TY - CONF TI - A Variable Selection Approach to Bayesian Monotonic Regression with Bernstien Polynomials AU - Ghosh, S. T2 - Seminar Bayesian Inference in Econometrics and Statistics C2 - 2009/5/1/ CY - Washington University, St. Louis, MO DA - 2009/5/1/ PY - 2009/5/1/ ER - TY - CONF TI - A Novel Bayesian Approach to Assessing the Risk of QT Prolongation AU - Ghosh, S. T2 - 5th Conference of the Eastern Mediterranean Region of the International Biometric Society C2 - 2009/5/10/ CY - Istanbul, Turkey DA - 2009/5/10/ PY - 2009/5/10/ ER - TY - SOUND TI - A Variable Selection Approach to Bayesian Monotonic Regression with Bernstein Polynomials AU - Ghosh, S. DA - 2009/5/19/ PY - 2009/5/19/ ER - TY - CONF TI - Bayesian Analysis in R AU - Ghosh, S. T2 - Joint Annual Meeting of the Agricultural & Applied Economics Association C2 - 2009/7/26/ CY - Milwaukee, WI DA - 2009/7/26/ PY - 2009/7/26/ ER - TY - CONF TI - Best applied practices for analysis of agricultural economics problems using Bayesian inferential techniques AU - Ghosh, S. T2 - Joint Annual Meeting of the Agricultural & Applied Economics Association C2 - 2009/7/26/ CY - Milwaukee, WI DA - 2009/7/26/ PY - 2009/7/26/ ER - TY - CONF TI - Guiding Young Professionals to Be Successful in Government, Academia, and Industries AU - Ghosh, S. T2 - Joint Statistical Meetings C2 - 2009/8/2/ CY - Washington, DC DA - 2009/8/2/ PY - 2009/8/2/ ER - TY - SOUND TI - A Variable Selection Approach to Monotonic Regression with Bernstein Polynomials AU - Ghosh, S. DA - 2009/11/11/ PY - 2009/11/11/ ER - TY - CONF TI - Semiparametric Inference Based on a Class of Zero-Altered Distributions AU - Ghosh, S. T2 - International Conference in Mathematics and Applications C2 - 2009/12/17/ CY - Bangkok, Thailand DA - 2009/12/17/ PY - 2009/12/17/ ER - TY - CONF TI - A Variable Selection Approach to Bayesian Monotonic Regression with Bernstein Polynomials AU - Ghosh, S. T2 - Seventh International Triennial Calcutta Symposium C2 - 2009/12/28/ CY - Kolkata, India DA - 2009/12/28/ PY - 2009/12/28/ ER - TY - CONF TI - Dynamic Pricing the Revenue Insurance Contracts: A Time-Varying Copula Model AU - Zhu, Y. AU - Ghosh, S.K. AU - Goodwin, B. T2 - Joint Statistical Meetings C2 - 2009/// DA - 2009/// PY - 2009/// ER - TY - CONF TI - A Variable Selection Approach to Bayesian Monotonic Regression with Bernstein Polynomials AU - Curtis, S.M. AU - Ghosh, S.K. T2 - Joint Statistical Meetings C2 - 2009/// DA - 2009/// PY - 2009/// ER - TY - CONF TI - Semi-parametric Bayesian Approach for Testing Non-inferiority Using Relative Risk and Odds Ratio for Binary Data AU - Osman, M. AU - Ghosh, S.K. T2 - Joint Statistical Meetings C2 - 2009/// DA - 2009/// PY - 2009/// ER - TY - CONF TI - Bayesian Independent Component Analysis Using Mixture Priors AU - Eloyan, A. AU - Ghosh, S.K. T2 - Joint Statistical Meetings C2 - 2009/// DA - 2009/// PY - 2009/// ER - TY - CONF TI - Joint Variable Selection of Fixed and Random E ects in a Linear Mixed-E ects Model and its Oracle Properties AU - Krishna, A. AU - Bondell, H. AU - Ghosh, S.K. T2 - Joint Statistical Meetings C2 - 2009/// DA - 2009/// PY - 2009/// ER - TY - CONF TI - A Bayesian Semiparametric Accelerated Failure Time Cure Model for Censored Data AU - Krachey, E. AU - Ghosh, S.K. AU - Lu, W. T2 - Joint Statistical Meetings C2 - 2009/// DA - 2009/// PY - 2009/// ER - TY - JOUR TI - Measuring and partitioning the high-order linkage disequilibrium by multiple order Markov chains AU - Kim, Yunjung AU - Feng, Sheng AU - Zeng, Zhao-Bang T2 - Genetic Epidemiology AB - Genetic EpidemiologyVolume 33, Issue 2 p. 181-181 ErratumFree Access Measuring and partitioning the high-order linkage disequilibrium by multiple order Markov chains Yunjung Kim, Yunjung Kim Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina Department of Statistics, North Carolina State University, Raleigh, North Carolina Y. Kim and S. Feng contributed equally to this work.Search for more papers by this authorSheng Feng, Sheng Feng Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina Department of Statistics, North Carolina State University, Raleigh, North Carolina Y. Kim and S. Feng contributed equally to this work.Search for more papers by this authorZhao-Bang Zeng, Zhao-Bang Zeng Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina Department of Statistics, North Carolina State University, Raleigh, North Carolina Department of Genetics, North Carolina State University, Raleigh, North CarolinaSearch for more papers by this author Yunjung Kim, Yunjung Kim Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina Department of Statistics, North Carolina State University, Raleigh, North Carolina Y. Kim and S. Feng contributed equally to this work.Search for more papers by this authorSheng Feng, Sheng Feng Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina Department of Statistics, North Carolina State University, Raleigh, North Carolina Y. Kim and S. Feng contributed equally to this work.Search for more papers by this authorZhao-Bang Zeng, Zhao-Bang Zeng Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina Department of Statistics, North Carolina State University, Raleigh, North Carolina Department of Genetics, North Carolina State University, Raleigh, North CarolinaSearch for more papers by this author First published: 12 June 2008 https://doi.org/10.1002/gepi.20349 AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume33, Issue2February 2009Pages 181-181 RelatedInformation DA - 2009/2// PY - 2009/2// DO - 10.1002/gepi.20349 VL - 33 IS - 2 SP - 181-181 J2 - Genet. Epidemiol. LA - en OP - SN - 0741-0395 1098-2272 UR - http://dx.doi.org/10.1002/gepi.20349 DB - Crossref ER - TY - JOUR TI - Bayesian Regression Models for the Quality Adjusted Lifetime Data with Zero Time Duration Health States AU - Mishra, Kaushal K. AU - Ghosh, Sujit K. T2 - Journal of Statistical Theory and Practice AB - Abstract Clinical trial studies are often conducted in which quality of life is accessed and recorded along with other clinically measurable endpoints. Consideration of the quality of life in addition to the survival time in the statistical analysis can result in a better assessment of the treatments being compared. Quality adjusted lifetime (QAL) data analysis can serve as an important tool to the medical and patient community. This article presents a Bayesian regression approach to the modeling of censored QAL data. The Bayesian hierarchical framework based on a progressive health state model with a data augmentation scheme which provides a nonzero probability to the zero time spent in any health state has been developed. Simulation studies using Markov Chain Monte Carlo (MCMC) methods were performed to validate the proposed method. A real data set was used to illustrate the application of the proposed method. Key Words: Bayesian inferenceData augmentationMarkov chain Monte CarloQuality adjusted survivalTWiST DA - 2009/6// PY - 2009/6// DO - 10.1080/15598608.2009.10411939 VL - 3 IS - 2 SP - 477-487 J2 - Journal of Statistical Theory and Practice LA - en OP - SN - 1559-8608 1559-8616 UR - http://dx.doi.org/10.1080/15598608.2009.10411939 DB - Crossref KW - Bayesian inference KW - Data augmentation KW - Markov chain Monte Carlo KW - Quality adjusted survival KW - TWiST ER - TY - JOUR TI - A Bayesian Approach for Investigating the Risk of QT Prolongation AU - Anand, Suraj P. AU - Ghosh, Sujit K. T2 - Journal of Statistical Theory and Practice AB - Abstract The standard approach to investigating a drug for its potential for QT prolongation is to construct a 90% two-sided (or a 95% one-sided) confidence interval (CI), for the difference in baseline corrected mean QTc (heart-rate corrected version of QT) between drug and placebo at each time-point, and to conclude non-inferiority if the upper limit for each CI is less than a pre-specified constant. An alternative approach is to base the non-inferiority inference on the largest time-matched difference in population mean QTc (baseline corrected) between drug and placebo. In this paper, we propose a Bayesian approach to resolving this problem using a Monte Carlo simulation method. We use simulated data to assess the performance of our proposed approach, discuss its advantages over the standard approach, and illustrate the method by applying it to a real data set obtained from a thorough QT study conducted at GlaxoSmithKline (GSK). DA - 2009/6// PY - 2009/6// DO - 10.1080/15598608.2009.10411936 VL - 3 IS - 2 SP - 445-454 J2 - Journal of Statistical Theory and Practice LA - en OP - SN - 1559-8608 1559-8616 UR - http://dx.doi.org/10.1080/15598608.2009.10411936 DB - Crossref KW - Bayesian inference KW - ICH E14 KW - Monte Carlo simulation KW - QT/QTc interval KW - Thorough QT/QTc study ER - TY - JOUR TI - Bayesian unit-root tests for Stochastic Volatility models AU - Kalaylıoğlu, Zeynep I. AU - Ghosh, Sujit K. T2 - Statistical Methodology AB - In this article, we consider Bayesian inference procedures to test for a unit root in Stochastic Volatility (SV) models. Unit-root tests for the persistence parameter of the SV models, based on the Bayes Factor (BF), have been recently introduced in the literature. In contrast, we propose a flexible class of priors that is non-informative over the entire support of the persistence parameter (including the non-stationarity region). In addition, we show that our model fitting procedure is computationally efficient (using the software WinBUGS). Finally, we show that our proposed test procedures have good frequentist properties in terms of achieving high statistical power, while maintaining low total error rates. We illustrate the above features of our method by extensive simulation studies, followed by an application to a real data set on exchange rates. DA - 2009/3// PY - 2009/3// DO - 10.1016/j.stamet.2008.07.002 VL - 6 IS - 2 SP - 189-201 J2 - Statistical Methodology LA - en OP - SN - 1572-3127 UR - http://dx.doi.org/10.1016/j.stamet.2008.07.002 DB - Crossref ER - TY - JOUR TI - A multivariate evaluation of Ex ante risks associated with fed cattle production AU - Belasco, E.J. AU - Ghosh, S.K. AU - Goodwin, B.K. T2 - American Journal of Agricultural Economics AB - Abstract The purpose of this paper is to evaluate production risks faced by fed cattle producers. We do this by jointly modeling a group of cattle production yield risk factors using a multivariate dynamic regression model. The proposed econometric model estimates parameters that influence the mean and variance of production yield factors, as well as the covariance between variables, while accounting for a high degree of censoring through the use of a dynamic multivariate Tobit model. The model provides insights into the relationship between production yield factors in fed cattle production. DA - 2009/// PY - 2009/// DO - 10.1111/j.1467-8276.2008.01244.x VL - 91 IS - 2 SP - 431-443 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-64649101928&partnerID=MN8TOARS KW - heteroskedastic multivariate Tobit KW - livestock yields KW - production risk ER - TY - JOUR TI - A comparative study of Bayesian model selection criteria for capture-recapture models for closed populations AU - Gosky, R.M. AU - Ghosh, S.K. T2 - Journal of Modern Applied Statistical Methods DA - 2009/// PY - 2009/// VL - 8 IS - 1 SP - 68-80 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-78650799398&partnerID=MN8TOARS ER - TY - JOUR TI - Overall and pairwise segregation tests based on nearest neighbor contingency tables AU - Ceyhan, Elvan T2 - Computational Statistics & Data Analysis AB - Multivariate interaction between two or more classes (or species) has important consequences in many fields and may cause multivariate clustering patterns such as spatial segregation or association. The spatial segregation occurs when members of a class tend to be found near members of the same class (i.e., near conspecifics) while spatial association occurs when members of a class tend to be found near members of the other class or classes. These patterns can be studied using a nearest neighbor contingency table (NNCT). The null hypothesis is randomness in the nearest neighbor (NN) structure, which may result from–among other patterns–random labeling (RL) or complete spatial randomness (CSR) of points from two or more classes (which is called the CSR independence, henceforth). New versions of overall and cell-specific tests based on NNCTs (i.e., NNCT-tests) are introduced and compared with Dixon’s overall and cell-specific tests and various other spatial clustering methods. Overall segregation tests are used to detect any deviation from the null case, while the cell-specific tests are post hoc pairwise spatial interaction tests that are applied when the overall test yields a significant result. The distributional properties of these tests are analyzed and finite sample performance of the tests are assessed by an extensive Monte Carlo simulation study. Furthermore, it is shown that the new NNCT-tests have better performance in terms of Type I error and power estimates. The methods are also applied on two real life data sets for illustrative purposes. DA - 2009/6// PY - 2009/6// DO - 10.1016/j.csda.2008.08.002 VL - 53 IS - 8 SP - 2786-2808 J2 - Computational Statistics & Data Analysis LA - en OP - SN - 0167-9473 UR - http://dx.doi.org/10.1016/j.csda.2008.08.002 DB - Crossref ER - TY - JOUR TI - Genetic Modifiers of Liver Disease in Cystic Fibrosis AU - Bartlett, Jaclyn R. AU - Friedman, Kenneth J. AU - Ling, Simon C. AU - Pace, Rhonda G. AU - Bell, Scott C. AU - Bourke, Billy AU - Castaldo, Giuseppe AU - Castellani, Carlo AU - Cipolli, Marco AU - Colombo, Carla AU - Colombo, John L. AU - Debray, Dominique AU - Fernandez, Adriana AU - Lacaille, Florence AU - Macek, Milan AU - Rowland, Marion AU - Salvatore, Francesco AU - Taylor, Christopher J. AU - Wainwright, Claire AU - Wilschanski, Michael AU - Zemkova, Dana AU - Hannah, William B. AU - Phillips, James AU - Corey, Mary AU - Zielenski, Julian AU - Dorfman, Ruslan AU - Wang, Yunfei AU - Zou, Fei AU - Silverman, Lawrence M. AU - Drumm, Mitchell L. AU - Wright, Fred A. AU - Lange, Ethan M. AU - Durie, Peter R. AU - Knowles, Michael R. T2 - JAMA AB -

Context

A subset (≈ 3%-5%) of patients with cystic fibrosis (CF) develops severe liver disease with portal hypertension.

Objective

To assess whether any of 9 polymorphisms in 5 candidate genes (α1-antitrypsin or α1-antiprotease [SERPINA1], angiotensin-converting enzyme [ACE], glutathione S-transferase [GSTP1], mannose-binding lectin 2 [MBL2], and transforming growth factor β1 [TGFB1]) are associated with severe liver disease in patients with CF.

Design, Setting, and Participants

Two-stage case-control study enrolling patients with CF and severe liver disease with portal hypertension (CFLD) from 63 CF centers in the United States as well as 32 in Canada and 18 outside of North America, with the University of North Carolina at Chapel Hill as the coordinating site. In the initial study, 124 patients with CFLD (enrolled January 1999-December 2004) and 843 control patients without CFLD were studied by genotyping 9 polymorphisms in 5 genes previously studied as modifiers of liver disease in CF. In the second stage, the SERPINA1 Z allele and TGFB1 codon 10 genotype were tested in an additional 136 patients with CFLD (enrolled January 2005-February 2007) and 1088 with no CFLD.

Main Outcome Measures

Differences in distribution of genotypes in patients with CFLD vs patients without CFLD.

Results

The initial study showed CFLD to be associated with the SERPINA1 Z allele (odds ratio [OR], 4.72; 95% confidence interval [CI], 2.31-9.61; P = 3.3 × 10−6) and with TGFB1 codon 10 CC genotype (OR, 1.53; 95% CI, 1.16-2.03; P = 2.8 × 10−3). In the replication study, CFLD was associated with the SERPINA1 Z allele (OR, 3.42; 95% CI, 1.54-7.59; P = 1.4 × 10−3) but not with TGFB1 codon 10. A combined analysis of the initial and replication studies by logistic regression showed CFLD to be associated with SERPINA1 Z allele (OR, 5.04; 95% CI, 2.88-8.83; P = 1.5 × 10−8).

Conclusions

The SERPINA1 Z allele is a risk factor for liver disease in CF. Patients who carry the Z allele are at greater risk (OR, ≈ 5) of developing severe liver disease with portal hypertension. DA - 2009/9/9/ PY - 2009/9/9/ DO - 10.1001/jama.2009.1295 VL - 302 IS - 10 SP - 1076-1083 SN - 0098-7484 UR - http://dx.doi.org/10.1001/jama.2009.1295 ER - TY - JOUR TI - Public vaccination policy using an age-structured model of pneumococcal infection dynamics AU - Sutton, Karyn L. AU - Banks, H. T. AU - Castillo-Chavez, Carlos T2 - Journal of Biological Dynamics AB - Public health professionals are charged with the task of designing prevention programs for the effective control of biologically intricate infectious diseases at a population level. The effective vaccination of a population for pneumococcal diseases (infections caused by Streptococcus pneumoniae) remains a relevant question in the scientific community. It is complicated by heterogeneity in individuals’ responses to exposure to the bacterium and their responses to vaccination. Due to these complexities, most modelling efforts in this area have been on the cellular/bacteria level. Here, we introduce an age-structured SEIS-type model of pneumococcal diseases and their vaccination. We discuss the use of this framework in predicting the impact of vaccine strategies, with pneumococcal diseases as an example. Using parameter values reasonable for a developed country, we discuss the effects of targeting the colonization and/or infection stages on the age profiles of morbidity in a population. DA - 2009/6/18/ PY - 2009/6/18/ DO - 10.1080/17513750903023715 VL - 4 IS - 2 SP - 176-195 J2 - Journal of Biological Dynamics LA - en OP - SN - 1751-3758 1751-3766 UR - http://dx.doi.org/10.1080/17513750903023715 DB - Crossref ER - TY - JOUR TI - The Imprecise Dirichlet Model for Multilevel System Reliability AU - Wilson, Alyson G. AU - Huzurbazar, Aparna V. AU - Sentz, Kari T2 - Journal of Statistical Theory and Practice DA - 2009/3// PY - 2009/3// DO - 10.1080/15598608.2009.10411921 VL - 3 IS - 1 SP - 211-223 J2 - Journal of Statistical Theory and Practice LA - en OP - SN - 1559-8608 1559-8616 UR - http://dx.doi.org/10.1080/15598608.2009.10411921 DB - Crossref KW - Fault tree KW - Bayesian network KW - Multilevel data KW - Reliability KW - Multinomial-Dirichlet model KW - Imprecise Dirichlet model ER - TY - JOUR TI - Multivariate Spatial-Temporal Modeling and Prediction of Speciated Fine Particles AU - Choi, Jungsoon AU - Reich, Brian J. AU - Fuentes, Montserrat AU - Davis, Jerry M. T2 - Journal of Statistical Theory and Practice AB - Fine particulate matter (PM(2.5)) is an atmospheric pollutant that has been linked to serious health problems, including mortality. PM(2.5) is a mixture of pollutants, and it has five main components: sulfate, nitrate, total carbonaceous mass, ammonium, and crustal material. These components have complex spatial-temporal dependency and cross dependency structures. It is important to gain insight and better understanding about the spatial-temporal distribution of each component of the total PM(2.5) mass, and also to estimate how the composition of PM(2.5) might change with space and time, by spatially interpolating speciated PM(2.5). This type of analysis is needed to conduct spatial-temporal epidemiological studies of the association of these pollutants and adverse health effect.We introduce a multivariate spatial-temporal model for speciated PM(2.5). We propose a Bayesian hierarchical framework with spatiotemporally varying coefficients. In addition, a linear model of coregionalization is developed to account for spatial and temporal dependency structures for each component as well as the associations among the components. We also introduce a statistical framework to combine different sources of data, which accounts for bias and measurement error. We apply our framework to speciated PM(2.5) data in the United States for the year 2004. Our study shows that sulfate concentrations are the highest during the summer while nitrate concentrations are the highest during the winter. The results also show total carbonaceous mass. DA - 2009/6// PY - 2009/6// DO - 10.1080/15598608.2009.10411933 VL - 3 IS - 2 SP - 407-418 J2 - Journal of Statistical Theory and Practice LA - en OP - SN - 1559-8608 1559-8616 UR - http://dx.doi.org/10.1080/15598608.2009.10411933 DB - Crossref KW - Air pollution KW - Bayesian inference KW - Linear coregionalization model KW - Multivariate spatiotemporal processes KW - Speciated particulate matter ER - TY - JOUR TI - A Comparison of Analysis of Covariate-Adjusted Residuals and Analysis of Covariance AU - Ceyhan, Elvan AU - Goad, Carla L. T2 - Communications in Statistics - Simulation and Computation AB - Abstract Various methods to control the influence of a covariate on a response variable are compared. These methods are ANOVA with or without homogeneity of variances (HOV) of errors and Kruskal–Wallis (K–W) tests on (covariate-adjusted) residuals and analysis of covariance (ANCOVA). Covariate-adjusted residuals are obtained from the overall regression line fit to the entire data set ignoring the treatment levels or factors. It is demonstrated that the methods on covariate-adjusted residuals are only appropriate when the regression lines are parallel and covariate means are equal for all treatments. Empirical size and power performance of the methods are compared by extensive Monte Carlo simulations. We manipulated the conditions such as assumptions of normality and HOV, sample size, and clustering of the covariates. The parametric methods on residuals and ANCOVA exhibited similar size and power when error terms have symmetric distributions with variances having the same functional form for each treatment, and covariates have uniform distributions within the same interval for each treatment. In such cases, parametric tests have higher power compared to the K–W test on residuals. When error terms have asymmetric distributions or have variances that are heterogeneous with different functional forms for each treatment, the tests are liberal with K–W test having higher power than others. The methods on covariate-adjusted residuals are severely affected by the clustering of the covariates relative to the treatment factors when covariate means are very different for treatments. For data clusters, ANCOVA method exhibits the appropriate level. However, such a clustering might suggest dependence between the covariates and the treatment factors, so makes ANCOVA less reliable as well. Keywords: AllometryANOVAClusteringHomogeneity of variancesIsometryKruskal–Wallis testLinear modelsParallel lines modelMathematics Subject Classification: 62J1062F0362J05 DA - 2009/9/29/ PY - 2009/9/29/ DO - 10.1080/03610910903243687 VL - 38 IS - 10 SP - 2019-2038 J2 - Communications in Statistics - Simulation and Computation LA - en OP - SN - 0361-0918 1532-4141 UR - http://dx.doi.org/10.1080/03610910903243687 DB - Crossref KW - Allometry KW - ANOVA KW - Clustering KW - Homogeneity of variances KW - Isometry KW - Kruskal-Wallis test KW - Linear models KW - Parallel lines model ER - TY - JOUR TI - A robust QTL mapping procedure AU - Zou, Fei AU - Nie, Lei AU - Wright, Fred. A. AU - Sen, Pranab K. T2 - Journal of Statistical Planning and Inference AB - In quantitative-trait linkage studies using experimental crosses, the conventional normal location-shift model or other parameterizations may be unnecessarily restrictive. We generalize the mapping problem to a genuine nonparametric setup and provide a robust estimation procedure for the situation where the underlying phenotype distributions are completely unspecified. Classical Wilcoxon-Mann-Whitney statistics are employed for point and interval estimation of QTL positions and effects. DA - 2009/3// PY - 2009/3// DO - 10.1016/j.jspi.2008.06.009 VL - 139 IS - 3 SP - 978-989 J2 - Journal of Statistical Planning and Inference LA - en OP - SN - 0378-3758 UR - http://dx.doi.org/10.1016/j.jspi.2008.06.009 DB - Crossref KW - GEE KW - Generalized least squares estimate KW - Quantitative trait KW - Weighted least squares estimate KW - Wilcoxon-Mann-Whitney statistic ER - TY - JOUR TI - Replication and narrowing of gene expression quantitative trait loci using inbred mice AU - Gatti, Daniel M. AU - Harrill, Alison H. AU - Wright, Fred A. AU - Threadgill, David W. AU - Rusyn, Ivan T2 - Mammalian Genome AB - Gene expression quantitative trait locus (eQTL) mapping has become a powerful tool in systems biology. While many authors have made important discoveries using this approach, one persistent challenge in eQTL studies is the selection of loci and genes that should receive further biological investigation. In this study we compared eQTL generated from gene expression profiling in the livers of two panels of mouse strains: 41 BXD recombinant inbred and 36 Mouse Diversity Panel (MDP) strains. Cis-eQTL, loci in which the transcript and its maximum QTL are colocated, have been shown to be more reproducible than trans-eQTL, which are not colocated with the transcript. We observed that between 9.9 and 12.1% of cis-eQTL and between 2.0 and 12.6% of trans-eQTL replicated between the two panels depending on the degree of statistical stringency. Notably, a significant eQTL hotspot on distal chromosome 12 observed in the BXD panel was reproduced in the MDP. Furthermore, the shorter linkage disequilibrium in the MDP strains allowed us to considerably narrow the locus and limit the number of candidate genes to a cluster of Serpin genes, which code for extracellular proteases. We conclude that this strategy has some utility in increasing confidence and resolution in eQTL mapping studies; however, due to the high false-positive rate in the MDP, eQTL mapping in inbred strains is best carried out in combination with an eQTL linkage study. DA - 2009/7// PY - 2009/7// DO - 10.1007/s00335-009-9199-0 VL - 20 IS - 7 SP - 437-446 J2 - Mamm Genome LA - en OP - SN - 0938-8990 1432-1777 UR - http://dx.doi.org/10.1007/s00335-009-9199-0 DB - Crossref ER - TY - JOUR TI - A susceptibility gene for type 2 diabetes confers substantial risk for diabetes complicating cystic fibrosis AU - Blackman, S. M. AU - Hsu, S. AU - Ritter, S. E. AU - Naughton, K. M. AU - Wright, F. A. AU - Drumm, M. L. AU - Knowles, M. R. AU - Cutting, G. R. T2 - Diabetologia AB - Insulin-requiring diabetes affects 25-50% of young adults with cystic fibrosis (CF). Although the cause of diabetes in CF is unknown, recent heritability studies in CF twins and siblings indicate that genetic modifiers play a substantial role. We sought to assess whether genes conferring risk for diabetes in the general population may play a risk modifying role in CF.We tested whether a family history of type 2 diabetes affected diabetes risk in CF patients in 539 families in the CF Twin and Sibling family-based study. A type 2 diabetes susceptibility gene (transcription factor 7-like 2, or TCF7L2) was evaluated for association with diabetes in CF using 998 patients from the family-based study and 802 unrelated CF patients in an independent case-control study.Family history of type 2 diabetes increased the risk of diabetes in CF (OR 3.1; p = 0.0009). A variant in TCF7L2 associated with type 2 diabetes (the T allele at rs7903146) was associated with diabetes in CF in the family study (p = 0.004) and in the case-control study (p = 0.02; combined p = 0.0002). In the family-based study, variation in TCF7L2 increased the risk of diabetes about three-fold (HR 1.75 per allele, 95% CI 1.3-2.4; p = 0.0006), and decreased the mean age at diabetes diagnosis by 7 years. In CF patients not treated with systemic glucocorticoids, the effect of TCF7L2 was even greater (HR 2.9 per allele, 95% CI 1.7-4.9, p = 0.00011).A genetic variant conferring risk for type 2 diabetes in the general population is a modifier of risk for diabetes in CF. DA - 2009/7/8/ PY - 2009/7/8/ DO - 10.1007/s00125-009-1436-2 VL - 52 IS - 9 SP - 1858-1865 J2 - Diabetologia LA - en OP - SN - 0012-186X 1432-0428 UR - http://dx.doi.org/10.1007/s00125-009-1436-2 DB - Crossref KW - Association KW - CFRD KW - Corticosteroid KW - Cystic fibrosis KW - Diabetes KW - Genetics KW - Glucocorticoid KW - Modifier gene KW - TCF7L2 ER - TY - JOUR TI - Shrinkage and model selection with correlated variables via weighted fusion AU - Daye, Z. John AU - Jeng, X. Jessie T2 - Computational Statistics & Data Analysis AB - In this paper, we propose the weighted fusion, a new penalized regression and variable selection method for data with correlated variables. The weighted fusion can potentially incorporate information redundancy among correlated variables for estimation and variable selection. Weighted fusion is also useful when the number of predictors p is larger than the number of observations n. It allows the selection of more than n variables in a motivated way. Real data and simulation examples show that weighted fusion can improve variable selection and prediction accuracy. DA - 2009/2// PY - 2009/2// DO - 10.1016/j.csda.2008.11.007 VL - 53 IS - 4 SP - 1284-1298 J2 - Computational Statistics & Data Analysis LA - en OP - SN - 0167-9473 UR - http://dx.doi.org/10.1016/j.csda.2008.11.007 DB - Crossref ER - TY - JOUR TI - A comprehensive approach to haplotype-specific analysis by penalized likelihood AU - Tzeng, Jung-Ying AU - Bondell, Howard D T2 - European Journal of Human Genetics AB - Haplotypes can hold key information to understand the role of candidate genes in disease etiology. However, standard haplotype analysis has yet been able to fully reveal the information retained by haplotypes. In most analysis, haplotype inference focuses on relative effects compared with an arbitrarily chosen baseline haplotype. It does not depict the effect structure unless an additional inference procedure is used in a secondary post hoc analysis, and such analysis tends to be lack of power. In this study, we propose a penalized regression approach to systematically evaluate the pattern and structure of the haplotype effects. By specifying an L1 penalty on the pairwise difference of the haplotype effects, we present a model-based haplotype analysis to detect and to characterize the haplotypic association signals. The proposed method avoids the need to choose a baseline haplotype; it simultaneously carries out the effect estimation and effect comparison of all haplotypes, and outputs the haplotype group structure based on their effect size. Finally, our penalty weights are theoretically designed to balance the likelihood and the penalty term in an appropriate manner. The proposed method can be used as a tool to comprehend candidate regions identified from a genome or chromosomal scan. Simulation studies reveal the better abilities of the proposed method to identify the haplotype effect structure compared with the traditional haplotype association methods, demonstrating the informativeness and powerfulness of the proposed method. DA - 2009/7/8/ PY - 2009/7/8/ DO - 10.1038/ejhg.2009.118 VL - 18 IS - 1 SP - 95-103 J2 - Eur J Hum Genet LA - en OP - SN - 1018-4813 1476-5438 UR - http://dx.doi.org/10.1038/ejhg.2009.118 DB - Crossref ER - TY - JOUR TI - What are secondary students’ expectations for teachers in virtual school environments? AU - Oliver, Kevin AU - Osborne, Jason AU - Brady, Kevin T2 - Distance Education AB - Abstract A recent evaluation of the new North Carolina Virtual Public School (NCVPS) in the USA revealed numerous expectations for virtual school teachers from secondary students. Specifically, students expected their teachers to actually teach rather than moderate a course shell, supplement course shells with content and projects that illustrate relevance, provide for both content and peer interaction, and respond to questions and provide feedback quickly. The data suggest a possible content‐related interaction where a limited course shell can be bolstered by a proactive teacher, but potentially flounder among teachers who do not expect or know how to supplement an online course. Data further suggest a potential communication‐related interaction where increased opportunities for student–student and student–teacher interaction could potentially decrease the actual or perceived need for individualized attention that is particularly challenging for virtual teachers to provide. These results can be used to establish teacher expectations and design professional development experiences that prepare teachers to undertake divergent roles unique to online instruction. Keywords: virtual schoolingdistance educationevaluationstudent expectationsteacher qualitycommunication Acknowledgements The North Carolina Department of Public Instruction provided the William and Ida Friday Institute for Educational Innovation with funding for the evaluation of NCVPS. Notes 1. Further, given a 32% response rate (n = 1648), many additional respondents with substantially different views would be required to alter the basic tenor of the results. In fact, the results were generally positive (satisfaction‐related items on a Likert scale of 1–5 averaged around 4), indicating that if there is bias, we missed many hundreds of strongly dissatisfied students. Yet in survey research, we tend to assume those who are strongly dissatisfied are most likely to respond when given an opportunity. In all, this leads us to believe that this sample is not substantially biased. 2. In general, validation is not required when engaging in survey research of this nature because we were not measuring latent constructs, but rather soliciting attitudes and impressions, and because these questions were developed in concert with experts from NCVPS. 