TY - JOUR
TI - Immunogenetics of CD4 Lymphocyte Count Recovery during Antiretroviral Therapy: An AIDS Clinical Trials Group Study
AU - Haas, David W.
AU - Geraghty, Daniel E.
AU - Andersen, Janet
AU - Mar, Jessica
AU - Motsinger, Alison A.
AU - D’Aquila, Richard T.
AU - Unutmaz, Derya
AU - Benson, Constance A.
AU - Ritchie, Marylyn D.
AU - Landay, Alan
T2 - The Journal of Infectious Diseases
AB - During antiretroviral therapy, CD4 lymphocyte count increases are modest in some patients despite virologic control. We explored whether polymorphisms in genes important for T cell expansion, survival, and apoptosis are associated with the magnitude of CD4 lymphocyte count recovery during antiretroviral therapy. We studied treatment-naive individuals who achieved sustained control of plasma viremia (<400 HIV-1 RNA copies/mL) for at least 48 weeks after initiation of antiretroviral therapy and compared genotypes among individuals who had an increase of either <200 or ⩾200 CD4 cells/mm3 from baseline. A total of 137 single-nucleotide polymorphisms across 17 genes were characterized in 873 study participants. In multivariate analyses that controlled for clinical variables, polymorphisms in genes encoding tumor necrosis factor (TNF)–related apoptosis-inducing ligand (TRAIL), TNF-α, Bcl-2–interacting molecule (Bim), interleukin (IL)–15, and IL-15 receptor α chain (IL-15Rα) were associated with the magnitude of the increase in CD4 lymphocyte count, as were haplotypes in genes encoding interferon-α, IL-2, and IL-15Rα (P<.05, for each). Multifactor dimensionality reduction identified a gene-gene interaction between IL-2/IL-15 receptor common β chain and IL-2/IL-7/IL-15 receptor common γ chain. Immune recovery during antiretroviral therapy is a complex phenotype that is influenced by multiple genetic variants. Future studies should validate these tentative associations and define underlying mechanisms
DA - 2006/10/15/
PY - 2006/10/15/
DO - 10.1086/507313
VL - 194
IS - 8
SP - 1098-1107
J2 - J INFECT DIS
LA - en
OP -
SN - 0022-1899 1537-6613
UR - http://dx.doi.org/10.1086/507313
DB - Crossref
ER -
TY - JOUR
TI - Drug Transporter and Metabolizing Enzyme Gene Variants and Nonnucleoside Reverse-Transcriptase Inhibitor Hepatotoxicity
AU - Ritchie, M. D.
AU - Haas, D. W.
AU - Motsinger, A. A.
AU - Donahue, J. P.
AU - Erdem, H.
AU - Raffanti, S.
AU - Rebeiro, P.
AU - George, A. L.
AU - Kim, R. B.
AU - Haines, J. L.
AU - Sterling, T. R.
T2 - Clinical Infectious Diseases
AB - This nested case-control study examined relationships between MDR1, CYP2B6, and CYP3A4 variants and hepatotoxicity during antiretroviral therapy with either efavirenz- or nevirapine-containing regimens. Decreased risk of hepatotoxicity was associated with MDR1 3435C→;T (odds ratio, 0.254; P = .021). An interaction between MDR1 and hepatitis B surface antigen status predicted risk with 82% accuracy (P < .001).
DA - 2006/9/15/
PY - 2006/9/15/
DO - 10.1086/507101
VL - 43
IS - 6
SP - 779-782
J2 - Clinical Infectious Diseases
LA - en
OP -
SN - 1058-4838 1537-6591
UR - http://dx.doi.org/10.1086/507101
DB - Crossref
ER -
TY - JOUR
TI - Multifactor dimensionality reduction reveals gene–gene interactions associated with multiple sclerosis susceptibility in African Americans
AU - Brassat, D
AU - Motsinger, A A
AU - Caillier, S J
AU - Erlich, H A
AU - Walker, K
AU - Steiner, L L
AU - Cree, B A C
AU - Barcellos, L F
AU - Pericak-Vance, M A
AU - Schmidt, S
AU - Gregory, S
AU - Hauser, S L
AU - Haines, J L
AU - Oksenberg, J R
AU - Ritchie, M D
T2 - Genes & Immunity
AB - Multiple sclerosis (MS) is a common disease of the central nervous system characterized by inflammation, myelin loss, gliosis, varying degrees of axonal pathology, and progressive neurological dysfunction. Multiple sclerosis exhibits many of the characteristics that distinguish complex genetic disorders including polygenic inheritance and environmental exposure risks. Here, we used a highly efficient multilocus genotyping assay representing variation in 34 genes associated with inflammatory pathways to explore gene–gene interactions and disease susceptibility in a well-characterized African-American case–control MS data set. We applied the multifactor dimensionality reduction (MDR) test to detect epistasis, and identified single-IL4R(Q576R)- and three-IL4R(Q576R), IL5RA(-80), CD14(-260)- locus association models that predict MS risk with 75–76% accuracy (P<0.01). These results demonstrate the importance of exploring both main effects and gene–gene interactions in the study of complex diseases.
DA - 2006/4/20/
PY - 2006/4/20/
DO - 10.1038/sj.gene.6364299
VL - 7
IS - 4
SP - 310-315
J2 - Genes Immun
LA - en
OP -
SN - 1466-4879 1476-5470
UR - http://dx.doi.org/10.1038/sj.gene.6364299
DB - Crossref
ER -
TY - CHAP
TI - Comparison of Neural Network Optimization Approaches for Studies of Human Genetics
AU - Motsinger, Alison A.
AU - Dudek, Scott M.
AU - Hahn, Lance W.
AU - Ritchie, Marylyn D.
T2 - Applications of Evolutionary Computing. EvoWorkshops 2006
A2 - Rothlauf, F.
T3 - Lecture Notes in Computer Science
AB - A major goal of human genetics is the identification of susceptibility genes associated with common, complex diseases. The preponderance of gene-gene and gene-environment interactions comprising the genetic architecture of common diseases presents a difficult challenge. To address this, novel computational approaches have been applied to studies of human disease. These novel approaches seek to capture the complexity inherent in common diseases. Previously, we developed a genetic programming neural network (GPNN) to optimize network architecture for the detection of disease susceptibility genes in association studies. While GPNN was a successful endeavor, we wanted to address the limitations in its flexibility and ease of development. To this end, we developed a grammatical evolution neural network (GENN) approach that accounts for the drawbacks of GPNN. In this study we show that this new method has high power to detect gene-gene interactions in simulated data. We also compare the performance of GENN to GPNN, a traditional back-propagation neural network (BPNN) and a random search algorithm. GENN outperforms both BPNN and the random search, and performs at least as well as GPNN. This study demonstrates the utility of using GE to evolve NN in studies of complex human disease.
PY - 2006///
DO - 10.1007/11732242_10
SP - 103–114
PB - Springer
SN - 9783540332374 9783540332381
SV - 3907
UR - http://dx.doi.org/10.1007/11732242_10
ER -
TY - JOUR
TI - The effect of reduction in cross-validation intervals on the performance of multifactor dimensionality reduction
AU - Motsinger, Alison A.
AU - Ritchie, Marylyn D.
T2 - Genetic Epidemiology
AB - Multifactor Dimensionality Reduction (MDR) was developed to detect genetic polymorphisms that present an increased risk of disease. Cross-validation (CV) is an important part of the MDR algorithm, as it prevents over-fitting and allows the predictive ability of a model to be evaluated. CV is a computationally intensive step in the MDR algorithm. Traditionally, MDR has been implemented using 10-fold CV. In order to reduce computation time and therefore allow MDR analysis to be applied to larger datasets, we evaluated the possibility of eliminating or reducing the number of CV intervals used for analysis. We found that eliminating CV made final model selection impossible, but that reducing the number of CV intervals from ten to five caused no loss of power, thereby reducing the computation time of the algorithm by half. The validity of this reduction was confirmed with data from an Alzheimer's disease (AD) study. Genet. Epidemiol. 2006. © 2006 Wiley-Liss, Inc.
DA - 2006///
PY - 2006///
DO - 10.1002/gepi.20166
VL - 30
IS - 6
SP - 546-555
J2 - Genet. Epidemiol.
LA - en
OP -
SN - 0741-0395 1098-2272
UR - http://dx.doi.org/10.1002/gepi.20166
DB - Crossref
KW - model validation
KW - MDR
KW - epistasis
KW - gene-gene interactions
ER -
TY - JOUR
TI - A recursive algorithm for computing the distribution of the number of successes in higher-order Markovian trials
AU - Martin, Donald E.K.
T2 - Computational Statistics & Data Analysis
AB - This paper presents a recursive method of computing the distribution of the number of successes in a sequence of binary trials that are Markovian of a general order. Waiting-time distributions are also obtained. Recurrence relations among probabilities of partitioned events are used to compute the desired probabilities. An advantage of computing the probabilities in the manner given is that the algorithm may be easily programmed on a computer, requiring no computer algebra system, as in computation based on conditional probability generating functions. The difference between calculated probabilities for various model orders emphasizes the importance of selecting a proper model order for a Markovian data set.
DA - 2006/2//
PY - 2006/2//
DO - 10.1016/j.csda.2004.09.005
VL - 50
IS - 3
SP - 604-610
J2 - Computational Statistics & Data Analysis
LA - en
OP -
SN - 0167-9473
UR - http://dx.doi.org/10.1016/j.csda.2004.09.005
DB - Crossref
KW - binary trials
KW - Markovian sequences
KW - probability
ER -
TY - JOUR
TI - Hot-hand effects in sports and a recursive method of computing probabilities for streaks
AU - Martin, Donald E.K.
T2 - Computers & Operations Research
AB - We give a recursive method of computing probabilities associated with the waiting time to the first occurrence of a run of arbitrary length in Markovian trials of a general order. Using data from the Oakland Athletics’ 2002 season as an example, we show that the assumed model order can make a large difference in computed probabilities. The algorithm is then applied to the computation of probabilities associated with strikes and nonstrikes in bowling. After showing that there is significant deviation from a model of Bernoulli trials for data from the 2003–2004 Professional Bowlers Association tour, we suggest a criterion based on the longest success run for choosing the order of Markovian dependence that gives the best fit to the streakiness characteristics of an individual bowler's data.
DA - 2006/7//
PY - 2006/7//
DO - 10.1016/j.cor.2004.09.023
VL - 33
IS - 7
SP - 1983-2001
J2 - Computers & Operations Research
LA - en
OP -
SN - 0305-0548
UR - http://dx.doi.org/10.1016/j.cor.2004.09.023
DB - Crossref
KW - binary trials
KW - higher-order Markovian sequences
KW - dependence
KW - run probabilities
KW - waiting-time distributions
KW - hot hand
KW - streaks
KW - longest run
ER -
TY - SOUND
TI - Spatial Statistics: a short course
AU - Ghosh, S.
DA - 2006/6/1/
PY - 2006/6/1/
ER -
TY - JOUR
TI - Semiparametric Accelerated Failure Time Models for Censored Data
AU - Ghosh, S.K.
