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
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 - Background 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. Objectives 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. Methods 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 ≥75% reduction in symptomatic AF burden or nonresponse if AF burden was unchanged, necessitating a change in drugs or therapy. Results 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). Conclusions 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. 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 ≥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
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 - 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 - 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. Une nouvelle famille de graphes aléatoires utile pour tester la ségrégation spatiale Les auteurs montrent comment on peut détecter des configurations de points dans l'espace à l'aide de graphes. Leur approche s'appuie sur la notion de graphe aléatoire observé, récemment introduite et utilisée en statistique pour la reconnaissance de formes. Les auteurs cherchent plus précisément à détecter la présence de ségrégation ou d'association entre deux ou plusieurs ensembles de points du plan en testant l'hypothèse d'absence complète de structure. Dans ce but, ils font appel à une classe paramétrique particulière de digraphes aléatoires appelés digraphes “à captation proximale” (DCP) qui tiennent compte de la disposition relative des éléments des diverses classes. Le test s'appuie sur la densité relative du DCP qui, une fois proprement normalisée, est une U-statistique. Les auteurs en déterminent la loi limite en invoquant la théorie asymptotique des U-statistiques. Ils en évaluent la performance à taille finie au moyen de simulations de Monte-Carlo et en étudient aussi le comportement limite sous l'angle de l'efficacité asymptotique de Pitman, dont découlent des choix optimaux de paramètres aux fins de test. Ils soulignent de plus que leur méthodologie reste valide en dimensions supérieures.
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 - 456â458
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. 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. Haplotypes of multiple SNPs are considered a more informative format of polymorphisms for genetic association analysis than single SNPs.1The International HapMap Consortium The International HapMap Project.Nature. 2003; 426: 789-796Crossref PubMed Scopus (4688) Google Scholar Haplotypes are more informative because they preserve the joint linkage disequilibrium (LD) structure among multiple adjacent markers.2Akey J Jin L Xiong M Haplotypes vs single marker linkage disequilibrium tests: what do we gain?.Eur J Hum Genet. 2001; 9: 291-300Crossref PubMed Scopus (351) Google Scholar Even when only tag SNPs are used, haplotypes serve as a proxy for unobserved SNPs and increase the predictive power for the genomic variation.3Pe’er I de Bakker PI Maller J Yelensky R Altshuler D Daly MJ Evaluating and improving power in whole-genome association studies using fixed marker sets.Nat Genet. 2006; 38: 663-667Crossref PubMed Scopus (238) Google Scholar, 4Zaitlen N Kang HM Eskin E Halperin E Leveraging the HapMap correlation structure in association studies.Am J Hum Genet. 2007; 80: 683-691Abstract Full Text Full Text PDF PubMed Scopus (53) Google Scholar However, in terms of practical efficacy, the power 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 for modeling the multimarker variations. To avoid the curse of dimensionality encountered in haplotype association analysis, various strategies have been proposed in the literature. They include (1) clustering evolutionarily close haplotypes,5Seltman H Roeder K Devlin B Evolutionary-based association analysis using haplotype data.Genet Epidemiol. 2003; 25: 48-58Crossref PubMed Scopus (93) Google Scholar, 6Durrant C Zondervan KT Cardon LR Hunt S Deloukas P Morris AP Linkage disequilibrium mapping via cladistic analysis of single-nucleotide polymorphism haplotypes.Am J Hum Genet. 