3. Other analyses, reported elsewhere, indicate that teachers were significantly more positive about their teaching performance than students, but not substantially so. 4. Of course, this issue is not unique to virtual classrooms. DA - 2009/5// PY - 2009/5// DO - 10.1080/01587910902845923 VL - 30 IS - 1 SP - 23-45 J2 - Distance Education LA - en OP - SN - 0158-7919 1475-0198 UR - http://dx.doi.org/10.1080/01587910902845923 DB - Crossref KW - virtual schooling KW - distance education KW - evaluation KW - student expectations KW - teacher quality KW - communication ER - TY - CONF TI - A Level Spreader — Vegetated Buffer System for Urban Stormwater Management AU - Winston, Ryan J. AU - Hunt, William F. T2 - World Environmental and Water Resources Congress 2009 AB - Vegetated filter strips (VFS) have been used to remove pollutants from contributing agricultural watersheds for decades. In order to improve effectiveness of vegetated buffers, level spreaders have been employed to distribute flow evenly across the length of the upstream end of the buffer. In North Carolina, level spreader- VFS systems are now gaining acceptance as a stormwater BMP for urbanized watersheds, as it promotes infiltration and reduces impervious surfaces, two tenets of Low Impact Development. A field study of four level spreader — vegetated filter strip systems was conducted at two urban watersheds in Louisburg and Apex, NC. At each site, stormwater was routed proportionately over two 13 ft long level spreaders, one draining to a 25 ft wide grassed buffer, the other to a 50 ft wide, half grassed, half forested buffer. Flow rates and flow volumes were measured at the inlet and outlets of the system. Composite, flow-weighted water quality samples were collected at the inlet and outlet of the system and analyzed for TKN, NO3+NO2, TN, NH3 TP, Orthophosphate, and TSS. The buffers promoted infiltration, which resulted in a substantial decrease in flow volume and peak flow rate between the inlet and outlet of the system. To date, 46 storm events have been monitored for hydrology in Louisburg, NC. Flow volume was reduced by an average of 83% and 80% for the 25 ft and 50 ft wide buffers, respectively. These buffers also reduced peak flow rate by an average of 86% and 83%, respectively. These results show that a level spreader — vegetated filter strip system can effectively reduce the hydrologic impacts of impervious surfaces. Water quality monitoring has been ongoing since March, 2008, with 19 and 20 storms monitored for Apex and Louisburg, respectively. Reductions in event mean concentrations for all buffer treatments occurred for TKN, TN, and TSS, while the other pollutants studied had mixed results. Because of the large reduction in volume due to infiltration, these BMPs provide a large reduction in mass of pollutants. The median percent mass removal for the Louisburg buffers was greater than 74% for all but one water quality constituent studied. A level spreader is relatively (1) easy to install, (2) inexpensive, and (3) requires little maintenance. Carefully selected and designed level spreader — vegetated buffer systems can be an effective method of controlling stormwater flow and its associated pollutants in small urban watersheds. C2 - 2009/5/12/ C3 - World Environmental and Water Resources Congress 2009 DA - 2009/5/12/ DO - 10.1061/41036(342)75 PB - American Society of Civil Engineers SN - 9780784410363 UR - http://dx.doi.org/10.1061/41036(342)75 DB - Crossref ER - TY - JOUR TI - Camp Golden Treasures: A multidisciplinary weight-loss and a healthy lifestyle camp for adolescent girls. AU - Pratt, Keeley J. AU - Lamson, Angela L. AU - Collier, David N. AU - Crawford, Yancey S. AU - Harris, Nancy AU - Gross, Kevin AU - Ballard, Sharon AU - Sarvey, Sharon AU - Saporito, Maria T2 - Families, Systems, & Health AB - Camp Golden Treasures, (CGT) the first non-profit weight loss camp for overweight adolescent girls in the nation, was held for six weeks from June 24 to August 3, 2007 at the East Carolina University campus in Greenville, NC. The primary goal was to support campers to lose weight, raise self esteem, and to learn the tools necessary to lead a healthy lifestyle while reducing risks for developing chronic disease or mitigating the effects of existing obesity-related conditions (sleep apnea, insulin resistance, hypertension, lower extremity dysfunction, etc.). While at CGT, campers learned about the importance of physical activity and proper nutrition through workshops, discussion groups and hands-on activities. Additionally campers were taught the necessary tools and strategies needed to make concrete, positive lifestyle changes so they can achieve a healthy weight. Due to the nature of a chronic disease such as obesity, multidisciplinary collaborators including physical therapy, nutrition, health education, management, family therapy, risk management, fundraising, public relations, medical, nursing, and physician coverage were involved in designing, planning, and implementing CGT. DA - 2009/// PY - 2009/// DO - 10.1037/a0014912 VL - 27 IS - 1 SP - 116-124 J2 - Families, Systems, & Health LA - en OP - SN - 1939-0602 1091-7527 UR - http://dx.doi.org/10.1037/a0014912 DB - Crossref KW - multidisciplinary KW - childhood obesity KW - residential camp ER - TY - JOUR TI - Erratum: Genomewide association for schizophrenia in the CATIE study: results of stage 1 AU - Sullivan, P F AU - Lin, D AU - Tzeng, J-Y AU - van den Oord, E AU - Perkins, D AU - Stroup, T S AU - Wagner, M AU - Lee, S AU - Wright, F A AU - Zou, F AU - Liu, W AU - Downing, A M AU - Lieberman, J AU - Close, S L T2 - Molecular Psychiatry AB - Correction to: Molecular Psychiatry (2008) 13, 570–584; doi: 10.1038/mp.2008.25 For technical reasons, Supplementary Tables 2, 3 and 4 were not published online. They now appear online at www.nature.com/mp. DA - 2009/11/18/ PY - 2009/11/18/ DO - 10.1038/mp.2008.74 VL - 14 IS - 12 SP - 1144-1144 J2 - Mol Psychiatry LA - en OP - SN - 1359-4184 1476-5578 UR - http://dx.doi.org/10.1038/mp.2008.74 DB - Crossref ER - TY - JOUR TI - A comparison of probabilistic and stochastic formulations in modelling growth uncertainty and variability AU - Banks, H. T. AU - Davis, J. L. AU - Ernstberger, S. L. AU - Hu, Shuhua AU - Artimovich, E. AU - Dhar, A. K. AU - Browdy, C. L. T2 - Journal of Biological Dynamics AB - We compare two approaches for inclusion of uncertainty/variability in modelling growth in size-structured population models. One entails imposing a probabilistic structure on growth rates in the population while the other involves formulating growth as a stochastic Markov diffusion process. We present a theoretical analysis that allows one to include comparable levels of uncertainty in the two distinct formulations in making comparisons of the two approaches. DA - 2009/5// PY - 2009/5// DO - 10.1080/17513750802304877 VL - 3 IS - 2-3 SP - 130-148 J2 - Journal of Biological Dynamics LA - en OP - SN - 1751-3758 1751-3766 UR - http://dx.doi.org/10.1080/17513750802304877 DB - Crossref ER - TY - CONF TI - Bioretention/Bioinfiltration Performance in the Mid-Atlantic AU - Brown, R. A. AU - Hunt, W. F. AU - Davis, A. P. AU - Traver, R. G. AU - Olszewski, J. M. T2 - World Environmental and Water Resources Congress 2009 AB - Researchers in Maryland, North Carolina, and Pennsylvania have been conducting parallel bioretention/bioinfiltration research since fall 2007. Various designs have been tested including those that rely on underdrains, have internal water storage (IWS) layers, or are underdrain-free. The cells provide a range of watershed practice size ratios and employ a variety of land covers. Researchers are pooling water quantity and quality data to help create new design standards. Initial results from the shared data will be presented, with specific attention to bioretention design parameters that control flow modification and water quality improvement. Two bioretention cells of varying vegetative cover are being monitored in Rocky Mount, NC. This site is located in the upper coastal plain with sandy in-situ soils. These cells were designed with a 0.9 m media depth and a 0.6 m deep internal water storage (IWS) layer. Another bioretention cell is being monitored in Silver Spring, MD. It was constructed with a 0.9 m media depth and a 0.3 m pooling depth. Finally, there are two bioinfiltration cells being monitored in Villanova, PA. The first is the "Traffic Island" bioinfiltration cell, which has been monitored since 2003. The bowl is only designed for 1.2 cm over the impervious surface, yet overflow rarely occurs for events less than 5.1 cm. The site had groundwater wells installed in 2007 and is the subject of an ongoing study on the groundwater effects. The second site has only been monitored for approximately six months. Cumulatively, the four bioretention cells extensively examined have dramatically reduced outflow volumes, completely assimilating all events less than 1.2 cm — and in some designs much greater events. By aggregating the data, runoff reduction by bioretention can be profound. C2 - 2009/5/12/ C3 - World Environmental and Water Resources Congress 2009 DA - 2009/5/12/ DO - 10.1061/41036(342)90 PB - American Society of Civil Engineers SN - 9780784410363 UR - http://dx.doi.org/10.1061/41036(342)90 DB - Crossref ER - TY - CONF TI - An Evaluation of Stormwater Wetlands in Series AU - Hathaway, J. M. AU - Hunt, W. F. T2 - World Environmental and Water Resources Congress 2009 AB - Retrofit BMPs are an important tool for achieving water quality goals in urban watersheds, providing treatment to areas not originally developed with stormwater management practices. One such BMP was installed and monitored in Mooresville, N.C. The system includes three wetlands built "in-series" to treat runoff from a highly impervious 30 acre watershed. The configuration of the wetlands allowed monitoring of water quality parameters at the outlet of each of the three stormwater wetlands. The results of this study indicate that water quality improvement for a number of pollutants experiences diminishing returns as it passes through the three wetland cells. For total suspended solids (TSS), approximately 95% of the total concentration reduction took place in the first wetland cell despite it only comprising 60% of the total surface area of the system. Analysis of the effluent concentrations of the first wetland cell indicates that undersized wetlands (roughly 1.5% of the contributing watershed in this case) may still contribute to water quality improvements in urban watersheds. Thus, retrofit BMPs may be desirable even in circumstances when they cannot be sized appropriately for the contributing watershed. C2 - 2009/5/12/ C3 - World Environmental and Water Resources Congress 2009 DA - 2009/5/12/ DO - 10.1061/41036(342)82 PB - American Society of Civil Engineers SN - 9780784410363 UR - http://dx.doi.org/10.1061/41036(342)82 DB - Crossref ER - TY - CONF TI - Water Quality Assessed by Benthic Macro-Invertebrates: Proposing the WQABI Method AU - McNett, J. K. AU - Hunt, W. F. T2 - World Environmental and Water Resources Congress 2009 AB - Stormwater experts agree that the currently used percent removal methodology metric has many flaws, and some have suggested utilizing a BMP effluent concentration metric. This paper examines a new method that establishes effluent target concentrations for BMPs based on the health of macro-invertebrates in the receiving water. 193 ambient water quality monitoring stations in North Carolina were paired with benthic macro-invertebrate health ratings collected in very close proximity. Water quality for the sites ranged from Excellent to Poor and was divided into three distinct eco-regions. Median NO3 + NO2, TKN, TN, and TP concentrations all increased with poorer benthic ratings; however, there was no such trend with respect to DO, TSS, and Fecal Coliforms. Overall, the new method was most effective in the Piedmont and Coastal eco-regions; however with more data collection, the Mountain eco-region may also benefit. For example, if regulators were to require "Good" water quality in the Piedmont eco-region, designers would have to limit effluent concentrations of TN and TP would be 0.99 mg/L and 0.11 mg/L, respectively, per the method presented herein. C2 - 2009/5/12/ C3 - World Environmental and Water Resources Congress 2009 DA - 2009/5/12/ DO - 10.1061/41036(342)542 PB - American Society of Civil Engineers SN - 9780784410363 UR - http://dx.doi.org/10.1061/41036(342)542 DB - Crossref ER - TY - CONF TI - Implementation and Performance of Stormwater Best Management Practice Retrofits in Wilmington, NC AU - Wright, J. D. AU - Hunt, W. F. AU - Burchell, II, M. R. AU - Perrin, C. A. AU - McCoy, E. R. T2 - World Environmental and Water Resources Congress 2009 AB - Burnt Mill Creek, located within downtown Wilmington, NC, is on the EPA's 303(d) list for impairment due in large part to urban stormwater runoff. The urban nature of the watershed presents challenges for restoration because of the varying land uses including single and multi-family residential areas, recreational parks, and commercial and industrial areas. Restoration efforts are multiplying in Burnt Mill Creek as a result of passionate involvement from local community leaders, and partnerships with state organizations. The Watershed Education for Communities and Local Officials (WECO) coordinated a partnership, with NCSU BAE, the City of Wilmington, as well as several other key state and local organizations and citizens groups, to obtain an EPA 319 grant that addresses stormwater management in the watershed. Community involvement has led to several retrofit BMP opportunities, including pervious pavement and rain gardens at a local YMCA, two bioretention cells installed in the parking lot at Port City Java's corporate headquarters, a stormwater wetland in a city owned communal area, and several residential scale rain gardens in an urban low income community. Twelve rain gardens and twenty four rain barrels were installed at citizen's private residences in an urban neighborhood in downtown Wilmington. Although restoration takes time, momentum continues to build in the Burnt Mill Creek watershed as resources are devoted to thoughtful education and engagement with the public. C2 - 2009/5/12/ C3 - World Environmental and Water Resources Congress 2009 DA - 2009/5/12/ DO - 10.1061/41036(342)536 PB - American Society of Civil Engineers SN - 9780784410363 UR - http://dx.doi.org/10.1061/41036(342)536 DB - Crossref ER - TY - CONF TI - Rainwater Harvesting Experiences in the Humid Southeast USA AU - Jones, Matthew AU - Hunt, William F. AU - Wright, Jason T2 - World Environmental and Water Resources Congress 2009 AB - Due to recent concerns over the environmental impact of stormwater runoff and increased water demands, interest in rainwater harvesting systems as an innovative stormwater treatment practice has developed in humid, well developed regions, such as the southeastern United States. Rainwater harvesting systems are designed to capture runoff from rooftops. The captured water can be used as an alternative to municipal or well water for non-potable applications. The water can be used for irrigation, vehicle washing, toilet flushing, and other non-potable uses. Harvested water can potentially be used for potable uses with proper treatment. Water harvesting systems can reduce peak flows and pollutant loads as well as conserve valuable resources. In order to better understand the anticipated usage and reliability of rainwater harvesting systems in the southeastern United States, a monitoring study was conducted at 5 rainwater harvesting systems in North Carolina, measuring cistern water levels and rainfall. Harvested water was used for a variety of applications including vehicle washing, irrigation, and toilet flushing. In order for water harvesting to be a viable solution for stormwater management the harvested water must be used between storm events. The system must be drained as much as possible to provide storage and peak flow mitigation for the next storm event. Results of the monitoring study showed that the rainwater harvesting systems were typically underutilized. Water usage was most consistent at the location where harvested rainwater was used to flush a toilet; however, the water level within the cistern only dropped below 80% of capacity on one occasion during the 30 month monitoring period. Research showed that the harvested water may require a dedicated use for water harvesting to be an effective stormwater management tool. C2 - 2009/5/12/ C3 - World Environmental and Water Resources Congress 2009 DA - 2009/5/12/ DO - 10.1061/41036(342)209 PB - American Society of Civil Engineers SN - 9780784410363 UR - http://dx.doi.org/10.1061/41036(342)209 DB - Crossref ER - TY - CONF TI - Effect of Bioretention on Runoff Temperature in Trout Sensitive Regions AU - Jones, Matthew AU - Hunt, William F. T2 - World Environmental and Water Resources Congress 2009 AB - Although it has been established that thermal pollution from urban stormwater can negatively impact the aquatic ecosystem, there are few mechanisms available to reduce the temperature or urban stormwater runoff. A monitoring study was conducted at 4 bioretention areas in western North Carolina, located along the southeastern extent of United States trout populations, to examine the effect these systems have on runoff temperature and identify any design criteria pertinent to temperature reduction. Median runoff temperatures leaving the pavement surfaces, based on storm events, exceeded the 21°C upper avoidance temperature of trout at all sites during the months of June through September. Of the bioretention areas studied, the two systems that covered an area smaller than 10% of their contributing watershed were able to significantly (p<0.01) reduce both maximum and median storm temperatures between the inlet and outlet. At the two bioretention areas that were larger than 10% of their contributing watershed area, maximum effluent temperatures were significantly (p<0.01) cooler than influent temperatures; however, there was no significant (p<0.05) difference between median influent and effluent temperatures. Despite reductions in temperature, effluent temperatures were not significantly (p<0.05) cooler than the upper avoidance temperature for trout at any of the monitoring locations. There was evidence that substantial reductions in runoff volume occurred at all bioretention areas, especially the systems that were larger than 10% of their contributing watershed. Overall, monitoring results indicated that bioretention areas served as effective treatment mechanisms for reducing, but not eliminating, the thermal impacts associated with urban stormwater runoff. C2 - 2009/5/12/ C3 - World Environmental and Water Resources Congress 2009 DA - 2009/5/12/ DO - 10.1061/41036(342)156 PB - American Society of Civil Engineers SN - 9780784410363 UR - http://dx.doi.org/10.1061/41036(342)156 DB - Crossref ER - TY - CONF TI - Research of Hydrologic and Water Quality Performance of 4 Linear Wetlands in Eastern North Carolina AU - Wright, J. D. AU - Hunt, W. F. T2 - World Environmental and Water Resources Congress 2009 AB - The North Carolina Department of Transportation is charged by an agreement with the North Carolina Department of Environment and Natural Resources to treat stormwater from NC DOT facilities across North Carolina. One heretofore unaccounted treatment is hundreds of miles of right-of-way swales in eastern North Carolina. It is possible that these serendipitous practices are improving runoff quality along theses highways. If so, an assessment of their performance is needed. Four existing right-of-way linear swales along I–40 east of I–95 will be monitored to determine their hydrologic and water quality effectiveness. Two different treatments are being examined: one swale that is unaltered and one that has been allowed to establish wetland conditions. There are two examples of each. Monitoring will also address the impact of the vegetated filter strip between the shoulder and the edge of the swale. Monitoring began in August of 2008. Samples are being collected from 18 events and analyzed for TN, TKN, NH4—N, NO2–3—N, TP, and TSS. C2 - 2009/5/12/ C3 - World Environmental and Water Resources Congress 2009 DA - 2009/5/12/ DO - 10.1061/41036(342)148 PB - American Society of Civil Engineers SN - 9780784410363 UR - http://dx.doi.org/10.1061/41036(342)148 DB - Crossref ER - TY - CONF TI - Field Testing Guidelines for Certification of Manufactured Stormwater BMPs: Part II AU - Sansalone, John AU - Benty, Jeff AU - Carrasco, Ernie AU - Gulliver, John AU - Hathaway, Jon AU - Hunt, Bill AU - Kayhanian, Masoud AU - Khambhammettu, Uday AU - Roseen, Robert M. AU - Rushton, Betty AU - Williams, Tim T2 - World Environmental and Water Resources Congress 2009 AB - Guidance from information and field testing concepts examined by the ASCE/EWRI Subcommittee on Field Testing is presented. Field-testing of manufactured treatment devices requires critical planning and implementation through all steps of the verification process from watershed/catchment selection, to testing and analytical protocols, to data evaluation and quality assurance and control measures, to data reporting guidelines. Ultimately the goal of field testing is to provide verification of analytical or numerical models for BMPs that have been developed through scaled or full-scale controlled physical model testing. The desired goals and outcomes must be known and designed into the entire verification process. Ultimately, the entire process leads to a defensible model that represents a quantitative yardstick for both deterministic and probabilistic evaluations of a BMP for stakeholders across a range of regional conditions. This committee is focused on field verification of a BMP for separation of particulate matter (PM) from rainfall-runoff and snowmelt. Towards this goal, the entire gradation of PM requires characterization for a BMP field evaluation, in particular the suspended fraction because of the mobility and acute bio-availability of this finer fraction. On the other hand, the coarse sediment fraction is of particular importance because this coarse fraction fills many BMPs and is most labile. A fundamental, transferable and defensible methodology is considered which includes particle size distributions (PSD) combined with gravimetric index tests for PM: total suspended solids (TSS) and suspended sediment concentration (SSC). TSS by definition is the PM fraction remaining suspended in an Imhoff Cone after one hour, although current methods utilize sub-sampling generate controversy as to the meaning of the measurement. However TSS remains in use because of ubiquitous usage, regulatory significance and as an important index of treatability. In contrast, SSC provides a gravimetric analysis of the entire sample and therefore limited bias, and outstanding reliability and repeatability. Quality assurance and feedback protocol are a necessary part of the testing protocol. We must recognize the range of challenges and collect sufficient representative data within an event and across events so that the role of such uniqueness can be quantified for the specific BMP or BMPs tested. C2 - 2009/5/12/ C3 - World Environmental and Water Resources Congress 2009 DA - 2009/5/12/ DO - 10.1061/41036(342)113 PB - American Society of Civil Engineers SN - 9780784410363 UR - http://dx.doi.org/10.1061/41036(342)113 DB - Crossref ER - TY - CONF TI - Field Evaluation of Indicator Bacteria Removal by Stormwater BMPs in North Carolina AU - Hathaway, J. M. AU - Hunt, W. F. AU - Wright, J. D. AU - Jadlocki, S. J. T2 - World Environmental and Water Resources Congress 2009 AB - In the United States Environmental Protection Agency's National Water Quality Inventory in 2000, 13% of the river and stream miles that were surveyed were impaired by pathogen indicator bacteria (USEPA 2002). Stormwater runoff is a transport mechanism for indicator bacteria to receiving waters, resulting in an increased risk to public health through consumption of contaminated shellfish or ingestion by swimmers. Urban stormwater is commonly treated by stormwater Best Management Practices (BMPs), each of which provides some combination of natural treatment mechanisms and fosters certain environmental conditions. Although BMPs have been studied in detail for many pollutants, little peer-reviewed literature is available which documents their ability to remove or inactivate indicator bacteria. The North Carolina State University Department of Biological and Agricultural Engineering evaluated 10 stormwater BMPs in Charlotte and Wilmington, NC, to evaluate their efficiency with respect to indicator bacteria removal. The study practices included two bioretention cells, four stormwater wetlands, two wet ponds, and two dry detention areas. Data collected from these studies indicates that positive removal of indicator bacteria is possible in many types of BMPs; however, removal can be highly variable from practice to practice. Further, stormwater BMPs may foster environments where indicator bacteria can persist, becoming sources of indicator bacteria. Finally, even if positive reductions in indicator bacteria are noted, research indicates that achieving effluent concentrations of indicator bacteria consistent with USEPA standards may be difficult with many types of BMPs. C2 - 2009/5/12/ C3 - World Environmental and Water Resources Congress 2009 DA - 2009/5/12/ DO - 10.1061/41036(342)112 PB - American Society of Civil Engineers SN - 9780784410363 UR - http://dx.doi.org/10.1061/41036(342)112 DB - Crossref ER - TY - CONF TI - Effects of Media Depth on Bioretention Performance in the Upper Coastal Plain of North Carolina and Bioretention Construction Impacts Study AU - Brown, R. A. AU - Hunt, W. F. T2 - World Environmental and Water Resources Congress 2009 AB - Bioretention is a principal low impact development (LID) practice. This paper examines two critical questions associated with bioretention design and construction. First, fill media is perhaps the major cost in constructing bioretention cells, so shallower media depths would be preferred, were they to work as well as deeper media systems. Two sets of bioretention cells of varying media depths in the upper coastal plain of North Carolina have been monitored since April 2008. They treat an impervious asphalt parking lot watershed in Nashville, NC. The bioretention cells were constructed with media depths of 0.6 and 0.9 m. Performance is being measured with respect to hydrology and water quality. Data show the deeper media depths meet the LID hydrology goal of volume reduction more frequently (35% compared to 9% of 45 events monitored). The second question examines how bioretention cells are excavated. Two excavation techniques, the conventional "scoop" method which purposefully smears the underlying soil surface and the "rake" method which uses the teeth of an excavator's bucket to scarify the underlying soil surface, were tested. Field tests were conducted on three soil types (sand, loamy sand, and clay) and under a variety of antecedent soil moisture conditions. Saturated hydraulic conductivity, surface infiltration, and soil compaction were measured for each excavated condition. In all cases, the rake method of excavation yielded more permeable, less compacted soils than the scoop method. The difference of infiltration and hydraulic conductivity between the two excavation techniques was statistically significant (p<0.05) when tests were conducted in wet soil conditions. Also, the infiltration rate at the clay site was significantly lower (p<0.05), and the hydraulic conductivity at the sandy site was significantly lower (p<0.05), when the scoop methodology was used. Based on results of this experiment and because there is essentially no extra cost associated with the rake method of excavating bioretention cells, the rake method of excavation is recommended over the conventional scoop method. The use of the rake method is expected to increase long term exfiltration from bioretention cells. C2 - 2009/5/12/ C3 - World Environmental and Water Resources Congress 2009 DA - 2009/5/12/ DO - 10.1061/41036(342)104 PB - American Society of Civil Engineers SN - 9780784410363 UR - http://dx.doi.org/10.1061/41036(342)104 DB - Crossref ER - TY - CONF TI - Data Reporting Guidelines for Certification of Manufactured Stormwater BMPs: Part II AU - Roseen, Robert M. AU - Carrasco, Ernie AU - Cheng, Yuan AU - Hunt, Bill AU - Johnston, Charlene AU - Mailloux, Jim AU - Stein, Walt AU - Williams, Tim T2 - World Environmental and Water Resources Congress 2009 AB - Data Reporting guidelines presented here were developed as part of the ASCE/EWRI Task Committee on Guidelines for Certification of Manufactured Stormwater BMPs. This work is the collaboration of the Stormwater Infrastructure Committee of EWRI's Water, Wastewater, and Stormwater Council (WWSC) and the Wet Weather Flow Technology Committee of the Urban Water Resources Research Council (UWRRC). These guidelines were developed by review of the major manufactured treatment device certification protocol requirements drawing primarily from the Technology Assessment Protocol-Ecology (TAPE) and the Technology Assessment Reciprocity Partnership (TARP). These reporting guidelines have been broadened to support the International Stormwater Best Management Practices (BMP) Database. With the increasing need for the field testing of proprietary devices comes the importance of consistent data reporting guidelines to be used when reporting to regulatory agencies or designers. The need for standardized reporting is underscored by the tremendous impact the range of testing factors can have upon testing results. These factors include the testing environment, experimental design, testing methodologies, statistical analysis, and data presentation. The need for consistency is underscored by the complex influence these factors have upon performance results. A clear and consistent data reporting approach can ensure that these biases are minimized, well understood, and that representative field testing can be effectively evaluated by the regulatory agency. A consistent reporting format is also needed to aid vendors to efficiently navigate the complicated application process for device certification. Finally, an independent third-party is needed to either conduct or review the testing to ensure testing impartiality. The committee membership includes stakeholders from the regulatory, academic, manufacturing, and design communities. C2 - 2009/5/12/ C3 - World Environmental and Water Resources Congress 2009 DA - 2009/5/12/ DO - 10.1061/41036(342)100 PB - American Society of Civil Engineers SN - 9780784410363 UR - http://dx.doi.org/10.1061/41036(342)100 DB - Crossref ER - TY - JOUR TI - Evaluation of algorithms used to order markers on genetic maps AU - Mollinari, M AU - Margarido, G R A AU - Vencovsky, R AU - Garcia, A A F T2 - Heredity AB - When building genetic maps, it is necessary to choose from several marker ordering algorithms and criteria, and the choice is not always simple. In this study, we evaluate the efficiency of algorithms try (TRY), seriation (SER), rapid chain delineation (RCD), recombination counting and ordering (RECORD) and unidirectional growth (UG), as well as the criteria PARF (product of adjacent recombination fractions), SARF (sum of adjacent recombination fractions), SALOD (sum of adjacent LOD scores) and LHMC (likelihood through hidden Markov chains), used with the RIPPLE algorithm for error verification, in the construction of genetic linkage maps. A linkage map of a hypothetical diploid and monoecious plant species was simulated containing one linkage group and 21 markers with fixed distance of 3 cM between them. In all, 700 F2 populations were randomly simulated with 100 and 400 individuals with different combinations of dominant and co-dominant markers, as well as 10 and 20% of missing data. The simulations showed that, in the presence of co-dominant markers only, any combination of algorithm and criteria may be used, even for a reduced population size. In the case of a smaller proportion of dominant markers, any of the algorithms and criteria (except SALOD) investigated may be used. In the presence of high proportions of dominant markers and smaller samples (around 100), the probability of repulsion linkage increases between them and, in this case, use of the algorithms TRY and SER associated to RIPPLE with criterion LHMC would provide better results. DA - 2009/7/29/ PY - 2009/7/29/ DO - 10.1038/hdy.2009.96 VL - 103 IS - 6 SP - 494-502 J2 - Heredity LA - en OP - SN - 0018-067X 1365-2540 UR - http://dx.doi.org/10.1038/hdy.2009.96 DB - Crossref KW - multipoint estimates KW - seriation KW - rapid chain delineation KW - recombination counting and ordering KW - unidirectional growth ER - TY - JOUR TI - Characterization of new polymorphic functional markers for sugarcane AU - Oliveira, K. M. AU - Pinto, L. R. AU - Marconi, T. G. AU - Mollinari, M. AU - Ulian, E. C. AU - Chabregas, S. M. AU - Falco, M. C. AU - Burnquist, W. AU - Garcia, A. A.F. AU - Souza, A. P. T2 - Genome AB - Expressed sequence tags (ESTs) offer the opportunity to exploit single, low-copy, conserved sequence motifs for the development of simple sequence repeats (SSRs). The authors have examined the Sugarcane Expressed Sequence Tag database for the presence of SSRs. To test the utility of EST-derived SSR markers, a total of 342 EST-SSRs, which represent a subset of over 2005 SSR-containing sequences that were located in the sugarcane EST database, could be designed from the nonredundant SSR-positive ESTs for possible use as potential genic markers. These EST-SSR markers were used to screen 18 sugarcane (Saccharum spp.) varieties. A high proportion (65.5%) of the above EST-SSRs, which gave amplified fragments of foreseen size, detected polymorphism. The number of alleles ranged from 2 to 24 