AU - Ghosal, S.
T2 - Bayesian Statistics and Its Applications
DA - 2006///
PY - 2006///
VL - 15
SP - 213–229
ER -
TY - CONF
TI - Bayesian Analysis and Model Selection in Closed-Population, Capture-Recapture Models
AU - Gosky, R.
AU - Ghosh, S.K.
T2 - Joint Statistical Meetings
C2 - 2006///
DA - 2006///
PY - 2006///
ER -
TY - CONF
TI - Bayesian Inference for NLME Models Involving ODEs
AU - Ghosh, S.K.
AU - Goyal, L.
T2 - Joint Statistical Meetings
C2 - 2006///
DA - 2006///
PY - 2006///
ER -
TY - CONF
TI - Bayesian Modeling of Longitudinal Data with Nonignorable Missing Data
AU - Zhu, L.
AU - Ghosh, S.K.
AU - Ghosal, S.
T2 - Joint Statistical Meetings
C2 - 2006///
DA - 2006///
PY - 2006///
ER -
TY - CONF
TI - A hierarchical Bayesian Analysis of Longitudinal Frequency Data Using Piecewise Linear Regression
AU - Kern, J.
AU - Bernini, N.
AU - Ghosh, S.K.
T2 - Joint Statistical Meetings
C2 - 2006///
DA - 2006///
PY - 2006///
ER -
TY - CONF
TI - Statistical Inference for Nonlinear Models Involving Ordinary Differential Equations
AU - Goyal, L.
AU - Ghosh, S.K.
T2 - Joint Statistical Meetings
C2 - 2006///
DA - 2006///
PY - 2006///
ER -
TY - SOUND
TI - Bayesian Methods in Environmental Science: A Brief Introduction
AU - Ghosh, S.
DA - 2006/2/15/
PY - 2006/2/15/
ER -
TY - CONF
TI - Application of Nonlinear Mixed Effects Models in Biomedical Sciences
AU - Ghosh, S.
T2 - Statistics Conference
C2 - 2006/5/25/
CY - Pattaya, Thailand
DA - 2006/5/25/
PY - 2006/5/25/
ER -
TY - CONF
TI - Bayesian Inference for NLME Models Involving ODEs
AU - Ghosh, S.
T2 - Joint Statistical Meetings
C2 - 2006/8/8/
CY - Seattle, WA, USA
DA - 2006/8/8/
PY - 2006/8/8/
ER -
TY - SOUND
TI - Bayesian Variable Selection Methods
AU - Ghosh, S.
DA - 2006/10/3/
PY - 2006/10/3/
ER -
TY - SOUND
TI - A Joint Modeling Approach for Analyzing Nonignorable Missing Data
AU - Ghosh, S.
DA - 2006/11/9/
PY - 2006/11/9/
ER -
TY - JOUR
TI - Physiologically-based pharmacokinetic modeling of genistein in rats, part I: Model development
AU - Schlosser, P.M.
AU - Borghoff, S.J.
AU - Coldham, N.G.
AU - David, J.A.
AU - Ghosh, S.K.
T2 - Risk Analysis
AB - Genistein is a phytoestrogen—a plant-derived compound that binds to and activates the estrogen receptor—occurring at high levels in soy beans and food products, leading to widespread human exposure. The numerous scientific publications available describing genistein's dosimetry, mechanisms of action, and identified or putative health effects in both experimental animals and humans make it ideal for examination as an example of endocrine-active compound (EAC). We developed a physiologically-based pharmacokinetic (PBPK) model to quantify the internal, target-tissue dosimetry of genistein in adult rats. Complexities of the model include enterohepatic circulation, binding of both genistein and its conjugates to plasma proteins, and the multiple compartments used to describe transport through the bile duct and gastrointestinal tract. Other aspects of the model are simple perfusion-limited transport to the tissue groups and first-order rates of metabolism, uptake, and excretion. We describe here the model structure and initial calibration of the model by fitting to a large data set for Wistar rats. The model structure can be readily extrapolated to describe genistein dosimetry in humans or modified to describe the dosimetry of other phytoestrogens and phenolic EACs. The model does a fair job of capturing the pharmacokinetics. Although it does not describe the interindividual variability and we have not identified a single set of parameters that provide a good fit to the data for both oral and intravenous exposures, we believe it provides a good initial attempt at PBPK modeling for genistein, which can serve as a template for other phytoestrogens and in the design of future experiments and research that can be used to fill data gaps and better estimate model parameters.
DA - 2006///
PY - 2006///
DO - 10.1111/j.1539-6924.2006.00743.x
VL - 26
IS - 2
SP - 483-500
UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-33645288581&partnerID=MN8TOARS
KW - endocrine-active
KW - genistein
KW - PBPK
KW - phytoestrogen
KW - rat
ER -
TY - JOUR
TI - Demonstration of vascular abnormalities compressing esophagus by MDCT: Special focus on dysphagia lusoria
AU - Alper, Fatih
AU - Akgun, Metin
AU - Kantarci, Mecit
AU - Eroglu, Atilla
AU - Ceyhan, Elvan
AU - Onbas, Omer
AU - Duran, Cihan
AU - Okur, Adnan
T2 - European Journal of Radiology
AB - Dysphagia lusoria (DL) is described in the literature as difficulty in swallowing caused by vascular abnormalities. The most common cause is an aberrant right subclavian artery (SCA) which passes behind the esophagus and is also called arteria lusoria (AL). Our aim was to demonstrate the use of multidetector computed tomography (MDCT) in the diagnosis of AL, as there is no comprehensive study investigating the role of MDCT in such cases.A total of 38 consecutive patients, comprising of 23 females (61%) and 15 males (39%), who had extrinsic compression were included in the study. These patients are selected from the cases who were admitted due to their gastrointestinal symptoms, such as dysphagia, epigastric pain, chronic nausea, vomiting, etc. The mean age of patients was 40 +/- 25 years (range 15-65). Following barium esophagogram and then endoscopy performed, MDCT angiography was carried out on the same or the following few days. MDCT sections were examined to determine the following: presence of vascular abnormality; the diameter and angle of that vascular structure; and the compressed area of esophagus. Radiological findings and dysphagia scores were also compared.In each of 15 cases, there was a compression due to vascular abnormality which were all located between the esophagus and the spine. There was an esophageal compression in each of 12 cases, due to right aberrant SCA, in one case due to right superior aortic arch and in two cases due to both right aortic arch and left SCA with Kommerell's diverticulum. The mean diameter and the angle of AL were 16.4 mm and 48.8 degrees , respectively, and the mean area of pressured esophagus was 194.7 mm2. Dysphagia scores of the cases was 1 in thirteen cases and 2 in two cases. However, dysphagia scores were not correlated with these parameters.MDCT angiography is a useful diagnostic tool for evaluation of patients with dysphagia, especially caused by a vascular abnormality.
DA - 2006/7//
PY - 2006/7//
DO - 10.1016/j.ejrad.2006.01.013
VL - 59
IS - 1
SP - 82-87
J2 - European Journal of Radiology
LA - en
OP -
SN - 0720-048X
UR - http://dx.doi.org/10.1016/j.ejrad.2006.01.013
DB - Crossref
KW - dysphagia lusoria
KW - esophagus
KW - MDCT
ER -
TY - JOUR
TI - Relative density of the random r-factor proximity catch digraph for testing spatial patterns of segregation and association
AU - Ceyhan, Elvan
AU - Priebe, Carey E.
AU - Wierman, John C.
T2 - Computational Statistics & Data Analysis
AB - Statistical pattern classification methods based on data-random graphs were introduced recently. In this approach, a random directed graph is constructed from the data using the relative positions of the data points from various classes. Different random graphs result from different definitions of the proximity region associated with each data point and different graph statistics can be employed for data reduction. The approach used in this article is based on a parameterized family of proximity maps determining an associated family of data-random digraphs. The relative arc density of the digraph is used as the summary statistic, providing an alternative to the domination number employed previously. An important advantage of the relative arc density is that, properly re-scaled, it is a U-statistic, facilitating analytic study of its asymptotic distribution using standard U-statistic central limit theory. The approach is illustrated with an application to the testing of spatial patterns of segregation and association. Knowledge of the asymptotic distribution allows evaluation of the Pitman and Hodges–Lehmann asymptotic efficacies, and selection of the proximity map parameter to optimize efficiency. Furthermore the approach presented here also has the advantage of validity for data in any dimension.
DA - 2006/4//
PY - 2006/4//
DO - 10.1016/j.csda.2005.03.002
VL - 50
IS - 8
SP - 1925-1964
J2 - Computational Statistics & Data Analysis
LA - en
OP -
SN - 0167-9473
UR - http://dx.doi.org/10.1016/j.csda.2005.03.002
DB - Crossref
KW - random proximity graphs
KW - delaunay triangulation
KW - relative density
KW - segregation
KW - association
ER -
TY - CONF
TI - Performance of BMPs
AU - Clark, Shirley E.
AU - Lenhart, James H.
AU - de Ridder, Scott A.
AU - Barrett, Michael E.
AU - Malina, Joseph F., Jr.
AU - Hunt, W. F.
AU - Jarrett, A. R.
T2 - Water Resources and Environment History Sessions at Environmental and Water Reources Institute Annual Meeting 2004
AB - Stormwater managers are increasingly faced with the need to address many potentially-conflicting issues as part of their activities. First, they need to control the potential flooding waters generated after urbanization. This has led to the use of detention facilities and control of peak flow rates to pre-development levels. However, these designs that focused on flow control for larger storms have been providing inconsistent performance for the control of other pollutants. Many other techniques, in addition to detention/sedimentation, have been proposed to alleviate these pollutant concerns. Stormwater ordinances/regulations and the development of TMDLs (with its subsequent need to control loadings to a stream) has driven the improvement of existing treatment technologies (often referred to as structural best management practices [BMPs]) and the development of new ones. Assumptions have made regarding the range of performance of these devices, based on the field data that currently exists, and as new data is submitted for publication, these new insights are added into the body of knowledge on BMP design and performance, specifically on the design needed to provide a specific performance.
C2 - 2006/5/17/
C3 - BMP Technology in Urban Watersheds
DA - 2006/5/17/
DO - 10.1061/9780784408728.008
PB - American Society of Civil Engineers
SN - 9780784408728 9780784471661
UR - http://dx.doi.org/10.1061/9780784408728.008
DB - Crossref
ER -
TY -
ER -
TY - JOUR
TI - Reliability
AU - Keller-McNulty, S.
AU - Wilson, A.
AU - Anderson-Cook, C.
T2 - Statistical Science
DA - 2006///
PY - 2006///
DO - 10.1214/088342306000000664
VL - 21
IS - 4
UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-34249333066&partnerID=MN8TOARS
ER -
TY - BOOK
TI - Statistical methods in counterterrorism: Game theory, modeling, syndromic surveillance, and biometric authentication
AU - Wilson, A.G.
AU - Wilson, G.D.
AU - Olwell, D.H.
