TY - JOUR TI - Nonparametric binary regression using a Gaussian process prior AU - Choudhuri, Nidhan AU - Ghosal, Subhashis AU - Roy, Anindya T2 - Statistical Methodology AB - The article describes a nonparametric Bayesian approach to estimating the regression function for binary response data measured with multiple covariates. A multiparameter Gaussian process, after some transformation, is used as a prior on the regression function. Such a prior does not require any assumptions like monotonicity or additivity of the covariate effects. However, additivity, if desired, may be imposed through the selection of appropriate parameters of the prior. By introducing some latent variables, the conditional distributions in the posterior may be shown to be conjugate, and thus an efficient Gibbs sampler to compute the posterior distribution may be developed. A hierarchical scheme to construct a prior around a parametric family is described. A robustification technique to protect the resulting Bayes estimator against miscoded observations is also designed. A detailed simulation study is conducted to investigate the performance of the proposed methods. We also analyze some real data using the methods developed in this article. DA - 2007/4// PY - 2007/4// DO - 10.1016/j.stamet.2006.07.003 VL - 4 IS - 2 SP - 227-243 J2 - Statistical Methodology LA - en OP - SN - 1572-3127 UR - http://dx.doi.org/10.1016/j.stamet.2006.07.003 DB - Crossref ER - TY - CONF TI - Conversion of a Drainage Ditch to Constructed Wetlands to Treat Stormwater Runoff AU - Burchell, M. R. AU - Line, D. AU - Hunt, III, W. F. AU - Wright, J. T2 - World Environmental and Water Resources Congress 2007 AB - A drainage ditch near Laney High School in Wilmington, N.C., designed to collect runoff from athletic fields and parking lots and deliver it to Smith Creek, was converted to a constructed wetland in August 2005: The approximately 0.1 ha wetland collects and treats drainage water from a 12 ha watershed, 2.4 ha of which is impervious surface. The wetland was designed with a variety of elevation features and planted with over 15 species of wetland plants, to encourage sedimentation, biogeochemical transformations of nutrients associated with runoff, and ecological diversity. Retention times are estimated to be 3–4 days. As of summer 2006, the wetland was vegetated and on-line. Preliminary nutrient data indicate a 50% reduction in TN and TP concentrations, and a 40% reduction in TSS. C2 - 2007/5/11/ C3 - World Environmental and Water Resources Congress 2007 DA - 2007/5/11/ DO - 10.1061/40927(243)246 PB - American Society of Civil Engineers SN - 9780784409275 UR - http://dx.doi.org/10.1061/40927(243)246 DB - Crossref ER - TY - JOUR TI - Complex gene–gene interactions in multiple sclerosis: a multifactorial approach reveals associations with inflammatory genes AU - Motsinger, Alison A. AU - Brassat, David AU - Caillier, Stacy J. AU - Erlich, Henry A. AU - Walker, Karen AU - Steiner, Lori L. AU - Barcellos, Lisa F. AU - Pericak-Vance, Margaret A. AU - Schmidt, Silke AU - Gregory, Simon AU - Hauser, Stephen L. AU - Haines, Jonathan L. AU - Oksenberg, Jorge R. AU - Ritchie, Marylyn D. T2 - Neurogenetics DA - 2007/// PY - 2007/// DO - 10.1007/S10048-006-0058-9 VL - 8 IS - 1 SP - 11–20 SN - 1364-6745 1364-6753 UR - http://dx.doi.org/10.1007/S10048-006-0058-9 KW - multiple sclerosis KW - multifactor dimensionality reduction KW - epistasis ER - TY - JOUR TI - Human Genomic Association Studies: A Primer for the Infectious Diseases Specialist AU - Motsinger, Alison A. AU - Haas, David W. AU - Hulgan, Todd AU - Ritchie, Marylyn D. T2 - The Journal of Infectious Diseases AB - Medical science is undergoing a genomic revolution. In coming years, insights from human genomic research will increasingly influence all aspects of infectious diseases, ranging from fundamental laboratory research and clinical care to epidemiology and global health. Infectious disease specialists unfamiliar with genomic methods and computational techniques may shy away from publications that involve human genomics analyses. In this article, we discuss selected aspects of study design and statistical analysis in this area, emphasizing important pitfalls that may compromise the validity of some studies. Our goal is to provide the infectious diseases specialist with information that will aid in the critical evaluation of publications that include human genomic analyses. DA - 2007/6/15/ PY - 2007/6/15/ DO - 10.1086/518247 VL - 195 IS - 12 SP - 1737-1744 J2 - J INFECT DIS LA - en OP - SN - 0022-1899 1537-6613 UR - http://dx.doi.org/10.1086/518247 DB - Crossref ER - TY - JOUR TI - Genetic variation in the mitochondrial enzyme carbamyl-phosphate synthetase I predisposes children to increased pulmonary artery pressure following surgical repair of congenital heart defects: A validated genetic association study AU - Canter, Jeffrey A. AU - Summar, Marshall L. AU - Smith, Heidi B. AU - Rice, Geraldine D. AU - Hall, Lynn D. AU - Ritchie, Marylyn D. AU - Motsinger, Alison A. AU - Christian, Karla G. AU - Drinkwater, Davis C., Jr. AU - Scholl, Frank G. AU - Dyer, Karrie L. AU - Kavanaugh-McHugh, Ann L. AU - Barr, Frederick E. T2 - Mitochondrion AB - Increased pulmonary artery pressure (PAP) can complicate the postoperative care of children undergoing surgical repair of congenital heart defects. Endogenous NO regulates PAP and is derived from arginine supplied by the urea cycle. The rate-limiting step in the urea cycle is catalyzed by a mitochondrial enzyme, carbamoyl-phosphate synthetase I (CPSI). A well-characterized polymorphism in the gene encoding CPSI (T1405N) has previously been implicated in neonatal pulmonary hypertension. A consecutive modeling cohort of children (N = 131) with congenital heart defects requiring surgery was prospectively evaluated to determine key factors associated with increased postoperative PAP, defined as a mean PAP > 20 mmHg for at least 1 h during the 48 h following surgery measured by an indwelling pulmonary artery catheter. Multiple dimensionality reduction (MDR) was used to both internally validate observations and develop optimal two-variable through five-variable models that were tested prospectively in a validation cohort (N = 41). Unconditional logistic regression analysis of the modeling cohort revealed that age (OR = 0.92, p = 0.01), CPSI T1405N genotype (AC vs. AA: OR = 4.08, p = 0.04, CC vs. AA: OR = 5.96, p = 0.01), and Down syndrome (OR = 5.25, p = 0.04) were independent predictors of this complex phenotype. MDR predicted that the best two-variable model consisted of age and CPSI T1405N genotype (p < 0.001). This two-variable model correctly predicted 73% of the outcomes from the validation cohort. A five-variable model that added race, gender and Down’s syndrome was not significantly better than the two-variable model. In conclusion, the CPSI T1405N genotype appears to be an important new factor in predicting susceptibility to increased PAP following surgical repair of congenital cardiac defects in children. DA - 2007/5// PY - 2007/5// DO - 10.1016/j.mito.2006.11.001 VL - 7 IS - 3 SP - 204-210 J2 - Mitochondrion LA - en OP - SN - 1567-7249 UR - http://dx.doi.org/10.1016/j.mito.2006.11.001 DB - Crossref KW - mitochondrial enzyme KW - CPSI KW - pulmonary artery pressure ER - TY - JOUR TI - Polymorphism modulates symptomatic response to antiarrhythmic drug therapy in patients with lone atrial fibrillation AU - Darbar, Dawood AU - Motsinger, Alison A. AU - Ritchie, Marylyn D. AU - Gainer, James V. AU - Roden, Dan M. T2 - Heart Rhythm AB - The angiotensin-converting enzyme (ACE) deletion allele, ACE D, is associated with increased ACE activity and adverse outcomes in cardiovascular disease. Although activation of the renin-angiotensin-aldosterone system (RAAS) now appears to play a role in the pathophysiology of atrial fibrillation (AF), it remains to be determined if ACE genotype impacts response to conventional AAD therapy in patients with AF.The purpose of this study was to investigate whether response to antiarrhythmic drug (AAD) therapy in patients with AF is modulated by the ACE I/D polymorphism.We studied 213 patients (147 men, 66 women; ages 52 +/- 15 years) prospectively enrolled in the Vanderbilt AF Registry. AAD therapy outcome was defined prospectively as response if there was a >or=75% reduction in symptomatic AF burden or nonresponse if AF burden was unchanged, necessitating a change in drugs or therapy.Lone AF (age <65 years, no identifiable cause) was present in 72 (34%) patients, whereas hypertension was the most common underlying disease in the remaining 141 (41%). AF was paroxysmal in 170 (80%) and persistent in 43 (20%). The frequencies of the DD, ID, and II genotypes were in Hardy-Weinberg equilibrium. Lone AF and DD/ID genotypes were highly significant predictors of failure of drug therapy (P <.005). In patients with lone AF, failure of drug response was 5%, 41%, and 47% in patients with II, ID, and DD genotypes, respectively, (P <.005, II vs. ID/DD).These results provide further evidence for a role of RAAS activation in the pathophysiology of AF and point to a potential role for stratification of therapeutic approaches by ACE genotype. DA - 2007/6// PY - 2007/6// DO - 10.1016/j.hrthm.2007.02.006 VL - 4 IS - 6 SP - 743-749 J2 - Heart Rhythm LA - en OP - SN - 1547-5271 UR - http://dx.doi.org/10.1016/j.hrthm.2007.02.006 DB - Crossref KW - atrial fibrillation KW - antiarrhythmic drugs KW - angiotensin-converting-enzyme KW - genetics ER - TY - JOUR TI - Genetic programming neural networks: A powerful bioinformatics tool for human genetics AU - Ritchie, Marylyn D. AU - Motsinger, Alison A. AU - Bush, William S. AU - Coffey, Christopher S. AU - Moore, Jason H. T2 - Applied Soft Computing AB - The identification of genes that influence the risk of common, complex disease primarily through interactions with other genes and environmental factors remains a statistical and computational challenge in genetic epidemiology. This challenge is partly due to the limitations of parametric statistical methods for detecting genetic effects that are dependent solely or partially on interactions. We have previously introduced a genetic programming neural network (GPNN) as a method for optimizing the architecture of a neural network to improve the identification of genetic and gene–environment combinations associated with disease risk. Previous empirical studies suggest GPNN has excellent power for identifying gene–gene and gene–environment interactions. The goal of this study was to compare the power of GPNN to stepwise logistic regression (SLR) and classification and regression trees (CART) for identifying gene–gene and gene–environment interactions. SLR and CART are standard methods of analysis for genetic association studies. Using simulated data, we show that GPNN has higher power to identify gene–gene and gene–environment interactions than SLR and CART. These results indicate that GPNN may be a useful pattern recognition approach for detecting gene–gene and gene–environment interactions in studies of human disease. DA - 2007/1// PY - 2007/1// DO - 10.1016/j.asoc.2006.01.013 VL - 7 IS - 1 SP - 471-479 J2 - Applied Soft Computing LA - en OP - SN - 1568-4946 UR - http://dx.doi.org/10.1016/j.asoc.2006.01.013 DB - Crossref KW - nueral networks KW - genetic programming KW - bioinformatics KW - epistasis KW - gene-gene interactions ER - TY - JOUR TI - Genetic heterogeneity is not as threatening as you might think AU - Ritchie, Marylyn D. AU - Edwards, Todd L. AU - Fanelli, Theresa J. AU - Motsinger, Alison A. T2 - Genetic Epidemiology AB - Genetic EpidemiologyVolume 31, Issue 7 p. 797-800 Letter to the Editor Genetic heterogeneity is not as threatening as you might think Marylyn D. Ritchie, Corresponding Author Marylyn D. Ritchie ritchie@chgr.mc.vanderbilt.edu Vanderbilt University, Center for Human Genetics Research, Nashville, TennesseeCenter for Human Genetics Research, Department of Molecular Physiology and Biophysics, 519 Light Hall, Vanderbilt University Medical School, Nashville, TN, 37232-0700===Search for more papers by this authorTodd L. Edwards, Todd L. Edwards Vanderbilt University, Center for Human Genetics Research, Nashville, TennesseeSearch for more papers by this authorTheresa J. Fanelli, Theresa J. Fanelli Vanderbilt University, Center for Human Genetics Research, Nashville, TennesseeSearch for more papers by this authorAlison A. Motsinger, Alison A. Motsinger Vanderbilt University, Center for Human Genetics Research, Nashville, TennesseeSearch for more papers by this author Marylyn D. Ritchie, Corresponding Author Marylyn D. Ritchie ritchie@chgr.mc.vanderbilt.edu Vanderbilt University, Center for Human Genetics Research, Nashville, TennesseeCenter for Human Genetics Research, Department of Molecular Physiology and Biophysics, 519 Light Hall, Vanderbilt University Medical School, Nashville, TN, 37232-0700===Search for more papers by this authorTodd L. Edwards, Todd L. Edwards Vanderbilt University, Center for Human Genetics Research, Nashville, TennesseeSearch for more papers by this authorTheresa J. Fanelli, Theresa J. Fanelli Vanderbilt University, Center for Human Genetics Research, Nashville, TennesseeSearch for more papers by this authorAlison A. Motsinger, Alison A. Motsinger Vanderbilt University, Center for Human Genetics Research, Nashville, TennesseeSearch for more papers by this author First published: 24 July 2007 https://doi.org/10.1002/gepi.20256Citations: 13AboutPDF 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 onFacebookTwitterLinked InRedditWechat Citing Literature Volume31, Issue7November 2007Pages 797-800 RelatedInformation DA - 2007/// PY - 2007/// DO - 10.1002/gepi.20256 VL - 31 IS - 7 SP - 797-800 J2 - Genet. Epidemiol. LA - en OP - SN - 0741-0395 1098-2272 UR - http://dx.doi.org/10.1002/gepi.20256 DB - Crossref ER - TY - JOUR TI - A balanced accuracy function for epistasis modeling in imbalanced datasets using multifactor dimensionality reduction AU - Velez, Digna R. AU - White, Bill C. AU - Motsinger, Alison A. AU - Bush, William S. AU - Ritchie, Marylyn D. AU - Williams, Scott M. AU - Moore, Jason H. T2 - Genetic Epidemiology AB - Multifactor dimensionality reduction (MDR) was developed as a method for detecting statistical patterns of epistasis. The overall goal of MDR is to change the representation space of the data to make interactions easier to detect. It is well known that machine learning methods may not provide robust models when the class variable (e.g. case-control status) is imbalanced and accuracy is used as the fitness measure. This is because most methods learn patterns that are relevant for the larger of the two classes. The goal of this study was to evaluate three different strategies for improving the power of MDR to detect epistasis in imbalanced datasets. The methods evaluated were: (1) over-sampling that resamples with replacement the smaller class until the data are balanced, (2) under-sampling that randomly removes subjects from the larger class until the data are balanced, and (3) balanced accuracy [(sensitivity+specificity)/2] as the fitness function with and without an adjusted threshold. These three methods were compared using simulated data with two-locus epistatic interactions of varying heritability (0.01, 0.025, 0.05, 0.1, 0.2, 0.3, 0.4) and minor allele frequency (0.2, 0.4) that were embedded in 100 replicate datasets of varying sample sizes (400, 800, 1600). Each dataset was generated with different ratios of cases to controls (1 : 1, 1 : 2, 1 : 4). We found that the balanced accuracy function with an adjusted threshold significantly outperformed both over-sampling and under-sampling and fully recovered the power. These results suggest that balanced accuracy should be used instead of accuracy for the MDR analysis of epistasis in imbalanced datasets. DA - 2007/5// PY - 2007/5// DO - 10.1002/gepi.20211 VL - 31 IS - 4 SP - 306-315 J2 - Genet. Epidemiol. LA - en OP - SN - 0741-0395 1098-2272 UR - http://dx.doi.org/10.1002/gepi.20211 DB - Crossref ER - TY - CONF TI - Bayesian Estimation of Scram Rate Trends in Nuclear Power Plants AU - Mishra, K. AU - Ghosh, S.K. T2 - Joint Statistical Meetings C2 - 2007/// DA - 2007/// PY - 2007/// ER - TY - CONF TI - A Joint Modeling Approach for Analyzing Nonignorable Missing Data AU - Ghosh, S.K. AU - Zhu, L. T2 - Joint Statistical Meetings C2 - 2007/// DA - 2007/// PY - 2007/// ER - TY - CONF TI - A Bayesian Approach to Assessing the Risk of QT Prolongation AU - Anand, S. AU - Ghosh, S.K. T2 - Joint Statistical Meetings C2 - 2007/// DA - 2007/// PY - 2007/// ER - TY - CONF TI - Nonparametric Estimation of Mean Residual Life Function AU - Liu, S. AU - Ghosh, S.K. T2 - Joint Statistical Meetings C2 - 2007/// DA - 2007/// PY - 2007/// ER - TY - CONF TI - A Variable Selection Method for Linear Models using Modi ed Zellner's Prior AU - Krishna, A. AU - Ghosh, S.K. AU - Bondell, H. T2 - Joint Statistical Meetings C2 - 2007/// DA - 2007/// PY - 2007/// ER - TY - CONF TI - Application of Nonlinear Mixed E ects Models in Biomedical Sciences AU - Ghosh, S. T2 - Statistics Seminar C2 - 2007/1/29/ CY - Glaxo-Smith-Kline Inc, Research Triangle Park, NC DA - 2007/1/29/ PY - 2007/1/29/ ER - TY - SOUND TI - A Class of Kernel-based CAR Models for Spatial Data AU - Ghosh, S. DA - 2007/4/14/ PY - 2007/4/14/ ER - TY - SOUND TI - Bayesian Methods for Nonlinear Mixed Models: a short course AU - Ghosh, S. DA - 2007/5/31/ PY - 2007/5/31/ ER - TY - CONF TI - Spatial Association between Speciated Fine Particles and Mortality AU - Ghosh, S. T2 - Office of Research and Methodology and Washington Statistical Society Seminar C2 - 2007/6/21/ CY - National Center for Health Statistics, Hyattsville, MD DA - 2007/6/21/ PY - 2007/6/21/ ER - TY - CONF TI - A Joint Modeling Approach for Analyzing Nonignorable Missing Data AU - Ghosh, S. T2 - Joint Statistical Meetings C2 - 2007/7/29/ CY - Salt Lake City, UT DA - 2007/7/29/ PY - 2007/7/29/ ER - TY - CONF TI - Spatial Association Between Speciated Fine Particles and Mortality AU - Ghosh, S. T2 - StatGIS Conference C2 - 2007/9/24/ CY - Klagenfurt, Austria DA - 2007/9/24/ PY - 2007/9/24/ ER - TY - CONF TI - A Joint Modeling Approach for Analyzing Non-ignorable Missing Data AU - Ghosh, S. T2 - International Conference on Advances in Interdisciplinary Statistics and Combinatorics C2 - 2007/10/12/ CY - Greensboro, NC DA - 2007/10/12/ PY - 2007/10/12/ ER - TY - CONF TI - Spatial Association between Speciated Fine Particles and Mortality AU - Ghosh, S. T2 - 17th Annual Conference of the International Society of Exposure Analysis C2 - 2007/10/18/ CY - Durham, NC DA - 2007/10/18/ PY - 2007/10/18/ ER - TY - SOUND TI - Application of Nonlinear Mixed Models involving ODEs in Biomedical Sciences AU - Ghosh, S. DA - 2007/11/2/ PY - 2007/11/2/ ER - TY - SOUND TI - Monte Carlo Statistical Methods: a short course AU - Ghosh, S. DA - 2007/12/17/ PY - 2007/12/17/ ER - TY - JOUR TI - A nonparametric plug-in rule for selecting optimal block lengths for block bootstrap methods AU - Lahiri, S.N. AU - Furukawa, K. AU - Lee, Y.