with an average of 7.55 alleles per locus, while polymorphism information content values ranged from 0.16 to 0.94, with an average of 0.73. The ability of each set of EST-SSR markers to discriminate between varieties was generally higher than the polymorphism information content analysis. When tested for functionality, 82.1% of these 224 EST-SSRs were found to be functional, showing homology to known genes. As the EST-SSRs are within the expressed portion of the genome, they are likely to be associated to a particular gene of interest, improving their utility for genetic mapping; identification of quantitative trait loci, and comparative genomics studies of sugarcane. The development of new EST-SSR markers will have important implications for the genetic analysis and exploitation of the genetic resources of sugarcane and related species and will provide a more direct estimate of functional diversity. DA - 2009/2// PY - 2009/2// DO - 10.1139/g08-105 VL - 52 IS - 2 SP - 191-209 J2 - Genome LA - en OP - SN - 0831-2796 1480-3321 UR - http://dx.doi.org/10.1139/G08-105 DB - Crossref KW - sugarcane KW - simple sequence repeat (SSR) KW - expressed sequence tag (EST) KW - functional markers ER - TY - CHAP TI - An Inverse Problem Statistical Methodology Summary AU - Banks, H. Thomas AU - Davidian, Marie AU - Samuels, John R. AU - Sutton, Karyn L. T2 - Mathematical and Statistical Estimation Approaches in Epidemiology AB - We discuss statistical and computational aspects of inverse or parameter estimation problems for deterministic dynamical systems based on Ordinary Least Squares and Generalized Least Squares with appropriate corresponding data noise assumptions of constant variance and nonconstant variance (relative error), respectively. Among the topics included here are mathematical model, statistical model and data assumptions, and some techniques (residual plots, sensitivity analysis, model comparison tests) for verifying these. The ideas are illustrated throughout with the popular logistic growth model of Verhulst and Pearl as well as with a recently developed population level model of pneumococcal disease spread. PY - 2009/// DO - 10.1007/978-90-481-2313-1_11 SP - 249-302 OP - PB - Springer Netherlands SN - 9789048123124 9789048123131 UR - http://dx.doi.org/10.1007/978-90-481-2313-1_11 DB - Crossref ER - TY - JOUR TI - On asymptotically optimal tests under loss of identifiability in semiparametric models AU - Song, Rui AU - Kosorok, Michael R. AU - Fine, Jason P. T2 - The Annals of Statistics AB - We consider tests of hypotheses when the parameters are not identifiable under the null in semiparametric models, where regularity conditions for profile likelihood theory fail. Exponential average tests based on integrated profile likelihood are constructed and shown to be asymptotically optimal under a weighted average power criterion with respect to a prior on the nonidentifiable aspect of the model. These results extend existing results for parametric models, which involve more restrictive assumptions on the form of the alternative than do our results. Moreover, the proposed tests accommodate models with infinite dimensional nuisance parameters which either may not be identifiable or may not be estimable at the usual parametric rate. Examples include tests of the presence of a change-point in the Cox model with current status data and tests of regression parameters in odds-rate models with right censored data. Optimal tests have not previously been studied for these scenarios. We study the asymptotic distribution of the proposed tests under the null, fixed contiguous alternatives and random contiguous alternatives. We also propose a weighted bootstrap procedure for computing the critical values of the test statistics. The optimal tests perform well in simulation studies, where they may exhibit improved power over alternative tests. DA - 2009/10// PY - 2009/10// DO - 10.1214/08-aos643 VL - 37 IS - 5A SP - 2409-2444 J2 - Ann. Statist. LA - en OP - SN - 0090-5364 UR - http://dx.doi.org/10.1214/08-aos643 DB - Crossref KW - Change-point models KW - contiguous alternative KW - empirical processes KW - exponential average test KW - nonstandard testing problem KW - odds-rate models KW - optimal test KW - power KW - profile likelihood ER - TY - JOUR TI - A note on semiparametric efficient inference for two-stage outcome-dependent sampling with a continuous outcome AU - Song, R. AU - Zhou, H. AU - Kosorok, M. R. T2 - Biometrika AB - Outcome-dependent sampling designs have been shown to be a cost effective way to enhance study efficiency. We show that the outcome-dependent sampling design with a continuous outcome can be viewed as an extension of the two-stage case-control designs to the continuous-outcome case. We further show that the two-stage outcome-dependent sampling has a natural link with the missing-data and biased-sampling framework. Through the use of semiparametric inference and missing-data techniques, we show that a certain semiparametric maximum likelihood estimator is computationally convenient and achieves the semiparametric efficient information bound. We demonstrate this both theoretically and through simulation. DA - 2009/1/24/ PY - 2009/1/24/ DO - 10.1093/biomet/asn073 VL - 96 IS - 1 SP - 221-228 J2 - Biometrika LA - en OP - SN - 0006-3444 1464-3510 UR - http://dx.doi.org/10.1093/biomet/asn073 DB - Crossref KW - Biased sampling KW - Empirical process KW - Maximum likelihood estimation KW - Missing data KW - Outcome-dependent KW - Profile likelihood KW - Two-stage sampling ER - TY - JOUR TI - Cardiac Resynchronization Therapy Reduces the Risk of Hospitalizations in Patients With Advanced Heart Failure AU - Anand, Inder S. AU - Carson, Peter AU - Galle, Elizabeth AU - Song, Rui AU - Boehmer, John AU - Ghali, Jalal K. AU - Jaski, Brian AU - Lindenfeld, JoAnn AU - O'Connor, Christopher AU - Steinberg, Jonathan S. AU - Leigh, Jill AU - Yong, Patrick AU - Kosorok, Michael R. AU - Feldman, Arthur M. AU - DeMets, David AU - Bristow, Michael R. T2 - Circulation AB - In the Comparison of Medical Therapy, Pacing and Defibrillation in Heart Failure (COMPANION) trial, 1520 patients with advanced heart failure were assigned in a 1:2:2 ratio to optimal pharmacological therapy or optimal pharmacological therapy plus cardiac resynchronization therapy (CRT-P) or CRT with defibrillator (CRT-D). Use of CRT-P and CRT-D was associated with a significant reduction in combined risk of death or all-cause hospitalizations. Because mortality also was significantly reduced (optimal pharmacological therapy versus CRT-D only), an assessment of the true reduction in hospitalization rates must consider the competing risk of death and varying follow-up times.To overcome the challenges of comparing treatment groups, we used a nonparametric test of right-censored recurrent events that accounts for multiple hospital admissions, differential follow-up time between treatment groups, and death as a competing risk. An end-point committee adjudicated and classified all hospitalizations. Compared with optimal pharmacological therapy, CRT-P and CRT-D were associated with a 21% and 25% reduction in all-cause, 34% and 37% reduction in cardiac, and 44% and 41% reduction in heart failure hospital admissions per patient-year of follow-up, respectively. Similar reductions were seen in hospitalization days per patient-year. The reduction in hospitalization rate for heart failure in the CRT groups appeared within days of randomization and remained sustained. Noncardiac hospitalization rates were not different between groups.Use of CRT with or without a defibrillator in advanced heart failure patients was associated with marked reductions in all-cause, cardiac, and heart failure hospitalization rates in an analysis that accounted for the competing risk of mortality and unequal follow-up time. DA - 2009/2/24/ PY - 2009/2/24/ DO - 10.1161/circulationaha.108.793273 VL - 119 IS - 7 SP - 969-977 J2 - Circulation LA - en OP - SN - 0009-7322 1524-4539 UR - http://dx.doi.org/10.1161/circulationaha.108.793273 DB - Crossref KW - cardiac resynchronization therapy KW - defibrillators, implantable KW - heart failure KW - hospitalizations KW - prognosis ER - TY - JOUR TI - Joint covariate-adjusted score test statistics for recurrent events and a terminal event AU - Song, Rui AU - Cai, Jianwen T2 - Lifetime Data Analysis AB - Recurrent events data are frequently encountered and could be stopped by a terminal event in clinical trials. It is of interest to assess the treatment efficacy simultaneously with respect to both the recurrent events and the terminal event in many applications. In this paper we propose joint covariate-adjusted score test statistics based on joint models of recurrent events and a terminal event. No assumptions on the functional form of the covariates are needed. Simulation results show that the proposed tests can improve the efficiency over tests based on covariate unadjusted model. The proposed tests are applied to the SOLVD data for illustration. DA - 2009/12/1/ PY - 2009/12/1/ DO - 10.1007/s10985-009-9140-6 VL - 16 IS - 4 SP - 491-508 J2 - Lifetime Data Anal LA - en OP - SN - 1380-7870 1572-9249 UR - http://dx.doi.org/10.1007/s10985-009-9140-6 DB - Crossref KW - Frailty KW - Proportional hazards KW - Proportional rates KW - Recurrent events data KW - Semiparametric model ER - TY - JOUR TI - Higher-order approximations for interval estimation in binomial settings AU - Staicu, Ana-Maria T2 - Journal of Statistical Planning and Inference AB - In this paper we revisit the classical problem of interval estimation for one-binomial parameter and for the log odds ratio of two binomial parameters. We examine the confidence intervals provided by two versions of the modified log likelihood root: the usual Barndorff-Nielsen's r* and a Bayesian version of the r* test statistic. For the one-binomial problem, this work updates the findings of Brown et al. [2003. Interval estimation in exponential families. Statistica Sinica 13, 19–49; 2002. Confidence intervals for a binomial proportion and asymptotic expansion. The Annals of Statistics 30, 160–201] and Cai [2005. One-sided confidence intervals in discrete distributions. Journal of Statistical Planning and Inference 131, 63–88] to higher-order methods. For the log odds ratio of two binomial parameters we show via Edgeworth expansion that both versions of the r* statistics give confidence intervals which nearly completely eliminate the systematic bias in the unconditional smooth coverage probability. We also give expansions for the length of the confidence intervals. DA - 2009/10// PY - 2009/10// DO - 10.1016/j.jspi.2009.03.021 VL - 139 IS - 10 SP - 3393-3404 J2 - Journal of Statistical Planning and Inference LA - en OP - SN - 0378-3758 UR - http://dx.doi.org/10.1016/j.jspi.2009.03.021 DB - Crossref KW - Binomial distribution KW - Confidence intervals KW - Edgeworth expansion KW - First-order matching intervals KW - Modified likelihood root ER - TY - JOUR TI - Response to Ezell and von Winterfeldt AU - Parnell, G.S. AU - Borio, L.L. AU - Cox, L.A. AU - Brown, G.G. AU - Pollock, S. AU - Wilson, A.G. T2 - Biosecurity and Bioterrorism AB - Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and ScienceVol. 7, No. 1 CommentaryResponse to Ezell and von WinterfeldtGregory S. Parnell, Luciana L. Borio, Louis A. (Tony) Cox, Gerald G. Brown, Stephen Pollock, and Alyson G. WilsonGregory S. ParnellSearch for more papers by this author, Luciana L. BorioSearch for more papers by this author, Louis A. (Tony) CoxSearch for more papers by this author, Gerald G. BrownSearch for more papers by this author, Stephen PollockSearch for more papers by this author, and Alyson G. WilsonSearch for more papers by this authorPublished Online:20 Apr 2009https://doi.org/10.1089/bsp.2009.0927AboutSectionsPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail "Response to Ezell and von Winterfeldt." , 7(1), pp. 111–112FiguresReferencesRelatedDetailsCited byIs ALARP applicable to the management of terrorist risks?Reliability Engineering & System Safety, Vol. 95, No. 8 Volume 7Issue 1Mar 2009 InformationMary Ann Liebert, Inc.To cite this article:Gregory S. Parnell, Luciana L. Borio, Louis A. (Tony) Cox, Gerald G. Brown, Stephen Pollock, and Alyson G. Wilson.Response to Ezell and von Winterfeldt.Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science.Mar 2009.111-112.http://doi.org/10.1089/bsp.2009.0927Published in Volume: 7 Issue 1: April 20, 2009PDF download DA - 2009/// PY - 2009/// DO - 10.1089/bsp.2009.0927 VL - 7 IS - 1 SP - 111-112 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-65349093369&partnerID=MN8TOARS ER - TY - JOUR TI - Probability, chance and the probability of chance AU - Singpurwalla, N.D. AU - Wilson, A.G. T2 - IIE Transactions (Institute of Industrial Engineers) AB - In our day-to-day discourse on uncertainty, words like belief, chance, plausible, likelihood and probability are commonly encountered. Often, these words are used interchangeably, because they are intended to encapsulate some loosely articulated notions about the unknowns. The purpose of this paper is to propose a framework that is able to show how each of these terms can be made precise, so that each reflects a distinct meaning. To construct our framework, we use a basic scenario upon which caveats are introduced. Each caveat motivates us to bring in one or more of the above notions. The scenario considered here is very basic; it arises in both the biomedical context of survival analysis and the industrial context of engineering reliability. This paper is expository and much of what is said here has been said before. However, the manner in which we introduce the material via a hierarchy of caveats that could arise in practice, namely our proposed framework, is the novel aspect of this paper. To appreciate all this, we require of the reader a knowledge of the calculus of probability. However, in order to make our distinctions transparent, probability has to be interpreted subjectively, not as an objective relative frequency. DA - 2009/// PY - 2009/// DO - 10.1080/07408170802322630 VL - 41 IS - 1 SP - 12-22 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-56849107795&partnerID=MN8TOARS KW - Belief functions KW - biometry KW - likelihood KW - plausibility KW - quality assurance KW - reliability KW - survival analysis KW - uncertainty KW - vagueness ER - TY - JOUR TI - On the finiteness of the cone spectrum of certain linear transformations on Euclidean Jordan algebras AU - Zhou, Yihui AU - Gowda, M. Seetharama T2 - Linear Algebra and its Applications AB - Let L be a linear transformation on a finite dimensional real Hilbert space H and K be a closed convex cone with dual K∗ in H. The cone spectrum of L relative to K is the set of all real λ for which the linear complementarity problemx∈K,y=L(x)-λx∈K∗,and〈x,y〉=0admits a nonzero solution x. In the setting of a Euclidean Jordan algebra H and the corresponding symmetric cone K, we discuss the finiteness of the cone spectrum for Z-transformations and quadratic representations on H. DA - 2009/8// PY - 2009/8// DO - 10.1016/j.laa.2009.03.031 VL - 431 IS - 5-7 SP - 772-782 J2 - Linear Algebra and its Applications LA - en OP - SN - 0024-3795 UR - http://dx.doi.org/10.1016/j.laa.2009.03.031 DB - Crossref KW - Euclidean Jordan algebra KW - Symmetric cone KW - Cone spectrum KW - Z-transformation KW - Quadratic representation ER - TY - JOUR TI - Testing in semiparametric models with interaction, with applications to gene-environment interactions AU - Maity, Arnab AU - Carroll, Raymond J. AU - Mammen, Enno AU - Chatterjee, Nilanjan T2 - Journal of the Royal Statistical Society. Series B: Statistical Methodology AB - Motivated from the problem of testing for genetic effects on complex traits in the presence of gene-environment interaction, we develop score tests in general semiparametric regression problems that involves Tukey style 1 degree-of-freedom form of interaction between parametrically and non-parametrically modelled covariates. We find that the score test in this type of model, as recently developed by Chatterjee and co-workers in the fully parametric setting, is biased and requires undersmoothing to be valid in the presence of non-parametric components. Moreover, in the presence of repeated outcomes, the asymptotic distribution of the score test depends on the estimation of functions which are defined as solutions of integral equations, making implementation difficult and computationally taxing. We develop profiled score statistics which are unbiased and asymptotically efficient and can be performed by using standard bandwidth selection methods. In addition, to overcome the difficulty of solving functional equations, we give easy interpretations of the target functions, which in turn allow us to develop estimation procedures that can be easily implemented by using standard computational methods. We present simulation studies to evaluate type I error and power of the method proposed compared with a naive test that does not consider interaction. Finally, we illustrate our methodology by analysing data from a case-control study of colorectal adenoma that was designed to investigate the association between colorectal adenoma and the candidate gene NAT2 in relation to smoking history. DA - 2009/// PY - 2009/// DO - 10.1111/j.1467-9868.2008.00671.x VL - 71 IS - 1 SP - 75–96 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-58149340050&partnerID=MN8TOARS KW - Additive models KW - Diplotypes KW - Function estimation KW - Non-parametric regression KW - Omnibus hypothesis testing KW - Partially linear model KW - Repeated measures KW - Score test KW - Semiparametric models KW - Smooth backfitting KW - Tukey's 1 degree-of-freedom model ER - TY - JOUR TI - Nonparametric Additive Regression for Repeatedly Measured Data AU - Carroll, R.J. AU - Maity, A. AU - Mammen, E. AU - Yu, K. T2 - Biometrika AB - We develop an easily computed smooth backfitting algorithm for additive model fitting in repeated measures problems. Our methodology easily copes with various settings, such as when some covariates are the same over repeated response measurements. We allow for a working covariance matrix for the regression errors, showing that our method is most efficient when the correct covariance matrix is used. The component functions achieve the known asymptotic variance lower bound for the scalar argument case. Smooth backfitting also leads directly to design-independent biases in the local linear case. Simulations show our estimator has smaller variance than the usual kernel estimator. This is also illustrated by an example from nutritional epidemiology. DA - 2009/// PY - 2009/// DO - 10.1093/biomet/asp015 VL - 96 IS - 2 SP - 383-398 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-66249142283&partnerID=MN8TOARS KW - Additive model KW - Generalized least square KW - Nonparametric regression KW - Repeated measure KW - Smooth backfitting ER - TY - JOUR TI - SIMEX and standard error estimation in semiparametric measurement error models AU - Apanasovich, Tatiyana V. AU - Carroll, Raymond J. AU - Maity, Arnab T2 - Electronic Journal of Statistics AB - SIMEX is a general-purpose technique for measurement error correction. There is a substantial literature on the application and theory of SIMEX for purely parametric problems, as well as for purely nonparametric regression problems, but there is neither application nor theory for semiparametric problems. Motivated by an example involving radiation dosimetry, we develop the basic theory for SIMEX in semiparametric problems using kernel-based estimation methods. This includes situations that the mismeasured variable is modeled purely parametrically, purely nonparametrically, or that the mismeasured variable has components that are modeled both parametrically and nonparametrically. Using our asymptotic expansions, easily computed standard error formulae are derived, as are the bias properties of the nonparametric estimator. The standard error method represents a new method for estimating variability of nonparametric estimators in semiparametric problems, and we show in both simulations and in our example that it improves dramatically on first order methods. We find that for estimating the parametric part of the model, standard bandwidth choices of order O(n−1/5) are sufficient to ensure asymptotic normality, and undersmoothing is not required. SIMEX has the property that it fits misspecified models, namely ones that ignore the measurement error. Our work thus also more generally describes the behavior of kernel-based methods in misspecified semiparametric problems. DA - 2009/// PY - 2009/// DO - 10.1214/08-ejs341 VL - 3 IS - 0 SP - 318–348 KW - Berkson measurement errors KW - measurement error KW - misspecified models KW - nonparametric regression KW - radiation epidemiology KW - semiparametric models KW - SIMEX KW - simulation-extrapolation KW - standard error estimation KW - uniform expansions ER - TY - JOUR TI - Efficient Semiparametric Marginal Estimation for the Partially Linear Additive Model for Longitudinal/Clustered Data AU - Carroll, Raymond AU - Maity, Arnab AU - Mammen, Enno AU - Yu, Kyusang T2 - Stat Biosci AB - We consider the efficient estimation of a regression parameter in a partially linear additive nonparametric regression model from repeated measures data when the covariates are multivariate. To date, while there is some literature in the scalar covariate case, the problem has not been addressed in the multivariate additive model case. Ours represents a first contribution in this direction. As part of this work, we first describe the behavior of nonparametric estimators for additive models with repeated measures when the underlying model is not additive. These results are critical when one considers variants of the basic additive model. We apply them to the partially linear additive repeated-measures model, deriving an explicit consistent estimator of the parametric component; if the errors are in addition Gaussian, the estimator is semiparametric efficient. We also apply our basic methods to a unique testing problem that arises in genetic epidemiology; in combination with a projection argument we develop an efficient and easily computed testing scheme. Simulations and an empirical example from nutritional epidemiology illustrate our methods. DA - 2009/// PY - 2009/// DO - 10.1007/s12561-009-9000-7 VL - 1 IS - 1 SP - 10–31 KW - Additive models KW - Generalized least squares KW - Interaction testing KW - Nonparametric regression KW - Partially linear model KW - Repeated measures KW - Smooth backfitting KW - Tukey-type models ER - TY - JOUR TI - Stepwise multiple quantile regression estimation using non-crossing constraints AU - Wu, Y. C. AU - Liu, Y. F. T2 - Statistics and its Interface AB - Quantile regression is an important statistical tool for statistical modeling. It has been widely used in various fields including econometrics, medicine, and bioinformatics. Despite its popularity in practice, individually estimated quantile regression functions often cross each other and consequently violate the basic properties of quantiles. In this paper we propose a new method for estimating multiple quantile regression functions without crossing. Both linear and kernel quantile regression models are considered. Several numerical examples are presented to illustrate competitive performance of the proposed method. DA - 2009/// PY - 2009/// DO - 10.4310/sii.2009.v2.n3.a4 VL - 2 IS - 3 SP - 299-310 ER - TY - JOUR TI - FIRST: Combining forward iterative selection and shrinkage in high dimensional sparse linear regression AU - Hwang, W. Y. AU - Zhang, H. H. AU - Ghosal, S. T2 - Statistics and its Interface AB - We propose a new class of variable selection techniques for regression in high dimensional linear models based on a forward selection version of the LASSO, adaptive LASSO or elastic net, respectively to be called as forward iterative regression and shrinkage technique (FIRST), adaptive FIRST and elastic FIRST. These methods seem to work effectively for extremely sparse high dimensional linear models. We exploit the fact that the LASSO, adaptive LASSO and elastic net have closed form solutions when the predictor is onedimensional. The explicit formula is then repeatedly used in an iterative fashion to build the model until convergence occurs. By carefully considering the relationship between estimators at successive stages, we develop fast algorithms to compute our estimators. The performance of our new estimators are compared with commonly used estimators in terms of predictive accuracy and errors in variable selection. AMS 2000 subject classifications: Primary 62J05, 62J05; secondary 62J07. DA - 2009/// PY - 2009/// DO - 10.4310/sii.2009.v2.n3.a7 VL - 2 IS - 3 SP - 341-348 ER - TY - JOUR TI - Viscoelastic models for passive arterial wall dynamics AU - Valdez-Jasso, D. AU - Banks, H. T. AU - Haider, M. A. AU - Bia, D. AU - Zocalo, Y. AU - Armentano, R. L. AU - Olufsen, M. S. T2 - Advances in Applied Mathematics & Mechanics DA - 2009/// PY - 2009/// VL - 1 IS - 2 SP - 151-165 ER - TY - JOUR TI - Detection of arterial occlusions using viscoelastic wave propagation AU - Banks, H. T. AU - Samuels, J. R. T2 - Advances in Applied Mathematics & Mechanics DA - 2009/// PY - 2009/// VL - 1 IS - 1 SP - 1-28 ER - TY - BOOK TI - Mathematical and experimental modeling of physical and biological processes AU - Banks, H. T. AU - Tran, H. T. DA - 2009/// PY - 2009/// PB - Boca Raton : CRC Press SN - 9781420073379 ER - TY - JOUR TI - Bayesian Inference for Directional Conditionally Autoregressive Models AU - Kyung, Minjung AU - Ghosh, Sujit K. T2 - BAYESIAN ANALYSIS AB - Counts or averages over arbitrary regions are often analyzed using conditionally autoregressive (CAR) models. The neighborhoods within CAR models are generally determined using only the inter-distances or boundaries between the sub-regions. To accommodate spatial variations that may depend on directions, a new class of models is developed using different weights given to neighbors in different directions. By accounting for such spatial anisotropy, the proposed model generalizes the usual CAR model that assigns equal weight to all directions. Within a fully hierarchical Bayesian framework, the posterior distributions of the parameters are derived using conjugate and non-informative priors. Efficient Markov chain Monte Carlo (MCMC) sampling algorithms are provided to generate samples from the marginal posterior distribution of the parameters. Simulation studies are presented to evaluate the performance of the estimators and are used to compare results with traditional CAR models. Finally the method is illustrated using data sets on local crime frequencies in Columbus, OH and on the elevated blood lead levels of children under the age of 72 months observed in Virginia counties for the year of 2000. DA - 2009/// PY - 2009/// DO - 10.1214/09-BA425 VL - 4 IS - 4 SP - 675-705 SN - 1936-0975 KW - Anisotropy KW - Bayesian estimation KW - Conditionally autoregressive models KW - Lattice data KW - Spatial analysis ER - TY - JOUR TI - Well-posedness of inverse problems for systems with time dependent parameters AU - Banks, H. T. AU - Pedersen, M. T2 - Arabian Journal for Science and Engineering DA - 2009/// PY - 2009/// VL - 34 IS - 1D SP - 39-58 ER - TY - JOUR TI - Ultrahigh dimensional feature selection: Beyond the linear model AU - Fan, J. Q. AU - Samworth, R. AU - Wu, Y. C. T2 - Journal of Machine Learning Research DA - 2009/// PY - 2009/// VL - 10 SP - 2013-2038 ER - TY - JOUR TI - NETWORK EXPLORATION VIA THE ADAPTIVE LASSO AND SCAD PENALTIES AU - Fan, Jianqing AU - Feng, Yang AU - Wu, Yichao T2 - ANNALS OF APPLIED STATISTICS AB - Graphical models are frequently used to explore networks, such as genetic networks, among a set of variables. This is usually carried out via exploring the sparsity of the precision matrix of the variables under consideration. Penalized likelihood methods are often used in such explorations. Yet, positive-definiteness constraints of precision matrices make the optimization problem challenging. We introduce nonconcave penalties and the adaptive LASSO penalty to attenuate the bias problem in the network estimation. Through the local linear approximation to the nonconcave penalty functions, the problem of precision matrix estimation is recast as a sequence of penalized likelihood problems with a weighted L1 penalty and solved using the efficient algorithm of Friedman et al. [Biostatistics 9 (2008) 432–441]. Our estimation schemes are applied to two real datasets. Simulation experiments and asymptotic theory are used to justify our proposed methods. DA - 2009/6// PY - 2009/6// DO - 10.1214/08-AOAS215 VL - 3 IS - 2 SP - 521-541 SN - 1932-6157 KW - Adaptive LASSO KW - covariance selection KW - Gaussian concentration graphical model KW - genetic network KW - LASSO KW - precision matrix KW - SCAD ER - TY - JOUR TI - Daily Activity Patterns of University Students AU - Eom, Jin Ki AU - Stone, John R. AU - Ghosh, Sujit K. T2 - JOURNAL OF URBAN PLANNING AND DEVELOPMENT AB - This paper presents a comprehensive analysis of students’ activity characteristics and travel patterns based on the 2001 North Carolina State University Student Activity Travel Survey. Results show that undergraduate students and on-campus residents are engaged in more activities than graduate students and off-campus students. Graduate students are more likely to engage in class and work activity in the afternoon than in the morning. There is no statistically significant difference between student groups in terms of the proportion of students involved in a certain activity at a certain hour of the day. Instead, the types of activities are different across all 24 h of a day. The insights gained from this study will serve as the basis of an activity-based university travel demand model for North Carolina State University. DA - 2009/12// PY - 2009/12// DO - 10.1061/(ASCE)UP.1943-5444.0000015 VL - 135 IS - 4 SP - 141-149 SN - 1943-5444 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-75949111868&partnerID=MN8TOARS ER - TY - JOUR TI - QUANTILE REGRESSION IN PARTIALLY LINEAR VARYING COEFFICIENT MODELS AU - Wang, Huixia Judy AU - Zhu, Zhongyi AU - Zhou, Jianhui T2 - ANNALS OF STATISTICS AB - Semiparametric models are often considered for analyzing longitudinal data for a good balance between flexibility and parsimony. In this paper, we study a class of marginal partially linear quantile models with possibly varying coefficients. The functional coefficients are estimated by basis function approximations. The estimation procedure is easy to implement, and it requires no specification of the error distributions. The asymptotic properties of the proposed estimators are established for the varying coefficients as well as for the constant coefficients. We develop rank score tests for hypotheses on the coefficients, including the hypotheses on the constancy of a subset of the varying coefficients. Hypothesis testing of this type is theoretically challenging, as the dimensions of the parameter spaces under both the null and the alternative hypotheses are growing with the sample size. We assess the finite sample performance of the proposed method by Monte Carlo simulation studies, and demonstrate its value by the analysis of an AIDS data set, where the modeling of quantiles provides more comprehensive information than the usual least squares approach. DA - 2009/12// PY - 2009/12// DO - 10.1214/09-AOS695 VL - 37 IS - 6B SP - 3841-3866 SN - 0090-5364 KW - Basis spline KW - longitudinal data KW - marginal model KW - rank score test KW - semiparametric ER - TY - JOUR TI - Nonlinear Models for Longitudinal Data AU - Serroyen, Jan AU - Molenberghs, Geert AU - Verbeke, Geert AU - Davidian, Marie T2 - AMERICAN STATISTICIAN AB - Whereas marginal models, random-effects models, and conditional models are routinely considered to be the three main modeling families for continuous and discrete repeated measures with linear and generalized linear mean structures, respectively, it is less common to consider nonlinear models, let alone frame them within the above taxonomy. In the latter situation, indeed, when considered at all, the focus is often exclusively on random-effects models. In this article, we consider all three families, exemplify their great flexibility and relative ease of use, and apply them to a simple but illustrative set of data on tree circumference growth of orange trees. This article has supplementary material online. DA - 2009/11// PY - 2009/11// DO - 10.1198/tast.2009.07256 VL - 63 IS - 4 SP - 378-388 SN - 1537-2731 KW - Conditional model KW - Marginal model KW - Random-effects model KW - Serial correlation KW - Transition model ER - TY - JOUR TI - LOCAL QUASI-LIKELIHOOD WITH A PARAMETRIC GUIDE AU - Fan, Jianqing AU - Wu, Yichao AU - Feng, Yang T2 - ANNALS OF STATISTICS AB - Generalized linear models and quasi-likelihood method extend the ordinary regression models to accommodate more general conditional distributions of the response. Nonparametric methods need no explicit parametric specification and the resulting model is completely determined by the data themselves. However nonparametric estimation schemes generally have a slower convergence rate such as the local polynomial smoothing estimation of nonparametric generalized linear models studied in Fan, Heckman and Wand (1995). In this work, we propose two parametrically guided nonparametric estimation schemes by incorporating prior shape information on the link transformation of the response variable's conditional mean in terms of the predictor variable. Asymptotic results and numerical simulations demonstrate the improvement of our new estimation schemes over the original nonparametric counterpart. DA - 2009/12// PY - 2009/12// DO - 10.1214/09-AOS713 VL - 37 IS - 6B SP - 4153-4183 SN - 0090-5364 KW - Generalized linear model KW - local polynomial smoothing KW - parametric guide KW - quasi-likelihood method ER - TY - JOUR TI - Indicator Bacteria Removal in Storm-Water Best Management Practices in Charlotte, North Carolina AU - Hathaway, J. M. AU - Hunt, W. F. AU - Jadlocki, S. T2 - JOURNAL OF ENVIRONMENTAL ENGINEERING-ASCE AB - Water quality degradation due to pathogen pollution is a major concern in the United States. Storm-water runoff is an important contributor to the transport of indicator bacteria from urbanized watersheds to nearby surface waters. With total maximum daily loads being established to reduce the export of indicator bacteria to surface waters, storm-water best management practices (BMPs) may be an important tool in treating indicator bacteria in runoff. However, the ability of these systems to remove indicator bacteria is not well established. A study in Charlotte, N.C., monitored nine storm-water BMPs (one wet pond, two storm-water wetlands, two dry detention basins, one bioretention area, and three proprietary devices) for fecal coliform and Escherichia coli (E. coli). A wet pond, two wetlands, a bioretention area, and a proprietary device all removed fecal coliform with an efficiency higher than 50%; however, only the wetlands and bioretention area had significantly different influent and effluent concentrations (p<0.05). For E. coli, only one of the wetlands and the bioretention area provided a concentration reduction greater than 50%, both of which had a significant difference in influent and effluent concentrations (p<0.05). Only one of the nine BMPs had a geometric mean effluent concentration of fecal coliform lower than the U.S. EPA target value, while four of the nine BMPs had geometric mean effluent concentrations lower than the U.S. EPA standard for E. coli. This study showed that some BMPs may be useful for treatment of indicator bacteria; however, other BMPs did not perform well. Because wet, nutrient-rich environments exist in many storm-water BMPs, there is a potential for indicator bacteria to persist in these systems. DA - 2009/12// PY - 2009/12// DO - 10.1061/(asce)ee.1943-7870.0000107 VL - 135 IS - 12 SP - 1275-1285 SN - 0733-9372 ER - TY - JOUR TI - Bayesian modeling of multivariate spatial binary data with applications to dental caries AU - Bandyopadhyay, Dipankar AU - Reich, Brian J. AU - Slate, Elizabeth H. T2 - STATISTICS IN MEDICINE AB - Dental research gives rise to data with potentially complex correlation structure. Assessments of dental caries yield a binary outcome indicating the presence or absence of caries experience for each surface of each tooth in a subject's mouth. In addition to this nesting, caries outcome exhibit spatial structure among neighboring teeth. We develop a Bayesian multivariate model for spatial binary data using random effects autologistic regression that controls for the correlation within tooth surfaces and spatial correlation among neighboring teeth. Using a sample from a clinical study conducted at the Medical University of South Carolina, we compare this autologistic model with covariates to alternative models to demonstrate the improvement in predictions and also to assess the effects of covariates on caries experience. DA - 2009/12/10/ PY - 2009/12/10/ DO - 10.1002/sim.3647 VL - 28 IS - 28 SP - 3492-3508 SN - 1097-0258 KW - autologistic KW - binary KW - caries KW - MCMC KW - spatial KW - WinBUGS ER - TY - JOUR TI - A model for hormonal control of the menstrual cycle: Structural consistency but sensitivity with regard to data AU - Selgrade, J. F. AU - Harris, L. A. AU - Pasteur, R. D. T2 - JOURNAL OF THEORETICAL BIOLOGY AB - This study presents a 13-dimensional system of delayed differential equations which predicts serum concentrations of five hormones important for regulation of the menstrual cycle. Parameters for the system are fit to two different data sets for normally cycling women. For these best fit parameter sets, model simulations agree well with the two different data sets but one model also has an abnormal stable periodic solution, which may represent polycystic ovarian syndrome. This abnormal cycle occurs for the model in which the normal cycle has estradiol levels at the high end of the normal range. Differences in model behavior are explained by studying hysteresis curves in bifurcation diagrams with respect to sensitive model parameters. For instance, one sensitive parameter is indicative of the estradiol concentration that promotes pituitary synthesis of a large amount of luteinizing hormone, which is required for ovulation. Also, it is observed that models with greater early follicular growth rates may have a greater risk of cycling abnormally. DA - 2009/10/21/ PY - 2009/10/21/ DO - 10.1016/j.jtbi.2009.06.017 VL - 260 IS - 4 SP - 572-580 SN - 1095-8541 KW - Estradiol KW - Follicle KW - Parameter KW - Bifurcation ER - TY - CONF TI - ReFormat: Automatic reverse engineering of encrypted messages AU - Wang, Z. AU - Jiang, X. X. AU - Cui, W. D. AU - Wang, X. Y. AU - Grace, M. C2 - 2009/// C3 - Computer security - esorics 2009, proceedings DA - 2009/// VL - 5789 SP - 200-215 ER - TY - JOUR TI - Generalized Multilevel Functional Regression AU - Crainiceanu, Ciprian M. AU - Staicu, Ana-Maria AU - Di, Chong-Zhi T2 - JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION AB - We introduce Generalized Multilevel Functional Linear Models (GMFLMs), a novel statistical framework for regression models where exposure has a multilevel functional structure. We show that GMFLMs are, in fact, generalized multilevel mixed models (GLMMs). Thus, GMFLMs can be analyzed using the mixed effects inferential machinery and can be generalized within a well researched statistical framework. We propose and compare two methods for inference: 1) a two-stage frequentist approach; and 2) a joint Bayesian analysis. Our methods are motivated by and applied to the Sleep Heart Health Study (SHHS), the largest community cohort study of sleep. However, our methods are general and easy to apply to a wide spectrum of emerging biological and medical data sets. Supplemental materials for this article are available online. DA - 2009/12// PY - 2009/12// DO - 10.1198/jasa.2009.tm08564 VL - 104 IS - 488 SP - 1550-1561 SN - 1537-274X KW - Functional principal components KW - Sleep EEG KW - Smoothing ER - TY - CONF TI - Bayesian nonparametric approach to multiple testing AU - Ghosal, S. AU - Roy, A. C2 - 2009/// C3 - Perspectives in mathematical sciences i: probability and statistics DA - 2009/// VL - 7 SP - 139-164 ER - TY - JOUR TI - Automatic model selection for partially linear models AU - Ni, Xiao AU - Zhang, Hao Helen AU - Zhang, Daowen T2 - JOURNAL OF MULTIVARIATE ANALYSIS AB - We propose and study a unified procedure for variable selection in partially linear models. A new type of double-penalized least squares is formulated, using the smoothing spline to estimate the nonparametric part and applying a shrinkage penalty on parametric components to achieve model parsimony. Theoretically we show that, with proper choices of the smoothing and regularization parameters, the proposed procedure can be as efficient as the oracle estimator (Fan and Li, 2001). We also study the asymptotic properties of the estimator when the number of parametric effects diverges with the sample size. Frequentist and Bayesian estimates of the covariance and confidence intervals are derived for the estimators. One great advantage of this procedure is its linear mixed model (LMM) representation, which greatly facilitates its implementation by using standard statistical software. Furthermore, the LMM framework enables one to treat the smoothing parameter as a variance component and hence conveniently estimate it together with other regression coefficients. Extensive numerical studies are conducted to demonstrate the effective performance of the proposed procedure. DA - 2009/10// PY - 2009/10// DO - 10.1016/j.jmva.2009.06.009 VL - 100 IS - 9 SP - 2100-2111 SN - 0047-259X KW - Semiparametric regression KW - Smoothing splines KW - Smoothly clipped absolute deviation KW - Variable selection ER - TY - JOUR TI - Are electricity prices affected by the US dollar to Euro exchange rate? The Spanish case AU - Pilar Munoz, M. AU - Dickey, David A. T2 - ENERGY ECONOMICS AB - The objective of this paper is to investigate the relationships between Spanish electricity spot prices and the US dollar/Euro (USD/Euro) exchange rate during the period 2005–2007, taking into account the study of the association between dollar and oil prices, in order to better understand the evolution of the former over time. The first finding in this study is that Spanish electricity spots prices, the USD/Euro exchange rate and oil prices are cointegrated; therefore there is a long-run equilibrium relationship between the three variables. Short-run relationships have been detected between oil prices and Spanish electricity prices and USD/Euro exchange rate in the sense that Spanish electricity prices and USD/Euro exchange rate are affected by oil prices in the short run. There is a transmission of volatility between USD/Euro exchange rate and oil prices to Spanish electricity prices; so although Spanish electricity prices are not affected in level by the movements of USD/Euro exchange rate, they are in volatility. In this kind of scenario the conclusions confirm that for countries so dependent on external causes as Spain, one possible solution for guarantying the energy security would be the promotion of the renewable energies. Therefore we cannot ignore the impact in the internal expenses of the cost of installation and generation of green energies so there must be a balance between the increase in renewables and the reasonable market price of the electricity. DA - 2009/11// PY - 2009/11// DO - 10.1016/j.eneco.2009.05.011 VL - 31 IS - 6 SP - 857-866 SN - 1873-6181 KW - Electricity price KW - Exchange rate KW - Unit roots KW - Cointegration KW - Short and long-run relationships KW - Volatility ER - TY - JOUR TI - A Comparison of Analytical Methods for Genetic Association Studies (vol 32, pg 767, 2008) AU - Motsinger-Reif, Alison A. AU - Reif, David M. AU - Fanelli, Theresa J. AU - Ritchie, Marylyn D. T2 - GENETIC EPIDEMIOLOGY AB - Genetic EpidemiologyVolume 33, Issue 8 p. 751-751 ErratumFree Access A comparison of analytical methods for genetic association studies Alison A. Motsinger-Reif, Alison A. Motsinger-Reif Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, North CarolinaSearch for more papers by this authorDavid M. Reif, David M. Reif National Center for Computational Toxicology, US Environmental Protection Agency, Research Triangle Park, North CarolinaSearch for more papers by this authorTheresa J. Fanelli, Theresa J. Fanelli Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TennesseeSearch for more papers by this authorMarylyn D. Ritchie, Marylyn D. Ritchie Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TennesseeSearch for more papers by this author Alison A. Motsinger-Reif, Alison A. Motsinger-Reif Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, North CarolinaSearch for more papers by this authorDavid M. Reif, David M. Reif National Center for Computational Toxicology, US Environmental Protection Agency, Research Triangle Park, North CarolinaSearch for more papers by this authorTheresa J. Fanelli, Theresa J. Fanelli Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TennesseeSearch for more papers by this authorMarylyn D. Ritchie, Marylyn D. Ritchie Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TennesseeSearch for more papers by this author First published: 17 March 2009 https://doi.org/10.1002/gepi.20420AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume33, Issue8December 2009Pages 751-751 RelatedInformation DA - 2009/12// PY - 2009/12// DO - 10.1002/gepi.20420 VL - 33 IS - 8 SP - 751-751 SN - 0741-0395 ER - TY - JOUR TI - The Genetic Architecture of Maize Flowering Time AU - Buckler, Edward S. AU - Holland, James B. AU - Bradbury, Peter J. AU - Acharya, Charlotte B. AU - Brown, Patrick J. AU - Browne, Chris AU - Ersoz, Elhan AU - Flint-Garcia, Sherry AU - Garcia, Arturo AU - Glaubitz, Jeffrey C. AU - Goodman, Major M. AU - Harjes, Carlos AU - Guill, Kate AU - Kroon, Dallas E. AU - Larsson, Sara AU - Lepak, Nicholas K. AU - Li, Huihui AU - Mitchell, Sharon E. AU - Pressoir, Gael AU - Peiffer, Jason A. AU - Rosas, Marco Oropeza AU - Rocheford, Torbert R. AU - Cinta Romay, M. AU - Romero, Susan AU - Salvo, Stella AU - Sanchez Villeda, Hector AU - Silva, H. Sofia AU - Sun, Qi AU - Tian, Feng AU - Upadyayula, Narasimham AU - Ware, Doreen AU - Yates, Heather AU - Yu, Jianming AU - Zhang, Zhiwu AU - Kresovich, Stephen AU - McMullen, Michael D. T2 - SCIENCE AB - Flowering time is a complex trait that controls adaptation of plants to their local environment in the outcrossing species Zea mays (maize). We dissected variation for flowering time with a set of 5000 recombinant inbred lines (maize Nested Association Mapping population, NAM). Nearly a million plants were assayed in eight environments but showed no evidence for any single large-effect quantitative trait loci (QTLs). Instead, we identified evidence for numerous small-effect QTLs shared among families; however, allelic effects differ across founder lines. We identified no individual QTLs at which allelic effects are determined by geographic origin or large effects for epistasis or environmental interactions. Thus, a simple additive model accurately predicts flowering time for maize, in contrast to the genetic architecture observed in the selfing plant species rice and Arabidopsis. DA - 2009/8/7/ PY - 2009/8/7/ DO - 10.1126/science.1174276 VL - 325 IS - 5941 SP - 714-718 SN - 1095-9203 ER - TY - JOUR TI - Species-specific seed dispersal in an obligate ant-plant mutualism AU - Youngsteadt, E. AU - Baca, J. A. AU - Osborne, J. AU - Schal, C. T2 - PLoS One DA - 2009/// PY - 2009/// VL - 4 IS - 2 ER - TY - JOUR TI - Longitudinal data analysis using sufficient dimension reduction method AU - Li, Lexin AU - Yin, Xiangrong T2 - COMPUTATIONAL STATISTICS & DATA ANALYSIS AB - There have been an increasing number of applications where the number of predictors is large, meanwhile data are repeatedly measured at a sequence of time points. In this article we investigate how dimension reduction method can be employed for analyzing such high-dimensional longitudinal data. Predictor dimension can be effectively reduced while full regression means information can be retained during dimension reduction. Simultaneous variable selection along with dimension reduction is studied, and graphical diagnosis and model fitting after dimension reduction are investigated. The method is flexible enough to encompass a variety of commonly used longitudinal models. DA - 2009/10/1/ PY - 2009/10/1/ DO - 10.1016/j.csda.2009.04.018 VL - 53 IS - 12 SP - 4106-4115 SN - 1872-7352 ER - TY - JOUR TI - Influence of genetic background on tumor karyotypes: Evidence for breed-associated cytogenetic aberrations in canine appendicular osteosarcoma AU - Thomas, Rachael AU - Wang, Huixia J. AU - Tsai, Pei-Chien AU - Langford, Cordelia F. AU - Fosmire, Susan P. AU - Jubala, Cristan M. AU - Getzy, David M. AU - Cutter, Gary R. AU - Modiano, Jaime F. AU - Breen, Matthew T2 - CHROMOSOME RESEARCH AB - Recurrent chromosomal aberrations in solid tumors can reveal the genetic pathways involved in the evolution of a malignancy and in some cases predict biological behavior. However, the role of individual genetic backgrounds in shaping karyotypes of sporadic tumors is unknown. The genetic structure of purebred dog breeds, coupled with their susceptibility to spontaneous cancers, provides a robust model with which to address this question. We tested the hypothesis that there is an association between breed and the distribution of genomic copy number imbalances in naturally occurring canine tumors through assessment of a cohort of Golden Retrievers and Rottweilers diagnosed with spontaneous appendicular osteosarcoma. Our findings reveal significant correlations between breed and tumor karyotypes that are independent of gender, age at diagnosis, and histological classification. These data indicate for the first time that individual genetic backgrounds, as defined by breed in dogs, influence tumor karyotypes in a cancer with extensive genomic instability. DA - 2009/4// PY - 2009/4// DO - 10.1007/s10577-009-9028-z VL - 17 IS - 3 SP - 365-377 SN - 1573-6849 KW - microarray KW - comparative genomic hybridization (CGH) KW - canine KW - osteosarcoma KW - chromosome ER - TY - JOUR TI - Fully Automated Common Carotid Artery and Internal Jugular Vein Identification and Tracking Using B-Mode Ultrasound AU - Wang, David C. AU - Klatzky, Roberta AU - Wu, Bing AU - Weller, Gregory AU - Sampson, Allan R. AU - Stetten, George D. T2 - IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING AB - We describe a fully automated ultrasound analysis system that tracks and identifies the common carotid artery (CCA) and the internal jugular vein (IJV). Our goal is to prevent inadvertent damage to the CCA when targeting the IJV for catheterization. The automated system starts by identifying and fitting ellipses to all the regions that look like major arteries or veins throughout each B-mode ultrasound image frame. The spokes ellipse algorithm described in this paper tracks these putative vessels and calculates their characteristics, which are then weighted and summed to identify the vessels. The optimum subset of characteristics and their weights were determined from a training set of 38 subjects, whose necks were scanned with a portable 10 MHz ultrasound system at 10 frames per second. Stepwise linear discriminant analysis (LDA) narrowed the characteristics to the five that best distinguish between the CCA and IJV. A paired version of Fisher's LDA was used to calculate the weights for each of the five parameters. Leave-one-out validation studies showed that the system could track and identify the CCA and IJV with 100% accuracy in this dataset. DA - 2009/6// PY - 2009/6// DO - 10.1109/TBME.2009.2015576 VL - 56 IS - 6 SP - 1691-1699 SN - 0018-9294 KW - Biomedical acoustic imaging KW - biomedical engineering KW - biomedical image processing KW - blood vessels ER - TY - JOUR TI - Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci AU - Choi, S. C. AU - Stone, E. A. AU - Kishino, H. AU - Thorne, J. L. T2 - Gene AB - We consider the inference of which of two alleles is ancestral when the alleles have a single nonsynonymous difference and when natural selection acts via protein tertiary structure. Whereas the probability that an allele is ancestral under neutrality is equal to its frequency, under selection this probability depends on allele frequency and on the magnitude and direction of selection pressure. Although allele frequencies can be well estimated from intraspecific data, small fitness differences have a large evolutionary impact but can be difficult to estimate with only intraspecific data. Methods for predicting aspects of phenotype from genotype can supplement intraspecific sequence data. Recently developed statistical techniques can assess effects of phenotypes, such as protein tertiary structure on molecular evolution. While these techniques were initially designed for comparing protein-coding genes from different species, the resulting interspecific inferences can be assigned population genetic interpretations to assess the effect of selection pressure, and we use them here along with intraspecific allele frequency data to estimate the probability that an allele is ancestral. We focus on 140 nonsynonymous single nucleotide polymorphisms of humans that are in proteins with known tertiary structures. We find that our technique for employing protein tertiary structure information yields some biologically plausible results but that it does not substantially improve the inference of ancestral human allele types. DA - 2009/// PY - 2009/// DO - 10.1016/j.gene.2008.07.020 VL - 441 IS - 1-2 SP - 45-52 ER - TY - JOUR TI - Effective Protection of Open Space: Does Planning Matter? AU - Steelman, Toddi A. AU - Hess, George R. T2 - ENVIRONMENTAL MANAGEMENT DA - 2009/7// PY - 2009/7// DO - 10.1007/s00267-009-9272-1 VL - 44 IS - 1 SP - 93-104 SN - 0364-152X KW - Land protection KW - Stakeholder involvement KW - Land use planning KW - Natural resource protection KW - Implementation KW - North Carolina ER - TY - JOUR TI - Azithromycin treatment alters gene expression in inflammatory, lipid metabolism, and cell cycle pathways in well-differentiated human airway epithelia AU - Ribeiro, C. M. P. AU - Hurd, H. AU - Wu, Y. C. AU - Martino, M. E. B. AU - Jones, L. AU - Brighton, B. AU - Boucher, R. C. AU - O'Neal, W. K. T2 - PLoS One DA - 2009/// PY - 2009/// VL - 4 IS - 6 ER - TY - JOUR TI - Automated Design Space Exploration for DSP Applications AU - Hourani, Ramsey AU - Jenkal, Ravi AU - Davis, W. Rhett AU - Alexander, Winser T2 - JOURNAL OF SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY DA - 2009/9// PY - 2009/9// DO - 10.1007/s11265-008-0226-2 VL - 56 IS - 2-3 SP - 199-216 SN - 1939-8115 KW - Hardware design KW - VLSI KW - Synthesis KW - RTL KW - Area KW - Throughput KW - Power dissipation KW - DSP KW - FIR filter ER - TY - JOUR TI - Analysis of the effects of ultrafine particulate matter while accounting for human exposure AU - Reich, Brian J. AU - Fuentes, Montserrat AU - Burke, Janet T2 - ENVIRONMETRICS AB - Abstract Particulate matter (PM) has been associated with mortality in several epidemiological studies. The US EPA currently regulates PM 10 and PM 2.5 (mass concentration of particles with diameter less than 10 and 2.5 µm, respectively), but it is not clear which size of particles are most responsible for adverse heath outcomes. A current hypothesis is that ultrafine particles with diameter less than 0.1 µm are particularly harmful because their small size allows them to deeply penetrate the lungs. This paper investigates the association between exposure to particles of varying diameter and daily mortality. We propose a new dynamic factor analysis model to relate the ambient concentrations of several sizes of particles with diameters ranging from 0.01 to 0.40 µm with mortality. We introduce a Bayesian model that converts ambient concentrations into simulated personal exposure using the EPA's Stochastic Human Exposure and Dose Simulator, and relates simulated exposure with mortality. Using new data from Fresno, CA, we find that the 4‐day lag of particles with diameter between 0.02 and 0.08 µm is associated with mortality. This is consistent with the small particles hypothesis. Copyright © 2008 John Wiley & Sons, Ltd. DA - 2009/3// PY - 2009/3// DO - 10.1002/env.915 VL - 20 IS - 2 SP - 131-146 SN - 1099-095X KW - ecological fallacy KW - human exposure KW - dynamic factor model KW - SHEDS KW - ultrafine particles ER - TY - JOUR TI - Variable Selection in Bayesian Smoothing Spline ANOVA Models: Application to Deterministic Computer Codes AU - Reich, Brian J. AU - Storlie, Curtis B. AU - Bondell, Howard D. T2 - TECHNOMETRICS AB - With many predictors, choosing an appropriate subset of the covariates is a crucial, and difficult, step in nonparametric regression. We propose a Bayesian nonparametric regression model for curve-fitting and variable selection. We use the smoothing spline ANOVA framework to decompose the regression function into interpretable main effect and interaction functions. Stochastic search variable selection via MCMC sampling is used to search for models that fit the data well. Also, we show that variable selection is highly-sensitive to hyperparameter choice and develop a technique to select hyperparameters that control the long-run false positive rate. The method is used to build an emulator for a complex computer model for two-phase fluid flow. DA - 2009/5// PY - 2009/5// DO - 10.1198/TECH.2009.0013 VL - 51 IS - 2 SP - 110-120 SN - 1537-2723 KW - Bayesian hierarchical modeling KW - Markov chain Monte Carlo KW - Nonparametric regression KW - Smoothing splines ANOVA KW - Variable selection ER - TY - JOUR TI - The Third International Conference of Quantitative Genetics AU - Weir, Bruce S. AU - Hill, William G. AU - Zhu, Jun AU - Zeng, Zhao-Bang T2 - GENETICA AB - The third International Conference of Quantitative Genetics was held at Zheijiang University, Hangzhou, China from August 18 to 24, 2007. The papers of invited speakers at the conference comprise this issue of Genetica. The first ICQG was held in Ames, Iowa in 1976 and the second in Raleigh, North Carolina in 1987. Since the conference in Raleigh statistical techniques then in their infancy, such as QTL mapping and MCMC analysis, have become standard but still developing practices. New molecular techniques have enabled individual genes contributing to variation in quantitative traits to be identified. The new technologies of genomics and gene expression arrays provide new opportunities to understand the genetic basis of quantitative characters, but also new problems in statistical inference. The application of quantitative genetics has broadened from primarily animal and plant breeding into the genetics of human disease and the analyses of natural populations and their evolution. Indeed, it is now often termed the genetics of complex traits, in recognition of the fact that most diseases, for example, are not determined by just one or a handful of genes. The death of quantitative genetics has been forecast for 40 years or more; but it lives on, strongly. The wide range of topics and methods discussed in these papers show the diversity of applications of quantitative genetics and of the technologies employed. The conference was run as a single session in order to foster interactions and exchange of ideas and problems among those working on these different systems, species and technologies. In addition a number of selected short papers were presented in the oral sessions and others as posters. There were a total of 201 delegates at the conference, including 129 from outside the home country, who had opportunity to see and hear about research in quantitative genetics in China. Zhejiang University is one of the five most highly ranked research institutions in China, and arose from the merger of four specialist universities in the city. A new campus is being built and part of the University is already on that site. The City of Hangzhou is one of the seven ancient capital cities of China, and has many attractive features, including the famed West Lake. It is the capital city of Zheijiang province and has a population of nearly 4 million. Participants in Hangzhou considered intervals of 10 or 20 years far too long to enable adequate discussion and review of a changing subject, and that 5 years should be aimed for. Accordingly, the fourth conference will be held in Edinburgh in 2012. Those from outside the University are grateful to Jun Zhu and to the large team of staff and students at Zheijiang University led by Longjian Fan who undertook all the work and were exposed to the stresses and strains of managing a successful large conference. The conference and social events were excellent and provided many visitors their first exposure to Chinese culture. We are also grateful to Ron B. S. Weir Department of Biostatistics, University of Washington, Seattle, WA 98915, USA DA - 2009/6// PY - 2009/6// DO - 10.1007/s10709-008-9315-1 VL - 136 IS - 2 SP - 211-212 SN - 1573-6857 ER - TY - JOUR TI - Spatial-temporal association between fine particulate matter and daily mortality AU - Choi, Jungsoon AU - Fuentes, Montserrat AU - Reich, Brian J. T2 - COMPUTATIONAL STATISTICS & DATA ANALYSIS AB - Fine particulate matter (PM(2.5)) is a mixture of pollutants that has been linked to serious health problems, including premature mortality. Since the chemical composition of PM(2.5) varies across space and time, the association between PM(2.5) and mortality could also change with space and season. In this work we develop and implement a statistical multi-stage Bayesian framework that provides a very broad, flexible approach to studying the spatiotemporal associations between mortality and population exposure to daily PM(2.5) mass, while accounting for different sources of uncertainty. In stage 1, we map ambient PM(2.5) air concentrations using all available monitoring data (IMPROVE and FRM) and an air quality model (CMAQ) at different spatial and temporal scales. In stage 2, we examine the spatial temporal relationships between the health end-points and the exposures to PM(2.5) by introducing a spatial-temporal generalized Poisson regression model. We adjust for time-varying confounders, such as seasonal trends. A common seasonal trends model is to use a fixed number of basis functions to account for these confounders, but the results can be sensitive to the number of basis functions. In this study, the number of the basis functions is treated as an unknown parameter in our Bayesian model and we use a space-time stochastic search variable selection approach. We apply our methods to a data set in North Carolina for the year 2001. DA - 2009/6/15/ PY - 2009/6/15/ DO - 10.1016/j.csda.2008.05.018 VL - 53 IS - 8 SP - 2989-3000 SN - 1872-7352 ER - TY - JOUR TI - Separating the influence of resource 'availability' from resource 'imbalance' on productivity-diversity relationships AU - Cardinale, Bradley J. AU - Hillebrand, Helmut AU - Harpole, W. S. AU - Gross, Kevin AU - Ptacnik, Robert T2 - ECOLOGY LETTERS AB - One of the oldest and richest questions in biology is that of how species diversity is related to the availability of resources that limit the productivity of ecosystems. Researchers from a variety of disciplines have pursued this question from at least three different theoretical perspectives. Species energy theory has argued that the summed quantities of all resources influence species richness by controlling population sizes and the probability of stochastic extinction. Resource ratio theory has argued that the imbalance in the supply of two or more resources, relative to the stoichiometric needs of the competitors, can dictate the strength of competition and, in turn, the diversity of coexisting species. In contrast to these, the field of Biodiversity and Ecosystem Functioning has argued that species diversity acts as an independent variable that controls how efficiently limited resources are utilized and converted into new tissue. Here we propose that all three of these fields give necessary, but not sufficient, conditions to explain productivity-diversity relationships (PDR) in nature. However, when taken collectively, these three paradigms suggest that PDR can be explained by interactions among four distinct, non-interchangeable variables: (i) the overall quantity of limiting resources, (ii) the stoichiometric ratios of different limiting resources, (iii) the summed biomass produced by a group of potential competitors and (iv) the richness of co-occurring species in a local competitive community. We detail a new multivariate hypothesis that outlines one way in which these four variables are directly and indirectly related to one another. We show how the predictions of this model can be fit to patterns of covariation relating the richness and biomass of lake phytoplankton to three biologically essential resources (N, P and light) in a large number of Norwegian lakes. DA - 2009/6// PY - 2009/6// DO - 10.1111/j.1461-0248.2009.01317.x VL - 12 IS - 6 SP - 475-487 SN - 1461-0248 KW - Biodiversity and ecosystem functioning KW - resource ratio theory KW - species energy theory ER - TY - JOUR TI - Locally Weighted Censored Quantile Regression AU - Wang, Huixia Judy AU - Wang, Lan T2 - JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION AB - Abstract Censored quantile regression offers a valuable supplement to Cox proportional hazards model for survival analysis. Existing work in the literature often requires stringent assumptions, such as unconditional independence of the survival time and the censoring variable or global linearity at all quantile levels. Moreover, some of the work uses recursive algorithms, making it challenging to derive asymptotic normality. To overcome these drawbacks, we propose a new locally weighted censored quantile regression approach that adopts the redistribution-of-mass idea and employs a local reweighting scheme. Its validity only requires conditional independence of the survival time and the censoring variable given the covariates, and linearity at the particular quantile level of interest. Our method leads to a simple algorithm that can be conveniently implemented with R software. Applying recent theory of M-estimation with infinite dimensional parameters, we establish the consistency and asymptotic normality of the proposed estimator. The proposed method is studied via simulations and is illustrated with the analysis of an acute myocardial infarction dataset. Keywords: : Kaplan–Meier estimatorKernelQuantile regressionRandom censoringSemiparametricSurvival analysis DA - 2009/9// PY - 2009/9// DO - 10.1198/jasa.2009.tm08230 VL - 104 IS - 487 SP - 1117-1128 SN - 0162-1459 KW - Kaplan-Meier estimator KW - Kernel KW - Quantile regression KW - Random censoring KW - Semiparametric KW - Survival analysis ER - TY - JOUR TI - Introduction to this special issue on statistics for wildfire processes AU - Gumpertz, Marcia T2 - ENVIRONMENTAL AND ECOLOGICAL STATISTICS AB - This special issue on statistics for wildfire processes brings together foresters, wildfire ecologists, statisticians,mathematicians, and economists. All of these disciplines bring different interests, approaches and expertise to the modeling of wildfire processes. It is not necessarily easy, however, to communicate