DA - 2006///
PY - 2006///
DO - 10.1007/0-387-35209-0
SE - 1-292
UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84889962244&partnerID=MN8TOARS
ER -
TY - JOUR
TI - Advances in data combination, analysis and collection for system reliability assessment
AU - Wilson, A.G.
AU - Graves, T.L.
AU - Hamada, M.S.
AU - Reese, C.S.
T2 - Statistical Science
AB - The systems that statisticians are asked to assess, such as nuclear weapons, infrastructure networks, supercomputer codes and munitions, have become increasingly complex. It is often costly to conduct full system tests. As such, we present a review of methodology that has been proposed for addressing system reliability with limited full system testing. The first approaches presented in this paper are concerned with the combination of multiple sources of information to assess the reliability of a single component. The second general set of methodology addresses the combination of multiple levels of data to determine system reliability. We then present developments for complex systems beyond traditional series/parallel representations through the use of Bayesian networks and flowgraph models. We also include methodological contributions to resource allocation considerations for system relability assessment. We illustrate each method with applications primarily encountered at Los Alamos National Laboratory.
DA - 2006///
PY - 2006///
DO - 10.1214/088342306000000439
VL - 21
IS - 4
SP - 514-531
UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-34249308477&partnerID=MN8TOARS
KW - Bayesian
KW - Bayesian network
KW - biased data
KW - complex system
KW - count data
KW - degradation data
KW - fault tree
KW - flowgraph
KW - genetic algorithm
KW - lifetime data
KW - logistic regression
KW - Markov chain Monte Carlo
KW - Metropolis algorithm
KW - multilevel data
KW - nonhomogeneous Poisson process
KW - prior elicitation
KW - reliability block diagram
KW - repairable system
KW - resource allocation
ER -
TY - JOUR
TI - Proton auroral intensifications and injections at synchronous altitude
AU - Chi, E.C.
AU - Mende, S.B.
AU - Fok, M.-C.
AU - Reeves, G.D.
T2 - Geophysical Research Letters
AB - [1] In sudden flux increases at synchronous altitude the lower energy channels often show progressively more delay or dispersion. It is usually assumed that the dispersion is caused by a simultaneous injection of particles of all energies at some location, and by the subsequent drift of these particles to the synchronous altitude measurement site “downstream” of the injection event. In this paper we present a method for timing and locating the injections from proton auroral precipitation inferred by the Lyman α emission data from the IMAGE FUV instrument. We compare the timing of the proton flux increases observed by the Los Alamos National Laboratory synchronous altitude satellites to the time delay predicted by a model describing the longitudinal drift of particles in the magnetosphere. We present comparisons for eleven substorm particle injections and find that the observed azimuthal drift times are reasonably consistent with those calculated by a simple model using the Tsyganenko 89 magnetic and Volland electric field models as input. This consistency supports the concept that the proton auroral intensification at substorm onset and the proton injection in the magnetosphere occur at the same magnetic local time (longitude).
DA - 2006///
PY - 2006///
DO - 10.1029/2005GL024656
VL - 33
IS - 6
UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-33646463820&partnerID=MN8TOARS
ER -
TY - JOUR
TI - Sycamore and sweetgum plantation productivity on former agricultural land in South Carolina
AU - Davis, A.A.
AU - Trettin, C.C.
T2 - Biomass and Bioenergy
AB - Former agricultural lands in the southern US comprise a significant land base to support short rotation woody crop (SRWC) plantations. This study presents the seven-year response of productivity and biomass allocation in operational-scale, first rotation sycamore (Plantanus occidentalis L.) and sweetgum (Liquidambar styraciflua L.) plantations that were established on drained Ultisols which were historically planted in cotton and soybeans. Three plantation systems, sycamore open drainage, sycamore plus water management, and sweetgum open drainage were established on replicate 3.5–5.5 ha catchments. Height, diameter, and mortality were measured annually. Allometric equations, based on three, five, and seven year-old trees, were used to estimate aboveground biomass. Below-ground biomass was measured in year-five. Water management did not affect sycamore productivity, probably a result of a 5 year drought. The sycamore plantations were more productive after seven growing seasons than the sweetgum. Sycamore were twice the height (11.6 vs. 5.5 m); fifty percent larger in diameter (10.9 vs. 7.0 cm); and accrued more than twice the biomass (38–42 vs. 17Mgha-1) of the sweetgum. Sweetgum plantation productivity was constrained by localized areas of high mortality (up to 88%) and vegetative competition. Mean annual height increment has not culminated for either species. Diameter growth slowed in the sycamore during growing seasons five through seven, but was still increasing in the sweetgum. Both species had similar partitioning of above-ground (60% of total) and below-ground biomass (40% of total).
DA - 2006///
PY - 2006///
DO - 10.1016/j.biombioe.2005.08.001
VL - 30
IS - 8-9
SP - 769–777
KW - Platanus occidentalis
KW - Liquidambar styraciflua
KW - short rotation woody crop
KW - productivity
KW - hardwood plantation
ER -
TY - JOUR
TI - The two-sample t test with one variance unknown
AU - Maity, A.
AU - Sherman, M.
T2 - American Statistician
AB - We consider the situation in two-sample testing when one variance is assumed to be known and the other variance is considered unknown. This situation arises, for example, when one is interested in comparing a standard treatment with a new treatment. Although this situation occurs relatively infrequently, our example discusses the important tool of moment matching and makes the classic two-sample Satterthwaite t approximation transparent.
DA - 2006///
PY - 2006///
DO - 10.1198/000313006X108567
VL - 60
IS - 2
SP - 163-166
UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-33744525717&partnerID=MN8TOARS
KW - Behrens-Fisher
KW - moments
KW - Satterthwaite
ER -
TY - CONF
TI - Planarization for reverse-tone step and flash imprint lithography - art. no. 61512G
AU - Lin, M. W.
AU - Chao, H. L.
AU - Hao, J. J.
AU - Kim, E. K.
AU - Palmieri, F.
AU - Kim, W. C.
AU - Dickey, M.
AU - Ho, P. S.
AU - Willson, C. G.
C2 - 2006///
C3 - Proceedings of the society of photo-optical instrumentation engineers
DA - 2006///
VL - 6151
SP - G1512-1512
ER -
TY - RPRT
TI - Guided by planning, powered by people: open space protection in the Triangle
AU - Hess, G.
AU - Steelman, T. A.
AU - Beechwood, B.
AU - Cavalieri, S.
AU - Crooks, L.
AU - Doig, S.
AU - Norwood, C.
AU - Paxton, D.
AU - Schuster, G.
AU - Trinks, M.
A3 - Raleigh: Department of Forestry and Environmental Resources, College of Natural Resources, North Carolina State University
DA - 2006///
PY - 2006///
PB - Raleigh: Department of Forestry and Environmental Resources, College of Natural Resources, North Carolina State University
ER -
TY - JOUR
TI - Electronic textiles and their potential
AU - Ghosh, T. K.
AU - Dhawan, A.
T2 - Indian Journal of Fibre & Textile Research
DA - 2006///
PY - 2006///
VL - 30
IS - 1
ER -
TY - CONF
TI - Predicting whole-stem wood properties in loblolly pine
AU - Aspinwall, M.
AU - Li, B.
AU - McKeand, S.
AU - Isik, F.
AU - Gumpertz, M.
C2 - 2006///
C3 - Information Exchange Group 40 Conference, Incorporating Genetic Advances into Forest Productivity Systems: Value for All Landowners.
Exchange Group 40 Conference, Incorporating Genetic Advances into Forest
Productivity Systems: Value for All Landowners.
DA - 2006///
VL - 40
ER -
TY - BOOK
TI - Measurement error in nonlinear models: A modern perspective. (2nd ed.)
AU - Carroll, R. J.
AU - Ruppert, D.
AU - Stefanski, L. A.
AU - Crainiceanu, C. A.
DA - 2006///
PY - 2006///
DO - 10.1201/9781420010138
PB - Boca Raton, FL: Chapman & Hall
SN - 1584886331
ER -
TY - JOUR
TI - Evaluating bioretention hydrology and nutrient removal at three field sites in North Carolina
AU - Hunt, W. F.
AU - Jarrett, A. R.
AU - Smith, J. T.
AU - Sharkey, L. J.
T2 - Journal of Irrigation and Drainage Engineering
AB - Three bioretention field sites in North Carolina were examined for pollutant removal abilities and hydrologic performance. The cells varied by fill media type or drainage configuration. The field studies confirmed high annual total nitrogen mass removal rates at two conventionally drained bioretention cells (40% reduction each). Nitrate-nitrogen mass removal rates varied between 75 and 13%, and calculated annual mass removal of zinc, copper, and lead from one Greensboro cell were 98, 99, and 81%, respectively. All high mass removal rates were due to a substantial decrease in outflow volume. The ratio of volume of water leaving the bioretention cell versus that which entered the cell varied from 0.07 (summer) to 0.54 (winter). There was a significant (p<0.05) change in the ratio of outflow volume to inflow volume when comparing warm seasons to winter. Cells using a fill soil media with a lower phosphorus index (P-index), Chapel Hill cell C1 and Greensboro cell G1, had much higher phosphorus removal than Gr...
DA - 2006///
PY - 2006///
DO - 10.1061/(ASCE)0733-9437(2006)132:6(600)
VL - 132
IS - 6
SP - 600-608
ER -
TY - JOUR
TI - Surrogates for the study of norovirus stability and inactivation in the environment: A comparison of murine norovirus and feline calicivirus
AU - Cannon, Jennifer L.
AU - Papafragkou, Efstathia
AU - Park, Geunwoo W.
AU - Osborne, Jason
AU - Jaykus, Lee-Ann
AU - Vinje, Jan
T2 - JOURNAL OF FOOD PROTECTION
AB - Human noroviruses (NoVs) are the leading cause of food- and waterborne outbreaks of acute nonbacterial gastroenteritis worldwide. As a result of the lack of a mammalian cell culture model for these viruses, studies on persistence, inactivation, and transmission have been limited to cultivable viruses, including feline calicivirus (FCV). Recently, reports of the successful cell culture of murine norovirus 1 (MNV-1) have provided investigators with an alternative surrogate for human NoVs. In this study, we compared the inactivation profiles of MNV-1 to FCV in an effort to establish the relevance of MNV-1 as a surrogate virus. Specifically, we evaluated (i) stability upon exposure to pH extremes; (ii) stability upon exposure to organic solvents; (iii) thermal inactivation; and (iv) surface persistence under wet and dry conditions. MNV-1 was stable across the entire pH range tested (pH 2 to 10) with less than 1 log reduction in infectivity at pH 2, whereas FCV was inactivated rapidly at pH values < 3 and > 9. FCV was more stable than MNV-1 at 56 degrees C, but both viruses exhibited similar inactivation at 63 and 72 degrees C. Long-term persistence of both viruses suspended in a fecal matrix and inoculated onto stainless steel coupons were similar at 4 degrees C, but at room temperature in solution, MNV-1 was more stable than FCV. The genetic relatedness of MNV-1 to human NoVs combined with its ability to survive under gastric pH levels makes this virus a promising and relevant surrogate for studying environmental survival of human NoVs.