-D. T2 - Statistical Methodology AB - In this paper, we consider the problem of empirical choice of optimal block sizes for block bootstrap estimation of population parameters. We suggest a nonparametric plug-in principle that can be used for estimating ‘mean squared error’-optimal smoothing parameters in general curve estimation problems, and establish its validity for estimating optimal block sizes in various block bootstrap estimation problems. A key feature of the proposed plug-in rule is that it can be applied without explicit analytical expressions for the constants that appear in the leading terms of the optimal block lengths. Furthermore, we also discuss the computational efficacy of the method and explore its finite sample properties through a simulation study. DA - 2007/7// PY - 2007/7// DO - 10.1016/j.stamet.2006.08.002 VL - 4 IS - 3 SP - 292-321 J2 - Statistical Methodology LA - en OP - SN - 1572-3127 UR - http://dx.doi.org/10.1016/j.stamet.2006.08.002 DB - Crossref ER - TY - JOUR TI - Normal approximation to the hypergeometric distribution in nonstandard cases and a sub-Gaussian Berry–Esseen theorem AU - Lahiri, S.N. AU - Chatterjee, A. AU - Maiti, T. T2 - Journal of Statistical Planning and Inference AB - In this paper, we consider simple random sampling without replacement from a dichotomous finite population. We investigate accuracy of the Normal approximation to the Hypergeometric probabilities for a wide range of parameter values, including the nonstandard cases where the sampling fraction tends to one and where the proportion of the objects of interest in the population tends to the boundary values, zero and one. We establish a non-uniform Berry–Esseen theorem for the Hypergeometric distribution which shows that in the nonstandard cases, the rate of Normal approximation to the Hypergeometric distribution can be considerably slower than the rate of Normal approximation to the Binomial distribution. We also report results from a moderately large numerical study and provide some guidelines for using the Normal approximation to the Hypergeometric distribution in finite samples. DA - 2007/11// PY - 2007/11// DO - 10.1016/j.jspi.2007.03.033 VL - 137 IS - 11 SP - 3570-3590 J2 - Journal of Statistical Planning and Inference LA - en OP - SN - 0378-3758 UR - http://dx.doi.org/10.1016/j.jspi.2007.03.033 DB - Crossref KW - finite population KW - sampling without replacement KW - simple random sampling KW - normal approximation KW - Berry-Esseen theorem ER - TY - JOUR TI - Bootstrapping the Empirical Distribution Function of a Spatial Process AU - Zhu, Jun AU - Lahiri, S. N. T2 - Statistical Inference for Stochastic Processes DA - 2007/7// PY - 2007/7// DO - 10.1007/s11203-005-2349-4 VL - 10 IS - 2 SP - 107-145 J2 - Stat Infer Stoch Process LA - en OP - SN - 1387-0874 1572-9311 UR - http://dx.doi.org/10.1007/s11203-005-2349-4 DB - Crossref ER - TY - JOUR TI - Bayesian Analysis of Quality Adjusted Lifetime (QAL) Data AU - Ghosh, Sujit K. AU - Mukhopadhyay, Pabak T2 - Journal of Statistical Theory and Practice DA - 2007/6// PY - 2007/6// DO - 10.1080/15598608.2007.10411836 VL - 1 IS - 2 SP - 233-251 J2 - Journal of Statistical Theory and Practice LA - en OP - SN - 1559-8608 1559-8616 UR - http://dx.doi.org/10.1080/15598608.2007.10411836 DB - Crossref KW - Bayesian Inference KW - Data Augmentation KW - Gibbs Sampling KW - Markov Chain Monte Carlo KW - Quality Adjusted Survival KW - TWiST ER - TY - JOUR TI - Semiparametric inference based on a class of zero-altered distributions AU - Ghosh, Sujit K. AU - Kim, Honggie T2 - Statistical Methodology AB - In modeling count data collected from manufacturing processes, economic series, disease outbreaks and ecological surveys, there are usually a relatively large or small number of zeros compared to positive counts. Such low or high frequencies of zero counts often require the use of underdispersed or overdispersed probability models for the underlying data generating mechanism. The commonly used models such as generalized or zero-inflated Poisson distributions are parametric and can usually account for only the overdispersion, but such distributions are often found to be inadequate in modeling underdispersion because of the need for awkward parameter or support restrictions. This article introduces a flexible class of semiparametric zero-altered models which account for both underdispersion and overdispersion and includes other familiar models such as those mentioned above as special cases. Consistency and asymptotic normality of the estimator of the dispersion parameter are derived under general conditions. Numerical support for the performance of the proposed method of inference is presented for the case of common discrete distributions. DA - 2007/7// PY - 2007/7// DO - 10.1016/j.stamet.2007.01.001 VL - 4 IS - 3 SP - 371-383 J2 - Statistical Methodology LA - en OP - SN - 1572-3127 UR - http://dx.doi.org/10.1016/j.stamet.2007.01.001 DB - Crossref ER - TY - CONF TI - Innovative Stormwater Treatment Practices in the Neuse and Tar-Pamlico Basins: A Partnership between the North Carolina Ecosystem Enhancement Program and the Biological and Agricultural Engineering Department at North Carolina State University AU - Hathaway, J. M. AU - Hunt, W. F. AU - Smith, R. A. AU - Bass, K. L. T2 - World Environmental and Water Resources Congress 2007 AB - Urbanization within North Carolina's watersheds and the need for proactive mitigation led to the establishment of the North Carolina Ecosystem Enhancement Program (EEP) in July 2003. The EEP is responsible for the majority of mitigation efforts throughout the state. These efforts include the restoration, enhancement, and preservation of streams and wetlands, as well as the creation of stormwater best management practices (BMPs) for the purpose of maintaining and improving water quality and riparian habitats across the state. This project involves a partnership between EEP and the Biological and Agricultural Engineering Department (BAE) at North Carolina State University for the purpose of locating, designing, and monitoring stormwater BMPs. In addition, local governments and the North Carolina Cooperative Extension Service assist in project site selection and development. Two large river basins in North Carolina, Neuse and Tar-Pamlico, have historic, significant degradation to water quality partially due to urbanization and agricultural practices. Primary pollutants within these basins include nitrogen and phosphorous. To change the trend of degradation, the State of North Carolina enacted regulations for nitrogen and phosphorous removal specifically for these basins. These regulations provided for the funding of the EEP Nutrient Reduction Program by authorizing impact fees. C2 - 2007/5/11/ C3 - World Environmental and Water Resources Congress 2007 DA - 2007/5/11/ DO - 10.1061/40927(243)570 PB - American Society of Civil Engineers SN - 9780784409275 UR - http://dx.doi.org/10.1061/40927(243)570 DB - Crossref ER - TY - JOUR TI - Southern two-lined salamanders in urbanizing watersheds AU - Miller, Jennifer E. AU - Hess, George R. AU - Moorman, Christopher E. T2 - Urban Ecosystems DA - 2007/// PY - 2007/// DO - 10.1007/s11252-006-0012-5 VL - 10 IS - 1 SP - 73–85 SN - 1083-8155 1573-1642 UR - http://dx.doi.org/10.1007/s11252-006-0012-5 ER - TY - JOUR TI - Inside Front Cover: Field-Driven Biofunctionalization of Polymer Fiber Surfaces during Electrospinning (Adv. Mater. 1/2007) AU - Sun, X.-Y. AU - Shankar, R. AU - Börner, H. G. AU - Ghosh, T. K. AU - Spontak, R. J. T2 - Advanced Materials AB - Abstract Surface‐biofunctionalized synthetic polymer fibers composed of a fiber‐forming host polymer and an oligopeptide conjugate can be prepared from electrospinning, report Spontak and co‐workers on p. 87. The conjugate consists of a polypeptide segment and a polymer block that is compatible with the host polymer. Because the more polarizable peptide segment migrates to the surface during electrospinning, peptide surface‐enrichment is achieved in a single step without further treatment. DA - 2007/1/8/ PY - 2007/1/8/ DO - 10.1002/adma.200790004 VL - 19 IS - 1 SP - NA-NA J2 - Adv. Mater. LA - en OP - SN - 0935-9648 1521-4095 UR - http://dx.doi.org/10.1002/adma.200790004 DB - Crossref ER - TY - JOUR TI - Hypotonic swelling of salicylate-treated cochlear outer hair cells AU - Zhi, Man AU - Ratnanather, J. Tilak AU - Ceyhan, Elvan AU - Popel, Aleksander S. AU - Brownell, William E. T2 - Hearing Research AB - The outer hair cell (OHC) is a hydrostat with a low hydraulic conductivity of Pf = 3 × 10−4 cm/s across the plasma membrane (PM) and subsurface cisterna that make up the OHC’s lateral wall. The SSC is structurally and functionally a transport barrier in normal cells that is known to be disrupted by salicylate. The effect of sodium salicylate on Pf is determined from osmotic experiments in which isolated, control and salicylate-treated OHCs were exposed to hypotonic solutions in a constant flow chamber. The value of Pf = 3.5 ± 0.5 × 10−4 cm/s (mean ± s.e.m., n = 34) for salicylate-treated OHCs was not significantly different from Pf = 2.4 ± 0.3 × 10−4 cm/s (mean ± s.e.m., n = 31) for untreated OHCs (p = .3302). Thus Pf is determined by the PM and is unaffected by salicylate treatment. The ratio of longitudinal strain to radial strain εz/εc = −0.76 for salicylate-treated OHCs was significantly smaller (p = .0143) from −0.72 for untreated OHCs, and is also independent of the magnitude of the applied osmotic challenge. Salicylate-treated OHCs took longer to attain a steady-state volume which is larger than that for untreated OHCs and increased in volume by 8–15% prior to hypotonic perfusion unlike sodium α-ketoglutarate-treated OHCs. It is suggested that depolymerization of cytoskeletal proteins and/or glycogen may be responsible for the large volume increase in salicylate-treated OHCs as well as the different responses to different modes of application of the hypotonic solution. DA - 2007/6// PY - 2007/6// DO - 10.1016/j.heares.2007.02.007 VL - 228 IS - 1-2 SP - 95-104 J2 - Hearing Research LA - en OP - SN - 0378-5955 UR - http://dx.doi.org/10.1016/j.heares.2007.02.007 DB - Crossref KW - hydraulic conductivity KW - extracisternal space KW - subsurface cisterna ER - TY - JOUR TI - A new family of random graphs for testing spatial segregation AU - Ceyhan, Elvan AU - Priebe, Carey E. AU - Marchette, David J. T2 - Canadian Journal of Statistics AB - Abstract The authors discuss a graph‐based approach for testing spatial point patterns. This approach falls under the category of data‐random graphs, which have been introduced and used for statistical pattern recognition in recent years. The authors address specifically the problem of testing complete spatial randomness against spatial patterns of segregation or association between two or more classes of points on the plane. To this end, they use a particular type of parameterized random digraph called a proximity catch digraph (PCD) which is based on relative positions of the data points from various classes. The statistic employed is the relative density of the PCD, which is a U ‐statistic when scaled properly. The authors derive the limiting distribution of the relative density, using the standard asymptotic theory of U ‐statistics. They evaluate the finite‐sample performance of their test statistic by Monte Carlo simulations and assess its asymptotic performance via Pitman's asymptotic efficiency, thereby yielding the optimal parameters for testing. They further stress that their methodology remains valid for data in higher dimensions. DA - 2007/3// PY - 2007/3// DO - 10.1002/cjs.5550350106 VL - 35 IS - 1 SP - 27-50 J2 - Can. J. Statistics LA - en OP - SN - 0319-5724 1708-945X UR - http://dx.doi.org/10.1002/cjs.5550350106 DB - Crossref KW - association KW - complete spatial randomness KW - Delaunay triangulation KW - proximity catch digraph KW - random graph KW - relative density KW - segregation ER - TY - JOUR TI - Monitoring the recovery of smalltooth sawfish, Pristis pectinata, using standardized relative indices of abundance AU - Carlson, John K. AU - Osborne, Jason AU - Schmidt, Thomas W. T2 - Biological Conservation AB - The US population of smalltooth sawfish, Pristis pectinata, is currently listed as endangered under the Endangered Species Act. An important component of monitoring the recovery of this species is establishing long-term baseline trends in abundance. In the absence of scientific survey data, assessing and monitoring the status of some marine species has required the utilization of fishery-dependent data. Using voluntary dockside interviews of sport fishers collected in Everglades National Park, a standardized index of abundance was created for smalltooth sawfish using the delta method. The index was developed as the product of separate generalized linear models of the proportion of positive trips and the positive catch rates on successful trips. Development of the final model included testing factors that were expected to influence the catch of smalltooth sawfish. The final model assumed a binomial distribution for the proportion of positive trips and a lognormal distribution for positive catch rates. Year was significant as a main effect in the binomial model whereas year and skill level of the fishing party were significant in the lognormal model. The relative abundance index shows a small increase in abundance at an average rate of about 5% per year since 1989. These results indicate that the population of smalltooth sawfish in Everglades National Park has at least stabilized and may be increasing. However, additional data and analyses from multiple sources are required before definitive conclusions on the recovery of smalltooth sawfish can be established. DA - 2007/4// PY - 2007/4// DO - 10.1016/j.biocon.2006.11.013 VL - 136 IS - 2 SP - 195-202 J2 - Biological Conservation LA - en OP - SN - 0006-3207 UR - http://dx.doi.org/10.1016/j.biocon.2006.11.013 DB - Crossref KW - index of abundance KW - endangered species KW - elasmobranch KW - GLM ER - TY - JOUR TI - Multiscale Considerations in Modeling of Nonlinear Elastomers AU - Banks, H. T. AU - Medhin, Negash G. AU - Pinter, Gabriella A. T2 - International Journal for Computational Methods in Engineering Science and Mechanics AB - We present a survey of results from an extended project focused on the understanding of the dynamic behavior of elastomers or filled rubbers. This entailed experimental, modeling, computational and theoretical efforts. Of particular emphasis are the nonlinear and hysteretic aspects of dynamic deformations. DA - 2007/2/13/ PY - 2007/2/13/ DO - 10.1080/15502280601149346 VL - 8 IS - 2 SP - 53-62 J2 - International Journal for Computational Methods in Engineering Science and Mechanics LA - en OP - SN - 1550-2287 1550-2295 UR - http://dx.doi.org/10.1080/15502280601149346 DB - Crossref KW - Nonlinear Partial Differential Equations KW - Computational Methods KW - Viscoelasticity KW - Hysteresis KW - Molecular Dynamics KW - Multiscale Modeling ER - TY - CONF TI - Pollutant Removal in Bioretention Cells with Grass Cover AU - Smith, Ryan A. AU - Hunt, William F. T2 - World Environmental and Water Resources Congress 2007 AB - North Carolina has spent considerable effort to improve water quality in the State and its estuaries. One area of focus has been stormwater runoff quality. Bioretention is often used to treat runoff from new developments and is retrofitted in areas where development has already occurred. Typical designs have trees and shrubs planted and mulch cover, which has become the design standard. There is significant interest in bioretention with grassed cover because maintenance could be less costly and because some owners consider them to be more aesthetically pleasing and usable. Some regulators are reluctant to allow grassed systems because of a lack of research data proving that they meet current standards for pollutant removal. The goals of this study were (1) to test the performance of grassed bioretention cells in removing nitrogen, phosphorous, metals and sediment and (2) to compare the pollutant removal between 2 identical grassed cells using induced storage zones with different fill media depths. An induced storage zone is a water storage layer at the bottom of the bioretention cell created by elevating the underdrain outlet above the bottom of the cell. A field system was built in the Piedmont of North Carolina for the study. Both cells lost volume during storm events through exfiltration, which decreased the volume of outflow through the underdrains. The induced storage zone caused an increase in the exfiltration volume, in some cases preventing any outflow from the underdrains, which improved the pollutant load reduction by the cells. Nutrient load reductions for TN were approximately 70 to 80%. Phosphorus load reductions were 35 to 50%. The higher load reduction estimates were associated with the cell with a greater media depth. Fecal conform concentration removal was excellent for one cell, 97%. However, due to a limited number of storms collected (6), there was not a statistically significant finding. C2 - 2007/5/11/ C3 - World Environmental and Water Resources Congress 2007 DA - 2007/5/11/ DO - 10.1061/40927(243)581 PB - American Society of Civil Engineers SN - 9780784409275 UR - http://dx.doi.org/10.1061/40927(243)581 DB - Crossref ER - TY - CONF TI - Field Evaluation of Level Spreaders in the Piedmont of North Carolina AU - Hathaway, J. M. AU - Hunt, W. F. T2 - World Environmental and Water Resources Congress 2007 AB - Level Spreaders are commonly used in combination with riparian buffers as a stormwater Best Management Practice (BMP) in many parts of the United States. These systems have not been extensively studied in urban environments to determine if they can provide a long term water quality benefit. In winter 2005, 24 level spreaders were evaluated in the Piedmont of North Carolina. Detailed observations were made at 20 of these locations. The results of the study indicate that level spreaders may not be the versatile structure they are perceived to be. No level spreader — riparian buffer system was able to provide diffuse flow through the riparian buffer from the level spreader to the stream. Common causes for failure to maintain diffuse flow included: lack of maintenance (12 cases), poor design (11), riparian topography / content (11), level spreader lip not level (7), built with easily eroded materials (6), poor construction methods (3), and human interference (2). This field evaluation indicates that level spreader systems may need design revisions, construction guidance, and maintenance requirements before they continue to be used en masse. C2 - 2007/5/11/ C3 - World Environmental and Water Resources Congress 2007 DA - 2007/5/11/ DO - 10.1061/40927(243)579 PB - American Society of Civil Engineers SN - 9780784409275 UR - http://dx.doi.org/10.1061/40927(243)579 DB - Crossref ER - TY - CONF TI - The Effect of Urban Stormwater BMPs on Runoff Temperature in Trout Sensitive Waters AU - Jones, Matthew P. AU - Hunt, William F. AU - Smith, Jonathan T. T2 - World Environmental and Water Resources Congress 2007 AB - Urbanization can increase the temperature of coldwater stream environments by transferring heat from solar radiation, captured by pavement materials, to receiving water bodies through stormwater runoff. A number of aquatic organisms, including trout, are sensitive to elevated stream temperatures and temperature increases associated with urbanization have been shown to have a negative impact on the aquatic ecosystem. Research was conducted in regions of trout sensitive waters in Western North Carolina to determine, the effect that urban stormwater BMPs have on the thermal load of stormwater runoff at 4 bioretention areas, 1 stormwater wetland, and 1 wet pond. Water temperature and associated flows were remotely logged every 5 minutes at all BMP inlets and outlets, with additional temperature sensors located at specified depths and receiving waters. Analysis focused on flow and temperature reductions between inlets and outlets, as well as temperature changes within the BMPs due to diurnal fluctuations and storm events. Variations in temperature throughout the soil and water columns suggest the opportunity for modified outlet structures to reduce the thermal load discharged from BMPs. Results have also indicated the possibility of lowering runoff temperatures through conveyance in buried pipes. A comparison of the effect shading within the BMPs has on thermal load is also presented. An understanding of the temperature reduction mechanisms involved in urban stormwater BMPs should provide engineers with design criteria tos effectively mitigate the effect of thermal loads from stormwater runoff. C2 - 2007/5/11/ C3 - World Environmental and Water Resources Congress 2007 DA - 2007/5/11/ DO - 10.1061/40927(243)438 PB - American Society of Civil Engineers SN - 9780784409275 UR - http://dx.doi.org/10.1061/40927(243)438 DB - Crossref ER - TY - CONF TI - Evaluation of Various Types of Permeable Pavements with Respect to Water Quality Improvement and Flood Control AU - Collins, Kelly A. AU - Hunt, William F. AU - Hathaway, Jon M. T2 - World Environmental and Water Resources Congress 2007 AB - In many U.S. states, different permeable pavement types are considered to have the same capabilities in reducing runoff, and they are not credited with improving water quality. To test various permeable pavement designs, a parking lot consisting of four different types of permeable pavements and standard asphalt was constructed in Kinston, NC. The permeable pavement sections consist of pervious concrete (PC), permeable interlocking concrete pavers (PICP) with 8.5 % void space, PICP with 12.9 % void space, and concrete grid pavers (CGP), each covering a 1200 sq. ft. area with a 10 in. gravel storage layer. The purpose of this study is to evaluate and compare the effects of each pavement type on water quality and runoff reduction. Site analyses on every rainfall event began in March, 2006, and will continue through March, 2007. Preliminary results indicate significant (p<0.05) peak flow and volume reductions from all permeable pavements. Additionally, there has been little to no runoff observed from any of the pervious sections. Pollutant removal performance by the pavements has widely varied. As a result of this study, it is expected that the state of North Carolina will make a judgment on how much pollutant removal credit permeable pavement types should receive. Also, this study may be used to determine whether or not stormwater credit should vary based on pavement type. C2 - 2007/5/11/ C3 - World Environmental and Water Resources Congress 2007 DA - 2007/5/11/ DO - 10.1061/40927(243)435 PB - American Society of Civil Engineers SN - 9780784409275 UR - http://dx.doi.org/10.1061/40927(243)435 DB - Crossref ER - TY - JOUR TI - Comment: Demystifying Double Robustness: A Comparison of Alternative Strategies for Estimating a Population Mean from Incomplete Data AU - Tsiatis, Anastasios A. AU - Davidian, Marie T2 - Statistical Science AB - Comment on ``Demystifying Double Robustness: A Comparison of Alternative Strategies for Estimating a Population Mean from Incomplete Data'' [arXiv:0804.2958] DA - 2007/11// PY - 2007/11// DO - 10.1214/07-sts227b VL - 22 IS - 4 SP - 569-573 J2 - Statist. Sci. LA - en OP - SN - 0883-4237 UR - http://dx.doi.org/10.1214/07-sts227b DB - Crossref ER - TY - JOUR TI - Inference under right censoring for transformation models with a change-point based on a covariate threshold AU - Kosorok, Michael R. AU - Song, Rui T2 - The Annals of Statistics AB - We consider linear transformation models applied to right censored survival data with a change-point in the regression coefficient based on a covariate threshold. We establish consistency and weak convergence of the nonparametric maximum likelihood estimators. The change-point parameter is shown to be n-consistent, while the remaining parameters are shown to have the expected root-n consistency. We show that the procedure is adaptive in the sense that the nonthreshold parameters are estimable with the same precision as if the true threshold value were known. We also develop Monte Carlo methods of inference for model parameters and score tests for the existence of a change-point. A key difficulty here is that some of