across disciplines or follow the developments in a variety of fields. Hence, the papers in this issue are primarily expository in nature, with the goal of facilitating and cross-fertilizing cross-disciplinary research on wildfire modeling. The papers in this issue were first presented in two conferences that brought wildfire modelers together. The first seed of the idea for the special issue was planted in a theme session of the 2005 annual meeting of the Eastern North American Region (ENAR) of the Biometric Society in Austin, TX, titled “Statistical Analysis of Wildfire Data.” The project was fertilized and grew in May of that year at a 5-day “Workshop on Forest Fires and Point Processes” at the Fields Institute in Toronto. This issue begins with a paper by B. M. Wotton explaining the Canadian forest fire danger rating system, which is used by Canadian fire management agencies. Fire managers usemodels to help predict forest fire growth and intensity andmakedecisions each day about where to position fire fighting resources. This paper gives statistical modelers a view of these uses of fire models, the current types of models employed by fire managers, and the need for understanding how the relationship between the Canadian Fire Weather Index System outputs and fuel moisture and the probability of fire occurrence vary among regions of the country and forest types. The next two papers describe ideas for stochastic wildfire models that could potentially be used for forecasting the spread of fires that have already started. The first of these, by Boychuk et al., describes a model in which fire spreads from cell to DA - 2009/6// PY - 2009/6// DO - 10.1007/s10651-007-0081-5 VL - 16 IS - 2 SP - 105-106 SN - 1352-8505 ER - TY - JOUR TI - Heart rate as a sublethal indicator of thermal stress in juvenile freshwater mussels AU - Pandolfo, Tamara J. AU - Cope, W. Gregory AU - Arellano, Consuelo T2 - COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY AB - Freshwater mussels (Unionoida) are one of the most sensitive and rapidly declining faunal groups in the world. Rising water temperatures, caused by industrial discharges, land development, or climate change can further challenge threatened unionid communities. The direct relationship between heart rate and temperature in ectotherms enables the use of heart rate as an indicator of whole-animal thermal stress. The purpose of this study was to assess the utility of heart rate as an indicator of thermal stress in freshwater mussels. Seven species of juvenile mussels (Lampsilis siliquoidea, Potamilus alatus, Ligumia recta, Ellipsaria lineolata, Megalonaias nervosa, Alasmidonta varicosa, and Villosa delumbis) were evaluated in response to a range of experimental temperatures (20–36 °C) at three acclimation temperatures (17, 22, and 27 °C). Heart rate was measured by direct visual observation through transparent mussel shells. The average heart rate for all 7 species at 20 °C was 55 bpm, with a range from 38 bpm (L. recta) to 65 bpm (P. alatus). L. recta and V. delumbis exhibited significant changes in heart rate with increasing temperature at each of the three acclimation temperatures. The use of heart rate appears to be a suitable indicator of thermal stress in some unionid mussels. DA - 2009/11// PY - 2009/11// DO - 10.1016/j.cbpa.2009.07.001 VL - 154 IS - 3 SP - 347-352 SN - 1531-4332 KW - Freshwater mussel KW - Heart rate KW - Temperature KW - Thermal stress KW - Unionidae ER - TY - JOUR TI - Evaluation of a Shape Memory Alloy Reinforced Annuloplasty Band for Minimally Invasive Mitral Valve Repair AU - Purser, Molly F. AU - Richards, Andrew L. AU - Cook, Richard C. AU - Osborne, Jason A. AU - Cormier, Denis R. AU - Buckner, Gregory D. T2 - ANNALS OF THORACIC SURGERY AB - An in vitro study using explanted porcine hearts was conducted to evaluate a novel annuloplasty band, reinforced with a two-phase, shape memory alloy, designed specifically for minimally invasive mitral valve repair.In its rigid (austenitic) phase, this band provides the same mechanical properties as the commercial semi-rigid bands. In its compliant (martensitic) phase, this band is flexible enough to be introduced through an 8-mm trocar and is easily manipulated within the heart.In its rigid phase, the prototype band displayed similar mechanical properties to commercially available semi-rigid rings. Dynamic flow testing demonstrated no statistical differences in the reduction of mitral valve regurgitation. In its flexible phase, the band was easily deployed through an 8-mm trocar, robotically manipulated and sutured into place.Experimental results suggest that the shape memory alloy reinforced band could be a viable alternative to flexible and semi-rigid bands in minimally invasive mitral valve repair. DA - 2009/10// PY - 2009/10// DO - 10.1016/j.athoracsur.2009.04.133 VL - 88 IS - 4 SP - 1312-1316 SN - 1552-6259 ER - TY - JOUR TI - Efficiency comparison between mean and log-rank tests for recurrent event time data AU - WenBin, Lu T2 - SCIENCE IN CHINA SERIES A-MATHEMATICS DA - 2009/6// PY - 2009/6// DO - 10.1007/s11425-009-0059-x VL - 52 IS - 6 SP - 1169-1180 SN - 1006-9283 KW - asymptotic relative efficiency KW - frailty model KW - log-rank test KW - proportional mean test KW - recurrent events KW - robust variance estimation ER - TY - JOUR TI - Creating effective poster presentations: AMEE Guide no. 40 AU - Hess, George R. AU - Tosney, Kathryn W. AU - Liegel, Leon H. T2 - MEDICAL TEACHER AB - Poster presentations have become an important part of professional meetings and are recognized as valuable tools for teaching and assessment. An effective poster is a visual communication tool that will help you engage colleagues in conversation, convey your main point to large numbers of people, and advertise your work. An effective poster is a highly condensed version of a research paper constructed primarily of visual displays of data with just enough supporting text to provide context, interpretation, and conclusions. A new AMEE Guide, 'Creating Effective Poster Presentations', provides guidance and is illustrated with annotated examples. DA - 2009/// PY - 2009/// DO - 10.1080/01421590902825131 VL - 31 IS - 4 SP - 356-358 SN - 0142-159X ER - TY - JOUR TI - Courses without Borders?: Collaborative graduate education across multiple campuses AU - Thompson, J. R. AU - Hess, G. R. AU - Bowman, T. A. AU - Magnusdottir, H. AU - Stubbs-Gipson, C. E. AU - Groom, M. AU - Miller, J. R. AU - Steelman, T. A. AU - Stokes, D. L. T2 - Journal of Natural Resources and Life Sciences Education DA - 2009/// PY - 2009/// VL - 38 ER - TY - JOUR TI - Analysis of Viscoelastic Wall Properties in Ovine Arteries AU - Valdez-Jasso, Daniela AU - Haider, Mansoor A. AU - Banks, H. T. AU - Santana, Daniel Bia AU - German, Yanina Zocalo AU - Armentano, Ricardo L. AU - Olufsen, Mette S. T2 - IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING AB - In this paper, we analyze how elastic and viscoelastic properties differ across seven locations along the large arteries in 11 sheep. We employ a two-parameter elastic model and a four-parameter Kelvin viscoelastic model to analyze experimental measurements of vessel diameter and blood pressure obtained in vitro at conditions mimicking in vivo dynamics. Elastic and viscoelastic wall properties were assessed via solutions to the associated inverse problem. We use sensitivity analysis to rank the model parameters from the most to the least sensitive, as well as to compute standard errors and confidence intervals. Results reveal that elastic properties in both models (including Young's modulus and the viscoelastic relaxation parameters) vary across locations (smaller arteries are stiffer than larger arteries). We also show that for all locations, the inclusion of viscoelastic behavior is important to capture pressure-area dynamics. DA - 2009/2// PY - 2009/2// DO - 10.1109/TBME.2008.2003093 VL - 56 IS - 2 SP - 210-219 SN - 1558-2531 KW - Arterial wall properties KW - data analysis KW - mathematical modeling KW - mechanics KW - parameter estimation KW - viscoelasticity ER - TY - JOUR TI - Analysis of Stability and Dispersion in a Finite Element Method for Debye and Lorentz Dispersive Media AU - Banks, H. T. AU - Bokil, V. A. AU - Gibson, N. L. T2 - NUMERICAL METHODS FOR PARTIAL DIFFERENTIAL EQUATIONS AB - Abstract We study the stability properties of, and the phase error present in, a finite element scheme for Maxwell's equations coupled with a Debye or Lorentz polarization model. In one dimension we consider a second order formulation for the electric field with an ordinary differential equation for the electric polarization added as an auxiliary constraint. The finite element method uses linear finite elements in space for the electric field as well as the electric polarization, and a theta scheme for the time discretization. Numerical experiments suggest the method is unconditionally stable for both Debye and Lorentz models. We compare the stability and phase error properties of the method presented here with those of finite difference methods that have been analyzed in the literature. We also conduct numerical simulations that verify the stability and dispersion properties of the scheme. © 2008 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2009 DA - 2009/7// PY - 2009/7// DO - 10.1002/num.20379 VL - 25 IS - 4 SP - 885-917 SN - 0749-159X KW - Maxwell's equations KW - Debye KW - Lorentz KW - finite elements KW - FDTD KW - dissipation KW - dispersion ER - TY - JOUR TI - An autoregressive point source model for spatial processes AU - Hughes-Oliver, Jacqueline M. AU - Heo, Tae-Young AU - Ghosh, Sujit K. T2 - ENVIRONMETRICS AB - We suggest a parametric modeling approach for nonstationary spatial processes driven by point sources. Baseline near-stationarity, which may be reasonable in the absence of a point source, is modeled using a conditional autoregressive (CAR) Markov random field. Variability due to the point source is captured by our proposed autoregressive point source (ARPS) model. Inference proceeds according to the Bayesian hierarchical paradigm, and is implemented using Markov chain Monte Carlo (MCMC) methods. The parametric approach allows a formal test of effectiveness of the point source. Application is made to a real dataset on electric potential measurements in a field containing a metal pole and the finding is that our approach captures the pole's impact on small-scale variability of the electric potential process. DA - 2009/8// PY - 2009/8// DO - 10.1002/env.957 VL - 20 IS - 5 SP - 575-594 SN - 1099-095X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-68149096814&partnerID=MN8TOARS KW - Bayesian inference KW - correlation nonstationarity KW - heterogeneity KW - hierarchical model KW - random effect KW - variance nonstationarity ER - TY - JOUR TI - A stochastic neighborhood conditional autoregressive model for spatial data AU - White, Gentry AU - Ghosh, Sujit K. T2 - COMPUTATIONAL STATISTICS & DATA ANALYSIS AB - A spatial process observed over a lattice or a set of irregular regions is usually modeled using a conditionally autoregressive (CAR) model. The neighborhoods within a CAR model are generally formed deterministically using the inter-distances or boundaries between the regions. An extension of CAR model is proposed in this article where the selection of the neighborhood depends on unknown parameter(s). This extension is called a Stochastic Neighborhood CAR (SNCAR) model. The resulting model shows flexibility in accurately estimating covariance structures for data generated from a variety of spatial covariance models. Specific examples are illustrated using data generated from some common spatial covariance functions as well as real data concerning radioactive contamination of the soil in Switzerland after the Chernobyl accident. DA - 2009/6/15/ PY - 2009/6/15/ DO - 10.1016/j.csda.2008.08.010 VL - 53 IS - 8 SP - 3033-3046 SN - 1872-7352 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-62849092527&partnerID=MN8TOARS ER - TY - JOUR TI - A new object-oriented method of impervious surface classification using feature analyst AU - Miller, J. A. AU - Nelson, S. A. C. AU - Hess, G. R. T2 - Professional Geographer DA - 2009/// PY - 2009/// VL - 61 SP - 1-15 ER - TY - JOUR TI - Sorghum sudangrass as a summer cover and hay crop for organic fall cabbage production AU - Finney, Denise M. AU - Creamer, Nancy G. AU - Schultheis, Jonathan R. AU - Wagger, Michael G. AU - Brownie, Cavell T2 - RENEWABLE AGRICULTURE AND FOOD SYSTEMS AB - Abstract No-tillage (NT) organic vegetable production presents several economic opportunities for growers in the southeastern United States while promoting natural resource conservation. This study was conducted to determine if removal of sorghum sudangrass (SS) cover crop biomass as hay, frequency at which the cover crop is mowed, and tillage affect weed suppression and head weight of transplanted organic cabbage. Sorghum sudangrass [ Sorghum bicolor (L.) Moench× Sorgum sudanense (Piper) Staph.] was planted in May 2004 at Reidsville and Goldsboro, NC, preceding the planting of organic ‘Bravo’ cabbage ( Brassica oleracea L. Capitata group) in August and September 2004, respectively. SS management systems included: low-frequency mowing with hay removed following the first mowing operation (LFM-H), low-frequency mowing with hay not removed (LFM), high-frequency mowing with hay not removed (HFM) and a no cover crop control. Two tillage treatments were applied within each management system: conventional tillage (CT) and NT. Under NT conditions, SS mulch generated by LFM offered broadleaf weed control in cabbage similar to that achieved under CT, regardless of whether cover crop biomass was removed as hay. Mowing with higher frequency reduced SS cover crop biomass by 18–33% and reduced weed suppression in NT cabbage. Mowing frequency did not influence the quantity of SS that re-grew in the cabbage crop. SS re-growth contributed to lower head weight in NT compared to CT cabbage in Goldsboro, and crop failure of NT cabbage in Reidsville. Cabbage head weight was highest when the crop was not preceded by SS in both CT and NT systems (1.6 as opposed to 1.3–1.4 kg head −1 ). Our findings suggest that the potential for growers to manage a cover crop also as a hay crop does exist; however, SS may not be a compatible cover crop species for organic fall cabbage production due to high amounts of re-growth. DA - 2009/9// PY - 2009/9// DO - 10.1017/S174217050999007X VL - 24 IS - 3 SP - 225-233 SN - 1742-1713 KW - Sorghum bicolor x Sorghum sudanense KW - Brassica oleracea KW - no-tillage KW - conservation tillage KW - organic vegetable production KW - cover cropping KW - weed management ER - TY - JOUR TI - Plant species loss decreases arthropod diversity and shifts trophic structure AU - Haddad, Nick M. AU - Crutsinger, Gregory M. AU - Gross, Kevin AU - Haarstad, John AU - Knops, Johannes M. H. AU - Tilman, David T2 - ECOLOGY LETTERS AB - Abstract Plant diversity is predicted to be positively linked to the diversity of herbivores and predators in a foodweb. Yet, the relationship between plant and animal diversity is explained by a variety of competing hypotheses, with mixed empirical results for each hypothesis. We sampled arthropods for over a decade in an experiment that manipulated the number of grassland plant species. We found that herbivore and predator species richness were strongly, positively related to plant species richness, and that these relationships were caused by different mechanisms at herbivore and predator trophic levels. Even more dramatic was the threefold increase, from low‐ to high‐plant species richness, in abundances of predatory and parasitoid arthropods relative to their herbivorous prey. Our results demonstrate that, over the long term, the loss of plant species propagates through food webs, greatly decreasing arthropod species richness, shifting a predator‐dominated trophic structure to being herbivore dominated, and likely impacting ecosystem functioning and services. DA - 2009/10// PY - 2009/10// DO - 10.1111/j.1461-0248.2009.01356.x VL - 12 IS - 10 SP - 1029-1039 SN - 1461-0248 KW - Arthropods KW - biodiversity KW - consumers KW - ecosystem function KW - herbivores KW - insects KW - long-term KW - plant diversity KW - predators KW - trophic structure ER - TY - JOUR TI - ON THE ADAPTIVE ELASTIC-NET WITH A DIVERGING NUMBER OF PARAMETERS AU - Zou, Hui AU - Zhang, Hao Helen T2 - ANNALS OF STATISTICS AB - We consider the problem of model selection and estimation in situations where the number of parameters diverges with the sample size. When the dimension is high, an ideal method should have the oracle property (Fan and Li, 2001; Fan and Peng, 2004) which ensures the optimal large sample performance. Furthermore, the high-dimensionality often induces the collinearity problem which should be properly handled by the ideal method. Many existing variable selection methods fail to achieve both goals simultaneously. In this paper, we propose the adaptive Elastic-Net that combines the strengths of the quadratic regularization and the adaptively weighted lasso shrinkage. Under weak regularity conditions, we establish the oracle property of the adaptive Elastic-Net. We show by simulations that the adaptive Elastic-Net deals with the collinearity problem better than the other oracle-like methods, thus enjoying much improved finite sample performance. DA - 2009/8// PY - 2009/8// DO - 10.1214/08-AOS625 VL - 37 IS - 4 SP - 1733-1751 SN - 0090-5364 KW - Adaptive regularization KW - elastic-net KW - high dimensionality KW - model selection KW - oracle property KW - shrinkage methods ER - TY - JOUR TI - Multiple testing in genome-wide association studies via hidden Markov models AU - Wei, Zhi AU - Sun, Wenguang AU - Wang, Kai AU - Hakonarson, Hakon T2 - BIOINFORMATICS AB - Genome-wide association studies (GWAS) interrogate common genetic variation across the entire human genome in an unbiased manner and hold promise in identifying genetic variants with moderate or weak effect sizes. However, conventional testing procedures, which are mostly P-value based, ignore the dependency and therefore suffer from loss of efficiency. The goal of this article is to exploit the dependency information among adjacent single nucleotide polymorphisms (SNPs) to improve the screening efficiency in GWAS.We propose to model the linear block dependency in the SNP data using hidden Markov models (HMMs). A compound decision-theoretic framework for testing HMM-dependent hypotheses is developed. We propose a powerful data-driven procedure [pooled local index of significance (PLIS)] that controls the false discovery rate (FDR) at the nominal level. PLIS is shown to be optimal in the sense that it has the smallest false negative rate (FNR) among all valid FDR procedures. By re-ranking significance for all SNPs with dependency considered, PLIS gains higher power than conventional P-value based methods. Simulation results demonstrate that PLIS dominates conventional FDR procedures in detecting disease-associated SNPs. Our method is applied to analysis of the SNP data from a GWAS of type 1 diabetes. Compared with the Benjamini-Hochberg (BH) procedure, PLIS yields more accurate results and has better reproducibility of findings.The genomic rankings based on our procedure are substantially different from the rankings based on the P-values. By integrating information from adjacent locations, the PLIS rankings benefit from the increased signal-to-noise ratio, hence our procedure often has higher statistical power and better reproducibility. It provides a promising direction in large-scale GWAS.An R package PLIS has been developed to implement the PLIS procedure. Source codes are available upon request and will be available on CRAN (http://cran.r-project.org/).zhiwei@njit.eduSupplementary data are available at Bioinformatics online. DA - 2009/11/1/ PY - 2009/11/1/ DO - 10.1093/bioinformatics/btp476 VL - 25 IS - 21 SP - 2802-2808 SN - 1460-2059 ER - TY - JOUR TI - Multiple interval mapping for gene expression QTL analysis AU - Zou, Wei AU - Zeng, Zhao-Bang T2 - GENETICA DA - 2009/11// PY - 2009/11// DO - 10.1007/s10709-009-9365-z VL - 137 IS - 2 SP - 125-134 SN - 1573-6857 KW - eQTL KW - FDR KW - MIM KW - Model selection ER - TY - JOUR TI - Latent-Model Robustness in Joint Models for a Primary Endpoint and a Longitudinal Process AU - Huang, Xianzheng AU - Stefanski, Leonard A. AU - Davidian, Marie T2 - BIOMETRICS AB - Summary Joint modeling of a primary response and a longitudinal process via shared random effects is widely used in many areas of application. Likelihood‐based inference on joint models requires model specification of the random effects. Inappropriate model specification of random effects can compromise inference. We present methods to diagnose random effect model misspecification of the type that leads to biased inference on joint models. The methods are illustrated via application to simulated data, and by application to data from a study of bone mineral density in perimenopausal women and data from an HIV clinical trial. DA - 2009/9// PY - 2009/9// DO - 10.1111/j.1541-0420.2008.01171.x VL - 65 IS - 3 SP - 719-727 SN - 1541-0420 KW - Censoring KW - Random effect KW - Remeasurement method KW - SIMEX ER - TY - JOUR TI - Joint Modeling and Analysis of Longitudinal Data with Informative Observation Times AU - Liang, Yu AU - Lu, Wenbin AU - Ying, Zhiliang T2 - BIOMETRICS AB - Summary In analysis of longitudinal data, it is often assumed that observation times are predetermined and are the same across study subjects. Such an assumption, however, is often violated in practice. As a result, the observation times may be highly irregular. It is well known that if the sampling scheme is correlated with the outcome values, the usual statistical analysis may yield bias. In this article, we propose joint modeling and analysis of longitudinal data with possibly informative observation times via latent variables. A two‐step estimation procedure is developed for parameter estimation. We show that the resulting estimators are consistent and asymptotically normal, and that the asymptotic variance can be consistently estimated using the bootstrap method. Simulation studies and a real data analysis demonstrate that our method performs well with realistic sample sizes and is appropriate for practical use. DA - 2009/6// PY - 2009/6// DO - 10.1111/j.1541-0420.2008.01104.x VL - 65 IS - 2 SP - 377-384 SN - 1541-0420 KW - Estimating equation KW - Frailty model KW - Informative follow-up KW - Longitudinal data KW - Semiparametric mixed effects model ER - TY - JOUR TI - Hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16S rRNA in the 30S ribosome AU - Huggins, W. AU - Ghosh, Sujit K. AU - Wollenzien, P. T2 - BMC Structural Biology AB - Conformational flexibility in structured RNA frequently is critical to function. The 30S ribosomal subunit exists in different conformations in different functional states due to changes in the central part of the 16S rRNA. We are interested in evaluating the factors that might be responsible for restricting flexibility to specific parts of the 16S rRNA using biochemical data obtained from the 30S subunit in solution. This problem was approached taking advantage of the observation that there must be a high degree of conformational flexibility at sites where UV photocrosslinking occurs and a lack of flexibility inhibits photoreactivity at many other sites that are otherwise suitable for reaction.We used 30S x-ray structures to quantify the properties of the nucleotide pairs at UV- and UVA-s4U-induced photocrosslinking sites in 16S rRNA and compared these to the properties of many hundreds of additional sites that have suitable geometry but do not undergo photocrosslinking. Five factors that might affect RNA flexibility were investigated - RNA interactions with ribosomal proteins, interactions with Mg2+ ions, the presence of long-range A minor motif interactions, hydrogen bonding and the count of neighboring heavy atoms around the center of each nucleobase to estimate the neighbor packing density. The two factors that are very different in the unreactive inflexible pairs compared to the reactive ones are the average number of hydrogen bonds and the average value for the number of neighboring atoms. In both cases, these factors are greater for the unreactive nucleotide pairs at a statistically very significant level.The greater extent of hydrogen bonding and neighbor atom density in the unreactive nucleotide pairs is consistent with reduced flexibility at a majority of the unreactive sites. The reactive photocrosslinking sites are clustered in the 30S subunit and this indicates nonuniform patterns of hydrogen bonding and packing density in the 16S rRNA tertiary structure. Because this analysis addresses inter-nucleotide distances and geometry between nucleotides distant in the primary sequence, the results indicate regional and global flexibility of the rRNA. DA - 2009/// PY - 2009/// DO - 10.1186/1472-6807-9-49 VL - 9 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-69249197790&partnerID=MN8TOARS ER - TY - JOUR TI - Field Study of the Ability of Two Grassed Bioretention Cells to Reduce Storm-Water Runoff Pollution AU - Passeport, Elodie AU - Hunt, William F. AU - Line, Daniel E. AU - Smith, Ryan A. AU - Brown, Robert A. T2 - JOURNAL OF IRRIGATION AND DRAINAGE ENGINEERING AB - Two grassed bioretention cells including internal storage zones (ISZs) were monitored for 16months in central North Carolina. Each cell had a surface area of 106m2 and fill media depths were 0.75 and 1.05m for the north (North) and the south (South) cells, respectively. Asphalt parking lot inflow and outflows were analyzed for nitrogen and phosphorus forms and fecal coliform (FC). Outflow volumes and peak flows for individual storms were generally less than those of inflow. Overall, except for NO2,3–N , effluent nitrogen species event mean concentrations (EMCs) and loads were significantly (α=0.05) lower than those of the inflow, and nitrogen species load reductions ranged from 47 to 88%. Apart from fall and winter, during which a longer hydraulic contact time seemed to be needed, the ISZs appeared to improve denitrification. Total phosphorus (TP) and OPO4-P EMCs were significantly lower than those of the inlet. Reductions were 58% (South) and 63% (North) for TP and 78% (North) and 74% (South) for OPO4–P . There was no significant difference in TP and OPO4–P loads between the inlet and the two outlets. Moreover, effluent concentrations for both phosphorus species were low, relative to other studies. The best nutrient EMC and load reductions occurred during the warm and humid seasons. When considering effluent concentrations in addition to removal rates, the grassed cells showed promising results for FC and nutrient pollution abatement when compared to conventionally vegetated bioretention (trees, shrubs, and mulch) previously studied in North Carolina. DA - 2009/// PY - 2009/// DO - 10.1061/(ASCE)IR.1943-4774.0000006 VL - 135 IS - 4 SP - 505-510 SN - 1943-4774 ER - TY - JOUR TI - Fast FSR Variable Selection with Applications to Clinical Trials AU - Boos, Dennis D. AU - Stefanski, Leonard A. AU - Wu, Yujun T2 - BIOMETRICS AB - A new version of the false selection rate variable selection method of Wu, Boos, and Stefanski (2007, Journal of the American Statistical Association 102, 235-243) is developed that requires no simulation. This version allows the tuning parameter in forward selection to be estimated simply by hand calculation from a summary table of output even for situations where the number of explanatory variables is larger than the sample size. Because of the computational simplicity, the method can be used in permutation tests and inside bagging loops for improved prediction. Illustration is provided in clinical trials for linear regression, logistic regression, and Cox proportional hazards regression. DA - 2009/9// PY - 2009/9// DO - 10.1111/j.1541-0420.2008.01127.x VL - 65 IS - 3 SP - 692-700 SN - 1541-0420 KW - Bagging KW - False discovery rate KW - False selection rate KW - Forward selection KW - LASSO KW - Model error KW - Model selection KW - Regression ER - TY - JOUR TI - Effect of Heliothis subflexa herbivory on fruit abscission by Physalis species: the roles of mechanical damage and chemical factors AU - Petzold, Jennifer AU - Brownie, Cavell AU - Gould, Fred T2 - ECOLOGICAL ENTOMOLOGY AB - Abstract. 1. Insect oral secretions are important for the induction of a number of plant responses, but the relative role of mechanical damage in the induction of these responses is often not well understood. Damage from the frugivore Heliothis subflexa , a specialist on Physalis species, causes herbivore‐induced fruit abscission. In this field study, we examined the separate and combined effects of mechanical damage and H. subflexa oral secretions on Physalis fruit abscission. 2. To determine the relative role of mechanical and chemical factors, the following treatments were administered to fruit: (1) three levels of mechanical damage, (2) natural herbivore damage by control larvae and by larvae surgically treated to inhibit saliva secretion, and (3) injection of H. subflexa oral secretions and a water control. Abscission of mechanically damaged fruit with and without the addition of oral secretions was also compared. 3. Mechanical damage was sufficient to cause fruit abscission, and the addition of oral secretions to mechanically damaged fruit did not cause an increase in fruit abscission. Normal caterpillars and those treated to inhibit saliva secretion caused similar abscission rates. 