DA - 2006/11//
PY - 2006/11//
DO - 10.4315/0362-028X-69.11.2761
VL - 69
IS - 11
SP - 2761-2765
SN - 1944-9097
ER -
TY - JOUR
TI - Posterior consistency of Gaussian process prior for nonparametric binary regression
AU - Ghosal, Subhashis
AU - Roy, Anindya
T2 - ANNALS OF STATISTICS
AB - Consider binary observations whose response probability is an unknown smooth function of a set of covariates. Suppose that a prior on the response probability function is induced by a Gaussian process mapped to the unit interval through a link function. In this paper we study consistency of the resulting posterior distribution. If the covariance kernel has derivatives up to a desired order and the bandwidth parameter of the kernel is allowed to take arbitrarily small values, we show that the posterior distribution is consistent in the L1-distance. As an auxiliary result to our proofs, we show that, under certain conditions, a Gaussian process assigns positive probabilities to the uniform neighborhoods of a continuous function. This result may be of independent interest in the literature for small ball probabilities of Gaussian processes.
DA - 2006/10//
PY - 2006/10//
DO - 10.1214/009053606000000795
VL - 34
IS - 5
SP - 2413-2429
SN - 0090-5364
KW - binary regression
KW - Gaussian process
KW - Karhunen-Loeve expansion
KW - maximal inequality
KW - posterior consistency
KW - reproducing kernel Hilbert space
ER -
TY - JOUR
TI - Model selection in nonparametric hazard regression
AU - Leng, Chenlei
AU - Zhang, Hao Helen
T2 - JOURNAL OF NONPARAMETRIC STATISTICS
AB - We propose a novel model selection method for a nonparametric extension of the Cox proportional hazard model, in the framework of smoothing splines ANOVA models. The method automates the model building and model selection processes simultaneously by penalizing the reproducing kernel Hilbert space norms. On the basis of a reformulation of the penalized partial likelihood, we propose an efficient algorithm to compute the estimate. The solution demonstrates great flexibility and easy interpretability in modeling relative risk functions for censored data. Adaptive choice of the smoothing parameter is discussed. Both simulations and a real example suggest that our proposal is a useful tool for multivariate function estimation and model selection in survival analysis.
DA - 2006///
PY - 2006///
DO - 10.1080/10485250601027042
VL - 18
IS - 7-8
SP - 417-429
SN - 1029-0311
KW - COSSO
KW - Cox proportional hazard model
KW - model selection
KW - penalized likelihood
ER -
TY - JOUR
TI - Interval mapping of quantitative trait loci for time-to-event data with the proportional hazards mixture cure model
AU - Liu, Mengling
AU - Lu, Wenbin
AU - Shao, Yongzhao
T2 - BIOMETRICS
AB - Summary Interval mapping using normal mixture models has been an important tool for analyzing quantitative traits in experimental organisms. When the primary phenotype is time-to-event, it is natural to use survival models such as Cox's proportional hazards model instead of normal mixtures to model the phenotype distribution. An extra challenge for modeling time-to-event data is that the underlying population may consist of susceptible and nonsusceptible subjects. In this article, we propose a semiparametric proportional hazards mixture cure model which allows missing covariates. We discuss applications to quantitative trait loci (QTL) mapping when the primary trait is time-to-event from a population of mixed susceptibility. This model can be used to characterize QTL effects on both susceptibility and time-to-event distribution, and to estimate QTL location. The model can naturally incorporate covariate effects of other risk factors. Maximum likelihood estimates for the parameters in the model as well as their corresponding variance estimates can be obtained numerically using an EM-type algorithm. The proposed methods are assessed by simulations under practical settings and illustrated using a real data set containing survival times of mice after infection with Listeria monocytogenes. An extension to multiple intervals is also discussed.
DA - 2006/12//
PY - 2006/12//
DO - 10.1111/j.1541-0420.2006.00585.x
VL - 62
IS - 4
SP - 1053-1061
SN - 0006-341X
KW - age-at-onset
KW - cure model
KW - EM algorithm
KW - proportional hazards model
KW - QTL mapping
ER -
TY - JOUR
TI - Heterosis and inbreeding depression in two soybean single crosses
AU - Burton, Joseph W.
AU - Brownie, Cavell
T2 - CROP SCIENCE
AB - Heterosis is considered to be of little importance in soybean (Glycine max L. Merr.) because the crop is produced as “pure-line” cultivars or blends of inbred lines. The F1 generations Holladay/Hutcheson (Cross 1) and Brim/Boggs (Cross 2) were generated by hand pollinations. Inbred generations were generated by bulk selfing. The F1, F2, F3, F4, and F5 generations were yield-tested in replicated bordered single row plots in multiple years and locations. The average yield of Cross 1 F1 was 16% greater than that of the highest-yielding parent and the average yield of the Cross 2 F1 was 5% greater than the highest-yielding parent. Cross 1 showed significant inbreeding depression when regressed on percentage inbreeding which is clear evidence of dominance for yield. Possible genetic bases for heterosis in soybean include gene complementation or interaction of duplicate favorable loci in repulsion, linked dominant alleles that are inherited as a unit, a greater number of dominant alleles in the F1 than either parent separately, multiple dosage-dependant regulatory loci, and/or overdominance. The existence of heterosis should be evidence that superior gene combinations are possible. The magnitude of yield heterosis may be a useful criterion for selection among biparental crosses.
DA - 2006///
PY - 2006///
DO - 10.2135/cropsci2006.03.0156
VL - 46
IS - 6
SP - 2643-2648
SN - 1435-0653
ER -
TY - JOUR
TI - Effects of residual smoothing on the posterior of the fixed effects in disease-mapping models
AU - Reich, Brian
AU - Hodges, J. S.
AU - Zadnik, V.
T2 - Biometrics
DA - 2006///
PY - 2006///
DO - 10.1111/j.1541-0420.2006.00617
VL - 62
IS - 4
SP - 1197–1206
ER -
TY - JOUR
TI - Differential gene expression in loblolly pine (Pinus taeda L.) challenged with the fusiform rust fungus, Cronartium quercuum f.sp fusiforme
AU - Myburg, Henrietta
AU - Morse, Alison M.
AU - Amerson, Henry V.
AU - Kubisiak, Thomas L.
AU - Huber, Dudley
AU - Osborne, Jason A.
AU - Garcia, Saul A.
AU - Nelson, C. Dana
AU - Davis, John M.
AU - Covert, Sarah F.
AU - Zyl, Leonel M.
T2 - PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY
AB - Cronartium quercuum f.sp. fusiforme is the pathogen that incites fusiform rust disease of southern pine species. To date, a number of host resistance genes have been mapped. Although genomic mapping studies have provided valuable information on the genetic basis of disease interactions in this pine-rust pathosystem, the interaction at the molecular level is poorly understood. To further our understanding of this interaction, we implemented a microarray study to examine the differential expression of genes in pathogen-challenged progeny of a full-sib loblolly pine family known to be segregating at a single dominant resistance gene ( Fr1 ). Statistical analyses revealed shifts in gene expression that may reflect discrete stages of gall development.
DA - 2006///
PY - 2006///
DO - 10.1016/j.pmpp.2006.07.002
VL - 68
IS - 1-3
SP - 79-91
SN - 0885-5765
KW - Cronartium quercuum f.sp fusiforme
KW - fusiform rust
KW - gene-for-gene interactions
KW - microarray analysis
ER -
TY - JOUR
TI - Component selection and smoothing in multivariate nonparametric regression
AU - Lin, Yi
AU - Zhang, Hao Helen
T2 - ANNALS OF STATISTICS
AB - We propose a new method for model selection and model fitting in multivariate nonparametric regression models, in the framework of smoothing spline ANOVA. The “COSSO” is a method of regularization with the penalty functional being the sum of component norms, instead of the squared norm employed in the traditional smoothing spline method. The COSSO provides a unified framework for several recent proposals for model selection in linear models and smoothing spline ANOVA models. Theoretical properties, such as the existence and the rate of convergence of the COSSO estimator, are studied. In the special case of a tensor product design with periodic functions, a detailed analysis reveals that the COSSO does model selection by applying a novel soft thresholding type operation to the function components. We give an equivalent formulation of the COSSO estimator which leads naturally to an iterative algorithm. We compare the COSSO with MARS, a popular method that builds functional ANOVA models, in simulations and real examples. The COSSO method can be extended to classification problems and we compare its performance with those of a number of machine learning algorithms on real datasets. The COSSO gives very competitive performance in these studies.
DA - 2006/10//
PY - 2006/10//
DO - 10.1214/009053606000000722
VL - 34
IS - 5
SP - 2272-2297
SN - 0090-5364
KW - smoothing spline ANOVA
KW - method of regularization
KW - nonparametric regression
KW - nonparametric classification
KW - model selection
KW - machine learning
ER -
TY - JOUR
TI - Recommendations for assessing the effectiveness of surrogate species approaches
AU - Favreau, Jorie M.
AU - Drew, C. Ashton
AU - Hess, George R.
AU - Rubino, Matthew J.
AU - Koch, Frank H.
AU - Eschelbach, Katherine A.
T2 - BIODIVERSITY AND CONSERVATION
DA - 2006/11//
PY - 2006/11//
DO - 10.1007/s10531-005-2631-1
VL - 15
IS - 12
SP - 3949-3969
SN - 1572-9710
KW - effectiveness
KW - flagship species
KW - focal species
KW - indicator species
KW - keystone species
KW - surrogate species
KW - umbrella species
ER -
TY - JOUR
TI - Mixture cure model with an application to interval mapping of quantitative trait loci
AU - Liu, Mengling
AU - Lu, Wenbin
AU - Shao, Yongzhao
T2 - LIFETIME DATA ANALYSIS
DA - 2006/12//
PY - 2006/12//
DO - 10.1007/s10985-006-9025-x
VL - 12
IS - 4
SP - 421-440
SN - 1572-9249
KW - EM algorithm
KW - genome-wide threshold
KW - parametric proportional hazards model
KW - QTL mapping
KW - time-to-event data
ER -
TY - JOUR
TI - Electromagnetic inverse problems involving distributions of dielectric mechanisms and parameters
AU - Banks, H. T.
AU - Gibson, N. L.
T2 - QUARTERLY OF APPLIED MATHEMATICS
AB - Abstract : We consider electromagnetic interrogation problems for complex materials involving distributions of polarization mechanisms and also distributions for the parameters in these mechanisms. a theoretical and computational framework for such problems is given. Computational results for specific problems with multiple Debye mechanisms are given in the case of discrete, uniform, log-normal, and log-Bi-Gaussian distributions.
DA - 2006/12//
PY - 2006/12//
DO - 10.1090/S0033-569X-06-01036-X
VL - 64
IS - 4
SP - 749-795
SN - 1552-4485
KW - electromagnetic interrogation
KW - pulsed antenna source microwaves
KW - inverse problems
KW - complex dielectric materials
KW - distributions of relaxation parameters and mechanisms
ER -
TY - JOUR
TI - Potential individual versus simultaneous climate change effects on soybean (C-3) and maize (C-4) crops: An agrotechnology model based study
AU - Mera, Roberto J.