2004; 75: 35-43Abstract Full Text Full Text PDF PubMed Scopus (162) Google Scholar, 7Tzeng JY Evolutionary-based grouping of haplotypes in association analysis.Genet Epidemiol. 2005; 28: 220-231Crossref PubMed Scopus (35) Google Scholar, 8Tzeng JY Wang CH Kao JT Hsiao CK Regression-based association analysis with clustered haplotypes through use of genotypes.Am J Hum Genet. 2006; 78: 231-242Abstract Full Text Full Text PDF PubMed Scopus (69) Google Scholar (2) modeling the level of haplotype sharing instead of the haplotypes themselves,9McPeek MS Strahs A Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping.Am J Hum Genet. 1999; 65: 858-875Abstract Full Text Full Text PDF PubMed Scopus (177) Google Scholar, 10der Meulen MAV te Meerman GJ Haplotype sharing analysis in affected individuals from nuclear families with at least one affected offspring.Genet Epidemiol. 1997; 14: 915-920Crossref PubMed Scopus (44) Google Scholar, 11Tzeng JY Devlin B Wasserman L Roeder K On the identification of disease mutations by the analysis of haplotype similarity and goodness of fit.Am J Hum Genet. 2003; 72: 891-902Abstract Full Text Full Text PDF PubMed Scopus (111) Google Scholar and (3) smoothing haplotype effects by introducing a correlation structure for the effects of similar haplotypes.12Thomas DC Morrison JL Clayton DG Bayes estimates of haplotype effects.Genet Epidemiol. 2001; 21: S712-S717PubMed Google Scholar, 13Molitor J Marjoram P Thomas D Application of Bayesian spatial statistical methods to analysis of haplotypes effects and gene mapping.Genet Epidemiol. 2003; 25: 95-105Crossref PubMed Scopus (33) Google Scholar, 14Schaid DJ Evaluating associations of haplotypes with traits.Genet Epidemiol. 2004; 27: 348-364Crossref PubMed Scopus (251) Google Scholar Although these strategies appear to be different, the fundamental principle is to use the evolutionary history of haplotypes to reduce the parameter space from individual haplotypes to haplotypes with similar ancestry. However, although the approaches of haplotype clustering and haplotype sharing enjoy a fair amount of power gain, empirical studies found that the smoothing approach may exhibit only similar or less power than the standard methods that regress trait values on haplotypes and impose no assumptions on haplotypes, even when there are many haplotypes.14Schaid DJ Evaluating associations of haplotypes with traits.Genet Epidemiol. 2004; 27: 348-364Crossref PubMed Scopus (251) Google Scholar In haplotype smoothing, a dependence structure is introduced to the effects of different haplotypes, according to the similarity between haplotypes, under a Bayesian hierarchical model or a mixed-model framework, and the overall gene-trait association can be studied via the variance components (VC).12Thomas DC Morrison JL Clayton DG Bayes estimates of haplotype effects.Genet Epidemiol. 2001; 21: S712-S717PubMed Google Scholar, 13Molitor J Marjoram P Thomas D Application of Bayesian spatial statistical methods to analysis of haplotypes effects and gene mapping.Genet Epidemiol. 2003; 25: 95-105Crossref PubMed Scopus (33) Google Scholar, 14Schaid DJ Evaluating associations of haplotypes with traits.Genet Epidemiol. 2004; 27: 348-364Crossref PubMed Scopus (251) Google Scholar The idea of correlating haplotype effect is based on the assumption that the present mutation-bearing haplotypes have descended from a small number of ancestral haplotypes, and, as a result, the disease haplotypes tend to be correlated because of this shared ancestry. Without losing generality, in this work, we refer to these methods as “VC” approaches and discuss them under a mixed-model framework. We also refer to the standard haplotype regression method as a “fixed-effect” approach. Schaid14Schaid DJ Evaluating associations of haplotypes with traits.Genet Epidemiol. 