the model parameters are not identifiable under the null hypothesis of no change-point. Simulation studies establish the validity of the proposed score tests for finite sample sizes. DA - 2007/7// PY - 2007/7// DO - 10.1214/009053606000001244 VL - 35 IS - 3 SP - 957-989 J2 - Ann. Statist. LA - en OP - SN - 0090-5364 UR - http://dx.doi.org/10.1214/009053606000001244 DB - Crossref KW - change-point models KW - empirical processes KW - nonparametric maximum KW - likelihood KW - proportional hazards model KW - proportional odds model KW - right censoring KW - semiparametric efficiency KW - transformation models ER - TY - JOUR TI - Robust Covariate-Adjusted Log-Rank Statistics and Corresponding Sample Size Formula for Recurrent Events Data AU - Song, Rui AU - Kosorok, Michael R. AU - Cai, Jianwen T2 - Biometrics AB - Recurrent events data are frequently encountered in clinical trials. This article develops robust covariate-adjusted log-rank statistics applied to recurrent events data with arbitrary numbers of events under independent censoring and the corresponding sample size formula. The proposed log-rank tests are robust with respect to different data-generating processes and are adjusted for predictive covariates. It reduces to the Kong and Slud (1997, Biometrika 84, 847-862) setting in the case of a single event. The sample size formula is derived based on the asymptotic normality of the covariate-adjusted log-rank statistics under certain local alternatives and a working model for baseline covariates in the recurrent event data context. When the effect size is small and the baseline covariates do not contain significant information about event times, it reduces to the same form as that of Schoenfeld (1983, Biometrics 39, 499-503) for cases of a single event or independent event times within a subject. We carry out simulations to study the control of type I error and the comparison of powers between several methods in finite samples. The proposed sample size formula is illustrated using data from an rhDNase study. DA - 2007/12/19/ PY - 2007/12/19/ DO - 10.1111/j.1541-0420.2007.00948.x VL - 64 IS - 3 SP - 741-750 LA - en OP - SN - 0006-341X UR - http://dx.doi.org/10.1111/j.1541-0420.2007.00948.x DB - Crossref KW - local alternative KW - log-rank statistic KW - power KW - proportional means KW - recurrent events data KW - sample size ER - TY - JOUR TI - Bayesian networks for multilevel system reliability AU - Wilson, A.G. AU - Huzurbazar, A.V. T2 - Reliability Engineering and System Safety AB - Bayesian networks have recently found many applications in systems reliability; however, the focus has been on binary outcomes. In this paper we extend their use to multilevel discrete data and discuss how to make joint inference about all of the nodes in the network. These methods are applicable when system structures are too complex to be represented by fault trees. The methods are illustrated through four examples that are structured to clarify the scope of the problem. DA - 2007/// PY - 2007/// DO - 10.1016/j.ress.2006.09.003 VL - 92 IS - 10 SP - 1413-1420 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-34250158140&partnerID=MN8TOARS KW - Bayesian belief network KW - system reliability KW - Bayesian reliability ER - TY - JOUR TI - Information integration for complex systems AU - Wilson, A.G. AU - McNamara, L.A. AU - Wilson, G.D. T2 - Reliability Engineering and System Safety AB - This paper develops a framework to determine the performance or reliability of a complex system. We consider a case study in missile reliability that focuses on the assessment of a high fidelity launch vehicle intended to emulate a ballistic missile threat. In particular, we address the case of how to make a system assessment when there are limited full-system tests. We address the development of a system model and the integration of a variety of data using a Bayesian network. DA - 2007/// PY - 2007/// DO - 10.1016/j.ress.2006.07.003 VL - 92 IS - 1 SP - 121-130 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-33748291454&partnerID=MN8TOARS KW - Bayesian network KW - prior elicitation KW - reliability KW - ethnography ER - TY - JOUR TI - Bayesian stockpile reliability methodology for complex systems AU - Anderson-Cook, C.M. AU - Graves, T. AU - Hamada, M. AU - Hengartner, N. AU - Johnson, V.E. AU - Reese, C.S. AU - Wilson, A.G. T2 - Military Operations Research DA - 2007/// PY - 2007/// VL - 12 IS - 2 SP - 25-37 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-44649175976&partnerID=MN8TOARS ER - TY - JOUR TI - Efficient estimation of population-level summaries in general semiparametric regression models AU - Maity, A. AU - Ma, Y. AU - Carroll, R.J. T2 - Journal of the American Statistical Association AB - This article considers a wide class of semiparametric regression models in which interest focuses on population-level quantities that combine both the parametric and the nonparametric parts of the model. Special cases in this approach include generalized partially linear models, generalized partially linear single-index models, structural measurement error models, and many others. For estimating the parametric part of the model efficiently, profile likelihood kernel estimation methods are well established in the literature. Here our focus is on estimating general population-level quantities that combine the parametric and nonparametric parts of the model (e.g., population mean, probabilities, etc.). We place this problem in a general context, provide a general kernel-based methodology, and derive the asymptotic distributions of estimates of these population-level quantities, showing that in many cases the estimates are semiparametric efficient. For estimating the population mean with no missing data, we show that the sample mean is semiparametric efficient for canonical exponential families, but not in general. We apply the methods to a problem in nutritional epidemiology, where estimating the distribution of usual intake is of primary interest and semiparametric methods are not available. Extensions to the case of missing response data are also discussed. DA - 2007/// PY - 2007/// DO - 10.1198/016214506000001103 VL - 102 IS - 477 SP - 123-139 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-33947277465&partnerID=MN8TOARS KW - generalized estimating equations KW - kernel methods KW - measurement error KW - missing data KW - nonparametric regression KW - nutrition KW - partially linear model KW - profile method KW - semiparametric efficient score KW - semiparametric information bound KW - single-index models ER - TY - JOUR TI - Comments on: Nonparametric inference with generalized likelihood ratio tests AU - Carroll, Raymond J. AU - Maity, Arnab T2 - Test DA - 2007/// PY - 2007/// DO - 10.1007/s11749-007-0085-3 VL - 16 IS - 3 SP - 456–458 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-36448987181&partnerID=MN8TOARS ER - TY - JOUR TI - The Hill–Robertson effect is a consequence of interplay between linkage, selection and drift: a commentary on ‘The effect of linkage on limits to artificial selection’ by W. G. Hill and A. Robertson AU - Zeng, Zhao Bang T2 - Genetics Research AB - The Hill–Robertson effect is a consequence of interplay between linkage, selection and drift: a commentary on ‘The effect of linkage on limits to artificial selection’ by W. G. Hill and A. Robertson - Volume 89 Issue 5-6 DA - 2007/12// PY - 2007/12// DO - 10.1017/s0016672308009506 VL - 89 IS - 5-6 SP - 309-310 J2 - Genet. Res. LA - en OP - SN - 0016-6723 1469-5073 UR - http://dx.doi.org/10.1017/s0016672308009506 DB - Crossref ER - TY - JOUR TI - Dynamic analysis of unwinding yarn from cylindrical packages, part III: The three-region model revisited AU - Pan, Z. AU - Ghosh, T. K. AU - Batra, S. K. T2 - Textile Research Journal DA - 2007/// PY - 2007/// VL - 77 ER - TY - JOUR TI - DISTRIBUTIONS ASSOCIATED WITH GENERAL RUNS AND PATTERNS IN HIDDEN MARKOV MODELS AU - Aston, John A. D. AU - Martin, Donald E. K. T2 - ANNALS OF APPLIED STATISTICS AB - This paper gives a method for computing distributions associated with patterns in the state sequence of a hidden Markov model, conditional on observing all or part of the observation sequence. Probabilities are computed for very general classes of patterns (competing patterns and generalized later patterns), and thus, the theory includes as special cases results for a large class of problems that have wide application. The unobserved state sequence is assumed to be Markovian with a general order of dependence. An auxiliary Markov chain is associated with the state sequence and is used to simplify the computations. Two examples are given to illustrate the use of the methodology. Whereas the first application is more to illustrate the basic steps in applying the theory, the second is a more detailed application to DNA sequences, and shows that the methods can be adapted to include restrictions related to biological knowledge. DA - 2007/12// PY - 2007/12// DO - 10.1214/07-AOAS125 VL - 1 IS - 2 SP - 585-611 SN - 1932-6157 KW - Competing patterns KW - CpG islands KW - finite Markov chain imbedding KW - generalized later patterns KW - higher-order hidden Markov models KW - sooner/later waiting time distributions ER - TY - JOUR TI - A MULTIVARIATE SEMIPARAMETRIC BAYESIAN SPATIAL MODELING FRAMEWORK FOR HURRICANE SURFACE WIND FIELDS AU - Reich, Brian J. AU - Fuentes, Montserrat T2 - ANNALS OF APPLIED STATISTICS AB - Storm surge, the onshore rush of sea water caused by the high winds and low pressure associated with a hurricane, can compound the effects of inland flooding caused by rainfall, leading to loss of property and loss of life for residents of coastal areas. Numerical ocean models are essential for creating storm surge forecasts for coastal areas. These models are driven primarily by the surface wind forcings. Currently, the gridded wind fields used by ocean models are specified by deterministic formulas that are based on the central pressure and location of the storm center. While these equations incorporate important physical knowledge about the structure of hurricane surface wind fields, they cannot always capture the asymmetric and dynamic nature of a hurricane. A new Bayesian multivariate spatial statistical modeling framework is introduced combining data with physical knowledge about the wind fields to improve the estimation of the wind vectors. Many spatial models assume the data follow a Gaussian distribution. However, this may be overly-restrictive for wind fields data which often display erratic behavior, such as sudden changes in time or space. In this paper we develop a semiparametric multivariate spatial model for these data. Our model builds on the stick-breaking prior, which is frequently used in Bayesian modeling to capture uncertainty in the parametric form of an outcome. The stick-breaking prior is extended to the spatial setting by assigning each location a different, unknown distribution, and smoothing the distributions in space with a series of kernel functions. This semiparametric spatial model is shown to improve prediction compared to usual Bayesian Kriging methods for the wind field of Hurricane Ivan. DA - 2007/6// PY - 2007/6// DO - 10.1214/07-AOAS108 VL - 1 IS - 1 SP - 249-264 SN - 1932-6157 KW - Hierarchical Bayesian model KW - multivariate data KW - spatial statistics KW - stick-breaking prior KW - wind fields ER - TY - JOUR TI - Eutrophication and cyanobacteria blooms in run-of-river impoundments in North Carolina, USA AU - Touchette, Brant W. AU - Burkholder, Joann M. AU - Allen, Elie H. AU - Alexander, Jessica L. AU - Kinder, Carol A. AU - Brownie, Cavell AU - James, Jennifer AU - Britton, Clay H. T2 - LAKE AND RESERVOIR MANAGEMENT AB - Abstract We compared monthly data taken during the dry summer growing season of 2002 in 11 potable water supply reservoirs (19–85 years old based on year filled) within the North Carolina Piedmont, including measures of watershed land use, watershed area, reservoir morphometry (depth, surface area, volume), suspended solids (SS), nutrient concentrations (total nitrogen, TN; total Kjeldahl nitrogen, TKN; nitrate + nitrite, NO3− + NO2−; total phosphorus, TP; total organic carbon), phytoplankton chlorophyll a (chla) concentrations, cyanobacteria assemblages, and microcystin concentrations from monthly data taken during the dry summer 2002 growing season. The reservoirs were considered collectively or as two subgroups by age as “mod.” (moderate age, 19–40 years post-fill, n = 5) and “old” (74–85 yr post-fill, n = 6). The run-of-river impoundments were meso-/eutrophic and turbid (means 25–125 μg TP/L, 410–1,800 μg TN/L, 3–70 μg chla/L and 5.7–41.9 mg SS/L). Under drought conditions in these turbid systems, there was a positive relationship between chla and both TN and TP, supported by correlation analyses and hierarchical ANOVA models. The models also indicated significant positive relationships between TN and TP, and between SS and both TP and TN. Agricultural land use was positively correlated with TKN for the reservoirs considered collectively, and with TN, TKN, TP, and chla in mod. reservoirs. In models considering the reservoirs by age group, TN:TP ratios were significantly lower and NO3− + NO2− was significantly higher in old reservoirs, and these relationships were stronger when reservoir age was used as a linear predictor. Cyanobacteria assemblages in the two reservoir age groups generally were comparable in abundance and species composition, and comprised 60–95% (up to 1.9 × 106 cells/mL) of the total phytoplankton cell number. Potentially toxic taxa were dominated by Cylindrospermopsis raciborskii and C. philippinensis. Although known microcystin producers were low in abundance, microcystin (< 0.8 μg/L) was detected in most samples. TP and chla were significant predictors of total cyanobacterial abundance. The data suggest that at present these turbid, meso-/eutrophic reservoirs have moderate cyanobacteria abundance and low cyanotoxin (microcystin) levels over the summer growing season, even in low-precipitation seasons that favor cyanobacteria. Accelerated eutrophication from further watershed development is expected to promote increased cyanobacterial abundance and adversely affect the value of these reservoirs as potable water supplies. DA - 2007/6// PY - 2007/6// DO - 10.1080/07438140709353921 VL - 23 IS - 2 SP - 179-192 SN - 1040-2381 KW - chlorophyll a KW - cyanobacteria KW - eutrophic KW - microcystin KW - nitrogen KW - nutrients KW - phosphorus KW - reservoirs KW - turbid ER - TY - JOUR TI - Tobit model estimation and sliced inverse regression AU - Li, Lexin AU - Simonoff, Jeffrey S. AU - Tsai, Chih-Ling T2 - STATISTICAL MODELLING AB - It is not unusual for the response variable in a regression model to be subject to censoring or truncation. Tobit regression models are specific examples of such a situation, where for some observations the observed response is not the actual response, but the censoring value (often zero), and an indicator that censoring (from below) has occurred. It is well-known that the maximum likelihood estimator for such a linear model assuming Gaussian errors is not consistent if the error term is not homoscedastic and normally distributed. In this paper, we consider estimation in the Tobit regression context when homoscedasticity and normality of errors do not hold, as well as when the true response is an unspecified nonlinear function of linear terms, using sliced inverse regression (SIR). The properties of SIR estimation for Tobit models are explored both theoretically and based on extensive Monte Carlo simulations.We show that the SIR estimator is a strong competitor to other Tobit regression estimators, in that it has good properties when the usual linear model assumptions hold, and can be much more effective than other Tobit model estimators when those assumptions break down. An example related to household charitable donations demonstrates the usefulness of the SIR estimator. DA - 2007/7// PY - 2007/7// DO - 10.1177/1471082X0700700201 VL - 7 IS - 2 SP - 107-123 SN - 1471-082X KW - dimension reduction KW - heteroscedasticity KW - nonnormality KW - single-index model ER - TY - JOUR TI - Lactoferrin supplementation to holstein calves during the preweaning and postweaning phases AU - English, E. A. AU - Hopkins, B. A. AU - Stroud, J. S. AU - Davidson, S. AU - Smith, G. AU - Brownie, C. AU - Whitlow, L. W. T2 - JOURNAL OF DAIRY SCIENCE AB - Sixty Holstein calves (30 bulls, 30 heifers) were used to examine the effects of supplemental lactoferrin on feed intake, growth, and health during the preweaning and postweaning periods. One of 3 levels of lactoferrin was supplemented from 3 to 56 d in either whole milk or water to produce 3 dietary treatments: 1) 0 g/d, 2) 0.5 g/d, and 3) 1 g/d. Whole milk (3.8 L/d) containing lactoferrin supplements was fed from bottles until weaning at 35 d. From d 36 to 56, lactoferrin supplements were added to water (15 to 25 mL) and fed from bottles. Lactoferrin supplementation had no effect on feed intake, body weight, average daily gain, heart girth, body temperature, fecal scores, respiratory scores, or haptoglobin concentrations. Calves were housed in individual pens in either an open-sided barn or hutches. Calves raised in the barn consumed more calf starter and therefore grew better than calves raised in hutches. Under the conditions of this study, lactoferrin supplementation was not beneficial. Further research is needed to fully elucidate the role of lactoferrin, and possible benefits during different feeding conditions or milk sources. DA - 2007/11/1/ PY - 2007/11/1/ DO - 10.3168/jds.2007-0361 VL - 90 IS - 11 SP - 5276-5281 SN - 1525-3198 KW - calf KW - lactoferrin KW - weaning ER - TY - JOUR TI - Haplotype-based association analysis via variance-components score test AU - Tzeng, Jung-Ying AU - Zhang, Daowen T2 - AMERICAN JOURNAL OF HUMAN GENETICS AB - Haplotypes provide a more informative format of polymorphisms for genetic association analysis than do individual single-nucleotide polymorphisms. However, the practical efficacy of haplotype-based association analysis is challenged by a trade-off between the benefits of modeling abundant variation and the cost of the extra degrees of freedom. To reduce the degrees of freedom, several strategies have been considered in the literature. They include (1) clustering evolutionarily close haplotypes, (2) modeling the level of haplotype sharing, and (3) smoothing haplotype effects by introducing a correlation structure for haplotype effects and studying the variance components (VC) for association. Although the first two strategies enjoy a fair extent of power gain, empirical evidence showed that VC methods may exhibit only similar or less power than the standard haplotype regression method, even in cases of many haplotypes. In this study, we report possible reasons that cause the underpowered phenomenon and show how the power of the VC strategy can be improved. We construct a score test based on the restricted maximum likelihood or the marginal likelihood function of the VC and identify its nontypical limiting distribution. Through simulation, we demonstrate the validity of the test and investigate the power performance of the VC approach and that of the standard haplotype regression approach. With suitable choices for the correlation structure, the proposed method can be directly applied to unphased genotypic data. Our method is applicable to a wide-ranging class of models and is computationally efficient and easy to implement. The broad coverage and the fast and easy implementation of this method make the VC strategy an effective tool for haplotype analysis, even in modern genomewide association studies. DA - 2007/11// PY - 2007/11// DO - 10.1086/521558 VL - 81 IS - 5 SP - 927-938 SN - 0002-9297 ER - TY - JOUR TI - Factor analysis of the aberrant behavior checklist in individuals with autism spectrum disorders AU - Brinkley, Jason AU - Nations, Laura AU - Abramson, Ruth K. AU - Hall, Alicia AU - Wright, Harry H. AU - Gabriels, Robin AU - Gilbert, John R. AU - Pericak-Vance, Margaret A. O. AU - Cuccaro, Michael L. T2 - JOURNAL OF AUTISM AND DEVELOPMENTAL DISORDERS DA - 2007/11// PY - 2007/11// DO - 10.1007/s10803-006-0327-3 VL - 37 IS - 10 SP - 1949-1959 SN - 1573-3432 KW - autism KW - aberrant behavior checklist KW - irritability KW - self-injury ER - TY - JOUR TI - Extreme value distributions for the skew-symmetric family of distributions AU - Chang, Sheng-Mao AU - Genton, Marc G. T2 - COMMUNICATIONS IN STATISTICS-THEORY AND METHODS AB - Abstract We derive the extreme value distribution of the skew-symmetric family, the probability density function of the latter being defined as twice the product of a symmetric density and a skewing function. We show that, under certain conditions on the skewing function, this extreme value distribution is the same as that for the symmetric density. We illustrate our results using various examples of skew-symmetric distributions as well as two data sets. Keywords: Flexible skew-symmetricGeneralized skew-normalHeavy tailsMultimodalitySelection modelsSkew-CauchySkew-t Mathematics Subject Classification: Primary 62H05Secondary 62E10 Acknowledgments The authors are most grateful to the guest editors and two referees for suggestions that improved the article. The work of Genton was partially supported by NSF grant DMS-0504896. DA - 2007/// PY - 2007/// DO - 10.1080/03610920601126159 VL - 36 IS - 9-12 SP - 1705-1717 SN - 0361-0926 KW - flexible skew-symmetric KW - generalized skew-normal KW - heavy tails KW - multimodality KW - selection models KW - skew-Cauchy KW - skew-t ER - TY - JOUR TI - Autism in African American families: Clinical-phenotypic findings AU - Cuccaro, Michael L. AU - Brinkley, Jason AU - Abramson, Ruth K. AU - Hall, Alicia AU - Wright, Harry H. AU - Hussman, John P. AU - Gilbert, John R. AU - Pericak-Vance, Margaret A. T2 - AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS AB - Unlike other complex diseases, the study of autism has been almost exclusively limited to Caucasian families. This study represents a first effort to examine clinical and phenotypic findings in individuals with autism from African American families. Drawing from an ongoing genetic study of autism we compared African American (N = 46, mean age = 118 months) and Caucasian (N = 298, mean age = 105 months) groups on autism symptoms and developmental language symptoms. The African American group showed greater delays in language but did not differ from the Caucasian group on core autism symptoms. These findings, while suggestive of a more severe phenotype, may reflect an ascertainment bias. Nonetheless, we believe that more studies of racial-ethnic groups should be conducted with several goals in mind including strengthening recruiting strategies to include more ethnic-racial groups and more thoughtful evaluation of phenotypic traits. Such considerations will aid greatly in the search for genetic variants in autism. DA - 2007/12/5/ PY - 2007/12/5/ DO - 10.1002/ajmg.b.30535 VL - 144B IS - 8 SP - 1022-1026 SN - 1552-485X KW - autism KW - phenotype KW - African American KW - racial-ethnic KW - genetics ER - TY - JOUR TI - Analysis of a binary composite endpoint with missing data in components AU - Quan, Hui AU - Zhang, Daowen AU - Zhang, Ji AU - Devlamynck, Laure T2 - STATISTICS IN MEDICINE AB - Composite endpoints are often used in clinical trials in order to increase the overall event rates, reduce the sizes of the trials and achieve desired power. For example, in a trial to study the effect of a treatment on the prevention of venous thromboembolic events after a major orthopaedic surgery of the lower limbs, the primary endpoint is usually a composite endpoint consisting of any deep vein thrombosis identified by systematic venography of lower limbs, symptomatic and well-documented non-fatal pulmonary embolism, and death from all causes. Just as any endpoints, missing data can occur in the components of the composite endpoint. If a patient has missing data on some of the components but not all the components, this patient may not have complete data but partial data for the composite endpoint. To be consistent with the intention-to-treat principle, the patient should not be discarded from the analysis. In this research, we propose an approach for the analysis of a composite endpoint with missing data in components. The main idea is to first derive the probabilities of all possible study outcomes based on the appropriate model and then to construct the overall rate for the composite endpoint. Simulations are conducted to compare the approach with several naïve methods. A data example is used to illustrate the application of the approach. DA - 2007/11/20/ PY - 2007/11/20/ DO - 10.1002/sim.2893 VL - 26 IS - 26 SP - 4703-4718 SN - 0277-6715 KW - EM algorithm KW - event rate KW - missing at random KW - maximum likelihood estimate ER - TY - JOUR TI - A field evaluation of distance measurement error in auditory avian point count surveys AU - Alldredge, Mathew W. AU - Simons, Theodore R. AU - Pollock, Kenneth H. T2 - JOURNAL OF WILDLIFE MANAGEMENT AB - ABSTRACT Detection distance is an important and common auxiliary variable measured during avian point count surveys. Distance data are used to determine the area sampled and to model the detection process using distance sampling theory. In densely forested habitats, visual detections of birds are rare, and most estimates of detection distance are based on auditory cues. Distance sampling theory assumes detection distances are measured accurately, but empirical validation of this assumption for auditory detections is lacking. We used a song playback system to simulate avian point counts with known distances in a forested habitat to determine the error structure of distance estimates based on auditory detections. We conducted field evaluations with 6 experienced observers both before and after distance estimation training. We conducted additional studies to determine the effect of height and speaker orientation (toward or away from observers) on distance estimation error. Distance estimation errors for all evaluations were substantial, although training reduced errors and bias in distance estimates by approximately 15%. Measurement errors showed a nonlinear relationship to distance. Our results suggest observers were not able to differentiate distances beyond 65 m. The height from which we played songs had no effect on distance estimation errors in this habitat. The orientation of the song source did have a large effect on distance estimation errors; observers generally doubled their distance estimates for songs played away from them compared with distance estimates for songs played directly toward them. These findings, which we based on realistic field conditions, suggest measures of uncertainty in distance estimates to auditory detections are substantially higher than assumed by most researchers. This means aural point count estimates of avian abundance based on distance methods deserve careful scrutiny because they are likely biased. DA - 2007/11// PY - 2007/11// DO - 10.2193/2006-161 VL - 71 IS - 8 SP - 2759-2766 SN - 1937-2817 KW - abundance KW - auditory detections KW - bird surveys KW - distance estimation KW - measurement error KW - point count surveys ER - TY - JOUR TI - Trranscript profiling of a conifer pathosystem: response of Pinus sylvestris root tissues to pathogen (Heterobasidion annosum) invasion AU - Adomas, Aleksandra AU - Heller, Gregory AU - Li, Guosheng AU - Olson, Ake AU - Chu, Tzu-Ming AU - Osborne, Jason AU - Craig, Deborah AU - Van Zyl, Len AU - Wolfinger, Russ AU - Sederoff, Ron AU - Dean, Ralph A. AU - Stenlid, Jan AU - Finlay, Roger AU - Asiegbu, Frederick O. T2 - TREE PHYSIOLOGY AB - The mechanisms underlying defence reactions to a pathogen attack, though well studied in crop plants, are poorly understood in conifers. To analyze changes in gene transcript abundance in Pinus sylvestris L. root tissues infected by Heterobasidion annosum (Fr.) Bref. s.l., a cDNA microarray containing 2109 ESTs from P. taeda L. was used. Mixed model statistical analysis identified 179 expressed sequence tags differentially expressed at 1, 5 or 15 days post inoculation. In general, the total number of genes differentially expressed during the infection increased over time. The most abundant group of genes up-regulated upon infection coded for enzymes involved in metabolism (phenylpropanoid pathway) and defence-related proteins with antimicrobial properties. A class III peroxidase responsible for lignin biosynthesis and cell wall thickening had increased transcript abundance at all measurement times. Real-time RT-PCR verified the microarray results with high reproducibility. The similarity of the expression profiling pattern observed in this pathosystem to those documented in crop pathology suggests that angiosperms and gymnosperms use similar genetic programs in responding to invasive growth by microbial pathogens. DA - 2007/10// PY - 2007/10// DO - 10.1093/treephys/27.10.1441 VL - 27 IS - 10 SP - 1441-1458 SN - 1758-4469 KW - antimicrobial peptide KW - microarray KW - peroxidase KW - phenylopropanoid pathway KW - pine KW - plant defence ER - TY - JOUR TI - Support vector machines with adaptive L-q penalty AU - Liu, Yufeng AU - Zhang, Hao Helen AU - Park, Cheolwoo AU - Ahn, Jeongyoun T2 - COMPUTATIONAL STATISTICS & DATA ANALYSIS AB - The standard support vector machine (SVM) minimizes the hinge loss function subject to the L2 penalty or the roughness penalty. Recently, the L1 SVM was suggested for variable selection by producing sparse solutions [Bradley, P., Mangasarian, O., 1998. Feature selection via concave minimization and support vector machines. In: Shavlik, J. (Ed.), ICML’98. Morgan Kaufmann, Los Altos, CA; Zhu, J., Hastie, T., Rosset, S., Tibshirani, R., 2003. 1-norm support vector machines. Neural Inform. Process. Systems 16]. These learning methods are non-adaptive since their penalty forms are pre-determined before looking at data, and they often perform well only in a certain type of situation. For instance, the L2 SVM generally works well except when there are too many noise inputs, while the L1 SVM is more preferred in the presence of many noise variables. In this article we propose and explore an adaptive learning procedure called the Lq SVM, where the best q>0 is automatically chosen by data. Both two- and multi-class classification problems are considered. We show that the new adaptive approach combines the benefit of a class of non-adaptive procedures and gives the best performance of this class across a variety of situations. Moreover, we observe that the proposed Lq penalty is more robust to noise variables than the L1 and L2 penalties. An iterative algorithm is suggested to solve the Lq SVM efficiently. Simulations and real data applications support the effectiveness of the proposed procedure. DA - 2007/8/15/ PY - 2007/8/15/ DO - 10.1016/j.csda.2007.02.006 VL - 51 IS - 12 SP - 6380-6394 SN - 1872-7352 KW - adaptive penalty KW - classification KW - shrinkage KW - support vector machine KW - variable selection ER - TY - JOUR TI - Sparse sufficient dimension reduction AU - Li, Lexin T2 - BIOMETRIKA AB - Existing sufficient dimension reduction methods suffer from the fact that each dimension reduction component is a linear combination of all the original predictors, so that it is difficult to interpret the resulting estimates. We propose a unified estimation strategy, which combines a regression-type formulation of sufficient dimension reduction methods and shrinkage estimation, to produce sparse and accurate solutions. The method can be applied to most existing sufficient dimension reduction methods such as sliced inverse regression, sliced average variance estimation and principal Hessian directions. We demonstrate the effectiveness of the proposed method by both simulations and real data analysis. DA - 2007/8// PY - 2007/8// DO - 10.1093/biomet/asm044 VL - 94 IS - 3 SP - 603-613 SN - 1464-3510 KW - lasso KW - shrinkage sparse estimator KW - sufficient dimension reduction ER - TY - JOUR TI - Partial inverse regression AU - Li, Lexin AU - Cook, Dennis AU - Tsai, Chih-Ling T2 - BIOMETRIKA AB - Journal Article Partial inverse regression Get access Lexin Li, Lexin Li Department of Statistics, North Carolina State University, Raleigh, North Carolina 27695, U.S.A. Search for other works by this author on: Oxford Academic Google Scholar R. Dennis Cook, R. Dennis Cook School of Statistics, University of Minnesota, St Paul, Minnesota 55108, U.S.A. Search for other works by this author on: Oxford Academic Google Scholar Chih-Ling Tsai Chih-Ling Tsai Graduate School of Management, University of California, Davis, California 95616, U.S.A. Search for other works by this author on: Oxford Academic Google Scholar Biometrika, Volume 94, Issue 3, August 2007, Pages 615–625, https://doi.org/10.1093/biomet/asm043 Published: 05 August 2007 Article history Received: 01 March 2005 Revision received: 01 December 2006 Published: 05 August 2007 DA - 2007/8// PY - 2007/8// DO - 10.1093/biomet/asm043 VL - 94 IS - 3 SP - 615-625 SN - 0006-3444 KW - partial least squares KW - single-index model KW - sliced inverse regression ER - TY - JOUR TI - Mechanistic computational model of ovarian steroidogenesis to predict biochemical responses to endocrine active compounds AU - Breen, Michael S. AU - Villeneuve, Daniel L. AU - Breen, Miyuki AU - Ankley, Gerald T. AU - Conolly, Rory B. T2 - ANNALS OF BIOMEDICAL ENGINEERING AB - Sex steroids, which have an important role in a wide range of physiological and pathological processes, are synthesized primarily in the gonads and adrenal glands through a series of enzyme-mediated reactions. The activity of steroidogenic enzymes can be altered by a variety of endocrine active compounds (EAC), some of which are therapeutics and others that are environmental contaminants. A steady-state computational model of the intraovarian metabolic network was developed to predict the synthesis and secretion of testosterone (T) and estradiol (E2), and their responses to EAC. Model predictions were compared to data from an in vitro steroidogenesis assay with ovary explants from a small fish model, the fathead minnow. Model parameters were estimated using an iterative optimization algorithm. Model-predicted concentrations of T and E2 closely correspond to the time-course data from baseline (control) experiments, and dose-response data from experiments with the EAC, fadrozole (FAD). A sensitivity analysis of the model parameters identified specific transport and metabolic processes that most influence the concentrations of T and E2, which included uptake of cholesterol into the ovary, secretion of androstenedione (AD) from the ovary, and conversions of AD to T, and AD to estrone (E1). The sensitivity analysis also indicated the E1 pathway as the preferred pathway for E2 synthesis, as compared to the T pathway. Our study demonstrates the feasibility of using the steroidogenesis model to predict T and E2 concentrations, in vitro, while reducing model complexity with a steady-state assumption. This capability could be useful for pharmaceutical development and environmental health assessments with EAC. DA - 2007/6// PY - 2007/6// DO - 10.1007/s10439-007-9309-7 VL - 35 IS - 6 SP - 970-981 SN - 1573-9686 KW - steroid biosynthesis KW - mathematical model KW - sensitivity analysis KW - endocrine disrupting chemicals KW - fadrozole KW - fish KW - cellular metabolism ER - TY - JOUR TI - Likelihood and pseudo-likelihood methods for semiparametric joint models for a primary endpoint and longitudinal data AU - Li, Erning AU - Zhang, Daowen AU - Davidian, Marie T2 - Computational Statistics & Data Analysis AB - Inference on the association between a primary endpoint and features of longitudinal profiles of a continuous response is of central interest in medical and public health research. Joint models that represent the association through shared dependence of the primary and longitudinal data on random effects are increasingly popular; however, existing inferential methods may be inefficient or sensitive to assumptions on the random effects distribution. We consider a semiparametric joint model that makes only mild assumptions on this distribution and develop likelihood-based inference on the association and distribution, which offers improved performance relative to existing methods that is insensitive to the true random effects distribution. Moreover, the estimated distribution can reveal interesting population features, as we demonstrate for a study of the association between longitudinal hormone levels and bone status in peri-menopausal women. DA - 2007/8// PY - 2007/8// DO - 10.1016/j.csda.2006.10.008 VL - 51 IS - 12 SP - 5776-5790 J2 - Computational Statistics & Data Analysis LA - en OP - SN - 0167-9473 UR - http://dx.doi.org/10.1016/j.csda.2006.10.008 DB - Crossref KW - conditional score KW - generalized linear model KW - mixed effects model KW - pseudo-likelihood KW - seminonparametric density ER - TY - JOUR TI - Evaluation of four permeable pavement sites in eastern North Carolina for runoff reduction and water quality impacts AU - Bean, E. Z. AU - Hunt, W. F. AU - Bidelspach, D. A. T2 - Journal of Irrigation and Drainage Engineering AB - Four permeable pavement applications in North Carolina’s Coastal Plain were constructed and monitored to determine their effectiveness of reducing runoff quantity and improving water quality. Sites were either constructed of permeable interlocking concrete pavers (2), porous concrete (1), or concrete grid pavers (1). One site of each pavement type was monitored for runoff reduction for periods ranging from 10 to 26 months. Measured runoff depths from rainfall events over 50mm were used to determine permeable pavement equivalent curve numbers for the sites, which ranged from 45 to 85. Only the two permeable interlocking concrete pavement (PICP) sites were monitored for water quality. Runoff and exfiltrate samples were intended to be collected, in addition to runoff monitoring, from the Swansboro PICP site. However, no runoff was produced during this study from the Swansboro PICP site for rainfall events up to 88mm. From exfiltrate concentrations, nutrient retention was estimated to be 3.4 and 0.4kg∕ha∕year for total nitrogen and total phosphorus, respectively. For the Goldsboro PICP site, water quality of asphalt runoff and PICP exfiltrate were compared. Analysis of water quality samples from the second site determined that concentrations of total Kjeldahl nitrogen, ammonia, total phosphorus, and zinc were significantly (p⩽0.05) lower in permeable pavement exfiltrate than asphalt runoff. DA - 2007/// PY - 2007/// DO - 10.1061/(ASCE)0733-9437(2007)133:6(583) VL - 133 IS - 6 SP - 583-592 ER - TY - JOUR TI - Elucidation of veA-dependent genes associated with aflatoxin and sclerotial production in Aspergillus flavus by functional genomics AU - Cary, J. W. AU - OBrian, G. R. AU - Nielsen, D. M. AU - Nierman, W. AU - Harris-Coward, P. AU - Bhatnagar, J. Yu D. AU - Cleveland, T. E. AU - Payne, G. A. AU - Calvo, A. M. T2 - APPLIED MICROBIOLOGY AND BIOTECHNOLOGY DA - 2007/10// PY - 2007/10// DO - 10.1007/s00253-007-1081-y VL - 76 IS - 5 SP - 1107-1118 SN - 0175-7598 KW - Aspergillus flavus KW - veA KW - aflatoxin KW - sclerotia KW - microarray ER - TY - JOUR TI - Effects and importance of soil wetness and neighbor vegetation on Solidago verna M. A. Curtis ex Torrey & A. Gray (spring-flowering goldenrod) [Asteraceae] transplant survivorship and growth AU - Fleming, M. S. AU - Stucky, J. M. AU - Brownie, C. T2 - Castanea AB - Solidago verna M. A. Curtis ex Torrey & A. Gray (spring-flowering goldenrod) [Asteraceae] is threatened in North Carolina, a species of federal concern, endemic to fire– adapted longleaf pine flatwoods in the Carolinas, and is in the Center for Plant Conservation's National Collection of Endangered Plants. Highway construction threatens the largest known population of S. verna. We conducted a transplant study to provide information for the plan being developed to mitigate for the impact of the highway. Plants of the threatened population were transplanted into study plots on seven Coastal Plain soils varying in wetness. Half of the plots on each soil were controls with unclipped neighbor vegetation; the others were experimental plots with clipped vegetation. Soil was the most important factor affecting transplant survival. Survival was lowest on soils that experienced ponding or flooding. Neighbor vegetation clipping tended to improve survival, with the greatest improvement on soils of intermediate wetness. Soil wetness and vegetation treatment (clipped or unclipped) accounted for only 16% of transplant growth variation. We recommend establishing a mitigation transplant population on moderately well drained or somewhat poorly drained soils such as Craven or Lenoir. Managing the transplant population could utilize mowing during those periods when fire is not practical. DA - 2007/// PY - 2007/// DO - 10.2179/06-35.1 VL - 72 IS - 4 SP - 205-213 ER - TY - JOUR TI - An overview of normal theory structural measurement error models AU - Thompson, Jeffrey R. AU - Carter, Randy L. T2 - INTERNATIONAL STATISTICAL REVIEW AB - Summary This paper gives an introduction and overview to the often under‐used measurement error model. The purpose is to provide a simple summary of problems that arise from measurement error and of the solutions that have been proposed. We start by describing how measurement error models occur in real‐world situations. Then we proceed with defining the measurement error model, initially introducing the multivariate form of the model, and then, starting with the simplest form of the model thoroughly discuss its features and solutions to the problems introduced due to measurement error. We discuss higher‐dimensional and more advanced forms of the model and give a brief numerical illustration. DA - 2007/8// PY - 2007/8// DO - 10.1111/j.1751-5823.2007.00014.x VL - 75 IS - 2 SP - 183-198 SN - 0306-7734 KW - instrumental variables KW - linear models KW - measurement error KW - nonlinear models KW - structural relationship ER - TY - JOUR TI - Adaptive lasso for Cox's proportional hazards model AU - Zhang, Hao Helen AU - Lu, Wenbin T2 - BIOMETRIKA AB - We investigate the variable selection problem for Cox's proportional hazards model, and propose a unified model selection and estimation procedure with desired theoretical properties and computational convenience. The new method is based on a penalized log partial likelihood with the adaptively weighted L1 penalty on regression coefficients, providing what we call the adaptive Lasso estimator. The method incorporates different penalties for different coefficients: unimportant variables receive larger penalties than important ones, so that important variables tend to be retained in the selection process, whereas unimportant variables are more likely to be dropped. Theoretical properties, such as consistency and rate of convergence of the estimator, are studied. We also show that, with proper choice of regularization parameters, the proposed estimator has the oracle properties. The convex optimization nature of the method leads to an efficient algorithm. Both simulated and real examples show that the method performs competitively. DA - 2007/8// PY - 2007/8// DO - 10.1093/biomet/asm037 VL - 94 IS - 3 SP - 691-703 