AU - Niyogi, Dev
AU - Buol, Gregory S.
AU - Wilkerson, Gail G.
AU - Semazzi, Fredrick H. M.
T2 - GLOBAL AND PLANETARY CHANGE
AB - Landuse/landcover change induced effects on regional weather and climate patterns and the associated plant response or agricultural productivity are coupled processes. Some of the basic responses to climate change can be detected via changes in radiation (R), precipitation (P), and temperature (T). Past studies indicate that each of these three variables can affect LCLUC response and the agricultural productivity. This study seeks to address the following question: What is the effect of individual versus simultaneous changes in R, P, and T on plant response such as crop yields in a C3 and a C4 plant? This question is addressed by conducting model experiments for soybean (C3) and maize (C4) crops using the DSSAT: Decision Support System for Agrotechnology Transfer, CROPGRO (soybean), and CERES-Maize (maize) models. These models were configured over an agricultural experiment station in Clayton, NC [35.65°N, 78.5°W]. Observed weather and field conditions corresponding to 1998 were used as the control. In the first set of experiments, the CROPGRO (soybean) and CERES-Maize (maize) responses to individual changes in R and P (25%, 50%, 75%, 150%) and T (± 1, ± 2 °C) with respect to control were studied. In the second set, R, P, and T were simultaneously changed by 50%, 150%, and ± 2 °C, and the interactions and direct effects of individual versus simultaneous variable changes were analyzed. For the model setting and the prescribed environmental changes, results from the first set of experiments indicate: (i) precipitation changes were most sensitive and directly affected yield and water loss due to evapotranspiration; (ii) radiation changes had a non-linear effect and were not as prominent as precipitation changes; (iii) temperature had a limited impact and the response was non-linear; (iv) soybeans and maize responded differently for R, P, and T, with maize being more sensitive. The results from the second set of experiments indicate that simultaneous change analyses do not necessarily agree with those from individual changes, particularly for temperature changes. Our analysis indicates that for the changing climate, precipitation (hydrological), temperature, and radiative feedbacks show a non-linear effect on yield. Study results also indicate that for studying the feedback between the land surface and the atmospheric changes, (i) there is a need for performing simultaneous parameter changes in the response assessment of cropping patterns and crop yield based on ensembles of projected climate change, and (ii) C3 crops are generally considered more sensitive than C4; however, the temperature–radiation related changes shown in this study also effected significant changes in C4 crops. Future studies assessing LCLUC impacts, including those from agricultural cropping patterns and other LCULC–climate couplings, should advance beyond the sensitivity mode and consider multivariable, ensemble approaches to identify the vulnerability and feedbacks in estimating climate-related impacts.
DA - 2006/11//
PY - 2006/11//
DO - 10.1016/j.gloplacha.2005.11.003
VL - 54
IS - 1-2
SP - 163-182
SN - 1872-6364
KW - land surface response
KW - climate change impacts
KW - crop yield
KW - soybeans
KW - maize
KW - crop models
KW - evapotranspiration
ER -
TY - JOUR
TI - Limitations to fruit and seed production by Lysimachia asperulifolia Poir. (Primulaceae), a rare plant species of the Carolinas
AU - Franklin, M. A.
AU - Stucky, J. M.
AU - Wentworth, T. R.
AU - Brownie, C.
AU - Roulston, T.
T2 - JOURNAL OF THE TORREY BOTANICAL SOCIETY
AB - Lysimachia asperulifolia Poir., rough–leaf loosestrife, is a federally endangered species that is restricted to longleaf pine savanna – pocosin ecotones in North and South Carolina. Potential causes of the limited fruit and seed production typical of this species and possible effects of prescribed fire on these causes were examined. It was determined that insects rarely visit flowers and that the visitors, Augochlorella spp. and Lasioglossum spp., are not effective pollinators. However, results of artificial pollinations do not support the hypothesis that pollinator limitation alone restricts seed production. Levels of fertility and S allele diversity may vary across natural populations and, combined with ineffective pollination, enforce restricted fruit and seed production. Pollen fertility, amount of flowering, and number of fruits produced in natural populations did not increase following prescribed fire. Restricted seed germination further limits recruitment of genetic variation into populations. Pollinations and propagule dispersal among populations are precluded by habitat fragmentation. Alternative courses of action designed to increase fruit and seed production and seedling recruitment are recommended to those developing loosestrife conservation plans.
DA - 2006///
PY - 2006///
DO - 10.3159/1095-5674(2006)133[403:LTFASP]2.0.CO;2
VL - 133
IS - 3
SP - 403-411
SN - 1940-0616
KW - fruit production
KW - habitat fragmentation
KW - pan trap sampling
KW - pollinator limitation
KW - S allele diversity
KW - seed germination
KW - seed production
KW - sterility
ER -
TY - JOUR
TI - A new architecture for coastal inundation and flood warning prediction
AU - Pietrafesa, L. J.
AU - Kelleher, K.
AU - Karl, T.
AU - Davidson, M.
AU - Peng, M.
AU - Bao, S.
AU - Dickey, D.
AU - Xie, L.
AU - Liu, H.
AU - Xia, M.
T2 - MARINE TECHNOLOGY SOCIETY JOURNAL
AB - The marine atmosphere, coastal ocean, estuary, harbor and river water systems constitute a physically coupled system. While these systems have always been heavily impacted by coastal storms, increases in population density, infrastructure, and personal and business merchandise have exacerbated the economic and personal impacts of these events over the past half century. As such there has been increased focus on the need for more timely and accurate forecasts of impending events. Traditionally model forecast architectures for coastal storm surge, flooding and inundation of coastal and inland areas have taken the approach of dealing with each system separately: rivers, estuaries, harbors and offshore facing areas. However, given advances in coupled modeling and the availability of real-time data, the ability to accurately predict and project coastal, estuary and inland flooding related to the passage of high energy and wet atmospheric events is rapidly emerging and requires a new paradigm in system architecture. No longer do monthly averaged winds or river discharge or water levels have to be invoked in developing hindcasts for planning purposes or for real-time forecasts. In 1999 a hurricane associated flood on the North Carolina coast took 56 lives and caused more than $6 billion in economic impacts. None of the models existing at that time were able to properly forecast the massive flooding and clearly called for a new model paradigm. Here we propose a model system that couples atmospheric information to fully three dimensional, non-linear time dependent ocean basin, coastal and estuary hydrodynamic models coupled to interactive river models with input of real or modeled winds, observed or modeled precipitation, measured and modeled water levels, and streamflow. The river and estuarine components must both be capable of going into modes of storage or accelerated discharge. Spatial scales must downscale in the horizontal from thousands to tens meters and in the vertical from hundreds to several centimeters. Topography and elevation data should be of the highest resolution available, necessary for highly accurate predictions of the timing and location of the inundation and retreat of flood waters. Precipitation information must be derived from the optimal mix of direct radar, satellite and ground-based observations. Creating the capability described above will advance the modernization of hydrologic services provided by the National Oceanic & Atmospheric Administration and provide more accurate and timely forecasts and climatologies of coastal and estuary flooding. The goal of these climatologies and improved forecasts is to provide better information to local and regional planners, emergency managers, highway patrols and to improve the capacity of coastal communities to mitigate against the impacts of coastal flooding.
DA - 2006///
PY - 2006///
DO - 10.4031/002533206787353205
VL - 40
IS - 4
SP - 71-77
SN - 0025-3324
ER -
TY - JOUR
TI - What is your diagnosis? Reluctant to dive: coelomic effusion in a frog
AU - Tarigo, Jaime
AU - Linder, Keith
AU - Neel, Jennifer
AU - Harvey, Stephen
AU - Remick, Amera
AU - Grindem, Carol
T2 - VETERINARY CLINICAL PATHOLOGY
AB - Abstract An adult female, albino South African Clawed frog (Xenopus laevis) from a research colony at the Biological Resources Facility of the College of Agriculture and Life Sciences at North Carolina State University (NCSU) was presented with depression, lethargy, loss of diving reflex, and a distended abdomen. Cytologic examination of coelomic effusion fluid at the NCSU veterinary teaching hospital revealed a mixed population of inflammatory cells, including heterophils and a predominance of large mononuclear cells (macrophages) that often contained intracytoplasmic, negatively-stained, rod-shaped to filamentous organisms consistent with Mycobacterium sp. Ziehl-Neelsen stain revealed bright pink to red, acid-fast organisms with a beaded appearance. Histopathologic findings in tissues obtained at necropsy included marked, multifocal to coalescing, heterophilic, granulomatous and fibrinous coelomitis as well as severe multifocal heterophilic and granulomatous hepatitis, interstitial pneumonia and sinusitis/rhinitis. Slender gram-positive, acid-fast bacterial rods were identified in sections of coelomic pleura, kidneys, nasal cavities, spleen, liver, and pulmonary interstitium, indicative of systemic mycobacteriosis. Based on mycobacterial culture, the organism was identified as M marinum complex. Mycobacteria are variably gram-positive, often acid-fast, small rods that are ubiquitous in aquatic environments. The clinical and pathologic spectrum of disease in amphibians depends on host and pathogen status. Xenopus sp and several other frogs are good models for studying the pathogenesis of M tuberculosis infection. In addition to culture, polymerase chain reaction assays may be used for definitive identification of the organisms; accurate speciation may require further genetic investigation.
DA - 2006/9//
PY - 2006/9//
DO - 10.1111/j.1939-165X.2006.tb00145.x
VL - 35
IS - 3
SP - 341-344
SN - 0275-6382
KW - amphibian
KW - cytology
KW - mycobacteriosis
KW - Xenopus
ER -
TY - JOUR
TI - Using multispectral satellite imagery to estimate leaf area and response to silvicultural treatments in loblolly pine stands
AU - Flores, FJ
AU - Allen, HL
AU - Cheshire, HM
AU - Davis, JM
AU - Fuentes, M
AU - Kelting, D
T2 - CANADIAN JOURNAL OF FOREST RESEARCH-REVUE CANADIENNE DE RECHERCHE FORESTIERE
AB - The relationship between leaf area index (LAI) of loblolly pine plantations and the broadband simple ratio (SR) vegetation index calculated from Landsat 7 Enhanced Thematic Mapper Plus (ETM+) data was examined. An equation was derived to estimate LAI from readily available Landsat 7 ETM+ data. The equation developed to predict LAI with Landsat 7 ETM+ data was tested with ground LAI measurements taken in 12 plots. The root mean square error of prediction was 0.29, an error of approximately 14% in prediction. The ability of Landsat 7 ETM+ data to consistently estimate SR over time was tested using two scenes acquired on different dates during the winter (December to early March). Comparison between the two images on a pixel-by-pixel basis showed that approximately 96% of the pixels had a difference of <0.5 units of SR (approximately 0.3 units of LAI). When the comparison was made on a stand-by-stand basis (average stand SR), a maximum difference of 0.2 units of SR (approximately 0.12 units of LAI) was found. These results suggest that stand LAI of loblolly pine plantations can be accurately estimated from readily available remote sensing data and provide an opportunity to apply the findings from ecophysiological studies in field plots to forest management decisions at an operational scale.