2004; 27: 348-364Crossref PubMed Scopus (251) Google Scholar first noted the underpowered phenomenon of the VC method, using the likelihood-ratio test (LRT), and explored potential reasons based on the noncentrality (NC) parameter of the distribution of the LRT statistics. The NC parameter reflects the distance between the alternative distribution and the null distribution of the test statistics, and the larger the null-to-alternative distance is, the higher the power a test possesses. By expressing the NC parameter as a function of heritability (h2), it can be seen that, although the NC parameter of a fixed-effect model is proportional to h2/1-h2, the NC parameter of a VC model is much smaller (proportional to h4). As a result, the power gain brought by the low degrees of freedom can be compromised with the small NC parameter in a VC-LRT approach. Here, we report other key factors that contribute to this underpowered phenomenon. In brief, unlike the usual VC model in which the VC represents the potential variability from a source that is independently distributed in the population (e.g., the family effect in the study of linkage or familial aggregation), in the population-based haplotype analysis, the source of variability is not independent. That is, the design matrix of the random haplotype effect does not have a diagonal or block-diagonal structure. Furthermore, the dimension of the random haplotype effect is fixed. Therefore, the data under the alternative hypothesis cannot be represented as a collection of independent data vectors. As a result, the distribution of the LRT statistic does not converge to the conventional 50:50 mixture of χ20 and χ21 (i.e., the limiting distribution predicted by the usual asymptotic theory15Self SG Liang KY Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions.J Am Stat Assoc. 1987; 82: 605-610Crossref Scopus (1780) Google Scholar). Instead, empirical evidence indicates that the distribution of VC-LRT statistics has higher weighting of χ20. Hence, the threshold value obtained from the 50:50 χ2 mixture is overstringent and causes a too-conservative testing result. Such overconservative findings of the LRT was obtained also by Crainiceanu and Ruppert16Crainiceanu CM Ruppert D Likelihood ratio tests in linear mixed models with one variance component.J R Statist Soc B. 2004; 66: 165-185Crossref Scopus (265) Google Scholar in certain linear mixed models. To overcome the problem of a lack of independence and also to generalize the VC approach to all types of trait values, we propose a score test under the generalized linear mixed-model (GLMM) framework. Specifically, we construct a score statistic based on the restricted maximum likelihood (REML) or the marginal likelihood function of the VC and identify its nontypical asymptotic distribution. The proposed test is easy to implement and computationally efficient yet is general enough to accommodate a broad class of phenotypes and correlation structures. It allows for covariate information and can be used for phase-unknown genotypic data. Through simulation, we demonstrate the validity of the test and investigate the power performance of the VC approach and the fixed-effect approach under general scenarios. We also apply the proposed method to a case-control data set from a genomewide association study of amyotrophic lateral sclerosis (ALS) conducted by Schymick et al.17Schymick JC Scholz SW Fung HC Britton A Arepalli S Gibbs JR Lombardo F Matarin M Kasperaviciute D Hernandez DG et al.Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data.Lancet Neurol. 2007; 6: 322-328Abstract Full Text Full Text PDF PubMed Scopus (179) Google Scholar In the analysis, we test for gene-trait association on chromosome 10 with the 275 ALS cases and 271 controls and examine statistical significance at the genomewide level. We verify the findings from the proposed method by comparing them with the results reported by Schymick et al.17Schymick JC Scholz SW Fung HC Britton A Arepalli S Gibbs JR Lombardo F Matarin M Kasperaviciute D Hernandez DG et al.Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data.Lancet Neurol. 