SN - 0006-3444 KW - adaptive lasso KW - lasso KW - penalized partial likelihood KW - proportional hazards model KW - variable selection ER - TY - JOUR TI - Yield and physiological response of peanut to glyphosate drift AU - Lassiter, Bridget R. AU - Burke, Ian C. AU - Thomas, Walter E. AU - Pline-Srnic, Wendy A. AU - Jordan, David L. AU - Wilcut, John W. AU - Wilkerson, Gall G. T2 - WEED TECHNOLOGY AB - Five experiments were conducted during 2001 and 2002 in North Carolina to evaluate peanut injury and pod yield when glyphosate was applied to 10 to 15 cm diameter peanut plants at rates ranging from 9 to 1,120 g ai/ha. Shikimic acid accumulation was determined in three of the five experiments. Visual foliar injury (necrosis and chlorosis) was noted 7 d after treatment (DAT) when glyphosate was applied at 18 g/ha or higher. Glyphosate at 280 g/ha or higher significantly injured the peanut plant and reduced pod yield. Shikimic acid accumulation was negatively correlated with visual injury and pod yield. The presence of shikimic acid can be detected using a leaf tissue assay, which is an effective diagnostic tool for determining exposure of peanut to glyphosate 7 DAT. DA - 2007/// PY - 2007/// DO - 10.1614/WT-07-045.1 VL - 21 IS - 4 SP - 954-960 SN - 0890-037X KW - herbicide drift KW - shikimic acid accumulation ER - TY - JOUR TI - The role of epistasis in the manifestation of heterosis: A systems-oriented approach AU - Melchinger, A. E. AU - Utz, H. F. AU - Piepho, H. -P. AU - Zeng, Z. -B. AU - Schoen, C. C. T2 - GENETICS AB - Abstract Heterosis is widely used in breeding, but the genetic basis of this biological phenomenon has not been elucidated. We postulate that additive and dominance genetic effects as well as two-locus interactions estimated in classical QTL analyses are not sufficient for quantifying the contributions of QTL to heterosis. A general theoretical framework for determining the contributions of different types of genetic effects to heterosis was developed. Additive × additive epistatic interactions of individual loci with the entire genetic background were identified as a major component of midparent heterosis. On the basis of these findings we defined a new type of heterotic effect denoted as augmented dominance effect di* that comprises the dominance effect at each QTL minus half the sum of additive × additive interactions with all other QTL. We demonstrate that genotypic expectations of QTL effects obtained from analyses with the design III using testcrosses of recombinant inbred lines and composite-interval mapping precisely equal genotypic expectations of midparent heterosis, thus identifying genomic regions relevant for expression of heterosis. The theory for QTL mapping of multiple traits is extended to the simultaneous mapping of newly defined genetic effects to improve the power of QTL detection and distinguish between dominance and overdominance. DA - 2007/11// PY - 2007/11// DO - 10.1534/genetics.107.077537 VL - 177 IS - 3 SP - 1815-1825 SN - 0016-6731 ER - TY - JOUR TI - Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypes AU - Bushel, Pierre R. AU - Wolfinger, Russell D. AU - Gibson, Greg T2 - BMC SYSTEMS BIOLOGY AB - Commonly employed clustering methods for analysis of gene expression data do not directly incorporate phenotypic data about the samples. Furthermore, clustering of samples with known phenotypes is typically performed in an informal fashion. The inability of clustering algorithms to incorporate biological data in the grouping process can limit proper interpretation of the data and its underlying biology. We present a more formal approach, the modk-prototypes algorithm, for clustering biological samples based on simultaneously considering microarray gene expression data and classes of known phenotypic variables such as clinical chemistry evaluations and histopathologic observations. The strategy involves constructing an objective function with the sum of the squared Euclidean distances for numeric microarray and clinical chemistry data and simple matching for histopathology categorical values in order to measure dissimilarity of the samples. Separate weighting terms are used for microarray, clinical chemistry and histopathology measurements to control the influence of each data domain on the clustering of the samples. The dynamic validity index for numeric data was modified with a category utility measure for determining the number of clusters in the data sets. A cluster's prototype, formed from the mean of the values for numeric features and the mode of the categorical values of all the samples in the group, is representative of the phenotype of the cluster members. The approach is shown to work well with a simulated mixed data set and two real data examples containing numeric and categorical data types. One from a heart disease study and another from acetaminophen (an analgesic) exposure in rat liver that causes centrilobular necrosis. The modk-prototypes algorithm partitioned the simulated data into clusters with samples in their respective class group and the heart disease samples into two groups (sick and buff denoting samples having pain type representative of angina and non-angina respectively) with an accuracy of 79%. This is on par with, or better than, the assignment accuracy of the heart disease samples by several well-known and successful clustering algorithms. Following modk-prototypes clustering of the acetaminophen-exposed samples, informative genes from the cluster prototypes were identified that are descriptive of, and phenotypically anchored to, levels of necrosis of the centrilobular region of the rat liver. The biological processes cell growth and/or maintenance, amine metabolism, and stress response were shown to discern between no and moderate levels of acetaminophen-induced centrilobular necrosis. The use of well-known and traditional measurements directly in the clustering provides some guarantee that the resulting clusters will be meaningfully interpretable. DA - 2007/2/23/ PY - 2007/2/23/ DO - 10.1186/1752-0509-1-15 VL - 1 SP - SN - 1752-0509 ER - TY - JOUR TI - Novel methods for detecting epistasis in pharmacogenomics studies AU - Motsinger, A. A. AU - Ritchie, M. D. AU - Reif, D. M. T2 - Pharmacogenomics DA - 2007/// PY - 2007/// VL - 8 IS - 9 SP - 1229-1241 ER - TY - JOUR TI - Electroactive nanostructured polymers as tunable actuators AU - Shankar, Ravi AU - Ghosh, Tushar K. AU - Spontak, Richard J. T2 - ADVANCED MATERIALS AB - Lightweight and conformable electroactive actuators stimulated by low electric fields are required for emerging responsive technologies. In this work, we demonstrate that selectively swollen triblock copolymers yield electroactive nanostructured polymers (ENPs) that exhibit excellent displacement (>200% areal strain) under an applied electric field (see figure). Such ENPs possess properties that can be broadly tailored and represent a viable avenue to designer organic actuators for advanced engineering, biomimetic, and biomedical applications. DA - 2007/9/3/ PY - 2007/9/3/ DO - 10.1002/adma.200602644 VL - 19 IS - 17 SP - 2218-+ SN - 1521-4095 ER - TY - JOUR TI - Effect of organnic, sustainable, and conventional management strategies in grower fields on soil physical, chemical, and biological factors and the incidence of Southern blight AU - Liu, Bo AU - Tu, Cong AU - Hu, Shuijin AU - Gumpertz, Marcia AU - Ristaino, Jean Beagle T2 - APPLIED SOIL ECOLOGY AB - The objectives of our research were to evaluate the impact of organic, sustainable, and conventional management strategies in grower fields on soil physical, chemical, and biological factors including soil microbial species and functional diversity and their effect on the Basidiomycete plant pathogen Sclerotium rolfsii, causal agent of Southern blight. Soils from 10 field locations including conventional, organic and sustainable farms were sampled and assayed for disease suppressiveness in greenhouse assays, and soil quality indicators. Soils from organic and sustainable farms were more suppressive to Southern blight than soils from conventional farms. Soils from organic farms had improved soil chemical factors and higher levels of extractable C and N, higher microbial biomass carbon and nitrogen, and net mineralizable N. In addition, soil microbial respiration was higher in soils from organic than sustainable or conventional farms, indicating that microbial activity was greater in these soils. Populations of fungi and thermophiles were significantly higher in soils from organic and sustainable than conventional fields. The diversity of bacterial functional communities was also greater in soils from organic farms, while species diversity was similar. Soils from organic and sustainable farms had improved soil health as indicated by a number of soil physical, chemical and biological factors and reduced disease. DA - 2007/11// PY - 2007/11// DO - 10.1016/j.apsoil.2007.06.007 VL - 37 IS - 3 SP - 202-214 SN - 1873-0272 KW - chemical and biological properties KW - organic and conventional farms KW - microbial communities KW - functional diversity KW - species diversity KW - biolog KW - DGGE ER - TY - JOUR TI - A semiparametric approach for composite functional mapping of dynamic quantitative traits AU - Yang, Runqing AU - Gao, Huijiang AU - Wang, Xin AU - Zhang, Ji AU - Zeng, Zhao-Bang AU - Wu, Rongling T2 - GENETICS AB - Abstract Functional mapping has emerged as a powerful tool for mapping quantitative trait loci (QTL) that control developmental patterns of complex dynamic traits. Original functional mapping has been constructed within the context of simple interval mapping, without consideration of separate multiple linked QTL for a dynamic trait. In this article, we present a statistical framework for mapping QTL that affect dynamic traits by capitalizing on the strengths of functional mapping and composite interval mapping. Within this so-called composite functional-mapping framework, functional mapping models the time-dependent genetic effects of a QTL tested within a marker interval using a biologically meaningful parametric function, whereas composite interval mapping models the time-dependent genetic effects of the markers outside the test interval to control the genome background using a flexible nonparametric approach based on Legendre polynomials. Such a semiparametric framework was formulated by a maximum-likelihood model and implemented with the EM algorithm, allowing for the estimation and the test of the mathematical parameters that define the QTL effects and the regression coefficients of the Legendre polynomials that describe the marker effects. Simulation studies were performed to investigate the statistical behavior of composite functional mapping and compare its advantage in separating multiple linked QTL as compared to functional mapping. We used the new mapping approach to analyze a genetic mapping example in rice, leading to the identification of multiple QTL, some of which are linked on the same chromosome, that control the developmental trajectory of leaf age. DA - 2007/11// PY - 2007/11// DO - 10.1534/genetics.107.077321 VL - 177 IS - 3 SP - 1859-1870 SN - 1943-2631 ER - TY - JOUR TI - The role of multi-modality adjuvant chemotherapy and radiation in women with advanced stage endometrial cancer AU - Secord, Angeles Alvarez AU - Havrilesky, Laura J. AU - Bae-Jump, Victoria AU - Chin, Jeanette AU - Calingaert, Brian AU - Bland, Amy AU - Rutledge, Teresa L. AU - Berchuck, Andrew AU - Clarke-Pearson, Daniel L. AU - Gehrig, Paola A. T2 - GYNECOLOGIC ONCOLOGY AB - : The optimal adjuvant therapy for women with stages III and IV endometrial cancer following surgical staging and cytoreductive surgery is controversial. We sought to determine the outcome of patients with advanced stage endometrial cancer treated with postoperative chemotherapy+/-radiation to determine whether there was an advantage to combining treatment modalities.: A retrospective analysis of patients with surgical stages III and IV endometrial cancer from 1975 to 2006 was conducted at Duke University and the University of North Carolina. Inclusion criteria were comprehensive staging procedure including hysterectomy, bilateral salpingo-oophorectomy, +/-selective pelvic/aortic lymphadenectomy, surgical debulking, and treatment with adjuvant chemotherapy and/or radiotherapy. Progression-free (PFS) and overall survival (OS) were analyzed using Kaplan-Meier method and Cox proportional hazards model.: 356 Patients with advanced stage endometrial cancer were identified who received postoperative adjuvant therapies; 48% (n=171) radiotherapy alone, 29% (n=102) chemotherapy alone, 23% (n=83) chemotherapy and radiation. The median age was 66 years; 38% had endometrioid tumors; and 83% were optimally debulked. There was a significant difference between the adjuvant treatment groups for both OS and PFS (p<0.001), with those receiving chemotherapy alone having poorer 3-year OS (33%) and PFS (19%) compared to either radiotherapy alone (70% and 59%) or combination therapy (79% and 62%). After adjusting for stage, age, grade, and debulking status the hazard ratio (HR) for OS was 1.60 (95% CI, 0.88 to 2.89; p=0.122) for chemotherapy alone and 2.01 (95% CI, 1.17 to 3.48; p=0.012) for radiotherapy alone, compared to combination therapy. When the analysis was restricted to optimally debulked patients the adjusted HR for patients who were treated with either chemotherapy or radiation alone indicated a significantly higher risk for disease progression [HR=1.84 (95% CI, 1.03 to 3.27; p=0.038); HR=1.80 (95% CI, 1.10 to 2.95; p=0.020)] and death [HR=2.33 (95% CI, 1.12 to 4.86; p=0.024); HR=2.64 (95% CI, 1.38 to 5.07; p=0.004)], respectively, compared to patients who received combination therapy.: Combined adjuvant chemotherapy and radiation was associated with improved survival in patients with advanced stage disease compared to either modality alone. Future clinical trials are needed to prospectively evaluate multi-modality adjuvant therapy in women with advanced staged endometrial cancer to determine the appropriate sequencing and types of chemotherapy and radiation. DA - 2007/11// PY - 2007/11// DO - 10.1016/j.ygyno.2007.06.014 VL - 107 IS - 2 SP - 285-291 SN - 0090-8258 KW - endometrial cancer KW - chemotherapy KW - radiotherapy ER - TY - JOUR TI - The large sample behaviour of the generalized method of moments estimator in misspecified models (vol 114, pg 361, 2003) AU - Hall, Alastair R. AU - Inoue, Atsushi T2 - JOURNAL OF ECONOMETRICS DA - 2007/12// PY - 2007/12// DO - 10.1016/j.jeconom.2007.02.006 VL - 141 IS - 2 SP - 1418-1418 SN - 0304-4076 ER - TY - JOUR TI - Speed-mapping quantitative trait loci using microarrays AU - Lai, Chao-Qiang AU - Leips, Jeff AU - Zou, Wei AU - Roberts, Jessica F. AU - Wollenberg, Kurt R. AU - Parnell, Laurence D. AU - Zeng, Zhao-Bang AU - Ordovas, Jose M. AU - Mackay, Trudy F. C. T2 - NATURE METHODS DA - 2007/10// PY - 2007/10// DO - 10.1038/NMETH1084 VL - 4 IS - 10 SP - 839-841 SN - 1548-7105 ER - TY - JOUR TI - Residual (sur)realism AU - Stefanski, Leonard A. T2 - AMERICAN STATISTICIAN AB - We show how to construct multiple linear regression datasets with the property that the plot of residuals versus predicted values from the least squares fit of the correct model reveals a hidden image or message. In the full PDF version of this article, the abstract itself is one such plot. DA - 2007/5// PY - 2007/5// DO - 10.1198/000313007X190079 VL - 61 IS - 2 SP - 163-177 SN - 1537-2731 KW - added-variable plot KW - backward selection KW - forward selection KW - hidden image KW - hidden message KW - linear regression KW - model selection KW - partial regression plot KW - residual plots KW - variable selection ER - TY - JOUR TI - Nonparametric Bayesian estimation of positive false discovery rates AU - Tang, Yongqiang AU - Ghosal, Subhashis AU - Roy, Anindya T2 - BIOMETRICS AB - Summary We propose a Dirichlet process mixture model (DPMM) for the P ‐value distribution in a multiple testing problem. The DPMM allows us to obtain posterior estimates of quantities such as the proportion of true null hypothesis and the probability of rejection of a single hypothesis. We describe a Markov chain Monte Carlo algorithm for computing the posterior and the posterior estimates. We propose an estimator of the positive false discovery rate based on these posterior estimates and investigate the performance of the proposed estimator via simulation. We also apply our methodology to analyze a leukemia data set. DA - 2007/12// PY - 2007/12// DO - 10.1111/j.1541-0420.2007.00819.x VL - 63 IS - 4 SP - 1126-1134 SN - 0006-341X KW - Dirichlet mixture KW - Dirichlet process KW - Markov chain Monte Carlo KW - multiple testing KW - positive false discovery rate KW - posterior estimates ER - TY - JOUR TI - Local annual survival and seasonal residency rates of semipalmated sandpipers (Calidris pusilla) in Puerto Rico AU - Rice, Susan M. AU - Collazo, Jaime A. AU - Alldredge, Mathew W. AU - Harrington, Brian A. AU - Lewis, Allen R. T2 - AUK AB - We report seasonal residency and local annual survival rates of migratory Semipalmated Sandpipers (Calidris pusilla) at the Cabo Rojo salt flats, Puerto Rico. Residency rate (daily probability of remaining on the flats) was 0.991 ± 0.001 (x̄ ± SE), yielding a mean length of stay of 110 days. This finding supports the inclusion of the Caribbean as part of the species' winter range. Average estimated percentage of fat was low but increased throughout the season, which suggests that birds replenish some spent fat reserves and strive for energetic maintenance. Local annual survival rate was 0.62 ± 0.04, within the range of values reported for breeding populations at Manitoba and Alaska (0.53–0.76). The similarity was not unexpected because estimates were obtained annually but at opposite sites of their annual migratory movements. Birds captured at the salt flats appeared to be a mix of birds from various parts of the breeding range, judging from morphology (culmen's coefficient of variation = 9.1, n = 106). This suggested that origin (breeding area) of birds and their proportion in the data should be ascertained and accounted for in analyses to glean the full conservation implications of winter-based annual survival estimates. Those data are needed to unravel the possibility that individuals of distinct populations are affected by differential mortality factors across different migratory routes. Mean length of stay strongly suggested that habitat quality at the salt flats was high. Rainfall and tidal flow combine to increase food availability during fall. The salt flats dry up gradually toward late January, at the onset of the dry season. Semipalmated Sandpipers may move west to other Greater Antilles or south to sites such as coastal Surinam until the onset of spring migration. They are not an oversummering species at the salt flats. Conservation efforts in the Caribbean region require understanding the dynamics of this species throughout winter to protect essential habitat. Tasas de Supervivencia Anual Local y de Residencia Estacional de Calidris pusilla en Puerto Rico DA - 2007/10// PY - 2007/10// DO - 10.1642/0004-8038(2007)124[1397:LASASR]2.0.CO;2 VL - 124 IS - 4 SP - 1397-1406 SN - 0004-8038 KW - apparent survival KW - Calidris pusilla KW - Caribbean KW - mark-recapture KW - migration KW - Semipalmated Sandpiper KW - stopover KW - winter distribution ER - TY - JOUR TI - Factors affecting aural detections of songbirds AU - Alldredge, Mathew W. AU - Simons, Theodore R. AU - Pollock, Kenneth H. T2 - ECOLOGICAL APPLICATIONS AB - Many factors affect the number of birds detected on point count surveys of breeding songbirds. The magnitude and importance of these factors are not well understood. We used a bird song simulation system to quantify the effects of detection distance, singing rate, species differences, and observer differences on detection probabilities of birds detected by ear. We simulated 40 point counts consisting of 10 birds per count for five primary species (Black-and-white Warbler Mniotilta varia, Black-throated Blue Warbler Dendroica caerulescens, Black-throated Green Warbler Dendroica virens, Hooded Warbler Wilsonia citrina, and Ovenbird Seiurus aurocapillus) over a range of 15 distances (34–143 m). Songs were played at low (two songs per count) and high (13–21 songs per count) singing rates. Detection probabilities averaged across observers ranged from 0.60 (Black-and-white Warbler) to 0.83 (Hooded Warbler) at the high singing rate and 0.41 (Black-and-white Warbler) to 0.67 (Hooded Warbler) at the low singing rate. Logistic regression analyses indicated that species, singing rate, distance, and observer were all significant factors affecting detection probabilities. Singing rate × species and singing rate × distance interactions were also significant. Simulations of expected counts, based on the best logistic model, indicated that observers detected between 19% (for the worst observer, lowest singing rate, and least detectable species) and 65% (for the best observer, highest singing rate, and most detectable species) of the true population. Detection probabilities on actual point count surveys are likely to vary even more because many sources of variability were controlled in our experiments. These findings strongly support the importance of adjusting measures of avian diversity or abundance from auditory point counts with direct estimates of detection probability. DA - 2007/4// PY - 2007/4// DO - 10.1890/06-0685 VL - 17 IS - 3 SP - 948-955 SN - 1939-5582 KW - auditory detection KW - detection probability KW - observer differences KW - point counts KW - singing rate KW - species difference KW - warblers ER - TY - JOUR TI - Estimation of dynamic rate parameters in insect populations undergoing sublethal exposure to pesticides AU - Banks, H. T. AU - Banks, John E. AU - Dick, Lara K. AU - Stark, John D. T2 - BULLETIN OF MATHEMATICAL BIOLOGY AB - With newer, more environmentally friendly and, subsequently less lethal, pesticides in use, evaluating efficacy of a pesticide now requires more than simply counting deaths after treatment. A discrete, age-structured matrix model that incorporates a species' life history traits (such as birth rate, death rate and fecundity) has previously been used by ecologists. This model will be presented and discussed along with an alternative continuous, age-structured model which offers significant advantage in considering sublethal damage. We use this continuous model to estimate time-dependent mortality parameters in an ordinary least-squares technique. Confidence intervals are given and results from tests for statistical significance of added parameters are presented. DA - 2007/10// PY - 2007/10// DO - 10.1007/s11538-007-9207-z VL - 69 IS - 7 SP - 2139-2180 SN - 1522-9602 KW - population models KW - Leslie KW - Sinko-Streifer KW - McKendrick-VonForester KW - time-dependent parameters ER - TY - JOUR TI - Variable selection for proportional odds model AU - Lu, Wenbin AU - Zhang, Hao H. T2 - STATISTICS IN MEDICINE AB - In this paper we study the problem of variable selection for the proportional odds model, which is a useful alternative to the proportional hazards model and might be appropriate when the proportional hazards assumption is not satisfied. We propose to fit the proportional odds model by maximizing the marginal likelihood subject to a shrinkage-type penalty, which encourages sparse solutions and hence facilitates the process of variable selection. Two types of shrinkage penalties are considered: the LASSO and the adaptive-LASSO (ALASSO) penalty. In the ALASSO penalty, different weights are imposed on different coefficients such that important variables are more protectively retained in the final model while unimportant ones are more likely to be shrunk to zeros. We further provide an efficient computation algorithm to implement the proposed methods, and demonstrate their performance through simulation studies and an application to real data. Numerical results indicate that both methods can produce accurate and interpretable models, and the ALASSO tends to work better than the usual LASSO. DA - 2007/9/10/ PY - 2007/9/10/ DO - 10.1002/sim.2833 VL - 26 IS - 20 SP - 3771-3781 SN - 1097-0258 KW - marginal likelihood KW - proportional odds model KW - variable selection KW - shrinkage estimate ER - TY - JOUR TI - Time delay systems with distribution dependent dynamics AU - Banks, H. T. AU - Dediu, Sava AU - Nguyen, Hoan K. T2 - ANNUAL REVIEWS IN CONTROL AB - General delay dynamical systems in which uncertainty is present in the form of probability measure dependent dynamics are considered. Several motivating examples arising in biology are discussed. A functional analytic framework for investigating well-posedness (existence, uniqueness and continuous dependence of solutions), inverse problems, sensitivity analysis and approximations of the measures for computational purposes is surveyed. DA - 2007/// PY - 2007/// DO - 10.1016/j.arcontrol.2007.02.002 VL - 31 IS - 1 SP - 17-26 SN - 1367-5788 KW - inverse dynamics problem KW - probability distribution function KW - sensitivity analysis KW - biomedical systems ER - TY - JOUR TI - The design and analysis of field studies to estimate catch-and-release mortality AU - Pollock, K. H. AU - Pine, W. E., III T2 - FISHERIES MANAGEMENT AND ECOLOGY AB - Abstract The practice of catch and release (CR) as a fisheries management tool to reduce fishing mortality is widely applied in both freshwater and marine fisheries, whether from shifts in angler attitudes related to harvest or from the increasing use of harvest restrictions such as closed seasons or length limits. This approach assumes that for CR fishing policies to benefit the stock, CR will result in much lower mortality than would otherwise occur. There are many challenges in the design of CR studies to assess mortality, and in many practical settings it is difficult to obtain accurate and precise estimates. The focus of this article is on the design and quantitative aspects of estimating CR mortality, the need for a comprehensive approach that explicitly states all components of CR mortality, and the assumptions behind these methods. A general conceptual model for CR mortality that is applicable to containment and tagging‐based studies with a slight modification is presented. This article reviews the design and analysis of containment and tagging studies to estimate CR mortality over both the short and long term and then compares these two approaches. Additionally, the potential population‐level impacts of CR mortality are discussed. A recurring theme is the difficulty of designing studies to estimate CR mortality comprehensively and the need for additional research into both statistical model development and field study design. DA - 2007/4// PY - 2007/4// DO - 10.1111/j.1365-2400.2007.00532.x VL - 14 IS - 2 SP - 123-130 SN - 0969-997X KW - cage studies KW - catch and release mortality KW - hooking mortality KW - tagging studies KW - telemetry studies ER - TY - JOUR TI - Testing goodness-of-fit in logistic case-control studies AU - Bondell, Howard D. T2 - BIOMETRIKA AB - We present a goodness-of-fit test for the logistic regression model under case-control sampling. The test statistic is constructed via a discrepancy between two competing kernel density estimators of the underlying conditional distributions given case-control status. The proposed goodness-of-fit test is shown to compare very favourably with previously proposed tests for case-control sampling in terms of power. The test statistic can be easily computed as a quadratic form in the residuals from a prospective logistic regression maximum likelihood fit. In addition, the proposed test is affine invariant and has an alternative representation in terms of empirical characteristic functions. DA - 2007/6// PY - 2007/6// DO - 10.1093/biomet/asm033 VL - 94 IS - 2 SP - 487-495 SN - 0006-3444 KW - biased sampling KW - case-control data KW - goodness-of-fit KW - Kernel density KW - logistic regression KW - retrospective sampling ER - TY - JOUR TI - Sampling hazelnuts for aflatoxin: Effect of sample size and accept/reject limit on reducing the risk of misclassifying lots AU - Ozay, G. AU - Seyhan, F. AU - Yilmaz, A. AU - Whitaker, T. B. AU - Slate, A. B. AU - Giesbrecht, F. C. T2 - Journal of AOAC International DA - 2007/// PY - 2007/// VL - 90 IS - 4 SP - 1028-1035 ER - TY - JOUR TI - Protein evolution constraints and model-based techniques to study them AU - Thorne, Jeffrey L. T2 - CURRENT OPINION IN STRUCTURAL BIOLOGY AB - There have been substantial improvements in statistical tools for assessing the evolutionary roles of mutation and natural selection from interspecific sequence data. The importance of having the rate at which a point mutation occurs depend on the DNA sequence at sites surrounding the mutation is now better appreciated and can be accommodated in probabilistic models of protein evolution. To quantify the evolutionary impact of some aspect of phenotype, one promising strategy is to develop a system for predicting phenotype from the DNA sequence and to then infer how the evolutionary rates of sequence change are affected by the predicted phenotypic consequences of the changes. Although statistical tools for characterizing protein evolution are improving, the list of candidate phenomena that can affect rates of protein evolution is long and the relative contributions of these phenomena are only beginning to be disentangled. DA - 2007/6// PY - 2007/6// DO - 10.1016/j.sbi.2007.05.006 VL - 17 IS - 3 SP - 337-341 SN - 1879-033X ER - TY - JOUR TI - Nonlinear feedback controllers and compensators: a state-dependent Riccati equation approach AU - Banks, H. T. AU - Lewis, B. M. AU - Tran, H. T. T2 - COMPUTATIONAL OPTIMIZATION AND APPLICATIONS AB - State-dependent Riccati equation (SDRE) techniques are rapidly emerging as general design and synthesis methods of nonlinear feedback controllers and estimators for a broad class of nonlinear regulator problems. In essence, the SDRE approach involves mimicking standard linear quadratic regulator (LQR) formulation for linear systems. In particular, the technique consists of using direct parameterization to bring the nonlinear system to a linear structure having state-dependent coefficient matrices. Theoretical advances have been made regarding the nonlinear regulator problem and the asymptotic stability properties of the system with full state feedback. However, there have not been any attempts at the theory regarding the asymptotic convergence of the estimator and the compensated system. This paper addresses these two issues as well as discussing numerical methods for approximating the solution to the SDRE. The Taylor series numerical methods works only for a certain class of systems, namely with constant control coefficient matrices, and only in small regions. The interpolation numerical method can be applied globally to a much larger class of systems. Examples will be provided to illustrate the effectiveness and potential of the SDRE technique for the design of nonlinear compensator-based feedback controllers. DA - 2007/6// PY - 2007/6// DO - 10.1007/s10589-007-9015-2 VL - 37 IS - 2 SP - 177-218 SN - 1573-2894 KW - nonlinear feedback control KW - nonlinear compensator KW - state-dependent Riccati equations ER - TY - JOUR TI - New confidence bounds for QT studies AU - Boos, Dennis D. AU - Hoffman, David AU - Kringle, Robert AU - Zhang, Ji T2 - STATISTICS IN MEDICINE AB - The proposed guidelines for the assessment of the effect of new pharmaceutical agents on the QT interval (beginning of QRS complex to end of T wave on the electrocardiogram) are based on the maximum of a series over time of simple one-sided 95 per cent upper confidence bounds. This procedure is typically very conservative as a procedure for obtaining a 95 per cent bound for the maximum of the population parameters. This paper proposes new bounds for the maximum, both analytical and bootstrap-based, that are lower but still achieve correct coverage in the context of crossover and parallel designs for the most realistic portions of the parameter space. DA - 2007/9/10/ PY - 2007/9/10/ DO - 10.1002/sim.2826 VL - 26 IS - 20 SP - 3801-3817 SN - 0277-6715 KW - repolarization KW - arrhythmia KW - electrocardiogram KW - crossover KW - parallel design ER - TY - JOUR TI - Long-term effects of organic and synthetic soil fertility amendments on soil microbial communities and the development of southern blight AU - Liu, Bo AU - Gumpertz, Marcia L. AU - Hu, Shuijin AU - Ristaino, Jean Beagle T2 - SOIL BIOLOGY & BIOCHEMISTRY AB - The effects of tillage and soil fertility amendments on the relationship between the suppressiveness of soils to southern blight and soil physical, chemical and biological factors were examined in experimental station plots in North Carolina. Main plots were either tilled frequently or surface-mulched after one initial tillage. Organic soil amendments including composted cotton gin trash, composted poultry manure, an incorporated rye–vetch green manure, or synthetic fertilizer were applied to subplots in a split-plot design experiment. Incidence of southern blight was lower in surfaced-mulched than tilled soils. Incidence of southern blight was also lower in soils amended with cotton gin trash than those amended with poultry manure, rye–vetch green manure or synthetic fertilizer. Soil water content was negatively correlated with the incidence of disease in both years. Disease incidence was negatively correlated with the level of potassium, calcium, cation exchange capacity (CEC), base saturation (BS) and humic matter in 2002, and net mineralizable nitrogen in 2001. Although, populations of thermophilic organisms were significantly higher in soils amended with cotton gin trash than the other three fertility amendments in each year, there was no significant correlation between the populations of thermophiles and incidence of the disease. Bacterial community diversity indices based on community-level physiological profiling (CLPP) and denaturing gradient gel electrophoresis (DGGE) were significantly higher in soils amended with cotton gin trash than those amended with poultry manure, green manure or synthetic fertilizer. There was a significant negative correlation between the incidence of southern blight, and CLPP and DGGE diversity indices. Greater differences in the richness of bacterial functional groups than genotypes were observed. These results demonstrate that organic soil fertility amendments and cotton gin trash in particular, reduced the development of the disease and affected soil physical, chemical and biological parameters. DA - 2007/9// PY - 2007/9// DO - 10.1016/j.soilbio.2007.04.001 VL - 39 IS - 9 SP - 2302-2316 SN - 1879-3428 KW - Sclerotium rolfsii KW - soil physical KW - chemical and biological parameters KW - organic and synthetic fertility amendments KW - disease KW - microbial communities KW - BIOLOG KW - DGGE ER - TY - JOUR TI - Information in generalized method of moments estimation and entropy-based moment selection AU - Hall, Alastair R. AU - Inoue, Atsushi AU - Jana, Kalidas AU - Shin, Changmock T2 - JOURNAL OF ECONOMETRICS AB - In this paper, we make five contributions to the literature on information and entropy in generalized method of moments (GMM) estimation. First, we introduce the concept of the long run canonical correlations (LRCCs) between the true score vector and the moment function f(vt,θ0) and show that they provide a metric for the information contained in the population moment condition E[f(vt,θ0)]=0. Second, we show that the entropy of the limiting distribution of the GMM estimator can be written in terms of these LRCCs. Third, motivated by the above results, we introduce an information criterion based on this entropy that can be used as a basis for moment selection. Fourth, we introduce the concept of nearly redundant moment conditions and use it to explore the connection between redundancy and weak identification. Fifth, we analyse the behaviour of the aforementioned entropy-based moment selection method in two scenarios of interest; these scenarios are: (i) nonlinear dynamic models where the parameter vector is identified by all the combinations of moment conditions considered; (ii) linear static models where the parameter vector may be weakly identified for some of the combinations considered. The first of these contributions rests on a generalized information equality that is proved in the paper, and may be of interest in its own right. DA - 2007/6// PY - 2007/6// DO - 10.1016/j.jeconom.2006.05.006 VL - 138 IS - 2 SP - 488-512 SN - 0304-4076 KW - long run canonical correlations KW - efficiency KW - near redundancy KW - weak identification ER - TY - JOUR TI - Global attractors for a discrete selection model with periodic immigration AU - Selgrade, James F. AU - Roberds, James H. T2 - JOURNAL OF DIFFERENCE EQUATIONS AND APPLICATIONS AB - A one-island selection-migration model is used to study the periodic immigration of a population of fixed allele frequency into a natural population. Density-dependent selection and immigration are the primary factors affecting the demographic and genetic change in the island population. With the assumptions of complete dominance (CD) or no dominance (ND) and homozygote superiority in fitness, the existence and location of global attractors are established. Analysis of this model provides rudimentary information about the migration of transgenes into a natural population. DA - 2007/4// PY - 2007/4// DO - 10.1080/10236190601079100 VL - 13 IS - 4 SP - 275-287 SN - 1023-6198 KW - natural selection KW - periodic immigration KW - complete dominance KW - no dominance KW - global attractor ER - TY - JOUR TI - Factors regulating cheese shreddability AU - Childs, J. L. AU - Daubert, C. R. AU - Stefanski, L. AU - Foegeding, E. A. T2 - JOURNAL OF DAIRY SCIENCE AB - Two sets of cheeses were evaluated to determine factors that affect shred quality. The first set of cheeses was made up of 3 commercial cheeses, Monterey Jack, Mozzarella, and process. The second set of cheeses was made up of 3 Mozzarella cheeses with varying levels of protein and fat at a constant moisture content. A shred distribution of long shreds, short shreds, and fines was obtained by shredding blocks of cheese in a food processor. A probe tack test was used to directly measure adhesion of the cheese to a stainless-steel surface. Surface energy was determined based on the contact angles of standard liquids, and rheological characterization was done by a creep and recovery test. Creep and recovery data were used to calculate the maximum and initial compliance and retardation time. Shredding defects of fines and adhesion to the blade were observed in commercial cheeses. Mozzarella did not adhere to the blade but did produce the most fines. Both Monterey Jack and process cheeses adhered to the blade and produced fines. Furthermore, adherence to the blade was correlated positively with tack energy and negatively with retardation time. Mozzarella cheese, with the highest fat and lowest protein contents, produced the most fines but showed little adherence to the blade, even though tack energy increased with fat content. Surface energy was not correlated with shredding defects in either group of cheese. Rheological properties and tack energy appeared to be the key factors involved in shredding defects. DA - 2007/5// PY - 2007/5// DO - 10.3168/jds.2006-618 VL - 90 IS - 5 SP - 2163-2174 SN - 0022-0302 KW - cheese KW - shreddability KW - pressure-sensitive adhesion KW - surface energy ER - TY - JOUR TI - Estimating fishing mortality, natural mortality, and selectivity using recoveries from tagging young fish AU - Jiang, Honghua AU - Brownie, Cavell AU - Hightower, Joseph E. AU - Pollock, Kenneth H. T2 - NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT AB - Abstract Current methods for estimation of age‐ and year‐specific instantaneous mortality rates based on multiyear, multiple‐age tagging studies assume that it is feasible to tag fish in a wide range of ages. For some species, however, only the youngest one or two age‐classes are readily available for tagging. Given the practical advantages of tagging young fish only, an important question is whether such studies would provide the information needed for estimation of age‐dependent mortality rates. We investigated three designs: tagging only the youngest available age‐class, tagging the two youngest age‐classes, and tagging the first five age‐classes. We carried out simulation studies to assess estimator performance under these three designs, in each case assuming the same total number of tagged fish. Data were generated assuming fishing mortality rates to be age and year dependent and natural mortality rates to be constant or with limited age dependence. Estimator performance is best when fish are tagged in five age‐classes, and tagging fish in the two youngest age‐classes shows substantial improvement compared with tagging one age‐class only. External information about the tag‐reporting rate is necessary to obtain estimators with reasonable properties, especially in the case of models with age‐dependent natural mortality. Such information can be obtained from auxiliary studies by means of high‐reward tags or planted tags. Collecting recovery information for several additional years after the last release produces small improvements in precision and bias. If tagging fish in multiple age‐classes is impractical, reasonable precision can be obtained by tagging one or preferably two age‐classes and obtaining supplemental information on the reporting rate. For illustration, estimates of age‐dependent fishing and natural mortality rates were obtained from tag returns on Chesapeake Bay striped bass Morone saxatilis tagged at ages 3 and 4 years. DA - 2007/8// PY - 2007/8// DO - 10.1577/M06-127.1 VL - 27 IS - 3 SP - 773-781 SN - 0275-5947 ER - TY - JOUR TI - Density-dependent growth and mortality in an estuary-dependent fish: an experimental approach with juvenile spot Leiostomus xanthurus AU - Craig, J. Kevin AU - Rice, James A. AU - Crowder, Larry B. AU - Nadeau, David A. T2 - MARINE ECOLOGY PROGRESS SERIES AB - MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 343:251-262 (2007) - DOI: https://doi.org/10.3354/meps06864 Density-dependent growth and mortality in an estuary-dependent fish: an experimental approach with juvenile spot Leiostomus xanthurus J. Kevin Craig1,5,*, James A. Rice2, Larry B. Crowder3, David A. Nadeau4 1Department of Zoology, Center for Marine Sciences and Technology, North Carolina State University, 303 College Circle, Morehead City, North Carolina 28557, USA 2Department of Zoology, North Carolina State University, Raleigh, North Carolina 27695-7617, USA 3Nicholas School of the Environment and Earth Sciences, Duke Center for Marine Conservation, 135 Duke Marine Lab Rd., Beaufort, North Carolina 28516-9721, USA 4MarineLab, Marine Resources Development Foundation, 51 Shoreland Drive, Key Largo, Florida 33037, USA 5Present address: Florida State University Coastal and Marine Laboratrory, 3618 Highway 98, St. Teresa, Florida 32358-2702, USA *Email: kevin_craig@ncsu.edu ABSTRACT: The abundance of demersal marine fishes is a function of both pre-settlement processes that influence recruitment to benthic juvenile habitats, as well as post-settlement density-dependent processes that act during the