DA - 2006/6//
PY - 2006/6//
DO - 10.1139/X06-030
VL - 36
IS - 6
SP - 1587-1596
SN - 0045-5067
ER -
TY - JOUR
TI - Soil cover and tillage influenced metolachlor mobility and dissipation in field lysimeters
AU - Weber, J. B.
AU - Taylor, K. A.
AU - Wilkerson, G. G.
T2 - Agronomy Journal
DA - 2006///
PY - 2006///
DO - 10.2134/argonj2004.0222
VL - 98
IS - 1
SP - 19-25
ER -
TY - JOUR
TI - Soil and herbicide properties influenced mobility of atrazine, metolachlor, and primisulfuron-methyl in field lysimeters
AU - Weber, J. B.
AU - Taylor, K. A.
AU - Wilkerson, G. G.
T2 - Agronomy Journal
DA - 2006///
PY - 2006///
DO - 10.2134/argonj2004.0221
VL - 98
IS - 1
SP - 8-18
ER -
TY - JOUR
TI - Remote sensing-informed variable-rate nitrogen management of wheat and corn: Agronomic and groundwater outcomes
AU - Hong, N
AU - White, JG
AU - Weisz, R
AU - Crozier, CR
AU - Gumpertz, ML
AU - Cassel, DK
T2 - AGRONOMY JOURNAL
AB - In‐season, site‐specific, variable‐rate (SS) N management based on remote sensing (RS) may reduce N losses to groundwater while maintaining or increasing yield and N fertilizer‐use efficiency. We compared in‐season, RS‐informed N management applied on a uniform, field‐average (FA) or SS basis with the current uniform best management practice (BMP) based on “Realistic Yield Expectations” (RYE) in a typical 2‐yr southeastern U.S. coastal plain rotation: winter wheat ( Triticum aestivum L.)–double‐crop soybean [ Glycine max (L.) Merr.]–corn ( Zea mays L.). Compared with the RYE‐based BMP, RS‐informed SS management achieved: (i) a maximum of 2.3 mg L −1 less groundwater NO 3 –N after 2001 wheat due to 39 kg ha −1 less fertilizer N and a 25% greater harvest N ratio (N in grain or forage/total N applied); (ii) 370 kg ha −1 more 2002 corn grain with 32 kg ha −1 greater N applied, similar harvest N ratio, and 37 kg ha −1 greater surplus N; (iii) 670 kg ha −1 more 2003 wheat grain associated with 14 kg ha −1 greater fertilizer N, 27% greater harvest N ratio, and 9 kg ha −1 less surplus N. Excepting one corn FA treatment that received excessive N, RS‐informed management produced equal or greater economic returns to N than RYE, and less surplus N for wheat. Treatments produced enduring effects on groundwater [NO 3 –N] consistent with agronomic results, but small relative to temporal [NO 3 –N] fluctuations that were positively correlated with water table elevation. To assess N management in leaching‐prone soils, frequent, periodic groundwater monitoring during and after the cropping season appears essential.
DA - 2006///
PY - 2006///
DO - 10.2134/agronj2005.0154
VL - 98
IS - 2
SP - 327-338
SN - 1435-0645
ER -
TY - JOUR
TI - Panzea: a database and resource for molecular and functional diversity in the maize genome
AU - Zhao, Wei
AU - Canaran, Payan
AU - Jurkuta, Rebecca
AU - Fulton, Theresa
AU - Glaubitz, Jeffrey
AU - Buckler, Edward
AU - Doebley, John
AU - Gaut, Brandon
AU - Goodman, Major
AU - Holland, Jim
AU - Kresovich, Stephen
AU - McMullen, Michael
AU - Stein, Lincoln
AU - Ware, Doreen
T2 - NUCLEIC ACIDS RESEARCH
AB - Serving as a community resource, Panzea (http://www.panzea.org) is the bioinformatics arm of the Molecular and Functional Diversity in the Maize Genome project. Maize, a classical model for genetic studies, is an important crop species and also the most diverse crop species known. On average, two randomly chosen maize lines have one single-nucleotide polymorphism every ∼100 bp; this divergence is roughly equivalent to the differences between humans and chimpanzees. This exceptional genotypic diversity underlies the phenotypic diversity maize needs to be cultivated in a wide range of environments. The Molecular and Functional Diversity in the Maize Genome project aims to understand how selection has shaped molecular diversity in maize and then relate molecular diversity to functional phenotypic variation. The project will screen 4000 loci for the signature of selection and create a wide range of maize and maize–teosinte mapping populations. These populations will be genotyped and phenotyped, permitting high-power and high-resolution dissection of the traits and relating the molecular diversity to functional variation. Panzea provides access to the genotype, phenotype and polymorphism data produced by the project through user-friendly web-based database searches and data retrieval/visualization tools, as well as a wide variety of information and services related to maize diversity.
DA - 2006/1/1/
PY - 2006/1/1/
DO - 10.1093/nar/gkj011
VL - 34
SP - D752-D757
SN - 1362-4962
ER -
TY - JOUR
TI - Occurrence and relative abundance of mosquitoes in stormwater retention facilities in North Carolina, USA
AU - Hunt, W. F., III
AU - Apperson, C. S.
AU - Kennedy, S. G.
AU - Harrison, B. A.
AU - Lord, W. G.
T2 - WATER SCIENCE AND TECHNOLOGY
AB - Throughout the 2004 mosquito season, 52 stormwater retention facilities were sampled to characterize the seasonal occurrence and relative abundance of mosquito species in relation to the structural complexity and biological diversity of the facilities. The three different types of facilities included standard wet ponds (n=20), innovative ponds (n=14), and wetland ponds (n=18). All retention structures were sampled at the beginning, middle and end of the mosquito season so that seasonal changes in mosquito production could be characterized. Overall samplings, mosquitoes were collected from 34% of the retention structures. Fourteen species representing 7 genera were collected, but only 5 species were commonly collected in all three types of stormwater management facilities. In general, the seasonal prevalence and relative abundance of mosquito species did not vary among three types of retention structures. A significant association (P < 0.01) between the presence of mosquito larvae or pupae and the absence of mosquitofish was found for innovative and wetland stormwater retention facilities but not for standard retention facilities (P > 0.05).
DA - 2006///
PY - 2006///
DO - 10.2166/wst.2006.625
VL - 54
IS - 6-7
SP - 315-321
SN - 1996-9732
KW - Gambusia
KW - mosquitoes
KW - North Carolina
KW - stormwater
KW - wetlands
KW - wet ponds
ER -
TY - JOUR
TI - It was one of my brothers
AU - Anderson, AD
AU - Weir, BS
T2 - INTERNATIONAL JOURNAL OF LEGAL MEDICINE
DA - 2006/3//
PY - 2006/3//
DO - 10.1007/s00414-005-0017-2
VL - 120
IS - 2
SP - 95-104
SN - 1437-1596
KW - forensic science
KW - match probability
KW - DNA profile
KW - relatives
ER -
TY - JOUR
TI - Geographic patterns of advanced breast cancer in Los Angeles: Associations with biological and sociodemographic factors (United States)
AU - Gumpertz, ML
AU - Pickle, LW
AU - Miller, BA
AU - Bell, BS
T2 - CANCER CAUSES & CONTROL
DA - 2006/4//
PY - 2006/4//
DO - 10.1007/s10552-005-0513-1
VL - 17
IS - 3
SP - 325-339
SN - 0957-5243
KW - breast neoplasms
KW - sociodemographic factors
KW - mammography
KW - logistic models
KW - spatial patterns
ER -
TY - JOUR
TI - Estimating detection probabilities from multiple-observer point counts
AU - Alldredge, Mathew W.
AU - Pollock, Kenneth H.
AU - Simons, Theodore R.
T2 - AUK
AB - Abstract Point counts are commonly used to obtain indices of bird population abundance. We present an independent-observer point-count method, a generalization of the dependent-observer approach, based on closed-population capture- recapture methods. The approach can incorporate individual covariates, such as detection distance, to account for individual differences in detection probabilities associated with measurable sources of variation. We demonstrate a negative bias in two-observer estimates by comparing abundance estimates from two- and four- observer point counts. Models incorporating data from four independent observers were capable of accounting for this bias. Modeling individual bird differences in detection probabilities produced abundance estimates 15–21% higher than models that did not account for individual differences, in four out of five data sets analyzed. Although independent-observer methods are expensive and impractical for large- scale applications, we believe they can provide importa...
DA - 2006/10//
PY - 2006/10//
DO - 10.1642/0004-8038(2006)123[1172:EDPFMP]2.0.CO;2
VL - 123
IS - 4
SP - 1172-1182
SN - 1938-4254
KW - bird surveys
KW - capture-recapture
KW - detection probability
KW - multiple observer
KW - point counts
ER -
TY - JOUR
TI - Effect of different reward levels on tag reporting rates and behavior of common snook anglers in southeast Florida
AU - Taylor, Ronald G.
AU - Whittington, James A.
AU - Pine, William E., III
AU - Pollock, Kenneth H.
T2 - NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT
AB - Based on the high-reward tagging method, we determined that reporting rates by recreational anglers for tagged common snook Centropomus undecimalis along the Atlantic coast of Florida were approximately 60–70%. Additionally, we found that angler reporting rates were influenced by the use of high-reward tags. To estimate reporting rates, we tagged 989 common snook (range = 600–1,132 mm total length) with internal anchor tags that bore one of eight variable-reward messages (the word “Reward” with or without a specified monetary amount from US$5 to $200) during the summer closed-harvest season of 1995. Approximately equal numbers and sizes of fish were tagged in each reward group. The $200 reward was assumed to be sufficient to elicit a reporting rate of 100%. Return rates during the first year were quite variable and ranged from 13.7% for $5 tags to 25.0% for $25 tags, while the $200 tags had a return rate of 18.7%. Return rates generally increased with increasing reward amount, reaching an asymptotic value at approximately $75 in year 1 and $100 in year 2, above which return rates did not change. In subsequent years, angler behavior appeared to change, as indicated by decreases in the reporting rate of unspecified “Reward” message tags and an increase in the asymptote of the reward level–return rate relationship. This may indicate that angler reporting behavior changed due to the use of high-reward tags. The results from this experiment will facilitate the deconstruction of total mortality into fishing and natural mortality components derived from tagging programs. They also provide insight into angler behavior related to the design and use of high-reward tagging programs to elicit tag returns.
DA - 2006/8//
PY - 2006/8//
DO - 10.1577/M04-185.1
VL - 26
IS - 3
SP - 645-651
SN - 1548-8675
ER -
TY - JOUR
TI - Dependence among sites in RNA evolution
AU - Yu, Jiaye
AU - Thorne, Jeffrey L.