2007; 6: 322-328Abstract Full Text Full Text PDF PubMed Scopus (179) Google Scholar We denote the data with the following notations. For individual i (i=1,2,…,n), we have trait value Yi, environmental covariates Xi (a K×1 vector including the intercept term), and haplotype Hi (an L×1 vector, where L is the number of distinct haplotypes observed in the population). Vector Hi records individual i’s haplotype pair via a certain scoring rule, such as by setting its hth element as the number of haplotype h that individual i carries. Throughout this article, we treat explanatory variables (e.g., Xi and Hi) as constants and will omit them in the lists of the conditional variables. This means that, for example, we will use Var (Yi) instead of Var(Yi|Xi,Hi). Assume that the trait value Yi follows some distribution with conditional mean E(Yi|β)=βi and conditional variance Var Yi|β=m−1iϕv βi, where mi is a known prior weight (e.g., binomial denominator), ϕ is the dispersion parameter (e.g., measurement-error variance for a normal quantitative trait), and v βi is the variance function. Then, the VC model can be expressed under the framework of GLMM asg(μi)=XiTγ+HiTββ~MN(0,τRβ) ,(1) where g(·) is a link function that connects the conditional mean βi and the explanatory variables, γK×1 represents the fixed effect of environmental covariates, and βL×1 is the random effect of haplotypes. The haplotype effect is assumed to have a multivariate normal (MN) prior. With model (1), the marginal phenotypic variance, Var (Yi), can be partitioned into genetic components and environment components, and the association between haplotypes and traits can be detected by testing for zero genetic VC (i.e., τ=0). Intuitively, τ=0 implies that all βh share the same value, and this is essentially the null hypothesis of the standard fixed-effect approaches. The correlation structure of βh is specified through the L×L matrix Rβ. Here, we consider a general formulation for Rβ by letting its (h,k) element, denoted by rhk, depend on the similarity level between haplotypes h and k, which is quantified by a certain similarity metric, s(h,k). One simple choice of the correlation structure is to let Rβ=I, where I is the identity matrix. This independence structure imposes no correlation among distinct haplotypes and reflects the “unstructured” variation among haplotypes. The independence prior may be reasonable if haplotype variants were created mainly by recombinations instead of mutations. In contrast, one can introduce local-dependence structures to account for the role of mutation and to reflect the conjecture that evolutionarily close haplotypes tend to have similar effects on traits. One convenient choice of such Rβ is the conditional autoregressive (CAR) structure. The CAR structure assumes that all βh are correlated but that the correlation diminishes as the haplotype similarity decays. With our representation, a CAR structure is to let Rβ=C, where C−1 has diagonal elements equal to 1 and off-diagonal elements equal to -s(h,k).18Carlin B Louis T Bayes and empirical Bayes methods for data analysis. 2nd ed. Chapman & Hall, New York2000: 262Google Scholar Alternatively, to avoid choosing between an independence prior and a sole CAR prior, an intermediate option, in practice, is the convolution model that combines the two: τRβ=τ1I+τ2C.12Thomas DC Morrison JL Clayton DG Bayes estimates of haplotype effects.Genet Epidemiol. 2001; 21: S712-S717PubMed Google Scholar, 13Molitor J Marjoram P Thomas D Application of Bayesian spatial statistical methods to analysis of haplotypes effects and gene mapping.Genet Epidemiol. 2003; 25: 95-105Crossref PubMed Scopus (33) Google Scholar In this work, we focus on the model that was considered by Schaid14Schaid DJ Evaluating associations of haplotypes with traits.Genet Epidemiol. 