juvenile stage. Few studies have investigated density-dependence for fishes that spawn offshore and recruit to inshore estuaries for the juvenile stage prior to returning to offshore waters as adults (i.e. estuary-dependent). We conducted 2 replicated experiments at different spatial scales to test for density-dependent growth and mortality in juvenile spot Leiostomus xanthurus, a common estuary-dependent species. In the small-scale experiment, we stocked spot in 1 m2 cages in a marsh creek at densities of 2, 5, and 10 fish m–2 and determined their growth and mortality after 51 d. In the large-scale experiment, we stocked spot in 79 m2 pond sections at 2, 5, and 10 fish m–2 and determined their growth and mortality after 52 d. We sampled benthic infauna at the end of the pond experiment to determine if prey availability mediated the effects of density on spot growth and mortality. Average spot growth rates decreased 83 to 97% and mortality increased 2- to 4-fold as density increased from 2 to 10 fish m–2. The density of benthic infauna at the end of the pond experiment was inversely related to spot density, consistent with competition for food as the underlying mechanism. Estimates of spot density compiled from the literature indicate that the density-dependent effects we observed occurred within the range of reported field densities. Our results provide strong experimental support for the hypothesis that density-dependent processes during the demersal juvenile stage in estuaries can modify patterns in the abundance of spot, and perhaps other estuary-dependent species, that are established prior to settlement. KEY WORDS: Density-dependent growth · Density-dependent mortality · Spot · Leiostomus xanthurus · Estuarine nursery · Food limitation Full text in pdf format PreviousNextCite this article as: Craig JK, Rice JA, Crowder LB, Nadeau DA (2007) Density-dependent growth and mortality in an estuary-dependent fish: an experimental approach with juvenile spot Leiostomus xanthurus. Mar Ecol Prog Ser 343:251-262. https://doi.org/10.3354/meps06864 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 343. Online publication date: August 07, 2007 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2007 Inter-Research. DA - 2007/// PY - 2007/// DO - 10.3354/meps06864 VL - 343 SP - 251-262 SN - 1616-1599 KW - density-dependent growth KW - density-dependent mortality KW - spot KW - Leiostomus xanthurus KW - estuarine nursery KW - food limitation ER - TY - JOUR TI - Comprehensive transcriptome profiling in tomato reveals a role for glycosyltransferase in Mi-mediated nematode resistance AU - Schaff, Jennifer E. AU - Nielsen, Dahlia M. AU - Smith, Chris P. AU - Scholl, Elizabeth H. AU - Bird, David Mck. T2 - PLANT PHYSIOLOGY AB - Root-knot nematode (RKN; Meloidogyne spp.) is a major crop pathogen worldwide. Effective resistance exists for a few plant species, including that conditioned by Mi in tomato (Solanum lycopersicum). We interrogated the root transcriptome of the resistant (Mi+) and susceptible (Mi-) cultivars 'Motelle' and 'Moneymaker,' respectively, during a time-course infection by the Mi-susceptible RKN species Meloidogyne incognita and the Mi-resistant species Meloidogyne hapla. In the absence of RKN infection, only a single significantly regulated gene, encoding a glycosyltransferase, was detected. However, RKN infection influenced the expression of broad suites of genes; more than half of the probes on the array identified differential gene regulation between infected and uninfected root tissue at some stage of RKN infection. We discovered 217 genes regulated during the time of RKN infection corresponding to establishment of feeding sites, and 58 genes that exhibited differential regulation in resistant roots compared to uninfected roots, including the glycosyltransferase. Using virus-induced gene silencing to silence the expression of this gene restored susceptibility to M. incognita in 'Motelle,' indicating that this gene is necessary for resistance to RKN. Collectively, our data provide a picture of global gene expression changes in roots during compatible and incompatible associations with RKN, and point to candidates for further investigation. DA - 2007/6// PY - 2007/6// DO - 10.1104/pp.106.090241 VL - 144 IS - 2 SP - 1079-1092 SN - 1532-2548 ER - TY - JOUR TI - Bayesian entropy for spatial sampling design of environmental data AU - Fuentes, Montserrat AU - Chaudhuri, Arin AU - Holland, David M. T2 - ENVIRONMENTAL AND ECOLOGICAL STATISTICS AB - We develop a spatial statistical methodology to design national air pollution monitoring networks with good predictive capabilities while minimizing the cost of monitoring. The underlying complexity of atmospheric processes and the urgent need to give credible assessments of environmental risk create problems requiring new statistical methodologies to meet these challenges. In this work, we present a new method of ranking various subnetworks taking both the environmental cost and the statistical information into account. A Bayesian algorithm is introduced to obtain an optimal subnetwork using an entropy framework. The final network and accuracy of the spatial predictions is heavily dependent on the underlying model of spatial correlation. Usually the simplifying assumption of stationarity, in the sense that the spatial dependency structure does not change location, is made for spatial prediction. However, it is not uncommon to find spatial data that show strong signs of nonstationary behavior. We build upon an existing approach that creates a nonstationary covariance by a mixture of a family of stationary processes, and we propose a Bayesian method of estimating the associated parameters using the technique of Reversible Jump Markov Chain Monte Carlo. We apply these methods for spatial prediction and network design to ambient ozone data from a monitoring network in the eastern US. DA - 2007/9// PY - 2007/9// DO - 10.1007/s10651-007-0017-0 VL - 14 IS - 3 SP - 323-340 SN - 1573-3009 KW - Bayesian inference KW - matern covariance KW - national air quality standards KW - nonstationarity KW - simulated annealing KW - spatial statistics ER - TY - JOUR TI - Application of complex demodulation on bZIP and bHLH-PAS protein domains AU - Wang, Z. AU - Smith, C. E. AU - Atchley, W. R. T2 - Mathematical Biosciences AB - Proteins are built with molecular modular building blocks such as an alpha-helix, beta-sheet, loop region and other structures. This is an economical way of constructing complex molecules. Periodicity analysis of protein sequences has allowed us to obtain meaningful information concerning their structure, function and evolution. In this work, complex demodulation (CDM) is introduced to detect functional regions in protein sequences data. More specifically, we analyzed bZIP and bHLH-PAS protein domains. Complex demodulation provided insightful information about changing amplitudes of periodic components in protein sequences. Furthermore, it was found that the local amplitude minimum or local amplitude maximum of the 3.6-aa periodic component is associated with protein structural or functional information due to the observation that the extrema are mainly located in the boundary area of two structural or functional regions. DA - 2007/// PY - 2007/// DO - 10.1016/j.mbs.2007.01.004 VL - 207 IS - 2 SP - 204-218 ER - TY - JOUR TI - Stochastic and deterministic models for agricultural production networks AU - Bai, P. AU - Banks, H. T. AU - Dediu, S. AU - Govan, A. Y. AU - Last, M. AU - Lloyd, A. L. AU - Nguyen, H. K. AU - Olufsen, M. S. AU - Rempala, G. AU - Slenning, B. D. T2 - Mathematical Biosciences and Engineering AB - An approach to modeling the impact of disturbances in an agricultural production network is presented. A stochastic model and its approximate deterministic model for averages over sample paths of the stochastic system are developed. Simulations, sensitivity and generalized sensitivity analyses are given. Finally, it is shown how diseases may be introduced into the network and corresponding simulations are discussed. DA - 2007/// PY - 2007/// DO - 10.3934/mbe.2007.4.373 VL - 4 IS - 3 SP - 373-402 ER - TY - JOUR TI - Statistical inference based on pooled data: A moment-based estimating equation approach AU - Bondell, Howard D. AU - Liu, Aiyi AU - Schisterman, Enrique F. T2 - JOURNAL OF APPLIED STATISTICS AB - Abstract We consider statistical inference on parameters of a distribution when only pooled data are observed. A moment-based estimating equation approach is proposed to deal with situations where likelihood functions based on pooled data are difficult to work with. We outline the method to obtain estimates and test statistics of the parameters of interest in the general setting. We demonstrate the approach on the family of distributions generated by the Box–Cox transformation model, and, in the process, construct tests for goodness of fit based on the pooled data. Keywords: Pooling biospecimensset-based observationsmomentsBox–Cox transformationgoodness-of-fitlognormal distribution Acknowledgements The authors thank W. Jack Hall and Kai F. Yu for helpful discussion and suggestions. DA - 2007/// PY - 2007/// DO - 10.1080/02664760600994844 VL - 34 IS - 2 SP - 129-140 SN - 1360-0532 KW - pooling biospecimens KW - set-based observations KW - moments KW - Box-Cox transformation KW - goodness-of-fit KW - lognormal distribution ER - TY - JOUR TI - Sampling almonds for aflatoxin, Part II: Estimating risks associated with various sampling plan designs AU - Whitaker, T. B. AU - Slate, A. B. AU - Hurley, J. M. AU - Giesbrecht, F. G. T2 - Journal of AOAC International DA - 2007/// PY - 2007/// VL - 90 IS - 3 SP - 778-785 ER - TY - JOUR TI - Quantifying the impact of protein tertiary structure on molecular evolution AU - Choi, Sang Chul AU - Hobolth, Asger AU - Robinson, Douglas M. AU - Kishino, Hirohisa AU - Thorne, Jeffrey L. T2 - MOLECULAR BIOLOGY AND EVOLUTION AB - To investigate the evolutionary impact of protein structure, the experimentally determined tertiary structure and the protein-coding DNA sequence were collected for each of 1,195 genes. These genes were studied via a model of sequence change that explicitly incorporates effects on evolutionary rates due to protein tertiary structure. In the model, these effects act via the solvent accessibility environments and pairwise amino acid interactions that are induced by tertiary structure. To compare the hypotheses that structure does and does not have a strong influence on evolution, Bayes factors were estimated for each of the 1,195 sequences. Most of the Bayes factors strongly support the hypothesis that protein structure affects protein evolution. Furthermore, both solvent accessibility and pairwise interactions among amino acids are inferred to have important roles in protein evolution. Our results also indicate that the strength of the relationship between tertiary structure and evolution has a weak but real correlation to the annotation information in the Gene Ontology database. Although their influences on rates of evolution vary among protein families, we find that the mean impacts of solvent accessibility and pairwise interactions are about the same. DA - 2007/8// PY - 2007/8// DO - 10.1093/molbev/msm097 VL - 24 IS - 8 SP - 1769-1782 SN - 0737-4038 KW - molecular evolution KW - protein structure impact KW - Gene Ontology KW - MCMC KW - Bayes factor ER - TY - JOUR TI - Posterior convergence rates of dirichlet mixtures at smooth densities AU - Ghosal, Subhashis AU - Vaart, Aad T2 - ANNALS OF STATISTICS AB - We study the rates of convergence of the posterior distribution for Bayesian density estimation with Dirichlet mixtures of normal distributions as the prior. The true density is assumed to be twice continuously differentiable. The bandwidth is given a sequence of priors which is obtained by scaling a single prior by an appropriate order. In order to handle this problem, we derive a new general rate theorem by considering a countable covering of the parameter space whose prior probabilities satisfy a summability condition together with certain individual bounds on the Hellinger metric entropy. We apply this new general theorem on posterior convergence rates by computing bounds for Hellinger (bracketing) entropy numbers for the involved class of densities, the error in the approximation of a smooth density by normal mixtures and the concentration rate of the prior. The best obtainable rate of convergence of the posterior turns out to be equivalent to the well-known frequentist rate for integrated mean squared error n−2/5 up to a logarithmic factor. DA - 2007/4// PY - 2007/4// DO - 10.1214/009053606000001271 VL - 35 IS - 2 SP - 697-723 SN - 0090-5364 KW - bracketing KW - dirichlet mixture KW - entropy KW - maximum likelihood KW - mixture of normals KW - posterior distribution KW - rate of convergence KW - sieve ER - TY - JOUR TI - Population genetics without intraspecific data AU - Thorne, Jeffrey L. AU - Choi, Sang Chul AU - Yu, Jiaye AU - Higgs, Paul G. AU - Kishino, Hirohisa T2 - MOLECULAR BIOLOGY AND EVOLUTION AB - A central goal of computational biology is the prediction of phenotype from DNA and protein sequence data. Recent models of sequence change use in silico prediction systems to incorporate the effects of phenotype on evolutionary rates. These models have been designed for analyzing sequence data from different species and have been accompanied by statistical techniques for estimating model parameters when the incorporation of phenotype induces dependent change among sequence positions. A difficulty with these efforts to link phenotype and interspecific evolution is that evolution occurs within populations, and parameters of interspecific models should have population genetic interpretations. We show, with two examples, how population genetic interpretations can be assigned to evolutionary models. The first example considers the impact of RNA secondary structure on sequence change, and the second reflects the tendency for protein tertiary structure to influence nonsynonymous substitution rates. We argue that statistical fit to data should not be the sole criterion for assessing models of sequence change. A good interspecific model should also yield a clear and biologically plausible population genetic interpretation. DA - 2007/8// PY - 2007/8// DO - 10.1093/molbev/msm085 VL - 24 IS - 8 SP - 1667-1677 SN - 1537-1719 KW - dependence among sites KW - fixation probability KW - protein structure KW - RNA structure ER - TY - JOUR TI - Estimation of detection probability in manatee aerial surveys at a winter aggregation site AU - Edwards, Holly H. AU - Pollock, Kenneth H. AU - Ackerman, Bruce B. AU - Reynolds, John E., III AU - Powell, James A. T2 - JOURNAL OF WILDLIFE MANAGEMENT AB - Abstract: Estimating components of detection probability is crucial to improving the design of aerial surveys for wildlife populations, and this is especially true for species of marine mammals that are threatened or endangered. To evaluate the probability that Florida manatees ( Trichechus manatus latirostris ) will be detected by observers during aerial surveys, we conducted 6 series of survey flights, during mornings and afternoons on 14‐16 consecutive days over the Tampa Electric Company's (TECO) Big Bend power plant discharge canal in Tampa Bay, Florida, USA (winter 2000 through 2003). Our objective was to understand how our ability to detect manatees at a winter aggregation site affects aerial survey counts, so that we may improve techniques for estimating manatee population size. We estimated the probability that manatees would be present at the warm‐water discharge of the plant during winter cold fronts and estimated the overall detection probability of manatees present at the plant and the 2 components that make up the probability of detection (the probability of being available and the probability of being detected given they are available). We used telemetry tags and marker flags ( n = 15) to facilitate capture‐recapture analyses. The probability that marked manatees would be at the plant varied from 48% to 68% across flight series and was inversely related to the ambient water temperature. Based on sightings of marked animals, estimates of the overall probability of detecting a manatee ranged from 45% to 69% across flight series (x̄ = 58%, n = 6). The probability that a manatee would be available to an observer ranged from 73% to 94% across flight series (x̄ = 83%) but was constant among years (83%, 81%, and 78%; x̄ = 81%). The probability that an available manatee would be detected by an aerial observer was variable across flight series (55‐95%) and years (73%, 86%, and 66%, x̄ = 73%). Independent estimates of the probability that a manatee would be available to the observer on one pass were obtained from time‐depth data loggers and ranged from 5% to 33% (x̄ = 19%, SE = 3.7%), and the probability that a manatee would be available during ≥1 of 10 passes ranged from 41% to 98% (x̄ = 88%, 95% confidence bounds 0.71‐0.95). We adjusted survey counts using measures of detectability. Although corrected counts presented here are site‐specific, adjusting counts based on detection probability will greatly improve reliability of population estimates from all aerial surveys. Special sampling to estimate components of detection probability should be built into all aerial surveys to ensure that reliable and unbiased information on species abundance is used to evaluate wildlife populations. DA - 2007/8// PY - 2007/8// DO - 10.2193/2005-645 VL - 71 IS - 6 SP - 2052-2060 SN - 0022-541X KW - aerial survey KW - capture-recapture KW - detection probability KW - Florida manatee KW - power plants KW - Tampa Bay KW - time-depth-temperature recorders (TDR) KW - Trichechus manatus latirostris KW - West Indian manatee ER - TY - JOUR TI - Dielectric elastomers as next-generation polymeric actuators AU - Shankar, Ravi AU - Ghosh, Tushar K. AU - Spontak, Richard J. T2 - SOFT MATTER AB - Due to their versatile properties, robust behavior, facile processability and low cost, organic polymers have become the material of choice for an increasing number of mature and cutting-edge technologies. In the last decade or so, a new class of polymers capable of responding to external electrical stimulation by displaying significant size or shape change has emerged. These responsive materials, collectively referred to as electroactive polymers (EAPs), are broadly classified as electronic or ionic according to their operational mechanism. Electronic EAPs generally exhibit superior performance relative to ionic EAPs in terms of actuation strain, reliability, durability and response time. Among electronic EAPs, dielectric elastomers exhibit the most promising properties that mimic natural muscle for use in advanced robotics and smart prosthetics, as well as in haptic and microfluidic devices. Elastomers derived from homopolymers such as acrylics and silicones have received considerable attention as dielectric EAPs, whereas novel dielectric EAPs based on selectively swollen nanostructured block copolymers with composition-tailorable properties have only recently been reported. Here, we provide an overview of various EAPs in terms of their operational mechanisms, uses and shortcomings, as well as a detailed account of dielectric elastomers as next-generation actuators. DA - 2007/// PY - 2007/// DO - 10.1039/b705737g VL - 3 IS - 9 SP - 1116-1129 SN - 1744-6848 ER - TY - JOUR TI - Correlation between perioperative factors and successful outcome in fibrosarcoma resection in cats AU - Davis, K. M. AU - Hardie, E. M. AU - Martin, F. R. AU - Zhu, J. AU - Brownie, C. T2 - VETERINARY RECORD AB - Veterinary RecordVolume 161, Issue 6 p. 199-200 Short Communication Correlation between perioperative factors and successful outcome in fibrosarcoma resection in cats K. M. Davis DVM, DipACVS, Corresponding Author K. M. Davis DVM, DipACVS n/[email protected] Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Drive, Raleigh, NC, 27606 USADr Davis's present address is Department of Small Animal Clinical Sciences, University of Florida Veterinary Medical Centre, 2015 SW 16th Avenue, Gainsville, FL 32610, USASearch for more papers by this authorE. M. Hardie DVM, PhD, DipACVS, E. M. Hardie DVM, PhD, DipACVS Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Drive, Raleigh, NC, 27606 USASearch for more papers by this authorF. R. Martin BA, F. R. Martin BA Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Drive, Raleigh, NC, 27606 USASearch for more papers by this authorJ. Zhu MStat, J. Zhu MStat Department of Statistics, North Carolina State University, Box 8203, Raleigh, NC, 27695-8203 USASearch for more papers by this authorC. Brownie PhD, C. Brownie PhD Department of Statistics, North Carolina State University, Box 8203, Raleigh, NC, 27695-8203 USASearch for more papers by this author K. M. Davis DVM, DipACVS, Corresponding Author K. M. Davis DVM, DipACVS n/[email protected] Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Drive, Raleigh, NC, 27606 USADr Davis's present address is Department of Small Animal Clinical Sciences, University of Florida Veterinary Medical Centre, 2015 SW 16th Avenue, Gainsville, FL 32610, USASearch for more papers by this authorE. M. Hardie DVM, PhD, DipACVS, E. M. Hardie DVM, PhD, DipACVS Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Drive, Raleigh, NC, 27606 USASearch for more papers by this authorF. R. Martin BA, F. R. Martin BA Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Drive, Raleigh, NC, 27606 USASearch for more papers by this authorJ. Zhu MStat, J. Zhu MStat Department of Statistics, North Carolina State University, Box 8203, Raleigh, NC, 27695-8203 USASearch for more papers