T2 - MOLECULAR BIOLOGY AND EVOLUTION
AB - Although probabilistic models of genotype (e.g., DNA sequence) evolution have been greatly elaborated, less attention has been paid to the effect of phenotype on the evolution of the genotype. Here we propose an evolutionary model and a Bayesian inference procedure that are aimed at filling this gap. In the model, RNA secondary structure links genotype and phenotype by treating the approximate free energy of a sequence folded into a secondary structure as a surrogate for fitness. The underlying idea is that a nucleotide substitution resulting in a more stable secondary structure should have a higher rate than a substitution that yields a less stable secondary structure. This free energy approach incorporates evolutionary dependencies among sequence positions beyond those that are reflected simply by jointly modeling change at paired positions in an RNA helix. Although there is not a formal requirement with this approach that secondary structure be known and nearly invariant over evolutionary time, computational considerations make these assumptions attractive and they have been adopted in a software program that permits statistical analysis of multiple homologous sequences that are related via a known phylogenetic tree topology. Analyses of 5S ribosomal RNA sequences are presented to illustrate and quantify the strong impact that RNA secondary structure has on substitution rates. Analyses on simulated sequences show that the new inference procedure has reasonable statistical properties. Potential applications of this procedure, including improved ancestral sequence inference and location of functionally interesting sites, are discussed.
DA - 2006/8//
PY - 2006/8//
DO - 10.1093/molbev/msl015
VL - 23
IS - 8
SP - 1525-1537
SN - 1537-1719
KW - RNA secondary structure
KW - dependence among sites
KW - substitution rate
ER -
TY - JOUR
TI - Cost-effectiveness of defibrillator therapy or amiodarone in chronic stable heart failure - Results from the Sudden Cardiac Death in Heart Failure Trial (SCD-HeFT)
AU - Mark, Daniel B.
AU - Nelson, Charlotte L.
AU - Anstrom, Kevin J.
AU - Al-Khatib, Sana M.
AU - Tsiatis, Anastasios A.
AU - Cowper, Patricia A.
AU - Clapp-Channing, Nancy E.
AU - Davidson-Ray, Linda
AU - Poole, Jeanne E.
AU - Johnson, George
AU - Anderson, Jill
AU - Lee, Kerry L.
AU - Bardy, Gust H.
T2 - CIRCULATION
AB - In the Sudden Cardiac Death in Heart Failure Trial (SCD-HeFT), implantable cardioverter-defibrillator (ICD) therapy significantly reduced all-cause mortality rates compared with medical therapy alone in patients with stable, moderately symptomatic heart failure, whereas amiodarone had no benefit on mortality rates. We examined long-term economic implications of these results.Medical costs were estimated by using hospital billing data and the Medicare Fee Schedule. Our base case cost-effectiveness analysis used empirical clinical and cost data to estimate the lifetime incremental cost of saving an extra life-year with ICD therapy relative to medical therapy alone. At 5 years, the amiodarone arm had a survival rate equivalent to that of the placebo arm and higher costs than the placebo arm. For ICD relative to medical therapy alone, the base case lifetime cost-effectiveness and cost-utility ratios (discounted at 3%) were dollar 38,389 per life-year saved (LYS) and dollar 41,530 per quality-adjusted LYS, respectively. A cost-effectiveness ratio < dollar 100,000 was obtained in 99% of 1000 bootstrap repetitions. The cost-effectiveness ratio was sensitive to the amount of extrapolation beyond the empirical 5-year trial data: dollar 127,503 per LYS at 5 years, dollar 88,657 per LYS at 8 years, and dollar 58,510 per LYS at 12 years. Because of a significant interaction between ICD treatment and New York Heart Association class, the cost-effectiveness ratio was dollar 29,872 per LYS for class II, whereas there was incremental cost but no incremental benefit in class III.Prophylactic use of single-lead, shock-only ICD therapy is economically attractive in patients with stable, moderately symptomatic heart failure with an ejection fraction < or = 35%, particularly those in NYHA class II, as long as the benefits of ICD therapy observed in the SCD-HeFT persist for at least 8 years.
DA - 2006/7/11/
PY - 2006/7/11/
DO - 10.1161/circulationaha.105.581884
VL - 114
IS - 2
SP - 135-142
SN - 0009-7322
KW - amiodarone
KW - defibrillators, implantable
KW - heart failure, congestive
KW - quality-adjusted life years
KW - cost-benefit analysis
ER -
TY - JOUR
TI - Computer simulation study of molecular recognition in model DNA microarrays
AU - Jayaraman, Arthi
AU - Hall, Carol K.
AU - Genzer, Jan
T2 - BIOPHYSICAL JOURNAL
AB - DNA microarrays have been widely adopted by the scientific community for a variety of applications. To improve the performance of microarrays there is a need for a fundamental understanding of the interplay between the various factors that affect microarray sensitivity and specificity. We use lattice Monte Carlo simulations to study the thermodynamics and kinetics of hybridization of single-stranded target genes in solution with complementary probe DNA molecules immobilized on a microarray surface. The target molecules in our system contain 48 segments and the probes tethered on a hard surface contain 8–24 segments. The segments on the probe and target are distinct and each segment represents a sequence of nucleotides (∼11 nucleotides). Each probe segment interacts exclusively with its unique complementary target segment with a single hybridization energy; all other interactions are zero. We examine how the probe length, temperature, or hybridization energy, and the stretch along the target that the probe segments complement, affect the extent of hybridization. For systems containing single probe and single target molecules, we observe that as the probe length increases, the probability of binding all probe segments to the target decreases, implying that the specificity decreases. We observe that probes 12–16 segments (∼132–176 nucleotides) long gave the highest specificity and sensitivity. This agrees with the experimental results obtained by another research group, who found an optimal probe length of 150 nucleotides. As the hybridization energy increases, the longer probes are able to bind all their segments to the target, thus improving their specificity. The hybridization kinetics reveals that the segments at the ends of the probe are most likely to start the hybridization. The segments toward the center of the probe remain bound to the target for a longer time than the segments at the ends of the probe.
DA - 2006/9//
PY - 2006/9//
DO - 10.1529/biophysj.106.086173
VL - 91
IS - 6
SP - 2227-2236
SN - 1542-0086
ER -
TY - JOUR
TI - Comparing and combining effort and catch estimates from aerial-access designs as applied to a large-scale angler survey in the Delaware River
AU - Volstad, Jon H.
AU - Pollock, Kenneth H.
AU - Richkus, Willlam A.
T2 - NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT
AB - Abstract We used probability‐based aerial−access surveys to estimate effort, catch, and harvest of American shad Alosa sapidissima and striped bass Morone saxatilis by recreational anglers in the Delaware River and upper estuary in 2002. Sampling of anglers at access points and flights over the river were conducted weekly from mid‐March through October. Daily flight times were randomly selected; probabilities were proportional to the observed distribution of daily angler effort in a prior aerial−access survey (random count). Additional experimental flights were scheduled to occur at the time of day with expected peak effort (maximum count). Effort estimates derived from these maximum counts were more precise than estimates derived from the random flights, but the maximum‐count observations caused bias except when the daily count expansions were based on effort distributions from the concurrent access survey. The aerial and access surveys produced similar estimates of boat angler effort and little evidence of bias, but shore anglers were undercounted in the aerial survey. We maximized the precision and minimized bias in total effort estimates by combining the estimates of boat angler effort and shore angler access. An estimated sevenfold increase in the access survey sampling effort (at nearly five times the cost) would be required to achieve the same precision in the total effort estimate produced by the aerial–access survey. Effective stratification and the use of efficient model‐based estimators helped us to achieve the target precision of 20% in relative standard error (RSE) for estimated recreational catch of American shad (mean = 26,885 fish; RSE = 16%) and striped bass (mean = 47,671 fish; RSE = 15%). A single access survey during the American shad run would have required a 10‐fold increase in sampling effort to achieve the same precision in estimated catch at six times the cost of the complemented surveys.
DA - 2006/8//
PY - 2006/8//
DO - 10.1577/M04-146.1
VL - 26
IS - 3
SP - 727-741
SN - 0275-5947
ER -
TY - JOUR
TI - A two-stage design for multiple testing in large-scale association studies
AU - Wen, Shu-Hui
AU - Tzeng, Jung-Ying
AU - Kao, Jau-Tsuen
AU - Hsiao, Chuhsing Kate
T2 - JOURNAL OF HUMAN GENETICS
AB - Modern association studies often involve a large number of markers and hence may encounter the problem of testing multiple hypotheses. Traditional procedures are usually over-conservative and with low power to detect mild genetic effects. From the design perspective, we propose a two-stage selection procedure to address this concern. Our main principle is to reduce the total number of tests by removing clearly unassociated markers in the first-stage test. Next, conditional on the findings of the first stage, which uses a less stringent nominal level, a more conservative test is conducted in the second stage using the augmented data and the data from the first stage. Previous studies have suggested using independent samples to avoid inflated errors. However, we found that, after accounting for the dependence between these two samples, the true discovery rate increases substantially. In addition, the cost of genotyping can be greatly reduced via this approach. Results from a study of hypertriglyceridemia and simulations suggest the two-stage method has a higher overall true positive rate (TPR) with a controlled overall false positive rate (FPR) when compared with single-stage approaches. We also report the analytical form of its overall FPR, which may be useful in guiding study design to achieve a high TPR while retaining the desired FPR.
DA - 2006/6//
PY - 2006/6//
DO - 10.1007/s10038-006-0393-6
VL - 51
IS - 6
SP - 523-532
SN - 1435-232X
KW - association studies
KW - cost-effectiveness
KW - false positive rate
KW - multiple testing
KW - two-stage design
ER -
TY - JOUR
TI - The mean squared error of the instrumental variables estimator when the disturbance has an elliptical distribution
AU - Peixe, FPM
AU - Hall, AR
AU - Kyriakoulis, K
T2 - ECONOMETRIC REVIEWS
AB - This paper generalizes Nagar's (1959 Nagar , A. L. ( 1959 ). The bias and moment matrix of the general k-class estimators of the parameters in simultaneous equations . Econometrica 27 : 575 – 595 . [CSA] [Crossref], [Web of Science ®] , [Google Scholar]) approximation to the finite sample mean squared error (MSE) of the instrumental variables (IV) estimator to the case in which the errors possess an elliptical distribution whose moments exist up to infinite order. This allows for types of excess kurtosis exhibited by some financial data series. This approximation is compared numerically to Knight's (1985 Knight , J. L. ( 1985 ). The moments of OLS and 2SLS when the disturbances are non-normal . J. Econometrics 27 : 39 – 60 . [CROSSREF] [CSA] [Crossref], [Web of Science ®] , [Google Scholar]) formulae for the exact moments of the IV estimator under nonnormality. We use the results to explore two questions on instrument selection. First, we complement Buse's (1992 Buse , A. ( 1992 ). The bias of instrumental variable estimators . Econometrica 60 : 173 – 180 . [CSA] [Crossref], [Web of Science ®] , [Google Scholar]) analysis by considering the impact of additional instruments on both bias and MSE. Second, we evaluate the properties of Andrews's (1999 Andrews , D. W. K. ( 1999 ). Consistent moment selection procedures for generalized method of moments estimation . Econometrica 67 : 543 – 564 . [CROSSREF] [CSA] [Crossref], [Web of Science ®] , [Google Scholar]) selection method in terms of the bias and MSE of the resulting IV estimator.