2004; 27: 348-364Crossref PubMed Scopus (251) Google Scholar and set rhk=s(h,k), with 0≤s(h,k)≤1. This model uses the haplotype similarity to reflect the correlation directly. It is more extreme but uses a simpler concept than the convolution model, by compromising between the dependence and the independence priors. It allows for correlation induced from partially similar haplotypes but assumes independence among haplotypes that share zero similarity. To motivate our VC-score test for haplotype-phenotype association, we illustrate the method, assuming a normally distributed trait (perhaps after some transformation, such as the logarithm transformation) with a known dispersion parameter, ϕ. We then present the VC-score test for general scenarios of unknown ϕ and trait values with an arbitrary distribution. We provide the derivation of the generalization in appendixes A and B. For quantitative traits that follow a normal distribution directly or after appropriate transformations, model (1) reduces to a linear mixed-model in matrix notation:Y=Xγ+Hβ+ε ,(2) where X is the design matrix for γ, whose ith row is XTi; H is the design matrix for β, whose ith row is HTi; β∼MN(0,τRβ) is the same as described in model (1); and ε∼N(0,ϕI) represents the uncertainty in measuring traits Y. Since our primary interest is to test H0:τ=0, we consider the REML log-likelihood function of VC (τ,ϕ). It is well known that the REML estimating equation for (τ,ϕ) is unbiased and will produce less biased estimates compared with the maximum-likelihood approach.19Searle S Casella G McCulloch C Variance components. Wiley, New York1992: 232-257Crossref Google Scholar Denote by ℓREML(τ,ϕ;Y) the REML log-likelihood function of τ and ϕ, which is given byℓREML(τ,φ;Y)=-12log|V|-12log|XTV-1X|-12YTPY ,(3) where V=τHRβHT+ϕI≡τS+ϕI is the marginal variance of Y and where P=V−1-V−1X(XTV−1X)−1XTV−1 is the projection matrix for the linear mixed model (2). The REML log-likelihood function (3) can also be viewed as the marginal log-likelihood of (τ,ϕ) from the Bayesian perspective obtained by specifying a flat prior for γ and integrating out γ from f(Y;γ,τ,ϕ). Simple algebra20Harville D Maximum likelihood approaches to variance component estimation and related problems.J Am Stat Assoc. 1977; 72: 322-340Google Scholar shows that the score statistic of τ evaluated under H0 on the basis of the REML function (3) is equal toUτ=∂lREML(τ,ϕ)∂τ|τ=0=12{YTP0SP0Y-tr(P0S)},(4) where P0=ϕ−1{I-X(XTX)−1XT}=ϕ−1Q is the projection matrix P evaluated under H0:τ=0 and where Q=I-X(XTX)−1XT. It is immediately seen from equation (4) that E(Uτ)=0 under H0:τ=0, and, when τ>0, E(Uτ)=τ·tr(QSQS)/(2ϕ2), which is a strictly increasing function of τ unless QS=0. Therefore, larger values of Uτ provide stronger evidence against H0. This suggests that the testing procedure for H0:τ=0 using Uτ should be one sided. In a situation where the VC τ represents the potential variability due to a source that is independently distributed in the population such as the subject-specific effects in a longitudinal study, the score statistic Uτ given in equation (4) under H0:τ=0 has an asymptotic normal distribution with zero mean and some variance when the number of independent clusters goes to infinity.21Lin X Variance component testing in generalized linear models with random effects.Biometrika. 1997; 84: 309-326Crossref Scopus (206) Google Scholar However, this condition does not satisfy in our case. In model (1), the design matrix H for the random effects β is not block diagonal and the dimension of β is fixed. Hence, the Lin’s21Lin X Variance component testing in generalized linear models with random effects.Biometrika. 1997; 84: 309-326Crossref Scopus (206) Google Scholar asymptotic result does not directly apply to Uτ. Since ϕ is known, the second term in Uτ is a constant. Therefore using the score statistic Uτ is equivalent to using the first term of Uτ (denoted by Tτ):Tτ=12YTP0SP0Y=12φ2YTQSQY .(5) We show in appendix A that Tτ has the same distribution as the weighted χ2 random variables Σci=1 λiχ21,i, where χ21,i’s are independent χ2 random variables with 1 df, and λi is the ordered non-zero eigenvalues of the semipositive definite matrix QSQ/(2ϕ) with λ1⩾λ2⩾·⩾λc>0 (c≤L). If the (1-α)th quantile of this weighted χ2 distribution is denoted by T(α), then a level α score test will reject H0 if Tτ⩾T(α). Here, we present the VC-score test for the general case in which the traits may not be normally distributed and the dispersion parameter ϕ may or may not be known. As indicated by the derivation given in appendix B, our test statistic can be defined