4. Though most studies examining the effects of insect oral secretions on induced plant responses find these chemical stimuli to be important or essential, the results of the present study showed that oral secretions are not necessary for fruit abscission. Future work is needed to determine the relative importance of mechanical damage in herbivore‐induced plant responses in other systems. DA - 2009/10// PY - 2009/10// DO - 10.1111/j.1365-2311.2009.01109.x VL - 34 IS - 5 SP - 603-613 SN - 1365-2311 KW - Fruit abscission KW - Heliothis subflexa KW - herbivore-induced plant defences KW - insect oral secretions KW - mechanical damage KW - Physalis ER - TY - JOUR TI - Dimension Reduction in Regressions With Exponential Family Predictors AU - Cook, R. Dennis AU - Li, Lexin T2 - JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS AB - We present first methodology for dimension reduction in regressions with predictors that, given the response, follow one-parameter exponential families. Our approach is based on modeling the conditional distribution of the predictors given the response, which allows us to derive and estimate a sufficient reduction of the predictors. We also propose a method of estimating the forward regression mean function without requiring an explicit forward regression model. Whereas nearly all existing estimators of the central subspace are limited to regressions with continuous predictors only, our proposed methodology extends estimation to regressions with all categorical or a mixture of categorical and continuous predictors. Supplementary materials including the proofs and the computer code are available from the JCGS website. DA - 2009/9// PY - 2009/9// DO - 10.1198/jcgs.2009.08005 VL - 18 IS - 3 SP - 774-791 SN - 1537-2715 KW - Central subspace KW - Grassmann manifolds KW - Inverse regression KW - Sufficient dimension reduction ER - TY - JOUR TI - Counting grass as a rich introduction to population estimation AU - Hess, G. R. AU - Keto, E. M. T2 - Journal of Natural Resources and Life Sciences Education DA - 2009/// PY - 2009/// VL - 38 SP - 56-60 ER - TY - JOUR TI - Contribution of genetic effects to genetic variance components with epistasis and linkage disequilibrium AU - Wang, Tao AU - Zeng, Zhao-Bang T2 - BMC GENETICS AB - Cockerham genetic models are commonly used in quantitative trait loci (QTL) analysis with a special feature of partitioning genotypic variances into various genetic variance components, while the F(infinity) genetic models are widely used in genetic association studies. Over years, there have been some confusion about the relationship between these two type of models. A link between the additive, dominance and epistatic effects in an F(infinity) model and the additive, dominance and epistatic variance components in a Cockerham model has not been well established, especially when there are multiple QTL in presence of epistasis and linkage disequilibrium (LD).In this paper, we further explore the differences and links between the F(infinity) and Cockerham models. First, we show that the Cockerham type models are allelic based models with a special modification to correct a confounding problem. Several important moment functions, which are useful for partition of variance components in Cockerham models, are also derived. Next, we discuss properties of the Finfinity models in partition of genotypic variances. Its difference from that of the Cockerham models is addressed. Finally, for a two-locus biallelic QTL model with epistasis and LD between the loci, we present detailed formulas for calculation of the genetic variance components in terms of the additive, dominant and epistatic effects in an F(infinity) model. A new way of linking the Cockerham and F(infinity) model parameters through their coding variables of genotypes is also proposed, which is especially useful when reduced F(infinity) models are applied.The Cockerham type models are allele-based models with a focus on partition of genotypic variances into various genetic variance components, which are contributed by allelic effects and their interactions. By contrast, the F(infinity) regression models are genotype-based models focusing on modeling and testing of within-locus genotypic effects and locus-by-locus genotypic interactions. When there is no need to distinguish the paternal and maternal allelic effects, these two types of models are transferable. Transformation between an F(infinity) model's parameters and its corresponding Cockerham model's parameters can be established through a relationship between their coding variables of genotypes. Genetic variance components in terms of the additive, dominance and epistatic genetic effects in an F(infinity) model can then be calculated by translating formulas derived for the Cockerham models. DA - 2009/9/4/ PY - 2009/9/4/ DO - 10.1186/1471-2156-10-52 VL - 10 SP - SN - 1471-2156 ER - TY - JOUR TI - Characterization of Conserved and Nonconserved Imprinted Genes in Swine AU - Bischoff, Steve R. AU - Tsai, Shengdar AU - Hardison, Nicholas AU - Motsinger-Reif, Alison A. AU - Freking, Brad A. AU - Nonneman, Dan AU - Rohrer, Gary AU - Piedrahita, Jorge A. T2 - BIOLOGY OF REPRODUCTION AB - To increase our understanding of imprinted genes in swine, we carried out a comprehensive analysis of this gene family using two complementary approaches: expression and phenotypic profiling of parthenogenetic fetuses, and analysis of imprinting by pyrosequencing. The parthenote placenta and fetus were smaller than those of controls but had no obvious morphological differences at Day 28 of gestation. By Day 30, however, the parthenote placentas had decreased chorioallantoic folding, decreased chorionic ruggae, and reduction of fetal-maternal interface surface in comparison with stage-matched control fetuses. Using Affymetrix Porcine GeneChip microarrays and/or semiquantitative PCR, brain, fibroblast, liver, and placenta of Day 30 fetuses were profiled, and 25 imprinted genes were identified as differentially expressed in at least one of the four tissue types: AMPD3, CDKN1C, COPG2, DHCR7, DIRAS3, IGF2 (isoform specific), IGF2AS, IGF2R, MEG3, MEST, NAP1L5, NDN, NNAT, OSBPL1A, PEG3, APEG3, PEG10, PLAGL1, PON2, PPP1R9A, SGCE, SLC38A4, SNORD107, SNRPN, and TFPI2. For DIRAS3, PLAGL1, SGCE, and SLC38A4, tissue-specific differences were detected. In addition, we examined the imprinting status of candidate genes by quantitative allelic pyrosequencing. Samples were collected from Day 30 pregnancies generated from reciprocal crosses of Meishan and White Composite breeds, and single-nucleotide polymorphisms were identified in candidate genes. Imprinting was confirmed for DIRAS3, DLK1, H19, IGF2AS, NNAT, MEST, PEG10, PHLDA2, PLAGL1, SGCE, and SNORD107. We also found no evidence of imprinting in ASB4, ASCL2, CD81, COMMD1, DCN, DLX5, and H13. Combined, these results represent the most comprehensive survey of imprinted genes in swine to date. DA - 2009/11// PY - 2009/11// DO - 10.1095/biolreprod.109.078139 VL - 81 IS - 5 SP - 906-920 SN - 1529-7268 KW - assisted reproductive technology KW - comparative genomic imprinting KW - epigenetics KW - gene regulation KW - genomic imprinting KW - parthenogenesis KW - placenta KW - swine parthenote ER - TY - JOUR TI - Bioretention Impact on Runoff Temperature in Trout Sensitive Waters AU - Jones, Matthew P. AU - Hunt, William F. T2 - JOURNAL OF ENVIRONMENTAL ENGINEERING AB - A study was conducted in western North Carolina, along the southeastern extent of the U.S. trout populations, to examine the effect of bioretention areas on runoff temperature. Four bioretention areas were monitored during the summers of 2006 and 2007. It was found that smaller bioretention areas, with respect to the size of their contributing watershed, were able to significantly reduce both maximum and median water temperatures between the inlet and outlet. The proportionately larger bioretention areas were only able to significantly reduce maximum water temperatures between the inlet and outlet; however, these systems showed evidence of substantial reductions in outflow quantity, effectively reducing the thermal impact. Despite temperature reductions, effluent temperatures still posed a potential threat to coldwater streams during the peak summer months. During the summer months, effluent temperatures were generally coolest at the greatest soil depths, supporting evidence of an optimum drain depth between 90 and 120 cm. The ability of bioretention areas to reduce storm-water temperature and flows supports their application to reduce the thermal impacts of urban storm-water runoff. DA - 2009/8// PY - 2009/8// DO - 10.1061/(asce)ee.1943-7870.0000022 VL - 135 IS - 8 SP - 577-585 SN - 1943-7870 ER - TY - JOUR TI - Bayesian variable selection using an adaptive powered correlation prior AU - Krishna, Arun AU - Bondell, Howard D. AU - Ghosh, Sujit K. T2 - JOURNAL OF STATISTICAL PLANNING AND INFERENCE AB - The problem of selecting the correct subset of predictors within a linear model has received much attention in recent literature. Within the Bayesian framework, a popular choice of prior has been Zellner's g-prior which is based on the inverse of empirical covariance matrix of the predictors. An extension of the Zellner's prior is proposed in this article which allow for a power parameter on the empirical covariance of the predictors. The power parameter helps control the degree to which correlated predictors are smoothed towards or away from one another. In addition, the empirical covariance of the predictors is used to obtain suitable priors over model space. In this manner, the power parameter also helps to determine whether models containing highly collinear predictors are preferred or avoided. The proposed power parameter can be chosen via an empirical Bayes method which leads to a data adaptive choice of prior. Simulation studies and a real data example are presented to show how the power parameter is well determined from the degree of cross-correlation within predictors. The proposed modification compares favorably to the standard use of Zellner's prior and an intrinsic prior in these examples. DA - 2009/8/1/ PY - 2009/8/1/ DO - 10.1016/j.jspi.2008.12.004 VL - 139 IS - 8 SP - 2665-2674 SN - 1873-1171 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-67349268430&partnerID=MN8TOARS KW - Bayesian variable selection KW - Collinearity KW - Powered correlation prior KW - Zellner's g-prior ER - TY - JOUR TI - Avian use of suburban greenways as stopover habitat AU - Kohut, S. AU - Hess, G. AU - Moorman, C. T2 - Urban Ecosystems AB - Greenways may provide stopover habitat for migrating birds in otherwise inhospitable suburban landscapes. We examined the effect of greenway forested corridor width, vegetation composition and structure, and adjacent land cover on the species richness and abundance of migrating songbirds during spring and fall migration in Raleigh and Cary, North Carolina, USA. Generally, migrating birds were more abundant in wider forest corridors during spring and fall migration. During the spring, migrants were detected more commonly in greenways with taller trees and a higher percentage of hardwood trees. In the fall, migrant richness and abundance was highest in greenways with lower canopy cover, possibly because of the increased vertical complexity of the vegetation at these sites. Forest-interior migrant richness was not correlated with corridor width in either season, but these species were more abundant in greenways bordered by less bare earth and pavement cover in the spring. No other bird groupings were correlated with adjacent land cover measures. Although migrants used greenways of all widths, forested corridors wider than 150 m should be conserved whenever possible to provide stopover habitat for forest-interior migrants. Shrub cover should be retained to maintain vegetative complexity. Habitat for the greatest diversity of migrants can be provided by constructing greenways in areas of lower development intensity and encouraging residents to retain shrubs and trees on properties bordering greenways. DA - 2009/// PY - 2009/// DO - 10.1007/s11252-009-0099-6 VL - 12 IS - 4 SP - 487-502 ER - TY - JOUR TI - Avian Response to Microclimate in Canopy Gaps in a Bottomland Hardwood Forest AU - Champlin, Tracey B. AU - Kilgo, John C. AU - Gumpertz, Marcia L. AU - Moorman, Christopher E. T2 - SOUTHEASTERN NATURALIST AB - Microclimate may influence use of early successional habitat by birds. We assessed the relationships between avian habitat use and microclimate (temperature, light intensity, and relative humidity) in experimentally created canopy gaps in a bottomland hardwood forest on the Savannah River Site, SC. Gaps were 2- to 3-year-old group-selection timber harvest openings of three sizes (0.13, 0.26, 0.50 ha). Our study was conducted from spring through fall, encompassing four bird-use periods (spring migration, breeding, post-breeding, and fall migration), in 2002 and 2003. We used mist netting and simultaneously recorded microclimate variables to determine the influence of microclimate on bird habitat use. Microclimate was strongly affected by net location within canopy gaps in both years. Temperature generally was higher on the west side of gaps, light intensity was greater in gap centers, and relative humidity was higher on the east side of gaps. However, we found few relationships between bird captures and the microclimate variables. Bird captures were inversely correlated with temperature during the breeding and post-breeding periods in 2002 and positively correlated with temperature during spring 2003. Captures were high where humidity was high during post-breeding 2002, and captures were low where humidity was high during spring 2003. We conclude that variations in the local microclimate had minor influence on avian habitat use within gaps. Instead, habitat selection in relatively mild regions like the southeastern US is based primarily on vegetation structure, while other factors, including microclimate, are less important. DA - 2009/// PY - 2009/// DO - 10.1656/058.008.0110 VL - 8 IS - 1 SP - 107-120 SN - 1938-5412 ER - TY - JOUR TI - A Model-Based Ensembling Approach for Developing QSARs AU - Zhang, Qianyi AU - Hughes-Oliver, Jacqueline M. AU - Ng, Raymond T. T2 - JOURNAL OF CHEMICAL INFORMATION AND MODELING AB - Ensemble methods have become popular for QSAR modeling, but most studies have assumed balanced data, consisting of approximately equal numbers of active and inactive compounds. Cheminformatics data are often far from being balanced. We extend the application of ensemble methods to include cases of imbalance of class membership and to more adequately assess model output. Based on the extension, we propose an ensemble method called MBEnsemble that automatically determines the appropriate tuning parameters to provide reliable predictions and maximize the F-measure. Results from multiple data sets demonstrate that the proposed ensemble technique works well on imbalanced data. DA - 2009/8// PY - 2009/8// DO - 10.1021/ci900080f VL - 49 IS - 8 SP - 1857-1865 SN - 1549-960X ER - TY - JOUR TI - Using Pulse Width Modulation for Wireless Transmission of Neural Signals in Multichannel Neural Recording Systems AU - Yin, Ming AU - Ghovanloo, Maysam T2 - IEEE TRANSACTIONS ON NEURAL SYSTEMS AND REHABILITATION ENGINEERING AB - We have used a well-known technique in wireless communication, pulse width modulation (PWM) of time division multiplexed (TDM) signals, within the architecture of a novel wireless integrated neural recording (WINeR) system. We have evaluated the performance of the PWM-based architecture and indicated its accuracy and potential sources of error through detailed theoretical analysis, simulations, and measurements on a setup consisting of a 15-channel WINeR prototype as the transmitter and two types of receivers; an Agilent 89600 vector signal analyzer and a custom wideband receiver, with 36 and 75 MHz of maximum bandwidth, respectively. Furthermore, we present simulation results from a realistic MATLAB-Simulink model of the entire WINeR system to observe the system behavior in response to changes in various parameters. We have concluded that the 15-ch WINeR prototype, which is fabricated in a 0.5-mum standard CMOS process and consumes 4.5 mW from plusmn1.5 V supplies, can acquire and wirelessly transmit up to 320 k-samples/s to a 75-MHz receiver with 8.4 bits of resolution, which is equivalent to a wireless data rate of ~ 2.56 Mb/s. DA - 2009/8// PY - 2009/8// DO - 10.1109/TNSRE.2009.2023302 VL - 17 IS - 4 SP - 354-363 SN - 1558-0210 KW - Frequency shift keying KW - implantable microelectronic devices KW - neural interfacing KW - pulse width modulation KW - telemetry KW - time division multiplexing ER - TY - JOUR TI - Improving efficiency and robustness of the doubly robust estimator for a population mean with incomplete data AU - Cao, Weihua AU - Tsiatis, Anastasios A. AU - Davidian, Marie T2 - BIOMETRIKA AB - Abstract Considerable recent interest has focused on doubly robust estimators for a population mean response in the presence of incomplete data, which involve models for both the propensity score and the regression of outcome on covariates. The usual doubly robust estimator may yield severely biased inferences if neither of these models is correctly specified and can exhibit nonnegligible bias if the estimated propensity score is close to zero for some observations. We propose alternative doubly robust estimators that achieve comparable or improved performance relative to existing methods, even with some estimated propensity scores close to zero. DA - 2009/9// PY - 2009/9// DO - 10.1093/biomet/asp033 VL - 96 IS - 3 SP - 723-734 SN - 0006-3444 KW - Causal inference KW - Enhanced propensity score model KW - Missing at random KW - No unmeasured confounders KW - Outcome regression ER - TY - JOUR TI - Gene-Trait Similarity Regression for Multimarker-Based Association Analysis AU - Tzeng, Jung-Ying AU - Zhang, Daowen AU - Chang, Sheng-Mao AU - Thomas, Duncan C. AU - Davidian, Marie T2 - Biometrics AB - We propose a similarity-based regression method to detect associations between traits and multimarker genotypes. The model regresses similarity in traits for pairs of "unrelated" individuals on their haplotype similarities, and detects the significance by a score test for which the limiting distribution is derived. The proposed method allows for covariates, uses phase-independent similarity measures to bypass the needs to impute phase information, and is applicable to traits of general types (e.g., quantitative and qualitative traits). We also show that the gene-trait similarity regression is closely connected with random effects haplotype analysis, although commonly they are considered as separate modeling tools. This connection unites the classic haplotype sharing methods with the variance-component approaches, which enables direct derivation of analytical properties of the sharing statistics even when the similarity regression model becomes analytically challenging. DA - 2009/2/5/ PY - 2009/2/5/ DO - 10.1111/j.1541-0420.2008.01176.x VL - 65 IS - 3 SP - 822-832 LA - en OP - SN - 0006-341X UR - http://dx.doi.org/10.1111/j.1541-0420.2008.01176.x DB - Crossref ER - TY - JOUR TI - Experimental design and estimation of growth rate distributions in size-structured shrimp populations AU - Banks, H T AU - Davis, Jimena L AU - Ernstberger, Stacey L AU - Hu, Shuhua AU - Artimovich, Elena AU - Dhar, Arun K T2 - Inverse Problems AB - We discuss inverse problem results for problems involving the estimation of probability distributions using aggregate data for growth in populations. We begin with a mathematical model describing variability in the early growth process of size-structured shrimp populations and discuss a computational methodology for the design of experiments to validate the model and estimate the growth-rate distributions in shrimp populations. Parameter-estimation findings using experimental data from experiments so designed for shrimp populations cultivated at Advanced BioNutrition Corporation are presented, illustrating the usefulness of mathematical and statistical modeling in understanding the uncertainty in the growth dynamics of such populations. DA - 2009/8/14/ PY - 2009/8/14/ DO - 10.1088/0266-5611/25/9/095003 VL - 25 IS - 9 SP - 095003 J2 - Inverse Problems OP - SN - 0266-5611 1361-6420 UR - http://dx.doi.org/10.1088/0266-5611/25/9/095003 DB - Crossref ER - TY - JOUR TI - Estimation of SCRAM Rate Trends in Nuclear Power Plants Using Hierarchical Bayes Models AU - Mishra, Kaushal K. AU - Ghosh, Sujit K. T2 - COMMUNICATIONS IN STATISTICS-THEORY AND METHODS AB - Nuclear reactors are equipped with reactor scram systems to ensure rapid shutdown of the system in the event of leaks, failure of power conversion systems, or other operational abnormalities. The U.S. Nuclear Regulatory Commission (NRC) collects data on scram rates from various nuclear power plants over time to estimate the trend of proper functioning of the plants which in turn is used to regulate them. The annual scram data obtained from 66 commercial nuclear power plants indicate an increase in the number of plants having no scrams from 1.5% in 1986 to 33% in 1993. To analyze correlated count data with excess zeros (e.g., no scrams), a zero-inflated model that accounts for both temporal and plant-to-plant variation is being developed in this article. A wide class of possibly non-nested models was fitted using Markov Chain Monte Carlo (MCMC) methods and compared using a predictive criterion. Out-of-sample tests were also performed to study the performance of the models in predicting the scram rates of the plants. For the NRC data on scram rates, the stochastic time trend models that account for zero-inflation were found to provide a much better fit compared to the deterministic trend models. DA - 2009/// PY - 2009/// DO - 10.1080/03610920902947196 VL - 38 IS - 16-17 SP - 2856-2871 SN - 1532-415X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-70249097019&partnerID=MN8TOARS KW - Bayesian inference KW - Markov Chain Monte Carlo (MCMC) KW - Scram KW - Zero-inflated model ER - TY - JOUR TI - Estimating Genetic Coefficients for the CSM-CERES-Maize Model in North Carolina Environments AU - Yang, Zhengyu AU - Wilkerson, Gail G. AU - Buol, Gregory S. AU - Bowman, Daryl T. AU - Heiniger, Ronnie W. T2 - AGRONOMY JOURNAL AB - CSM‐CERES‐Maize has been extensively used worldwide to simulate corn growth and grain production, but has not been evaluated for use in North Carolina. The objectives of this study were to calibrate CSM‐CERES‐Maize soil parameters and genetic coefficients using official variety trial data, evaluate model performance in North Carolina, and determine the suitability of the fitting technique using variety trial data for model calibration. The study used yield data for 53 maize genotypes collected from multiple locations over a 10‐yr period. A stepwise calibration procedure was utilized: (i) two genetic coefficients which determine anthesis and physiological maturity dates were adjusted based on growing degree day requirements for each hybrid; and (ii) plant available soil water and rooting profile were adjusted iteratively with two other genetic coefficients affecting yield. Cross validation was used to evaluate the suitability of this approach for estimating soil and genetic coefficients. The root mean squared errors of prediction (RMSEPs) were similar to fitting errors. Results indicate that CSM‐CERES‐Maize can be used in North Carolina to simulate corn growth under nonlimiting N conditions and variety trial data can be used for estimating genetic coefficients. Hybrid average simulated yields matched measured yields well across a wide range of environments, and simulated hybrid yield rankings were in close agreement with rankings based on measured yields. Data from several site‐years could not be used in fitting genetic coefficients due to large root mean squared errors. In some cases, this could be attributed to a weather event, such as a late‐season hurricane. DA - 2009/// PY - 2009/// DO - 10.2134/agronj2008.0234x VL - 101 IS - 5 SP - 1276-1285 SN - 1435-0645 ER - TY - JOUR TI - Economic analysis of US textile production activities under the North American Free Trade Agreement AU - Lim, M. AU - Suh, M. W. AU - Gaskill, L. T2 - JOURNAL OF THE TEXTILE INSTITUTE AB - This economic analysis investigates the US textile industry's output supply and input demand pattern under the influence of North American Free Trade Agreement (NAFTA) and determines the significance of the agreement on the industry. This analysis employs the normalized restricted translog profit model as an analytical tool and introduces a time dummy variable in the model to distinguish the pre- and post-NAFTA years. The outcome of analysis shows the significant but negative effect of NAFTA on the industry's profit performance in the early years of the agreement, probably due to intensified import competition, fall of real output prices, and numerous mill closings. NAFTA, however, is identified as less significant than variable input prices of labor, material, and electricity. The elasticity estimates show the dominant role of maintenance and capital expenditures, followed by textile output and variable input prices in order, in determining the industry's output supply and input demand. Overall, NAFTA is identified as a short-term solution to the US textile industry's fundamental problems of high labor costs and declining price competitiveness. DA - 2009/// PY - 2009/// DO - 10.1080/00405000802125170 VL - 100 IS - 7 SP - 612-625 SN - 0040-5000 KW - economic analysis KW - NAFTA KW - textile production KW - normalized restricted translog profit model ER - TY - JOUR TI - Does productivity drive diversity or vice versa? A test of the multivariate productivity-diversity hypothesis in streams AU - Cardinale, Bradley J. AU - Bennett, Danuta M. AU - Nelson, Craig E. AU - Gross, Kevin T2 - ECOLOGY AB - The idea that productivity regulates species diversity is deeply ingrained in the field of ecology. Yet, over the past few decades, an increasing number of experiments have shown that species diversity controls, rather than simply responds to, biomass production. These contrasting perspectives have led to a seeming paradox: Is diversity the cause or the consequence of biological production? Here we present empirical evidence for the multivariate productivity-diversity (MPD) hypothesis, which argues that differing perspectives on productivity-diversity relationships can be resolved by recognizing that historical research has focused on how resource supply regulates both the productivity and richness of local competitors, whereas more recent studies have focused on how the richness of a colonist pool regulates the efficiency by which resources are captured and converted into new tissue. The MPD hypothesis predicts that three pathways operate concurrently to generate productivity diversity relationships in nature: (1) resource supply directly limits the standing biomass and/or rate of new production by primary producers, (2) producer biomass is directly influenced by the richness of species that locally compete for resources, and (3) resource supply rate indirectly affects producer biomass by influencing the fraction of species from a colonist pool that locally coexist. To examine whether this set of pathways explains covariation between productivity and diversity in natural streams, we used nutrient-diffusing agar "patches" to manipulate resource supply rates in 20 streams throughout the Sierra Nevada mountain range, California, USA. We then measured the fraction of periphyton species from the stream colonist pool co-occurring on each nutrient patch, as well as the standing biomass and rates of primary production. Natural patterns of covariation agreed with predictions of the MPD hypothesis. Algal biomass was an increasing function of nutrient supply, and an increasing function of local richness. The fraction of species from the colonist pool found co-occurring on a patch was a concave-down function of nutrient supply, causing nutrients to indirectly affect biomass via control over local richness. These results suggest that the MPD hypothesis is a viable explanation of patterns of diversity and productivity in natural stream ecosystems, and that it has potential to merge the historical view that productivity drives diversity with a parallel view that diversity drives productivity. DA - 2009/5// PY - 2009/5// DO - 10.1890/08-1038.1 VL - 90 IS - 5 SP - 1227-1241 SN - 1939-9170 KW - biodiversity KW - ecosystem production and function KW - freshwater algae KW - species richness ER - TY - PCOMM TI - Comment on 'New confidence bounds for QT studies' REPLY AU - Boos, D. D. AU - Hoffman, D. AU - Kringle, R. AU - Zhang, J. DA - 2009/// PY - 2009/// SP - 2938-2940 ER - TY - JOUR TI - CHARACTERISTICS OF CEREBROSPINAL FLUID FLOW IN CAVALIER KING CHARLES SPANIELS ANALYZED USING PHASE VELOCITY CINE MAGNETIC RESONANCE IMAGING AU - Cerda-Gonzalez, Sofia AU - Olby, Natasha J. AU - Broadstone, Richard AU - McCullough, Susan AU - Osborne, Jason A. T2 - VETERINARY RADIOLOGY & ULTRASOUND AB - Syringomyelia is an important morbidity source in Cavalier King Charles Spaniels. Although abnormal cerebrospinal fluid (CSF) flow secondary to Chiari malformations is thought to cause syringomyelia in humans, this relationship is unknown in dogs. We used phase‐contrast magnetic resonance (MR) imaging to evaluate CSF flow in dogs. Fifty‐nine Cavalier King Charles Spaniels were assigned a neurologic grade reflecting their neurologic status. Five normal control dogs of other breeding were imaged for comparison. The presence of syringomyelia was noted from sagittal MR images. The pattern and velocity of CSF flow were assessed using phase‐contrast cine MRI at the foramen magnum, C2–C3 disc space, and within syrinxes. Flow was measured most easily with the neck flexed to mimic standing. CSF flow velocity in the dorsal aspect of the subarachnoid space at the foramen magnum was significantly higher in control dogs than Cavalier King Charles Spaniels ( P =0.035). Flow was obstructed at the foramen magnum in 41 of 59 Cavalier King Charles Spaniels. Turbulent flow and jets were associated with syringomyelia presence and severity, and CSF flow velocity at C2/3 dorsally was inversely related to the presence of syringomyelia ( P =0.0197). Peak dorsal subarachnoid space CSF flow velocity at the foramen magnum and C2–C3 were together highly predictive of syringomyelia. CSF flow can be assessed in dogs using phase‐contrast cine MRI. Obstruction to flow at the foramen magnum is common in Cavalier King Charles Spaniels and CSF flow pattern and velocity are related to the presence of syringomyelia. DA - 2009/// PY - 2009/// DO - 10.1111/j.1740-8261.2009.01571.x VL - 50 IS - 5 SP - 467-476 SN - 1740-8261 KW - caudal occipital malformation syndrome KW - Chiari malformation KW - cine MRI KW - occipital hypoplasia KW - phase velocity contrast KW - syringohydromyelia ER - TY - JOUR TI - Bootstrapping Spatial Median for Location Problems AU - Jhun, Myoungshic AU - Shin, Seungjun T2 - COMMUNICATIONS IN STATISTICS-SIMULATION AND COMPUTATION AB - In multivariate location problems, the sample mean is most widely used, having various advantages. It is, however, very sensitive to outlying observations and inefficient for data from heavy tailed distributions. In this situation, the spatial median is more robust than the sample mean and could be a reasonable alternative. We reviewed several spatial median based testing methods for multivariate location and compared their significance level and power through Monte Carlo simulations. The results show that bootstrap method is efficient for the estimation of the covariance matrix of the sample spatial median. We also proposed bootstrap simultaneous confidence intervals based on the spatial median for multiple comparisons in the multi-sample case. DA - 2009/// PY - 2009/// DO - 10.1080/03610910903249528 VL - 38 IS - 10 SP - 2123-2133 SN - 0361-0918 KW - Bootstrap KW - Multivariate location KW - Simultaneous confidence interval KW - Spatial median ER - TY - JOUR TI - An Object Extraction Approach for Impervious Surface Classification with Very-High-Resolution Imagery AU - Miller, Jennifer Elizabeth AU - Nelson, Stacy A. C. AU - Hess, George R. T2 - PROFESSIONAL GEOGRAPHER AB - Detailed land cover maps provide important information for research and decision-making but are often expensive to develop and can become outdated quickly. Widespread availability of aerial photography provides increased accessibility of high-resolution imagery and the potential to produce high-accuracy land cover classifications. However, these classifications often require expert knowledge and are time consuming. Our goal was to develop an efficient, accurate technique for classifying impervious surface in urbanizing Wake County, North Carolina. Using an iterative training technique, we classified 111 nonmosaicked, very-high-resolution images using the Feature Analyst software developed by Visual Learning Systems. Feature Analyst provides object extraction classifications by analyzing spatial context in relation to spectral data to classify high-resolution imagery. Our image classification results were 95 percent accurate in impervious surface extraction, with an overall total accuracy of 92 percent. Using this method, users with relatively limited geographic information system (GIS) training and modest budgets can produce highly accurate object-extracted classifications of impervious and pervious surface that are easily manipulated in a GIS. DA - 2009/// PY - 2009/// DO - 10.1080/00330120902742920 VL - 61 IS - 2 SP - 250-264 SN - 1467-9272 KW - aerial photography KW - Feature Analyst KW - GIS KW - impervious surface KW - land cover ER - TY - JOUR TI - A sensitivity matrix based methodology for inverse problem formulation AU - Cintron-Arias, A. AU - Banks, H. T. AU - Capaldi, A. AU - Lloyd, A. L. T2 - JOURNAL OF INVERSE AND ILL-POSED PROBLEMS AB - We propose an algorithm to select parameter subset combinations that can be estimated using an ordinary least-squares (OLS) inverse problem formulation with a given data set. First, the algorithm selects the parameter combinations that correspond to sensitivity matrices with full rank. Second, the algorithm involves uncertainty quantification by using the inverse of the Fisher Information Matrix. Nominal values of parameters are used to construct synthetic data sets, and explore the effects of removing certain parameters from those to be estimated using OLS procedures. We quantify these effects in a score for a vector parameter defined using the norm of the vector of standard errors for components of estimates divided by the estimates. In some cases the method leads to reduction of the standard error for a parameter to less than 1% of the estimate. DA - 2009/8// PY - 2009/8// DO - 10.1515/JIIP.2009.034 VL - 17 IS - 6 SP - 545-564 SN - 1569-3945 KW - Inverse problems KW - ordinary least squares KW - sensitivity matrix KW - Fisher Information matrix KW - parameter selection KW - standard errors ER - TY - JOUR TI - A Simple Definition of Detection Limit (vol 13, pg 99, 2008) AU - Proctor, Charles H. T2 - JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS DA - 2009/3// PY - 2009/3// DO - 10.1198/jabes.2009.0008 VL - 14 IS - 1 SP - 133-133 SN - 1085-7117 ER - TY - JOUR TI - A Regression-based Association Test for Case-control Studies that Uses Inferred Ancestral Haplotype Similarity AU - Liu, Youfang AU - Li, Yi-Ju AU - Satten, Glen A. AU - Allen, Andrew S. AU - Tzeng, Jung-Ying T2 - ANNALS OF HUMAN GENETICS AB - Association methods based on haplotype similarity (HS) can overcome power and stability issues encountered in standard haplotype analyses. Current HS methods can be generally classified into evolutionary and two-sample approaches. We propose a new regression-based HS association method for case-control studies that incorporates covariate information and combines the advantages of the two classes of approaches by using inferred ancestral haplotypes. We first estimate the ancestral haplotypes of case individuals and then, for each individual, an ancestral-haplotype-based similarity score is computed by comparing that individual's observed genotype with the estimated ancestral haplotypes. Trait values are then regressed on the similarity scores. Covariates can easily be incorporated into this regression framework. To account for the bias in the raw p-values due to the use of case data in constructing ancestral haplotypes, as well as to account for variation in ancestral haplotype estimation, a permutation procedure is adopted to obtain empirical p-values. Compared with the standard haplotype score test and the multilocus T(2) test, our method improves power when neither the allele frequency nor linkage disequilibrium between the disease locus and its neighboring SNPs is too low and is comparable in other scenarios. We applied our method to the Genetic Analysis Workshop 15 simulated SNP data and successfully pinpointed a stretch of SNPs that covers the fine-scale region where the causal locus is located. DA - 2009/9// PY - 2009/9// DO - 10.1111/j.1469-1809.2009.00536.x VL - 73 SP - 520-526 SN - 1469-1809 KW - Case-control studies KW - haplotype similarity KW - haplotype sharing KW - haplotype-based association test KW - covariates KW - regression-based association analysis ER - TY - JOUR TI - SNP Selection and Multidimensional Scaling to Quantify Population Structure AU - Miclaus, Kelci AU - Wolfinger, Russ AU - Czika, Wendy T2 - GENETIC EPIDEMIOLOGY AB - In the new era of large-scale collaborative Genome Wide Association Studies (GWAS), population stratification has become a critical issue that must be addressed. In order to build upon the methods developed to control the confounding effect of a structured population, it is extremely important to visualize