by this authorC. Brownie PhD, C. Brownie PhD Department of Statistics, North Carolina State University, Box 8203, Raleigh, NC, 27695-8203 USASearch for more papers by this author First published: 11 August 2007 https://doi.org/10.1136/vr.161.6.199Citations: 17AboutPDF 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.Citing Literature Volume161, Issue6August 2007Pages 199-200 RelatedInformation DA - 2007/8/11/ PY - 2007/8/11/ DO - 10.1136/vr.161.6.199 VL - 161 IS - 6 SP - 199-200 SN - 0042-4900 ER - TY - JOUR TI - Convergence rates of posterior distributions for noniid observations AU - Ghosal, Subhashis AU - Van Der Vaart, Aad T2 - ANNALS OF STATISTICS AB - We consider the asymptotic behavior of posterior distributions and Bayes estimators based on observations which are required to be neither independent nor identically distributed. We give general results on the rate of convergence of the posterior measure relative to distances derived from a testing criterion. We then specialize our results to independent, nonidentically distributed observations, Markov processes, stationary Gaussian time series and the white noise model. We apply our general results to several examples of infinite-dimensional statistical models including nonparametric regression with normal errors, binary regression, Poisson regression, an interval censoring model, Whittle estimation of the spectral density of a time series and a nonlinear autoregressive model. DA - 2007/2// PY - 2007/2// DO - 10.1214/009053606000001172 VL - 35 IS - 1 SP - 192-223 SN - 0090-5364 KW - covering numbers KW - Hellinger distance KW - independent nonidentically distributed observations KW - infinite dimensional model KW - Markov chains KW - posterior distribution KW - rate of convergence KW - tests ER - TY - JOUR TI - A sampling-based computational strategy for the representation of epistemic uncertainty in model predictions with evidence theory AU - Helton, J. C. AU - Johnson, J. D. AU - Oberkampf, W. L. AU - Storlie, C. B. T2 - COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING AB - Evidence theory provides an alternative to probability theory for the representation of epistemic uncertainty in model predictions that derives from epistemic uncertainty in model inputs, where the descriptor epistemic is used to indicate uncertainty that derives from a lack of knowledge with respect to the appropriate values to use for various inputs to the model. The potential benefit, and hence appeal, of evidence theory is that it allows a less restrictive specification of uncertainty than is possible within the axiomatic structure on which probability theory is based. Unfortunately, the propagation of an evidence theory representation for uncertainty through a model is more computationally demanding than the propagation of a probabilistic representation for uncertainty, with this difficulty constituting a serious obstacle to the use of evidence theory in the representation of uncertainty in predictions obtained from computationally intensive models. This presentation describes and illustrates a sampling-based computational strategy for the representation of epistemic uncertainty in model predictions with evidence theory. Preliminary trials indicate that the presented strategy can be used to propagate uncertainty representations based on evidence theory in analysis situations where naïve sampling-based (i.e., unsophisticated Monte Carlo) procedures are impracticable due to computational cost. DA - 2007/// PY - 2007/// DO - 10.1016/j.cma.2006.10.049 VL - 196 IS - 37-40 SP - 3980-3998 SN - 1879-2138 KW - dempster-shafer theory KW - epistemic uncertainty KW - evidence theory KW - Monte Carlo KW - numerical uncertainty propagation KW - sensitivity analysis KW - uncertainty analysis ER - TY - JOUR TI - A consistent nonparametric Bayesian procedure for estimating autoregressive conditional densities AU - Tang, Yongqiang AU - Ghosal, Subhashis T2 - Computational Statistics & Data Analysis AB - This article proposes a Bayesian infinite mixture model for the estimation of the conditional density of an ergodic time series. A nonparametric prior on the conditional density is described through the Dirichlet process. In the mixture model, a kernel is used leading to a dynamic nonlinear autoregressive model. This model can approximate any linear autoregressive model arbitrarily closely while imposing no constraint on parameters to ensure stationarity. We establish sufficient conditions for posterior consistency in two different topologies. The proposed method is compared with the mixture of autoregressive model [Wong and Li, 2000. On a mixture autoregressive model. J. Roy. Statist. Soc. Ser. B 62(1), 91–115] and the double-kernel local linear approach [Fan et al., 1996. Estimation of conditional densities and sensitivity measures in nonlinear dynamical systems. Biometrika 83, 189–206] by simulations and real examples. Our method shows excellent performances in these studies. DA - 2007/5// PY - 2007/5// DO - 10.1016/j.csda.2006.06.020 VL - 51 IS - 9 SP - 4424-4437 J2 - Computational Statistics & Data Analysis LA - en OP - SN - 0167-9473 UR - http://dx.doi.org/10.1016/j.csda.2006.06.020 DB - Crossref KW - Dirichlet process mixture models KW - posterior consistency KW - no-gaps algorithm ER - TY - JOUR TI - A comparison of approximation methods for the estimation of probability distributions on parameters AU - Banks, H. T. AU - Davis, Jimena L. T2 - APPLIED NUMERICAL MATHEMATICS AB - In this paper, we compare two computationally efficient approximation methods for the estimation of growth rate distributions in size-structured population models. After summarizing the underlying theoretical framework, we present several numerical examples as validation of the theory. Furthermore, we compare the results from a spline based approximation method and a delta function based approximation method for the inverse problem involving the estimation of the distributions of growth rates in size-structured mosquitofish populations. Convergence as well as sensitivity of the estimates with respect to noise in the data are discussed for both approximation methods. DA - 2007/// PY - 2007/// DO - 10.1016/j.apnum.2006.07.016 VL - 57 IS - 5-7 SP - 753-777 SN - 1873-5460 ER - TY - JOUR TI - Viscoelasticity in polymers: Phenomenological to molecular mathematical modeling AU - Banks, H. T. AU - Luke, N. S. AU - Samuels, J. R., Jr. T2 - NUMERICAL METHODS FOR PARTIAL DIFFERENTIAL EQUATIONS AB - Abstract We report on two recent advances in the modeling of viscoelastic polymers: (i) a new constitutive model that combines the virtual stick‐slip continuum “molecular‐based” ideas of Johnson and Stacer with the Rouse bead chain ideas; (ii) a two‐dimensional version of a model that accounts for stenosis‐driven shear wave propagation in biotissue. © 2007 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 23: 817–831, 2007 DA - 2007/7// PY - 2007/7// DO - 10.1002/num.20250 VL - 23 IS - 4 SP - 817-831 SN - 1098-2426 KW - viscoelastic polymers KW - constitutive models KW - biotissue KW - stenosis KW - shear wave propagation ER - TY - JOUR TI - Using artificial canopy gaps to restore Puerto Rican Parrot (Amazona vittata) habitat in tropical timber plantations AU - Inman, Faith M. AU - Wentworth, Thomas R. AU - Groom, Martha AU - Brownie, Cavell AU - Lea, Russ T2 - FOREST ECOLOGY AND MANAGEMENT AB - Timber plantations have the potential to catalyze regeneration of natural forest on degraded land. However, effective management methods to restore native tree diversity and wildlife habitat in areas planted with non-native timber species are needed. Our study investigated the effectiveness of creating artificial canopy gaps within timber plantations to increase germination, growth, and survival of native tree species that may be important food plants for the Puerto Rican Parrot (Amazona vittata). Seedling growth increased significantly in gaps; however, there were no differences in percent germination or survival between gap and closed (control) plots. Percent cover of grasses, shrubs, and vines increased in gaps, but the increased growth of competitors did not prevent tree seedlings from growing significantly more rapidly in gaps. Removing leaf litter at time of sowing had no effect on germination, growth, or survival of direct seeded species. Creation of canopy gaps by girdling timber trees reduced basal area of non-native tree species to levels comparable with those of native trees. Both local and landscape level diversity were predicted to increase in canopy gaps; however, plantations will continue to be dominated by non-native and timber tree species because advance regeneration of these species is common in plantation understories. Our results suggest that restoration of native tree diversity and wildlife habitat in plantations will require continued management to remove non-native species and to promote growth of tree species with high wildlife habitat value. DA - 2007/5/31/ PY - 2007/5/31/ DO - 10.1016/j.foreco.2007.02.003 VL - 243 IS - 2-3 SP - 169-177 SN - 0378-1127 KW - habitat restoration KW - Hibiscus elatus KW - tropical timber plantations KW - Puerto Rico KW - Puerto Rican Parrot KW - canopy gaps ER - TY - JOUR TI - Robustness and uncertainty in estimates of butterfly abundance from transect counts AU - Gross, Kevin AU - Kalendra, Eric J. AU - Hudgens, Brian R. AU - Haddad, Nick M. T2 - POPULATION ECOLOGY AB - Abstract Many butterfly populations are monitored by counting the number of butterflies observed while walking transects during the butterfly's flight season. Methods for estimating population abundance from these transect counts are appealing because they allow rare populations to be monitored without capture–recapture studies that could harm fragile individuals. An increasingly popular method for estimating abundance from transect counts relies on strong assumptions about the counting process and the processes that govern butterfly population dynamics. Here, we study the statistical performance of this method when underlying model assumptions are violated. We find that estimates of population size are robust to departures from underlying model assumptions, but that the uncertainty in these estimates (i.e., confidence intervals) is substantially underestimated. Alternative bootstrap and Bayesian methods provide better measures of the uncertainty in estimated population size, but are conditional upon knowledge of butterfly detectability. Because of these requirements, a mixed approach that combines data from small capture–recapture studies with transect counts strikes the best balance between accurate monitoring and minimal injury to individuals. Our study is motivated by monitoring studies for St. Francis satyr ( Neonympha mitchelli francisci ), a rare and relatively immobile butterfly occurring only in the sandhills region of south‐central North Carolina, USA. DA - 2007/7// PY - 2007/7// DO - 10.1007/s10144-007-0034-8 VL - 49 IS - 3 SP - 191-200 SN - 1438-390X KW - abundance KW - Bayesian statistics KW - estimation KW - parametric bootstrap KW - population monitoring ER - TY - JOUR TI - Polymeric resins adsorb and release oryzalin in response to pH AU - Fain, Glenn B. AU - Grey, Timothy L. AU - Wehtje, Glenn R. AU - Gilliam, Charles H. AU - Osborne, Jason A. T2 - WEED SCIENCE AB - Two polymeric anion-exchange resins and one sorbent resin were evaluated for their propensity to adsorb, and subsequently desorb, oryzalin. The intent was to determine whether these resins could adsorb and subsequently release oryzalin in a manner that would render these resins as an option for slow-release herbicide delivery. The dinitroaniline herbicide oryzalin is weakly acidic with a dissociation constant (p K a ) of 8.6. An additional objective was to determine whether altering the pH between sorption and desorption would enhance the desired performance. Maximum oryzalin sorption by the two anion-exchange resins was between 127 and 132 mg g −1 ai. The sorbent resin was adsorbed at a maximum concentration of 191 mg g −1 ai. Maximum sorption occurred with the pH 10 solutions with all resins. Average oryzalin desorption by the anion-exchange resin was between 0.12 and 3.84 mg g −1 per desorption event. Maximum desorption occurred at pH 6.0. Results reveal that the resins evaluated may have merit for slow-release herbicide delivery. DA - 2007/// PY - 2007/// DO - 10.1614/WS-06-013.1 VL - 55 IS - 2 SP - 157-163 SN - 1550-2759 KW - herbicide KW - adsorption KW - container-grown plants KW - nursery ER - TY - JOUR TI - MRI-guided thermal ablation therapy: Model and parameter estimates to predict cell death from MR thermometry images AU - Breen, Michael S. AU - Breen, Miyuki AU - Butts, Kim AU - Chen, Lili AU - Saidel, Gerald M. AU - Wilson, David L. T2 - ANNALS OF BIOMEDICAL ENGINEERING DA - 2007/8// PY - 2007/8// DO - 10.1007/s10439-007-9300-3 VL - 35 IS - 8 SP - 1391-1403 SN - 1573-9686 KW - cell death model KW - interventional MRI KW - laser thermal ablation KW - MR thermometry ER - TY - JOUR TI - Growth characteristics and allometry of Robinia pseudoacacia as a silvopastoral system component AU - Snyder, L. J. Unruh AU - Mueller, J. P. AU - Luginbuhl, J. M. AU - Brownie, C. T2 - AGROFORESTRY SYSTEMS DA - 2007/5// PY - 2007/5// DO - 10.1007/s10457-007-9035-z VL - 70 IS - 1 SP - 41-51 SN - 1572-9680 KW - black locust KW - tree herbage biomass KW - goat KW - prediction equation KW - plant population ER - TY - JOUR TI - Experimental analysis of the auditory detection process on avian point counts AU - Simons, Theodore R. AU - Alldredge, Mathew W. AU - Pollock, Kenneth H. AU - Wettroth, John M. T2 - AUK AB - We have developed a system for simulating the conditions of avian surveys in which birds are identified by sound. The system uses a laptop computer to control a set of amplified MP3 players placed at known locations around a survey point. The system can realistically simulate a known population of songbirds under a range of factors that affect detection probabilities. The goals of our research are to describe the sources and range of variability affecting point-count estimates and to find applications of sampling theory and methodologies that produce practical improvements in the quality of bird-census data. Initial experiments in an open field showed that, on average, observers tend to undercount birds on unlimited-radius counts, though the proportion of birds counted by individual observers ranged from 81% to 132% of the actual total. In contrast to the unlimited-radius counts, when data were truncated at a 50-m radius around the point, observers overestimated the total population by 17% to 122%. Results also illustrate how detection distances decline and identification errors increase with increasing levels of ambient noise. Overall, the proportion of birds heard by observers decreased by 28 ± 4.7% under breezy conditions, 41 ± 5.2% with the presence of additional background birds, and 42 ± 3.4% with the addition of 10 dB of white noise. These findings illustrate some of the inherent difficulties in interpreting avian abundance estimates based on auditory detections, and why estimates that do not account for variations in detection probability will not withstand critical scrutiny. DA - 2007/7// PY - 2007/7// DO - 10.1642/0004-8038(2007)124[986:EAOTAD]2.0.CO;2 VL - 124 IS - 3 SP - 986-999 SN - 1938-4254 KW - ambient noise KW - detection probability KW - measurement error KW - point counts ER - TY - JOUR TI - Data-reduction method for spatial data using a structured wavelet model AU - Jeong, Myong K. AU - Lu, Jye-Chyi AU - Zhou, Weixin AU - Ghosh, Sujit K. T2 - INTERNATIONAL JOURNAL OF PRODUCTION RESEARCH AB - Recent advances in sensor instrumentation have provided opportunities for process engineers to collect data at various process steps in order to detect process problems and develop remedial procedures. This article presents a structured wavelet model for the reduction of two-dimensional data having distinct structures. The wavelet component of our model can handle irregular data patterns exhibiting many peaks and valleys, while the existence of a distinct data structure prompts the use of polynomial functions on wavelet coefficients. The two-dimensional antenna data is reduced with a structured wavelet model followed by some procedures for the detection of process defects based on the reduced-size data. A real-life example is presented to illustrate the usefulness of the proposed tools in detecting process problems from a potentially large volume of data exhibiting many peaks and valleys. DA - 2007/// PY - 2007/// DO - 10.1080/00207540600793547 VL - 45 IS - 10 SP - 2295-2311 SN - 0020-7543 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-34247605442&partnerID=MN8TOARS KW - fault detection KW - intelligent manufacturing KW - process control KW - structured model KW - wavelets ER - TY - JOUR TI - Atomic scale design of nanostructures AU - Bernholc, J. AU - Lu, W. AU - Nakhmanson, S. M. AU - Hahn, P. H. AU - Meunier, V. AU - Nardelli, M. Buongiorno AU - Schmidt, W. G. T2 - MOLECULAR PHYSICS AB - Abstract Recent advances in theoretical methods and high performance computing allow for reliable first-principles predictions of complex nanostructured materials and devices. This paper describes three examples: (i) non-equilibrium electron transport through molecular junctions, as a stepping stone for the design of molecular-scale devices and for integration of biomolecules with Si technology; (ii) polarization and piezoelectric properties of PVDF and related polymers; and (iii) the many-body optical spectrum of water. For the molecular junction, our results provide a qualitative picture and quantitative understanding of the mechanism leading to negative differential resistance for a large class of small molecules. For ferroelectric polymers, the calculations show that their polarization is described by cooperative, quantum-mechanical interactions between polymer chains. Nevertheless, the ab initio results lead to a simple parameterization of polarization as a function of copolymer concentration. Finally, our calculations explain the well-known redshift in the fundamental absorption of water as due to exciton delocalization upon aggregation. DA - 2007/// PY - 2007/// DO - 10.1080/00268970701189186 VL - 105 IS - 2-3 SP - 147-156 SN - 1362-3028 ER - TY - JOUR TI - Age-dependent tag return models for estimating fishing mortality, natural mortality, and selectivity AU - Jiang, Honghua AU - Pollock, Kenneth H. AU - Brownie, Cavell AU - Hightower, Joseph E. AU - Hoenig, John M. AU - Hearn, William S. T2 - JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS AB - Tag return studies play an important role in providing estimates of mortality rates needed for management of many fisheries, but current methods of estimation do not allow age dependence of instantaneous mortality rates. We present models that allow age-dependent fishing and natural mortality rates, an important advance, because there is often substantial variation in age (and size) of fish at tagging. Age dependence of fishing mortality is modeled by assuming that availability to the fishery, that is, selectivity, depends on age but is constant over years. We assume that all age classes are tagged each year, and allow for incomplete mixing of newly tagged fish and for fisheries that are year-long or limited to a fishing season. We investigate parameter redundancy and estimator performance using analytic and simulation methods, and show that estimator properties are poor if the tag reporting rate is estimated (without auxiliary data such as planted tags). We analyzed multiple age class tag return data from a 13-year study on striped bass (Morone saxatilis) and saw clear evidence that selectivity increases with age. Assuming that the tag reporting rate is constant and known, results also demonstrate age dependence of natural mortality rates, and an increase in natural mortality rates from about 1999 coinciding with observation of a bacterial disease in the fish. DA - 2007/6// PY - 2007/6// DO - 10.1198/108571107x197382 VL - 12 IS - 2 SP - 177-194 SN - 1537-2693 KW - instantaneous mortality rates KW - near-singularity KW - parameter redundancy KW - striped bass KW - tag reporting rate ER - TY - JOUR TI - A comparison of chemical pretreatment methods for improving saccharification of cotton stalks AU - Silverstein, Rebecca A. AU - Chen, Ye AU - Sharma-Shivappa, Ratna R. AU - Boyette, Michael D. AU - Osborne, Jason T2 - BIORESOURCE TECHNOLOGY AB - The effectiveness of sulfuric acid (H(2)SO(4)), sodium hydroxide (NaOH), hydrogen peroxide (H(2)O(2)), and ozone pretreatments for conversion of cotton stalks to ethanol was investigated. Ground cotton stalks at a solid loading of 10% (w/v) were pretreated with H(2)SO(4), NaOH, and H(2)O(2) at concentrations of 0.5%, 1%, and 2% (w/v). Treatment temperatures of 90 degrees C and 121 degrees C at 15 psi were investigated for residence times of 30, 60, and 90 min. Ozone pretreatment was performed at 4 degrees C with constant sparging of stalks in water. Solids from H(2)SO(4), NaOH, and H(2)O(2) pretreatments (at 2%, 60 min, 121 degrees C/15 psi) showed significant lignin degradation and/or high sugar availability and hence were hydrolyzed by Celluclast 1.5L and Novozym 188 at 50 degrees C. Sulfuric acid pretreatment resulted in the highest xylan reduction (95.23% for 2% acid, 90 min, 121 degrees C/15 psi) but the lowest cellulose to glucose conversion during hydrolysis (23.85%). Sodium hydroxide pretreatment resulted in the highest level of delignification (65.63% for 2% NaOH, 90 min, 121 degrees C/15 psi) and cellulose conversion (60.8%). Hydrogen peroxide pretreatment resulted in significantly lower (p