asTτ=12(Y-μ)TΔWSWΔ(Y-μ)|τ=0,ϕ=ϕˆ,γ=γˆ,(6) where μ=g−1(Xγ), Δ=diag{g′(βi)},γ^ is the maximum-likelihood estimate of γ under H0, andϕ^ is the REML type of estimate (such as the one that uses Pearson residuals) of ϕ under H0. Matrix W=diag{wi}, with wi={ϕm−1iv(βi)[g′(βi)]2}−1. These quantities are readily available by fitting a standard generalized linear model, g(β)=Xγ. We derive in appendix B that Tτ also follows approximately the weighted χ2 distribution Σci=1λiχ21,i, where λ1⩾λ2⩾·⩾λc>0 (c≤L) is the nonzero eigenvalues of matrix W−1/2P0SP0W−1/2/2. We note that the conclusions given in the previous section are a special case of the results given here. For normally distributed traits, Δ=I, and W=V−1, which equals ϕ−1I under H0. Hence, equation (6) reduces to equation (5), and the matrix W−1/2P0SP0W−1/2/2 reduces to QSQ/(2ϕ). Given the fact that Tτ follows a weighted χ2 distribution, one can obtain the significance threshold Tα at level α from simulation. However, such a task may not be trivial when α is small. As an alternative, we introduce a Gamma approximation of the distribution of Tτ. Empirical evidence indicates that the eigenvalues λ1,λ2,·,λc of the matrix W−1/2P0SP0W−1/2/2 are dominated by the first few ones and decay rapidly to 0 (fig. 1). Following the work of Zhang and Lin,22Zhang D Lin X Hypothesis testing in semiparametric additive mixed models.Biostatistics. 2003; 4: 57-74Crossref PubMed Scopus (94) Google Scholar we use the Satterthwaite method to approximate the null distribution of Tτ by a Gamma distribution with parameters (a,b). Let E and V denote the mean and variance of Tτ, respectively. We match the mean and the variance of the Gamma distribution and those of the test statistic by setting ab=E and ab2=V, and we get a=E2/V and b=V/E. We can then obtain T(α) or calculate the P value of the test statistic from the distribution of Gamma (a,b). The mean, E, and variance, V, of Tτ can be calculated (appendixes A and B) byE∧=12tr(P0S)andV∧=I∧ττ-I∧τφ2/I∧φφ ,whereVˆ=Iˆττ-Iˆτϕ2/Iˆϕϕ,andI∧φφ=12φ∧2tr(P0W-1)=n-K2φ∧2 . Although we have described our test, assuming that the haplotype information H is observed, the phase information can be not crucial. From equations (5) and (6), we see that the haplotype information appears in Tτ only through S=HRβHT, whose (i,j) element, denoted by Sij, can be rewritten asSij=HiTRβHj=∑h,kHi,hHj,k×s(h,k) .The right-hand side of the equation states that Sij is simply the similarity score between the haplotype pair of person i and that of person j measured by metric s(h,k). As a result, by choosing those metrics that do not require phase information, we can calculate S without resorting to the phased data. One choice is to set s(h,k) as the proportion of matching alleles between two haplotypes, h and k. As demonstrated by Tzeng et al.11Tzeng JY Devlin B Wasserman L Roeder K On the identification of disease mutations by the analysis of haplotype similarity and goodness of fit.Am J Hum Genet. 2003; 72: 891-902Abstract Full Text Full Text PDF PubMed Scopus (111) Google Scholar and Schaid,14Schaid DJ Evaluating associations of haplotypes with traits.Genet Epidemiol. 2004; 27: 348-364Crossref PubMed Scopus (251) Google Scholar such Sij is equivalent to the proportion of matching alleles between the genotypes of individual i and individual j and hence can be calculated directly from genotypes with unknown phase. We conduct simulation studies to examine the performance of the proposed score test. In the simulation, we generated covariates Xi, haplotypes Hi, and trait values Yi, given Xi and Hi, for each individual. The covariate Xi is drawn from a standard normal distribution, and the haplotype Hi is generated using a technique similar to those reported by Roeder et al.23Roeder K Bacanu SA Sonpar V Zhang X Devlin B Analysis of single-locus tests to detect gene-disease associations.Genet Epidemiol. 2005; 28: 207-219Crossref PubMed Scopus (81) Google Scholar and Tzeng et al.8Tzeng JY Wang CH Kao JT Hsiao CK Regression-based association analysis with clustered haplotypes through use of genotypes.Am J Hum Genet. 