and quantify that effect. In this work, we develop methodology for single nucleotide polymorphism (SNP) selection and subsequent population stratification visualization based on deviation from Hardy-Weinberg equilibrium in conjunction with non-metric multidimensional scaling (MDS); a distance-based multivariate technique. Through simulation, it is shown that SNP selection based on Hardy-Weinberg disequilibrium (HWD) is robust against confounding linkage disequilibrium patterns that have been problematic in past studies and methods as well as producing a differentiated SNP set. Non-metric MDS is shown to be a multivariate visualization tool preferable to principal components in conjunction with HWD SNP selection through theoretical and empirical study from HapMap samples. The proposed selection tool offers a simple and effective way to select appropriate substructure-informative markers for use in exploring the effect that population stratification may have in association studies. DA - 2009/9// PY - 2009/9// DO - 10.1002/gepi.20401 VL - 33 IS - 6 SP - 488-496 SN - 1098-2272 KW - population stratification KW - substructure-informative SNP selection KW - Hardy-Weinberg disequilibrium KW - nonmetric MDS KW - association studies ER - TY - JOUR TI - Robust time series analysis via measurement error modeling AU - Wang, Q. AU - Stefanski, L. A. AU - Genton, M. G. AU - Boos, D. D. T2 - Statistica Sinica DA - 2009/// PY - 2009/// VL - 19 IS - 3 SP - 1263-1280 ER - TY - JOUR TI - Model free multivariate reduced-rank regression with categorical predictors AU - Setodji, C. M. AU - Li, L. X. T2 - Statistica Sinica DA - 2009/// PY - 2009/// VL - 19 IS - 3 SP - 1119-1136 ER - TY - JOUR TI - Long-Term Effects of Changing Land Use Practices on Surface Water Quality in a Coastal River and Lagoonal Estuary AU - Rothenberger, Meghan B. AU - Burkholder, JoAnn M. AU - Brownie, Cavell T2 - ENVIRONMENTAL MANAGEMENT DA - 2009/9// PY - 2009/9// DO - 10.1007/s00267-009-9330-8 VL - 44 IS - 3 SP - 505-523 SN - 1432-1009 KW - Agriculture KW - Estuary KW - Eutrophication KW - Land use KW - Longitudinal regression models KW - Urban KW - Watershed ER - TY - JOUR TI - Inference on quantile regression for heteroscedastic mixed models AU - Wang, H. J. T2 - Statistica Sinica DA - 2009/// PY - 2009/// VL - 19 IS - 3 SP - 1247-1261 ER - TY - JOUR TI - Genetic properties of the maize nested association mapping population AU - McMullen, M. D. AU - Kresovich, S. AU - Villeda, H. S. AU - Bradbury, P. AU - Li, H. H. AU - Sun, Q. AU - Flint-Garcia, S. AU - Thornsberry, J. AU - Acharya, C. AU - Bottoms, C. AU - Brown, P. AU - Browne, C. AU - Eller, M. AU - Guill, K. AU - Harjes, C. AU - Kroon, D. AU - Lepak, N. AU - Mitchell, S. E. T2 - Science AB - Codifying Maize Modifications Maize, one of our most important crop species, has been the target of genetic investigation and experimentation for more than 100 years. Crossing two inbred lines tends to result in “better” offspring, in a process known as heterosis. Attempts to map the genetic loci that control traits important for farming have been made, but few have been successful (see the Perspective by Mackay ). Buckler et al. (p. 714 ) and McMullen et al. (p. 737 ) produced a genomic map of maize that relates recombination to genome structure. Even tremendous adaptations in very diverse species were produced by numerous, small additive steps. Differences in flowering time in maize among inbred lines were not caused by a few genes with large effects, but by the cumulative effects of numerous quantitative trait loci—each of which has only a small impact on the trait. DA - 2009/// PY - 2009/// DO - 10.1126/science.1174320 VL - 325 IS - 5941 SP - 737-740 ER - TY - JOUR TI - Exploiting predictor domain information in sufficient dimension reduction AU - Li, Lexin T2 - COMPUTATIONAL STATISTICS & DATA ANALYSIS AB - Analysis of high-dimensional data is becoming the norm in a variety of scientific studies and dimension reduction methods are widely employed. As the predictor domain knowledge is often available, it is useful to incorporate such domain information into dimension reduction and subsequent model formulation. Existing solutions such as simple average, principal components analysis and partial least squares cannot assure preservation of full regression information when reducing the dimension. In this article we investigate sufficient dimension reduction strategies that can retain full regression information meanwhile utilizing prior domain knowledge. Both simulations and a real data analysis demonstrate that the new methods are effective and often superior than the existing solutions. DA - 2009/5/15/ PY - 2009/5/15/ DO - 10.1016/j.csda.2009.01.007 VL - 53 IS - 7 SP - 2665-2672 SN - 0167-9473 ER - TY - JOUR TI - Effects of Toll-like receptor 4 on Porphyromonas gingivalis-induced bone loss in mice AU - Costalonga, M. AU - Batas, L. AU - Reich, B. J. T2 - JOURNAL OF PERIODONTAL RESEARCH AB - Background and Objective: Toll‐like receptor 4 (TLR‐4)/myeloid differentiation protein‐2 complex ligation by lipopolysaccharide induces production of pro‐inflammatory cytokines and co‐stimulatory molecules on antigen presenting cells. The aim of this study was to determine the role of the TLR‐4 in bone loss‐resistant C57BL mice and in bone loss‐susceptible BALB/c mice after infection with Porphyromonas gingivalis . Material and Methods: The BALB/c and C57BL/10 mice, either normal or TLR‐4 deficient, were infected or sham‐infected orally four times, at 4 day intervals, with 10 9 colony forming units of P. gingivalis . At 47 days, defleshed jaws were stained and photographed in a standardized position. We measured the surface area of the root trunk to assess the alveolar bone loss. Results: Porphyromonas gingivalis ‐infected wild‐type BALB/c mice lost 13.8% more bone than P. gingivalis ‐infected wild‐type C57BL/10 mice. In contrast, P. gingivalis ‐infected TLR‐4‐deficient C57BL/10 mice lost 12.7% more bone than P. gingivalis ‐infected TLR‐4‐deficient BALB/c mice. Porphyromonas gingivalis ‐infected wild‐type C57BL/6 and TLR‐2 knockout C57BL/6 mice had similar bone levels to sham‐infected control mice. Conclusion: Toll‐like receptor 4 is protective for C57BL/10 but detrimental to BALB/c mice, since its absence allowed C57BL/10 but not BALB/c mice to lose alveolar bone. Toll‐like receptor 2 does not contribute to this protection in genetically similar C57BL/6 mice. DA - 2009/8// PY - 2009/8// DO - 10.1111/j.1600-0765.2008.01152.x VL - 44 IS - 4 SP - 537-542 SN - 1600-0765 KW - Toll-like receptor 4 KW - alveolar bone loss KW - mice-inbred BALB C KW - mice-inbred C57BL ER - TY - JOUR TI - A mathematical model for the first-pass dynamics of antibiotics acting on the cardiovascular system AU - Banks, H. T. AU - Holm, Kathleen AU - Wanner, Nathan C. AU - Cintron-Arias, Ariel AU - Kepler, Grace M. AU - Wetherington, Jeffrey D. T2 - MATHEMATICAL AND COMPUTER MODELLING AB - We present a preliminary first-pass dynamic model for delivery of drug compounds to the lungs and heart. We use a compartmental mass balance approach to develop a system of nonlinear differential equations for mass accumulated in the heart as a result of intravenous injection. We discuss sensitivity analysis as well as methodology for minimizing mass in the heart while maximizing mass delivered to the lungs on a first circulatory pass. DA - 2009/10// PY - 2009/10// DO - 10.1016/j.mcm.2009.02.007 VL - 50 IS - 7-8 SP - 959-974 SN - 1872-9479 KW - Compartmental model KW - Circulatory system KW - Drug delivery KW - Differential equations KW - Optimal dosing strategies KW - Sensitivity ER - TY - JOUR TI - 'Putting our heads together': insights into genomic conservation between human and canine intracranial tumors AU - Thomas, Rachael AU - Duke, Shannon E. AU - Wang, Huixia J. AU - Breen, Tessa E. AU - Higgins, Robert J. AU - Linder, Keith E. AU - Ellis, Peter AU - Langford, Cordelia F. AU - Dickinson, Peter J. AU - Olby, Natasha J. AU - Breen, Matthew T2 - JOURNAL OF NEURO-ONCOLOGY AB - Numerous attributes render the domestic dog a highly pertinent model for cancer-associated gene discovery. We performed microarray-based comparative genomic hybridization analysis of 60 spontaneous canine intracranial tumors to examine the degree to which dog and human patients exhibit aberrations of ancestrally related chromosome regions, consistent with a shared pathogenesis. Canine gliomas and meningiomas both demonstrated chromosome copy number aberrations (CNAs) that share evolutionarily conserved synteny with those previously reported in their human counterpart. Interestingly, however, genomic imbalances orthologous to some of the hallmark aberrations of human intracranial tumors, including chromosome 22/NF2 deletions in meningiomas and chromosome 1p/19q deletions in oligodendrogliomas, were not major events in the dog. Furthermore, and perhaps most significantly, we identified highly recurrent CNAs in canine intracranial tumors for which the human orthologue has been reported previously at low frequency but which have not, thus far, been associated intimately with the pathogenesis of the tumor. The presence of orthologous CNAs in canine and human intracranial cancers is strongly suggestive of their biological significance in tumor development and/or progression. Moreover, the limited genetic heterogenity within purebred dog populations, coupled with the contrasting organization of the dog and human karyotypes, offers tremendous opportunities for refining evolutionarily conserved regions of tumor-associated genomic imbalance that may harbor novel candidate genes involved in their pathogenesis. A comparative approach to the study of canine and human intracranial tumors may therefore provide new insights into their genetic etiology, towards development of more sophisticated molecular subclassification and tailored therapies in both species. DA - 2009/9// PY - 2009/9// DO - 10.1007/s11060-009-9877-5 VL - 94 IS - 3 SP - 333-349 SN - 1573-7373 KW - Comparative genomic hybridization KW - Canine KW - Brain tumor KW - Chromosome KW - Microarray ER - TY - JOUR TI - Simultaneous Factor Selection and Collapsing Levels in ANOVA AU - Bondell, Howard D. AU - Reich, Brian J. T2 - BIOMETRICS AB - When performing an analysis of variance, the investigator often has two main goals: to determine which of the factors have a significant effect on the response, and to detect differences among the levels of the significant factors. Level comparisons are done via a post-hoc analysis based on pairwise differences. This article proposes a novel constrained regression approach to simultaneously accomplish both goals via shrinkage within a single automated procedure. The form of this shrinkage has the ability to collapse levels within a factor by setting their effects to be equal, while also achieving factor selection by zeroing out entire factors. Using this approach also leads to the identification of a structure within each factor, as levels can be automatically collapsed to form groups. In contrast to the traditional pairwise comparison methods, these groups are necessarily nonoverlapping so that the results are interpretable in terms of distinct subsets of levels. The proposed procedure is shown to have the oracle property in that asymptotically it performs as well as if the exact structure were known beforehand. A simulation and real data examples show the strong performance of the method. DA - 2009/3// PY - 2009/3// DO - 10.1111/j.1541-0420.2008.01061.x VL - 65 IS - 1 SP - 169-177 SN - 0006-341X KW - ANOVA KW - Grouping KW - Multiple comparisons KW - Oracle property KW - Shrinkage KW - Variable selection ER - TY - JOUR TI - Public investment and industry incentives in life-science research AU - Belasco, E. J. AU - Ghosh, S. K. AU - Goodwin, B. K. T2 - American Journal of Agricultural Economics DA - 2009/// PY - 2009/// VL - 91 IS - 2 SP - 431-443 ER - TY - JOUR TI - Estimation in time-delay modeling of insecticide-induced mortality AU - Banks, H. T. AU - Banks, J. E. AU - Joyner, S. L. T2 - JOURNAL OF INVERSE AND ILL-POSED PROBLEMS AB - We present a mathematical and statistical computational framework for inverse problems involving delay or hysteretic differential equations. We demonstrate efficacy of the methodology in the context of models for insect maturation and mortality due to insecticide exposure. DA - 2009/3// PY - 2009/3// DO - 10.1515/JIIP.2009.012 VL - 17 IS - 2 SP - 101-125 SN - 1569-3945 KW - Inverse problems KW - ordinary and generalized least squares KW - delay-differential equation models KW - insect populations KW - insecticide exposure KW - time-varying mortality and maturation rates ER - TY - JOUR TI - Bayesian ROC curve estimation under binormality using a rank likelihood AU - Gu, Jiezhun AU - Ghosal, Subhashis T2 - Journal of Statistical Planning and Inference AB - There are various methods to estimate the parameters in the binormal model for the ROC curve. In this paper, we propose a conceptually simple and computationally feasible Bayesian estimation method using a rank-based likelihood. Posterior consistency is also established. We compare the new method with other estimation methods and conclude that our estimator generally performs better than its competitors. DA - 2009/6// PY - 2009/6// DO - 10.1016/j.jspi.2008.09.014 VL - 139 IS - 6 SP - 2076-2083 J2 - Journal of Statistical Planning and Inference LA - en OP - SN - 0378-3758 UR - http://dx.doi.org/10.1016/j.jspi.2008.09.014 DB - Crossref KW - Binormal model KW - MCMC KW - Rank-based likelihood KW - ROC curve KW - Posterior consistency ER - TY - JOUR TI - Variable selection in quantile regression AU - Wu, Y. C. AU - Liu, Y. F. T2 - Statistica Sinica DA - 2009/// PY - 2009/// VL - 19 IS - 2 SP - 801-817 ER - TY - JOUR TI - Mechanical and actuation behavior of electroactive nanostructured polymers AU - Shankar, Ravi AU - Ghosh, Tushar K. AU - Spontak, Richard J. T2 - SENSORS AND ACTUATORS A-PHYSICAL AB - Electroactive polymers (EAPs) can exhibit relatively large actuation strain responses upon electrical stimulation. For this reason, in conjunction with their light weight, robust properties, low cost and facile processability, EAPs are of considerable interest in the development of next-generation organic actuators. Within this class of materials, dielectric electroactive polymers (D-EAPs) have repeatedly exhibited the most promising and versatile properties. A new family of D-EAPs derived from swollen poly[styrene-b-(ethylene-co-butylene)-b-styrene] triblock copolymers has been recently found to undergo ultrahigh displacement at relatively low electric fields compared to previously reported D-EAPs. The present work examines the mechanical and actuation response of these electroactive nanostructured polymer (ENP) systems under quasi-static, and electromechanical loading conditions. Careful measurement of the quasi-static properties under tensile and compressive loading yield similar results that are significantly influenced by the introduction of in-plane strain, as well as by copolymer concentration or molecular weight. Blocking stress measurements reveal that the actuation effectiveness achieved by some of the ENPs is comparable to that of the VHB 4910 acrylic D-EAP, thus providing a novel and efficient avenue to designer D-EAPs for advanced engineering, biomimetic and biomedical applications. DA - 2009/4/8/ PY - 2009/4/8/ DO - 10.1016/j.sna.2009.01.002 VL - 151 IS - 1 SP - 46-52 SN - 0924-4247 KW - Electroactive nanostructured polymer KW - Compressive modulus KW - Blocking stress ER - TY - JOUR TI - INFERENCE FOR CENSORED QUANTILE REGRESSION MODELS IN LONGITUDINAL STUDIES AU - Wang, Huixia Judy AU - Fygenson, Mendel T2 - ANNALS OF STATISTICS AB - We develop inference procedures for longitudinal data where some of the measurements are censored by fixed constants. We consider a semi-parametric quantile regression model that makes no distributional assumptions. Our research is motivated by the lack of proper inference procedures for data from biomedical studies where measurements are censored due to a fixed quantification limit. In such studies the focus is often on testing hypotheses about treatment equality. To this end, we propose a rank score test for large sample inference on a subset of the covariates. We demonstrate the importance of accounting for both censoring and intra-subject dependency and evaluate the performance of our proposed methodology in a simulation study. We then apply the proposed inference procedures to data from an AIDS-related clinical trial. We conclude that our framework and proposed methodology is very valuable for differentiating the influences of predictors at different locations in the conditional distribution of a response variable. DA - 2009/4// PY - 2009/4// DO - 10.1214/07-AOS564 VL - 37 IS - 2 SP - 756-781 SN - 0090-5364 KW - Fixed censoring KW - logitudinal data KW - quantile regression KW - rank score test KW - tobit model KW - viral load ER - TY - JOUR TI - Dynamical behaviour of a discrete selection-migration model with arbitrary dominance AU - Selgrade, James F. AU - Bostic, Jordan West AU - Roberds, James H. T2 - JOURNAL OF DIFFERENCE EQUATIONS AND APPLICATIONS AB - To study the effects of immigration of genes (possibly transgenic) into a natural population, a one-island selection-migration model with density-dependent regulation is used to track allele frequency and population size. The existence and uniqueness of a polymorphic genetic equilibrium is proved under a general assumption about dominance in fitnesses. Also, conditions are found which guarantee the existence of and determine the location of the global attractor for this model. The rate at which solutions approach the attractor is approximated. A measure of allelic diversity is introduced. DA - 2009/// PY - 2009/// DO - 10.1080/10236190802400741 VL - 15 IS - 4 SP - 371-385 SN - 1563-5120 KW - natural selection KW - immigration KW - transgene KW - dominance KW - attractor ER - TY - JOUR TI - THE ESTIMATION OF THE EFFECTIVE REPRODUCTIVE NUMBER FROM DISEASE OUTBREAK DATA AU - Cintron-Arias, Ariel AU - Castillo-Chavez, Carlos AU - Bettencourt, Luis M. A. AU - Lloyd, Alun L. AU - Banks, H. T. T2 - MATHEMATICAL BIOSCIENCES AND ENGINEERING AB - We consider a single outbreak susceptible-infected-recovered (SIR) model and corresponding estimation procedures for the effective reproductive number $\mathcal{R}(t)$. We discuss the estimation of the underlying SIR parameters with a generalized least squares (GLS) estimation technique. We do this in the context of appropriate statistical models for the measurement process. We use asymptotic statistical theories to derive the mean and variance of the limiting (Gaussian) sampling distribution and to perform post statistical analysis of the inverse problems. We illustrate the ideas and pitfalls (e.g., large condition numbers on the corresponding Fisher information matrix) with both synthetic and influenza incidence data sets. DA - 2009/4// PY - 2009/4// DO - 10.3934/mbe.2009.6.261 VL - 6 IS - 2 SP - 261-282 SN - 1551-0018 KW - effective reproductive number KW - basic reproduction ratio KW - reproduction number KW - R KW - R(t) KW - R-0 KW - parameter estimation KW - generalized least squares KW - residual plots ER - TY - JOUR TI - M-estimation of Boolean models for particle flow experiments AU - Osborne, Jason A. AU - Grift, Tony E. T2 - JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS AB - Summary Probability models are proposed for passage time data collected in experiments with a device that was designed to measure particle flow during aerial application of fertilizer. Maximum likelihood estimation of flow intensity is reviewed for the simple linear Boolean model, which arises with the assumption that each particle requires the same known passage time. M-estimation is developed for a generalization of the model in which passage times behave as a random sample from a distribution with a known mean. The generalized model improves the fit in these experiments. An estimator of total particle flow is constructed by conditioning on lengths of multiparticle clumps. DA - 2009/// PY - 2009/// DO - 10.1111/j.1467-9876.2008.00655.x VL - 58 SP - 197-210 SN - 1467-9876 KW - Boolean models KW - Coverage processes KW - Infinite server queues KW - Likelihood KW - M-estimation ER - TY - JOUR TI - Genome-wide association for major depressive disorder: A possible role for the presynaptic protein piccolo AU - Sullivan, P. F. AU - Geus, E. J. C. AU - Willemsen, G. AU - James, M. R. AU - Smit, J. H. AU - Zandbelt, T. AU - Arolt, V. AU - Baune, B. T. AU - Blackwood, D. AU - Cichon, S. AU - Coventry, W. L. AU - Domschke, K. AU - Farmer, A. AU - Fava, M. AU - Gordon, S. D. AU - He, Q. AU - Heath, A. C. AU - Heutink, P. T2 - Molecular Psychiatry DA - 2009/// PY - 2009/// VL - 14 IS - 4 SP - 359-375 ER - TY - JOUR TI - Use of selection with recurrent backcrossing and QTL mapping to identify loci contributing to southern leaf blight resistance in a highly resistant maize line AU - Zwonitzer, John C. AU - Bubeck, David M. AU - Bhattramakki, Dinakar AU - Goodman, Major M. AU - Arellano, Consuelo AU - Balint-Kurti, Peter J. T2 - THEORETICAL AND APPLIED GENETICS DA - 2009/3// PY - 2009/3// DO - 10.1007/s00122-008-0949-2 VL - 118 IS - 5 SP - 911-925 SN - 1432-2242 ER - TY - JOUR TI - A model for HCMV infection in immunosuppressed patients AU - Kepler, G. M. AU - Banksa, H. T. AU - Davidian, M. AU - Rosenberg, E. S. T2 - MATHEMATICAL AND COMPUTER MODELLING AB - We propose a model for HCMV infection in healthy and immunosuppressed patients. First, we present the biological model and formulate a system of ordinary differential equations to describe the pathogenesis of primary HCMV infection in immunocompetent and immunosuppressed individuals. We then investigate how clinical data can be applied to this model. Approximate parameter values for the model are derived from data available in the literature and from mathematical and physiological considerations. Simulations with the approximated parameter values demonstrates that the model is capable of describing primary, latent, and secondary (reactivated) HCMV infection. Reactivation simulations with this model provide a window into the dynamics of HCMV infection in (D-R+) transplant situations, where latently-infected recipients (R+) receive transplant tissue from HCMV-naive donors (D-). DA - 2009/4// PY - 2009/4// DO - 10.1016/j.mcm.2008.06.003 VL - 49 IS - 7-8 SP - 1653-1663 SN - 1872-9479 KW - HCMV KW - CMV KW - Herpes KW - Transplantation KW - Mathematical model KW - Immunosuppression ER - TY - JOUR TI - Power and sample size calculation for log-rank test with a time lag in treatment effect AU - Zhang, Daomen AU - Quan, Hui T2 - STATISTICS IN MEDICINE AB - Abstract The log‐rank test is the most powerful non‐parametric test for detecting a proportional hazards alternative and thus is the most commonly used testing procedure for comparing time‐to‐event distributions between different treatments in clinical trials. When the log‐rank test is used for the primary data analysis, the sample size calculation should also be based on the test to ensure the desired power for the study. In some clinical trials, the treatment effect may not manifest itself right after patients receive the treatment. Therefore, the proportional hazards assumption may not hold. Furthermore, patients may discontinue the study treatment prematurely and thus may have diluted treatment effect after treatment discontinuation. If a patient's treatment termination time is independent of his/her time‐to‐event of interest, the termination time can be treated as a censoring time in the final data analysis. Alternatively, we may keep collecting time‐to‐event data until study termination from those patients who discontinued the treatment and conduct an intent‐to‐treat analysis by including them in the original treatment groups. We derive formulas necessary to calculate the asymptotic power of the log‐rank test under this non‐proportional hazards alternative for the two data analysis strategies. Simulation studies indicate that the formulas provide accurate power for a variety of trial settings. A clinical trial example is used to illustrate the application of the proposed methods. Copyright © 2009 John Wiley & Sons, Ltd. DA - 2009/2/28/ PY - 2009/2/28/ DO - 10.1002/sim.3501 VL - 28 IS - 5 SP - 864-879 SN - 0277-6715 KW - censoring KW - intent-to-treat analysis KW - treatment termination ER - TY - JOUR TI - Orthology-based multilevel modeling of differentially expressed mouse and human gene pairs AU - Ogorek, B. A. AU - Stefanski, L. A. T2 - Statistical Applications in Genetics and Molecular Biology DA - 2009/// PY - 2009/// VL - 8 IS - 1 ER - TY - JOUR TI - Modeling misidentification errors in capture-recapture studies using photographic identification of evolving marks AU - Yoshizaki, Jun AU - Pollock, Kenneth H. AU - Brownie, Cavell AU - Webster, Raymond A. T2 - ECOLOGY AB - Misidentification of animals is potentially important when naturally existing features (natural tags) are used to identify individual animals in a capture-recapture study. Photographic identification (photoID) typically uses photographic images of animals' naturally existing features as tags (photographic tags) and is subject to two main causes of identification errors: those related to quality of photographs (non-evolving natural tags) and those related to changes in natural marks (evolving natural tags). The conventional methods for analysis of capture-recapture data do not account for identification errors, and to do so requires a detailed understanding of the misidentification mechanism. Focusing on the situation where errors are due to evolving natural tags, we propose a misidentification mechanism and outline a framework for modeling the effect of misidentification in closed population studies. We introduce methods for estimating population size based on this model. Using a simulation study, we show that conventional estimators can seriously overestimate population size when errors due to misidentification are ignored, and that, in comparison, our new estimators have better properties except in cases with low capture probabilities (< 0.2) or low misidentification rates (< 2.5%). DA - 2009/1// PY - 2009/1// DO - 10.1890/08-0304.1 VL - 90 IS - 1 SP - 3-9 SN - 1939-9170 KW - capture-recapture KW - closed-population models KW - evolving tags KW - misidentification KW - natural tags KW - photographic identification KW - population size estimate ER - TY - JOUR TI - Estimating probabilities under the three-parameter gamma distribution using composite sampling AU - Jonkman, Jeffrey N. AU - Gerard, Patrick D. AU - Swallow, William H. T2 - COMPUTATIONAL STATISTICS & DATA ANALYSIS AB - Composite sampling may be used in industrial or environmental settings for the purpose of quality monitoring and regulation, particularly if the cost of testing samples is high relative to the cost of collecting samples. In such settings, it is often of interest to estimate the proportion of individual sampling units in the population that are above or below a given threshold value, C. We consider estimation of a proportion of the form p=P(X>C) from composite sample data, assuming that X follows a three-parameter gamma distribution. The gamma distribution is useful for modeling skewed data, which arise in many applications, and adding a shift parameter to the usual two-parameter gamma distribution also allows the analyst to model a minimum or baseline level of the response. We propose an estimator of p that is based on maximum likelihood estimates of the parameters @a, @b, and @c, and an associated variance estimator based on the observed information matrix. Theoretical properties of the estimator are briefly discussed, and simulation results are given to assess the performance of the estimator. We illustrate the proposed estimator using an example of composite sample data from the meat products industry. DA - 2009/2/15/ PY - 2009/2/15/ DO - 10.1016/j.csda.2008.10.005 VL - 53 IS - 4 SP - 1099-1109 SN - 0167-9473 ER - TY - JOUR TI - Differential Responses of Cotton Cultivars when Applying Mepiquat Pentaborate AU - Nathan B. O'Berry, AU - Faircloth, Joel C. AU - Jones, Michael A. AU - Herbert, David A., Jr. AU - Abaye, Azenegashe O. AU - McKemie, Thomas E. AU - Brownie, Cavell T2 - AGRONOMY JOURNAL AB - Plant growth regulators are routinely used in cotton ( Gossypium hirsutum L.) production to reduce plant height and hasten maturity. The objective of this research was to determine the response of several cotton cultivars to mepiquat pentaborate (MPB) application in environments accumulating different levels of heat units. Four MPB application regimes were imposed on three cultivars in Virginia and South Carolina in 2005 and 2006. Total MPB season rates of 0.0, 54.9, 85.3, or 121.9 g ai ha −1 applied at the five‐leaf stage, pin‐head square, match‐head square, and early bloom were used. The cultivars were: Deltapine (DP) 444 BG/RR, an “early‐maturing” cultivar; Fibermax (FM) 960 BR, a “medium‐maturing” cultivar; and DP 555 BG/RR, a “late‐maturing” cultivar. In South Carolina in 2006, FM 960 BR July plant height was reduced by 25% with MPB application compared to only 12 and 13% for DP 444 BG/RR and DP 555 BG/RR, respectively, although actual plant height reductions were not different among cultivars. Mepiquat pentaborate applications decreased plant height at harvest by 8 to 34%, height‐to‐node ratio by 10 to 32%, enhanced maturity as measured by nodes above white flower for all cultivars, and decreased lint yield by 3.7 to 8.5% compared to untreated cotton. Higher seasonal totals and earlier initiation of MPB application resulted in the greatest decrease in lint yield. DA - 2009/// PY - 2009/// DO - 10.2134/agronj2007.0333 VL - 101 IS - 1 SP - 25-31 SN - 0002-1962 ER - TY - JOUR TI - Bioretention technology: Overview of current practice and future needs AU - Davis, A. P. AU - Hunt, W. F. AU - Traver, R. G. AU - Clar, M. T2 - Journal of Environmental Engineering (New York, N.Y.) AB - Bioretention, or variations such as bioinfiltration and rain gardens, has become one of the most frequently used storm-water management tools in urbanized watersheds. Incorporating both filtration and infiltration, initial research into bioretention has shown that these facilities substantially reduce runoff volumes and peak flows. Low impact development, which has a goal of modifying postdevelopment hydrology to more closely mimic that of predevelopment, is a driver for the use of bioretention in many parts of the country. Research over the past decade has shown that bioretention effluent loads are low for suspended solids, nutrients, hydrocarbons, and heavy metals. Pollutant removal mechanisms include filtration, adsorption, and possibly biological treatment. Limited research suggests that bioretention can effectively manage other pollutants, such as pathogenic bacteria and thermal pollution, as well. Reductions in pollutant load result from the combination of concentration reduction and runoff volume attenuation, linking water quality and hydrologic performance. Nonetheless, many design questions persist for this practice, such as maximum pooling bowl depth, minimum fill media depth, fill media composition and configuration, underdrain configuration, pretreatment options, and vegetation selection. Moreover, the exact nature and impact of bioretention maintenance is still evolving, which will dictate long-term performance and life-cycle costs. Bioretention usage will grow as design guidance matures as a result of continued research and application. DA - 2009/// PY - 2009/// DO - 10.1061/(asce)0733-9372(2009)135:3(109) VL - 135 IS - 3 SP - 109-117 ER - TY - JOUR TI - A new chi-square approximation to the distribution of non-negative definite quadratic forms in non-central normal variables AU - Liu, Huan AU - Tang, Yongqiang AU - Zhang, Hao Helen T2 - COMPUTATIONAL STATISTICS & DATA ANALYSIS AB - This note proposes a new chi-square approximation to the distribution of non-negative definite quadratic forms in non-central normal variables. The unknown parameters are determined by the first four cumulants of the quadratic forms. The proposed method is compared with Pearson’s three-moment central χ2 approximation approach, by means of numerical examples. Our method yields a better approximation to the distribution of the non-central quadratic forms than Pearson’s method, particularly in the upper tail of the quadratic form, the tail most often needed in practical work. DA - 2009/2/15/ PY - 2009/2/15/ DO - 10.1016/j.csda.2008.11.025 VL - 53 IS - 4 SP - 853-856 SN - 1872-7352 ER - TY - JOUR TI - Mitigation of impervious surface hydrology using bioretention in North Carolina and Maryland AU - Li, H. AU - Sharkey, L. J. AU - Hunt, W. F. AU - Davis, A. P. T2 - Journal of Hydrologic Engineering AB - As an increasingly adopted storm water best management practice to remedy hydrologic impairment from urban imperviousness, bioretention facilities need rigorous field performance research and monitoring to confirm performance and improve design and maintenance recommendations. This study investigated hydrologic performance at six bioretention cells in Maryland [College Park (CP), a 181m2 cell, 50–80cm media depth, monitored for 22 events, and Silver Spring (SS), a 102m2 cell, 90cm media depth, monitored for 60 events] and North Carolina [Greensboro (G1 and G2), each approximately 317m2, 120cm media depth, both monitored for 46 events, and Louisburg (L1=surface area of 162m2, L2=surface area of 99m2); each had 50–60cm fill depths, monitored for 31 and 33 events, respectively] over 10–15month periods. Outflow from each cell was recorded and inflow was either recorded or calculated from rainfall data. In Louisburg, L2 was lined