2006; 78: 231-242Abstract Full Text Full Text PDF PubMed Scopus (69) Google Scholar Specifically, we simulated 100 haplotypes under the coalescent model,24Wall JD Pritchard JK Assessing the performance of the haplotype block model of linkage disequilibrium.Am J Hum Genet. 2003; 73: 502-515Abstract Full Text Full Text PDF PubMed Scopus (122) Google Scholar with an effective population size of 104, a scaled mutation rate of 5.6×10−4 per bp, and a scaled recombination rate of ∼6×10−3 per bp for the cold spots and a rate 45 times greater for the hotspots. These parameters are chosen to roughly match the genes observed in the SeattleSNP database. We discarded SNPs with minor-allele frequencies <0.05. The hypothetical disease locus is selected on the basis of a predetermined minor-allele frequency, q, and the diversity of haplotypes flanking the SNP. In the simulation, we considered q=0.1, 0.3, and 0.5 and haplotype-diversity levels of high (11–16 distinct haplotypes), moderate (9–11 distinct haplotypes), and low (6–9 distinct haplotypes). We set a haplotype region to be a segment of five adjacent SNPs, including the two SNPs on the left and the three SNPs on the right of the disease locus. Given that the disease SNP is excluded, we also considered whether the disease SNP is “tagged” or “not tagged” by the surrounding five SNPs under each scenario. We defined that the disease SNP is “tagged” if there is at least one SNP whose R2 with the disease SNP is >0.7, and it is “not tagged” otherwise. We then randomly sampled with replacement of 2 haplotypes from the 100 haplotypes to form an individual. The simulated haplotype data were then converted into unphased genotype data. We next generated the trait values Yi on the basis of Xi and the genotypes at the disease locus. We determined the trait value of individual i according to Xi and the number of disease alleles (Gi), using an additive-effect model. In the simulation study, we considered both quantitative traits and binary traits and adopted the same trait-generating scheme as did Lake et al.25Lake SL Lyon H Tantisira K Silverman EK Weiss ST Laird NM Schaid DJ Estimation and tests of haplotype-environment interaction when linkage phase is ambiguous.Hum Hered. 2003; 55: 56-65Crossref PubMed Scopus (385) Google Scholar and Tzeng et al.8Tzeng JY Wang CH Kao JT Hsiao CK Regression-based association analysis with clustered haplotypes through use of genotypes.Am J Hum Genet. 2006; 78: 231-242Abstract Full Text Full Text PDF PubMed Scopus (69) Google Scholar For quantitative traits, we used a random-sampling scheme and generated 200 trait values from the normal conditional distribution of Yi with mean γ0+γ1×Xi+(Gi-1) and variance 2q(1-q)×(1-h2)/h2. We set the heritability (h2) at 0.1 and γ0=γ1=1. For binary traits, we used a case-control sampling scheme and generated trait values of 0 or 1, using the penetrance function logitP(Y=1|Gi,Xi)=γ0+γ1×Xi+θ×Gi. We set the odds ratio (OR) (eθ) at 2.0 and set the disease prevalence at 0.01 by letting γ0=-4.5 and γ1=0. We repeated the process until we collected 100 cases and 100 controls. We analyzed these simulated data to evaluate the power performance of the VC-score method. To compare, we also conducted haplotype analyses, using the fixed-effect method and, in addition, the VC method via regular LRT (VC-LRT) under some scenarios. These analyses were performed assuming unknown phases. For fixed-effect analysis, we use
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 - 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.
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. © 2007 Wiley-Liss, Inc.
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 - ABSTRACT 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 intermedia...
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 - 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 m2 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 m2 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 m2. 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.
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 naive 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