with an impermeable membrane to eliminate exfiltration while L1 was unlined to allow both exfiltration and evapotranspiration. Results indicate that bioretention facilities can achieve substantial hydrologic benefits through delaying and reducing peak flows and decreasing runoff volume. A large cell media volume: drainage area ratio, and adjustments to the drainage configuration appear to improve the performance. Media layer depth may be the primary design parameter controlling hydrologic performance. Performance diminishes as rainfall depths increase and rainfall durations become longer. Annual water budget analysis suggests that approximately 20–50% of runoff entering the bioretention cells was lost to exfiltration and evapotranspiration. DA - 2009/// PY - 2009/// DO - 10.1061/(ASCE)1084-0699(2009)14:4(407) VL - 14 IS - 4 SP - 407-415 ER - TY - JOUR TI - Mesenchymal stem cell-seeded collagen matrices for bone repair: Effects of cyclic tensile strain, cell density, and media conditions on matrix contraction in vitro AU - Sumanasinghe, Ruwan D. AU - Osborne, Jason A. AU - Loboa, Elizabeth G. T2 - JOURNAL OF BIOMEDICAL MATERIALS RESEARCH PART A AB - Abstract Type I collagen is the most abundant extracellular matrix protein in bone and contains arginine– glycine–aspartic acid sequences that promote cell adhesion and proliferation. We have previously shown that human mesenchymal stem cells (hMSCs) seeded in three‐dimensional (3D) collagen gels upregulate BMP‐2 mRNA expression in response to tensile strain, indicative of osteogenesis. Therefore, collagen could be a promising scaffold material for functional bone tissue engineering using hMSCs. However, high contraction of the collagen gels by hMSCs poses a challenge to creating large, tissue‐engineered bone constructs. The effects of cyclic tensile strain, medium (with and without dexamethasone), and hMSC seeding density on contraction of collagen matrices have not been investigated. hMSCs were seeded in 3D collagen gels and subjected to cyclic tensile strain of 10% or 12% for 4 h/day at a frequency of 1 Hz in osteogenic‐differentiating or complete MSC growth media for up to 14 days. Viability of hMSCs was not affected by strain or media conditions. While initial seeding density affected matrix contraction alone, there was a high interdependence of strain and medium on matrix contraction. These findings suggest a correlation between hMSC proliferation and osteogenic differentiation on collagen matrix contraction that is affected by media, cell‐seeding density, and cyclic tensile strain. It is vital to understand the effects of culture conditions on collagen matrix contraction by hMSCs in order to consider hMSC‐seeded collagen constructs for functional bone tissue engineering in vitro . © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009 DA - 2009/3/1/ PY - 2009/3/1/ DO - 10.1002/jbm.a.31913 VL - 88A IS - 3 SP - 778-786 SN - 1552-4965 KW - bone tissue engineering KW - mechanical stimulation KW - osteogenic differentiation KW - collagen contraction KW - mesenchymal stem cells ER - TY - JOUR TI - Mercury(II) Bioaccumulation and Antioxidant Physiology in Four Aquatic Insects AU - Xie, Lingtian AU - Flippin, Jennifer L. AU - Deighton, Nigel AU - Funk, David H. AU - Dickey, David A. AU - Buchwalter, David B. T2 - ENVIRONMENTAL SCIENCE & TECHNOLOGY AB - We examined Hg(II) bioaccumulation and compartmentalization patterns in conjunction with antioxidant responses in four aquatic insect species: two caddisflies (Chimarra sp. and Hydropsyche betteni) and two mayflies (Maccaffertium modestum and Isonychia sp). Total antioxidant capabilities differed among unexposed larvae, with both caddisfly species exhibiting elevated antioxidant activities relative to the mayflies. We were able to account for these differences by examining the constitutive activities of catalase (CAT), glutathione peroxidase (GPx), glutathione S-transferase (GST), and superoxide dismutase (SOD), in the four species. We also examined levels of reduced and oxidized glutathione and cysteine in the insects. Glutathione peroxidase and SOD were the most responsive to Hg exposure, with GPx catalytic activity increasing between 50 and 310%. Superoxide dismutase activity decreased between 35 and 50%. This SOD suppression was shown to be dose-dependent in both caddisflies, butthe strength of this suppression did not appear to be related to rates of uptake. Surprisingly, little Hg (<10%) was found in the heat-stable cytosolic protein subcellular compartment in each of the four species, suggesting that Hg was not well detoxified. By combining bioaccumulation studies with other physiological measures, we can begin to better understand the consequences of trace metal pollutants in nature. DA - 2009/2/1/ PY - 2009/2/1/ DO - 10.1021/es802323r VL - 43 IS - 3 SP - 934-940 SN - 1520-5851 ER - TY - JOUR TI - Measuring and partitioning the high-order linkage disequilibrium by multiple order Markov chains (vol 32, pg 301, 2008) AU - Kim, Y. J. AU - Feng, S. AU - Zeng, Z. B. T2 - Genetic Epidemiology DA - 2009/// PY - 2009/// VL - 33 IS - 2 SP - 181-181 ER - TY - JOUR TI - Lifespan changes in working memory in fragile X premutation males AU - Cornish, Kim M. AU - Kogan, Cary S. AU - Li, Lexin AU - Turk, Jeremy AU - Jacquemont, Sebastien AU - Hagerman, Randi J. T2 - BRAIN AND COGNITION AB - Fragile X syndrome is the world's most common hereditary cause of developmental delay in males and is now well characterized at the biological, brain and cognitive levels. The disorder is caused by the silencing of a single gene on the X chromosome, the FMR1 gene. The premutation (carrier) status, however, is less well documented but has an emerging literature that highlights a more subtle profile of executive cognitive deficiencies that mirror those reported in fully affected males. Rarely, however, has the issue of age-related declines in cognitive performance in premutation males been addressed. In the present study, we focus specifically on the cognitive domain of working memory and its subcomponents (verbal, spatial and central executive memory) and explore performance across a broad sample of premutation males aged 18-69 years matched on age and IQ to unaffected comparison males. We further tease apart the premutation status into those males with symptoms of the newly identified neurodegenerative disorder, the fragile X-associated tremor/ataxia syndrome (FXTAS) and those males currently symptom-free. Our findings indicate a specific vulnerability in premutation males on tasks that require simultaneous manipulation and storage of new information, so-called executive control of memory. Furthermore, this vulnerability appears to exist regardless of the presence of FXTAS symptoms. Males with FXTAS symptoms demonstrated a more general impairment encompassing phonological working memory in addition to central executive working memory. Among asymptomatic premutation males, we observed the novel finding of a relationship between increased CGG repeat size and impairment to central executive working memory. DA - 2009/4// PY - 2009/4// DO - 10.1016/j.bandc.2008.11.006 VL - 69 IS - 3 SP - 551-558 SN - 1090-2147 KW - Fragile X syndrome KW - Fragile X tremor and ataxia syndrome KW - Premutation status KW - Working memory KW - Central executive KW - Phonological loop KW - Visual-spatial sketchpad KW - Development KW - Aging ER - TY - JOUR TI - Identification of protein-coding sequences using the hybridization of 18S rRNA and mRNA during translation AU - Xing, Chuanhua AU - Bitzer, Donald L. AU - Alexander, Winser E. AU - Vouk, Mladen A. AU - Stomp, Anne-Marie T2 - NUCLEIC ACIDS RESEARCH AB - We introduce a new approach in this article to distinguish protein-coding sequences from non-coding sequences utilizing a period-3, free energy signal that arises from the interactions of the 3′-terminal nucleotides of the 18S rRNA with mRNA. We extracted the special features of the amplitude and the phase of the period-3 signal in protein-coding regions, which is not found in non-coding regions, and used them to distinguish protein-coding sequences from non-coding sequences. We tested on all the experimental genes from Saccharomyces cerevisiae and Schizosaccharomyces pombe . The identification was consistent with the corresponding information from GenBank, and produced better performance compared to existing methods that use a period-3 signal. The primary tests on some fly, mouse and human genes suggests that our method is applicable to higher eukaryotic genes. The tests on pseudogenes indicated that most pseudogenes have no period-3 signal. Some exploration of the 3′-tail of 18S rRNA and pattern analysis of protein-coding sequences supported further our assumption that the 3′-tail of 18S rRNA has a role of synchronization throughout translation elongation process. This, in turn, can be utilized for the identification of protein-coding sequences. DA - 2009/2// PY - 2009/2// DO - 10.1093/nar/gkn917 VL - 37 IS - 2 SP - 591-601 SN - 1362-4962 ER - TY - JOUR TI - Asphalt parking lot runoff nutrient characterization for eight sites in North Carolina, USA AU - Passeport, E. AU - Hunt, W. F. T2 - Journal of Hydrologic Engineering AB - The objectives of this study were to characterize asphalt parking lot runoff quality and determine factors influencing nutrient concentrations and loads. Event mean concentrations (EMCs) and loads were measured from eight asphalt parking lots in North Carolina using automated flow meters and rain gauges. The number of water quality samples collected varied from 11 to 26 per site. EMCs and loads were statistically analyzed for six nutrient forms: total nitrogen, total Kjeldahl nitrogen, ammonia-nitrogen, nitrate-nitrogen, total phosphorus, and ortho-phosphate. The mean EMCs (in mg/L) were 1.57, 1.19, 0.32, 0.36, 0.19 and 0.07, respectively. Nitrogen species’ concentrations were slightly lower than those from highway runoff found in the literature; whereas, phosphorus EMCs were similar to those in highway runoff. Current load prediction models, generally based on highway or roadway nutrient concentrations, are therefore expected to over-estimate nitrogen loads from asphalt parking lots. Spring and summer presented the highest EMCs and loads, respectively. Significant seasonal differences in concentration (p<0.05) were found mainly between spring and the other three seasons, while loads in summer differed from those of fall and winter. In an attempt to determine the factors affecting EMCs and loads, Pearson correlation tests and multiple linear regression analyses were performed. Strong correlations were found among the variables of each group of factors referred to as climate, physical characteristics and surrounding land use. Rainfall depth, catchment area, the percentage of asphalt and natural surrounding land use were good predictors of nutrient concentrations and loads. DA - 2009/// PY - 2009/// DO - 10.1061/(ASCE)1084-0699(2009)14:4(352) VL - 14 IS - 4 SP - 352-361 ER - TY - JOUR TI - A Joint Association Test for Multiple SNPs in Genetic Case-Control Studies AU - Wang, Tao AU - Jacob, Howard AU - Ghosh, Soumitra AU - Wang, Xujing AU - Zeng, Zhao-Bang T2 - GENETIC EPIDEMIOLOGY AB - For a dense set of genetic markers such as single nucleotide polymorphisms (SNPs) on high linkage disequilibrium within a small candidate region, a haplotype-based approach for testing association between a disease phenotype and the set of markers is attractive in reducing the data complexity and increasing the statistical power. However, due to unknown status of the underlying disease variant, a comprehensive association test may require consideration of various combinations of the SNPs, which often leads to severe multiple testing problems. In this paper, we propose a latent variable approach to test for association of multiple tightly linked SNPs in case-control studies. First, we introduce a latent variable into the penetrance model to characterize a putative disease susceptible locus (DSL) that may consist of a marker allele, a haplotype from a subset of the markers, or an allele at a putative locus between the markers. Next, through using of a retrospective likelihood to adjust for the case-control sampling ascertainment and appropriately handle the Hardy-Weinberg equilibrium constraint, we develop an expectation-maximization (EM)-based algorithm to fit the penetrance model and estimate the joint haplotype frequencies of the DSL and markers simultaneously. With the latent variable to describe a flexible role of the DSL, the likelihood ratio statistic can then provide a joint association test for the set of markers without requiring an adjustment for testing of multiple haplotypes. Our simulation results also reveal that the latent variable approach may have improved power under certain scenarios comparing with classical haplotype association methods. DA - 2009/2// PY - 2009/2// DO - 10.1002/gepi.20368 VL - 33 IS - 2 SP - 151-163 SN - 0741-0395 KW - haplotype association KW - retrospective likelihood KW - latent variable KW - logistic mixture model KW - EM algorithm ER - TY - JOUR TI - The addition of cottonseed hulls to the starter and supplementation of live yeast or mannanoligosaccharide in the milk for young calves AU - Hill, S. R. AU - Hopkins, B. A. AU - Davidson, S. AU - Bolt, S. M. AU - Diaz, D. E. AU - Brownie, C. AU - Brown, T. AU - Huntington, G. B. AU - Whitlow, L. W. T2 - JOURNAL OF DAIRY SCIENCE AB - The objectives of this study were to investigate the effects of the addition of cottonseed hulls (CSH) to the starter and the supplementation of live yeast product (YST) or mannanoligosaccharide product (MOS) to milk, on growth, intake, rumen development, and health parameters in young calves. Holstein (n = 116) and Jersey (n = 46) bull (n = 74) and heifer (n = 88) calves were assigned randomly within sex at birth to treatments. All calves were fed 3.8 L of colostrum daily for the first 2 d. Holstein calves were fed 3.8 L of whole milk, and Jersey calves were fed 2.8 L of whole milk through weaning at 42 d. Calves continued on trial through 63 d. Six treatments were arranged as a 2 × 3 factorial. Calves received either a corn-soybean meal-based starter (21% crude protein and 6% acid detergent fiber; −CSH) or a blend of 85% corn-soybean meal-based starter and 15% CSH (18% crude protein and 14% acid detergent fiber; +CSH) ad libitum. In addition, calves received whole milk with either no supplement (NONE) or supplemented with 3 g/d of mannanoligosaccharide product (MOS) or 4 g/d of live yeast product (YST) through weaning at 42 d. Twelve Holstein steers [n = 6 (per starter type); n = 4 (per supplement type)] were euthanized for collection and examination of rumen tissue samples. Dry matter intake (DMI) was greater for Holstein calves fed +CSH (0.90 kg/d) than −CSH (0.76 kg/d). Final body weight at 63 d of Holstein calves fed +CSH (75.8 kg) was greater than that of those fed −CSH (71.0 kg). Average daily gain (ADG) was greater for Holstein calves fed +CSH (0.58 kg/d) than −CSH (0.52 kg/d). However, Holstein calves fed −CSH had a greater feed efficiency (FE; 0.71 kg of ADG/kg of DMI) than those fed +CSH (0.65 kg of ADG/kg of DMI). Also, Holstein calves fed +CSH had narrower rumen papillae (0.32 mm) compared with those fed −CSH (0.41 mm). There were no significant effects of CSH on DMI, ADG, or FE in Jersey calves. There were no significant effects of YST or MOS on DMI, ADG, FE, or rumen papillae measures in Holstein calves. Jersey calves fed YST or MOS had greater final body weight at 63 d (51.2 kg and 51.0 kg, respectively) than calves fed NONE (47.5 kg). However, there were no significant effects of YST or MOS on DMI, ADG, or FE in Jersey calves. DA - 2009/2// PY - 2009/2// DO - 10.3168/jds.2008-1320 VL - 92 IS - 2 SP - 790-798 SN - 1525-3198 KW - cottonseed hull KW - calf KW - yeast KW - mannanoligosaccharide ER - TY - JOUR TI - Shrinkage inverse regression estimation for model-free variable selection AU - Bondell, Howard D. AU - Li, Lexin T2 - JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY AB - Summary The family of inverse regression estimators that was recently proposed by Cook and Ni has proven effective in dimension reduction by transforming the high dimensional predictor vector to its low dimensional projections. We propose a general shrinkage estimation strategy for the entire inverse regression estimation family that is capable of simultaneous dimension reduction and variable selection. We demonstrate that the new estimators achieve consistency in variable selection without requiring any traditional model, meanwhile retaining the root n estimation consistency of the dimension reduction basis. We also show the effectiveness of the new estimators through both simulation and real data analysis. DA - 2009/// PY - 2009/// DO - 10.1111/j.1467-9868.2008.00686.x VL - 71 SP - 287-299 SN - 1467-9868 KW - Inverse regression estimation KW - Non-negative garrotte KW - Sliced inverse regression KW - Sufficient dimension reduction KW - Variable selection ER - TY - JOUR TI - Sampling and Analytical Variability Associated with the Determination of Total Aflatoxins and Ochratoxin A in Powdered Ginger Sold As a Dietary Supplement in Capsules AU - Trucksess, Mary W. AU - Whitaker, Thomas B. AU - Weaver, Carol M. AU - Slate, Andrew AU - Giesbrecht, Francis G. AU - Rader, Jeanne I. AU - Betz, Joseph M. T2 - JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY AB - The U.S. Food and Drug Administration is studying the need to monitor dietary supplements for mycotoxins such as total aflatoxins and ochratoxin A. An effective mycotoxin-monitoring program requires knowledge of the sampling and analytical variability associated with the determination of total aflatoxins (AF) and ochratoxin A (OTA) in dietary supplements. Three lots of ginger sold as a powder in capsule form and packaged in individual bottles were analyzed for both AF and OTA. The total variability associated with measuring AF and OTA in powdered ginger was partitioned into bottle-to-bottle, within bottle, and analytical variances. The variances were estimated using a nested design. For AF and OTA, the within-bottle variance associated with the 5 g laboratory sample size was the largest component of variability accounting for about 43% and 85% of the total variance, respectively; the analytical variance accounted for about 34% and 9% of the total variability, respectively; and the bottle-to-bottle variance accounted for about 23% and 7% of the total variance, respectively. When the total variance is converted into the coefficient of variation (CV or standard deviation relative to the mean concentration), the CV is lower for AF (16.9%) than OTA (24.7%). DA - 2009/1/28/ PY - 2009/1/28/ DO - 10.1021/jf8017854 VL - 57 IS - 2 SP - 321-325 SN - 0021-8561 KW - Sampling KW - analytical uncertainty KW - aflatoxins KW - ochratoxin A KW - ginger capsules KW - dietary supplements ER - TY - JOUR TI - Performance of a bioretention area and a level spreader-grass filter strip at two highway sites in North Carolina AU - Line, D. E. AU - Hunt, W. F. T2 - Journal of Irrigation and Drainage Engineering AB - The pollutant removal efficiency of a bioretention area and a level spreader-grass filter strip implemented at North Carolina highway facilities was assessed. The assessment consisted of monitoring inflow, outflow, and on-site rainfall for at least 13 storm events. Monitoring included continuous discharge measurement and collecting and analyzing flow-proportional samples for each event. All samples were analyzed for solids, turbidity, and nitrogen and phosphorus forms and selected samples were analyzed for metals. The level spreader-grass filter strip had the best overall efficiency with load reduction efficiencies in all pollutants ranging from 24 to 83% and the highest reduction for total suspended solids (TSS). Much of the efficiency of this best management practice can be attributed to the 49% reduction in runoff volume from inflow to outflow. Pollutant reduction efficiencies for the bioretention area ranged from −254 to 76% with the highest reduction for TSS. The lowest or large negative efficiency was for nitrate+nitrite nitrogen (NO2+3–N). The increase in NO2+3–N likely resulted from a combination of nitrogen additions within the cell and conversion of other forms of nitrogen to NO2+3–N. Statistical analyses suggested that all of the mass reductions for the grass filter strip and many of those for the bioretention area were significant. DA - 2009/// PY - 2009/// DO - 10.1061/(ASCE)0733-9437(2009)135:2(217) VL - 135 IS - 2 SP - 217-224 ER - TY - JOUR TI - MORPHOLOGY OF THE CAUDAL FOSSA IN CAVALIER KING CHARLES SPANIELS AU - Cerda-Gonzalez, Sofia AU - Olby, Natasha J. AU - McCullough, Susan AU - Pease, Anthony P. AU - Broadstone, Richard AU - Osborne, Jason A. T2 - VETERINARY RADIOLOGY & ULTRASOUND AB - Chiari malformations and syringohydromyelia are an important disease complex in Cavalier King Charles Spaniels. Although abnormalities in caudal fossa morphology are considered major contributors to the development of this disease, limited information exists on the range of morphologies in Cavalier King Charles Spaniels and on the relationship of these to clinically evident disease. Sixty‐four Cavalier King Charles Spaniels were studied. Each underwent a neurologic examination and magnetic resonance imaging of the cervical spine and brain. T2‐weighted sagittal images were used to determine both the morphologic characteristics and volume of the caudal fossa in each dog. This volume was also analyzed as a percentage of total cranial cavity volume. Each attribute was correlated with neurological grade and presence of syringohydromyelia. Fifteen dogs had neurologic signs, and 59 had morphologic abnormalities of the craniocervical junction. While 27 dogs had syringohydromyelia, 13 of these were clinically normal. Cerebellar herniation and occipital dysplasia were common findings but were not associated with syringohydromyelia. Dorsal compressive lesions were noted at the first and second cervical vertebral junction. Factors associated with the presence of neurologic signs included syringohydromyelia and the ratio of caudal fossa/total cranial cavity volume; dogs with signs had significantly larger syringohydromyelia than asymptomatic dogs. Caudal fossa size was not associated with syringohydromyelia. A positive association was identified between foramen magnum size and length of cerebellar herniation. The prevalence of craniocervical junction abnormalities is high in Cavalier King Charles Spaniels. While several factors are associated with neurologic signs, occipital hypoplasia appears to be the most important factor. DA - 2009/// PY - 2009/// DO - 10.1111/j.1740-8261.2008.01487.x VL - 50 IS - 1 SP - 37-46 SN - 1740-8261 KW - chiari-like KW - occipital hypoplasia KW - syringomyelia KW - MRI ER - TY - JOUR TI - Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination AU - Reif, D. M. AU - Motsinger-Reif, A. A. AU - McKinney, B. A. AU - Rock, M. T. AU - Crowe, J. E., Jr. AU - Moore, J. H. T2 - GENES AND IMMUNITY AB - Complex clinical outcomes, such as adverse reaction to vaccination, arise from the concerted interactions among the myriad components of a biological system. Therefore, comprehensive etiological models can be developed only through the integrated study of multiple types of experimental data. In this study, we apply this paradigm to high-dimensional genetic and proteomic data collected to elucidate the mechanisms underlying the development of adverse events (AEs) in patients after smallpox vaccination. As vaccination was successful in all of the patients under study, the AE outcomes reported likely represent the result of interactions among immune system components that result in excessive or prolonged immune stimulation. In this study, we examined 1442 genetic variables (single nucleotide polymorphisms) and 108 proteomic variables (serum cytokine concentrations) to model AE risk. To accomplish this daunting analytical task, we employed the Random Forests (RF) method to filter the most important attributes, then we used the selected attributes to build a final decision tree model. This strategy is well suited to integrated analysis, as relevant attributes may be selected from categorical or continuous data. Importantly, RF is a natural approach for studying the type of gene–gene, gene–protein and protein–protein interactions we hypothesize to be involved in the development of clinical AEs. RF importance scores for particular attributes take interactions into account, and there may be interactions across data types. Combining information from previous studies on AEs related to smallpox vaccination with the genetic and proteomic attributes identified by RF, we built a comprehensive model of AE development that includes the cytokines intercellular adhesion molecule-1 (ICAM-1 or CD54), interleukin-10 (IL-10), and colony stimulating factor-3 (CSF-3 or G-CSF) and a genetic polymorphism in the cyokine gene interleukin-4 (IL4). The biological factors included in the model support our hypothesized mechanism for the development of AEs involving prolonged stimulation of inflammatory pathways and an imbalance of normal tissue damage repair pathways. This study shows the utility of RF for such analytical tasks, while both enhancing and reinforcing our working model of AE development after smallpox vaccination. DA - 2009/3// PY - 2009/3// DO - 10.1038/gene.2008.80 VL - 10 IS - 2 SP - 112-119 SN - 1476-5470 KW - smallpox KW - Random Forests KW - integrated analysis KW - genetic KW - proteomic KW - interactions ER - TY - JOUR TI - Nonparametric autocovariance estimation from censored time series by Gaussian imputation AU - Park, Jung Wook AU - Genton, Marc G. AU - Ghosh, Sujit K. T2 - JOURNAL OF NONPARAMETRIC STATISTICS AB - One of the most frequently used methods to model the autocovariance function of a second-order stationary time series is to use the parametric framework of autoregressive and moving average models developed by Box and Jenkins. However, such parametric models, though very flexible, may not always be adequate to model autocovariance functions with sharp changes. Furthermore, if the data do not follow the parametric model and are censored at a certain value, the estimation results may not be reliable. We develop a Gaussian imputation method to estimate an autocovariance structure via nonparametric estimation of the autocovariance function in order to address both censoring and incorrect model specification. We demonstrate the effectiveness of the technique in terms of bias and efficiency with simulations under various rates of censoring and underlying models. We describe its application to a time series of silicon concentrations in the Arctic. DA - 2009/// PY - 2009/// DO - 10.1080/10485250802570964 VL - 21 IS - 2 SP - 241-259 SN - 1029-0311 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-61749094603&partnerID=MN8TOARS KW - censoring KW - Gibbs sampling KW - imputation KW - nonparametric estimation KW - truncated multivariate normal distribution ER - TY - JOUR TI - A novel statistical model for mandibular helical axis analysis AU - Hayashi, K. AU - Reich, B. AU - Delong, R. AU - Lee, S. -P. AU - Mizoguchi, I. T2 - JOURNAL OF ORAL REHABILITATION AB - Summary The purpose of this study was to establish a new statistical method for the analysis of noisy mandibular helical axis parameters, especially the position vector of the finite helical axis (FHA). The subjects were children with anterior cross‐bite who had received orthodontic treatment. Maximum mouth‐opening was measured by means of an opto‐electronic motion analysis system. These movements were compared with similar movement in the same group after treatment of their anterior cross‐bite. Each curve of FHA position vectors was modelled as a spline function with random coefficients. To determine the optimal number of knots, two criteria were used: deviance information criteria (DIC) and mean squared prediction error (MSE). We were interested in estimating a typical curve for a population. Self‐modelling regression (SEMOR) was extended to three dimensions to model groups of three‐dimensional curves. Each curve was modelled as a spline function using nine knots. Population average curves were created using SEMOR. This study provided detailed information about jaw movement for comparing cross‐bite to normal occlusion by calculating the population mean curves of the position vector of the FHA. Our results suggested that the two population mean curves for the position vector of the FHA were significantly different in the closing phase. The combination of a spline function with random coefficients and SEMOR extended to three dimensions can be used not only for FHA analysis but also for the analysis of other jaw movements. DA - 2009/2// PY - 2009/2// DO - 10.1111/j.1365-2842.2008.01890.x VL - 36 IS - 2 SP - 102-109 SN - 1365-2842 KW - finite helical axis KW - statistical model KW - spline KW - self-modelling regression KW - mandibular movement ER - TY - JOUR TI - Performance of information criteria for spatial models AU - Lee, Hyeyoung AU - Ghosh, Sujit K. T2 - JOURNAL OF STATISTICAL COMPUTATION AND SIMULATION AB - Model choice is one of the most crucial aspect in any statistical data analysis. It is well known that most models are just an approximation to the true data-generating process but among such model approximations, it is our goal to select the ‘best’ one. Researchers typically consider a finite number of plausible models in statistical applications, and the related statistical inference depends on the chosen model. Hence, model comparison is required to identify the ‘best’ model among several such candidate models. This article considers the problem of model selection for spatial data. The issue of model selection for spatial models has been addressed in the literature by the use of traditional information criteria-based methods, even though such criteria have been developed based on the assumption of independent observations. We evaluate the performance of some of the popular model selection critera via Monte Carlo simulation experiments using small to moderate samples. In particular, we compare the performance of some of the most popular information criteria such as Akaike information criterion (AIC), Bayesian information criterion, and corrected AIC in selecting the true model. The ability of these criteria to select the correct model is evaluated under several scenarios. This comparison is made using various spatial covariance models ranging from stationary isotropic to nonstationary models. DA - 2009/// PY - 2009/// DO - 10.1080/00949650701611143 VL - 79 IS - 1 SP - 93-106 SN - 1563-5163 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-57049088072&partnerID=MN8TOARS KW - Model selection KW - Spatial models KW - Information criteria ER - TY - JOUR TI - Fruit abscission by Physalis species as defense against frugivory AU - Benda, Nicole D. AU - Brownie, Cavell AU - Schal, Coby AU - Gould, Fred T2 - ENTOMOLOGIA EXPERIMENTALIS ET APPLICATA AB - Abstract Fruit abscission as a response to herbivory is well‐documented in many plant species, but its effect on further damage by mobile herbivores that survive fruit abscission is relatively unstudied. Physalis plants (Solanaceae) abscise fruit containing feeding larvae of their main frugivore, Heliothis subflexa Guenée (Lepidoptera: Noctuidae), a specialist moth. We tested the ability of H. subflexa larvae placed under the plant canopy to find and climb onto two architecturally different Physalis species. Physalis pubescens L., a low, shrub‐like, spreading plant, abscises its fruit at a higher rate than Physalis angulata L., a tall arborescent plant. As a result, small larvae are more often dropped from P. pubescens . Third and fifth instars located P. pubescens faster and with a higher probability than P. angulata . Although fifth instars outperformed third‐instar caterpillars at finding P. angulata , P. pubescens was located equally fast by the two instars. Heliothis subflexa located Physalis plants more successfully and more quickly than a close relative, the generalist Heliothis virescens Fabricius. The higher fruit abscission rates in P. pubescens may be an evolved response to its greater susceptibility to searching caterpillars. DA - 2009/1// PY - 2009/1// DO - 10.1111/j.1570-7458.2008.00792.x VL - 130 IS - 1 SP - 21-27 SN - 1570-7458 KW - caterpillar foraging KW - host plant location KW - Heliothis subflexa KW - Heliothis virescens KW - specialist behavior KW - plant architecture KW - Lepidoptera KW - Noctuidae KW - Solanaceae ER - TY - JOUR TI - Convergence properties of sequential Bayesian D-optimal designs AU - Roy, Anindya AU - Ghosal, Subhashis AU - Rosenberger, William F. T2 - Journal of Statistical Planning and Inference AB - We establish convergence properties of sequential Bayesian optimal designs. In particular, for sequential D-optimality under a general nonlinear location-scale model for binary experiments, we establish posterior consistency, consistency of the design measure, and the asymptotic normality of posterior following the design. We illustrate our results in the context of a particular application in the design of phase I clinical trials, namely a sequential design of Haines et al. [2003. Bayesian optimal designs for phase I clinical trials. Biometrics 59, 591--600] that incorporates an ethical constraint on overdosing. DA - 2009/2// PY - 2009/2// DO - 10.1016/j.jspi.2008.04.025 VL - 139 IS - 2 SP - 425-440 J2 - Journal of Statistical Planning and Inference LA - en OP - SN - 0378-3758 UR - http://dx.doi.org/10.1016/j.jspi.2008.04.025 DB - Crossref KW - Adaptive designs KW - Asymptotic normality KW - Discrete optimal design KW - Dose-response KW - Posterior convergence ER -