DA - 2006///
PY - 2006///
DO - 10.1080/07474930500545488
VL - 25
IS - 1
SP - 117-138
SN - 1532-4168
ER -
TY - JOUR
TI - Spatial association between speciated fine particles and mortality
AU - Fuentes, Montserrat
AU - Song, Hae-Ryoung
AU - Ghosh, Sujit K.
AU - Holland, David M.
AU - Davis, Jerry M.
T2 - BIOMETRICS
AB - Particulate matter (PM) has been linked to a range of serious cardiovascular and respiratory health problems, including premature mortality. The main objective of our research is to quantify uncertainties about the impacts of fine PM exposure on mortality. We develop a multivariate spatial regression model for the estimation of the risk of mortality associated with fine PM and its components across all counties in the conterminous United States. We characterize different sources of uncertainty in the data and model the spatial structure of the mortality data and the speciated fine PM. We consider a flexible Bayesian hierarchical model for a space-time series of counts (mortality) by constructing a likelihood-based version of a generalized Poisson regression model that combines methods for point-level misaligned data and change of support regression. Our results seem to suggest an increase by a factor of two in the risk of mortality due to fine particles with respect to coarse particles. Our study also shows that in the Western United States, the nitrate and crustal components of the speciated fine PM seem to have more impact on mortality than the other components. On the other hand, in the Eastern United States, sulfate and ammonium explain most of the fine PM effect.
DA - 2006/9//
PY - 2006/9//
DO - 10.1111/j.1541-0420.2006.00526.x
VL - 62
IS - 3
SP - 855-863
SN - 1541-0420
UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-33748768427&partnerID=MN8TOARS
KW - ambient air pollution
KW - Bayesian hierarchical models
KW - conditional autoregressive models
KW - environmental epidemiology
KW - particulate matter
KW - spatial statistics
ER -
TY - JOUR
TI - Sparse sliced inverse regression
AU - Li, Lexin
AU - Nachtsheim, Christopher J.
T2 - TECHNOMETRICS
AB - Sliced inverse regression (SIR) is an innovative and effective method for dimension reduction and data visualization of high-dimensional problems. It replaces the original variables with low-dimensional linear combinations of predictors without any loss of regression information and without the need to prespecify a model or an error distribution. However, it suffers from the fact that each SIR component is a linear combination of all the original predictors; thus, it is often difficult to interpret the extracted components. By representing SIR as a regression-type optimization problem, we propose in this article a new method, called sparse SIR, that combines the shrinkage idea of the lasso with SIR to produce both accurate and sparse solutions. The efficacy of the proposed method is verified by simulation, and a real data example is given.
DA - 2006/11//
PY - 2006/11//
DO - 10.1198/004017006000000129
VL - 48
IS - 4
SP - 503-510
SN - 1537-2723
KW - lasso
KW - regression shrinkage
KW - sliced inverse regression
KW - sufficient dimension reduction
ER -
TY - JOUR
TI - Smoothing spline-based score tests for proportional hazards models
AU - Lin, Jiang
AU - Zhang, Daowen
AU - Davidian, Marie
T2 - BIOMETRICS
AB - Summary We propose “score-type” tests for the proportional hazards assumption and for covariate effects in the Cox model using the natural smoothing spline representation of the corresponding nonparametric functions of time or covariate. The tests are based on the penalized partial likelihood and are derived by viewing the inverse of the smoothing parameter as a variance component and testing an equivalent null hypothesis that the variance component is zero. We show that the tests have a size close to the nominal level and good power against general alternatives, and we apply them to data from a cancer clinical trial.
DA - 2006/9//
PY - 2006/9//
DO - 10.1111/j.1541-0420.2005.00521.x
VL - 62
IS - 3
SP - 803-812
SN - 0006-341X
KW - Cox model
KW - penalized partial likelihood
KW - smoothing parameter
KW - variance component
ER -
TY - JOUR
TI - Semiparametric transformation models for the case-cohort study
AU - Lu, WB
AU - Tsiatis, AA
T2 - BIOMETRIKA
AB - A general class of semiparametric transformation models is studied for analysing survival data from the case-cohort design, which was introduced by Prentice (1986). Weighted estimating equations are proposed for simultaneous estimation of the regression parameters and the transformation function. It is shown that the resulting regression estimators are asymptotically normal, with variance-covariance matrix that has a closed form and can be consistently estimated by the usual plug-in method. Simulation studies show that the proposed approach is appropriate for practical use. An application to a case-cohort dataset from the Atherosclerosis Risk in Communities study is also given to illustrate the methodology.
DA - 2006/3//
PY - 2006/3//
DO - 10.1093/biomet/93.1.207
VL - 93
IS - 1
SP - 207-214
SN - 0006-3444
KW - case-cohort design
KW - martingale
KW - transformation model
KW - weighted estimating equation
ER -
TY - JOUR
TI - Professor C. R. Mudgeon and the "order," or writing regression questions so that students do not need a calculator
AU - Monahan, JF
T2 - AMERICAN STATISTICIAN
AB - Professor Mudgeon writes simple linear regression questions so that the numbers always work out nicely. A student uses knowledge of linear models to learn that by constructing errors that are orthogonal to the design matrix, regression coefficients can be set to any desired value. An example is provided to construct data to follow a particular example.
DA - 2006/2//
PY - 2006/2//
DO - 10.1198/000313006X90323
VL - 60
IS - 1
SP - 50-52
SN - 1537-2731
KW - design matrix
KW - orthogonal contrasts
KW - simple linear regression
ER -
TY - JOUR
TI - Material surface design to counter electromagnetic interrogation of targets
AU - Banks, HT
AU - Ito, K
AU - Kepler, GM
AU - Toivanen, JA
T2 - SIAM JOURNAL ON APPLIED MATHEMATICS
AB - Utilization of controllable ferromagnetic layers coating a conducting object to provide an attenuation capability against electromagnetic interrogation is discussed. The problem is formulated as a differential game and/or a robust optimization. The scattered field due to interrogation can be attenuated with the assumption of an uncertainty in the interrogation wave numbers. The controllable layer composed of ferromagnetic materials [H. How and C. Vittoria, Implementation of Microwave Active Nulling, private communication; H. How and C. Vittoria, IEEE Trans. Microwave Theory Tech., 52 (2004), pp. 2177-2182] is incorporated in a mathematical formulation based on the time-harmonic Maxwell equation. Fresnel's law for the reflectance index is extended to the electromagnetic propagation in anisotropic composite layers of ferromagnetic and electronic devices and is used to demonstrate feasibility of control of reflections. Our methodology is also tested for a nonplanar geometry of the conducting object (an NACA airfoil) in which we report our findings in the form of reduced radar cross sections (RCS)\@.
DA - 2006///
PY - 2006///
DO - 10.1137/040621430
VL - 66
IS - 3
SP - 1027-1049
SN - 1095-712X
KW - electromagnetic
KW - inverse scattering
KW - attenuation
ER -
TY - JOUR
TI - Increasing kernel density for two inbred lines of maize
AU - Thompson, Donald L.
AU - Goodman, Major M.
T2 - CROP SCIENCE
AB - Improving grain quality of maize (Zea mays L.), including endosperm hardness and density, is often a breeding objective. Dense seed is preferred by dry millers and for alkaline processing, and can command a price premium at market. This study attempted to increase kernel density in a backcrossing program for two inbreds of maize using two selection techniques, specific gravity of kernels and the percentage of sinking kernels in a salt solution (or sinkers). Two inbreds, B73G and A632, were crossed with synthetics exhibiting apparent high kernel density, and several generations of backcrossing and self-pollination followed. Examples of mean comparisons of backcross-derived inbreds with the recurrent parents, B73G and A632 are as follows: B73G–Specific gravity, 1.251 and 1.206; Sinkers, 62.3 and 14.9%; and A632–Specific gravity, 1.266 and 1.250; Sinkers 45.4 and 29.1%. Both the specific gravity and sinkers techniques were successful for increasing kernel density during backcrossing.
DA - 2006///
PY - 2006///
DO - 10.2135/cropsci2006.02.0111
VL - 46
IS - 5
SP - 2179-2182
SN - 1435-0653
ER -
TY - JOUR
TI - Identification of quantitative trait loci for resistance to southern leaf blight and days to anthesis in a maize recombinant inbred line population
AU - Balint-Kurti, P. J.
AU - Krakowsky, M. D.
AU - Jines, M. P.
AU - Robertson, L. A.
AU - Molnar, T. L.
AU - Goodman, M. M.
AU - Holland, J. B.
T2 - PHYTOPATHOLOGY
AB - A recombinant inbred line population derived from a cross between the maize lines NC300 (resistant) and B104 (susceptible) was evaluated for resistance to southern leaf blight (SLB) disease caused by Cochliobolus heterostrophus race O and for days to anthesis in four environments (Clayton, NC, and Tifton, GA, in both 2004 and 2005). Entry mean and average genetic correlations between disease ratings in different environments were high (0.78 to 0.89 and 0.9, respectively) and the overall entry mean heritability for SLB resistance was 0.89. When weighted mean disease ratings were fitted to a model using multiple interval mapping, seven potential quantitative trait loci (QTL) were identified, the two strongest being on chromosomes 3 (bin 3.04) and 9 (bin 9.03–9.04). These QTL explained a combined 80% of the phenotypic variation for SLB resistance. Some time-point-specific SLB resistance QTL were also identified. There was no significant correlation between disease resistance and days to anthesis. Six putative QTL for time to anthesis were identified, none of which coincided with any SLB resistance QTL.
DA - 2006/10//
PY - 2006/10//
DO - 10.1094/PHYTO-96-1067
VL - 96
IS - 10
SP - 1067-1071
SN - 1943-7684
KW - flowering
KW - Helminthosporium
ER -
TY - JOUR
TI - Homogenization of periodically varying coefficients in electromagnetic materials
AU - Banks, H. T.
AU - Bokil, V. A.
AU - Cioranescu, D.
AU - Gibson, N. L.
AU - Griso, G.
AU - Miara, B.
T2 - JOURNAL OF SCIENTIFIC COMPUTING
AB - In this paper, we employ the periodic unfolding method for simulating the electromagnetic field in a composite material exhibiting heterogeneous microstructures which are described by spatially periodic parameters. We consider cell problems to calculate the effective parameters for a Debye dielectric medium in the case of a circular microstructure in two dimensions. We assume that the composite materials are quasi-static in nature, i.e., the wavelength of the electromagnetic field is much larger than the relevant dimensions of the microstructure.
DA - 2006/9//
PY - 2006/9//
DO - 10.1007/s10915-006-9091-y
VL - 28
IS - 2-3
SP - 191-221
SN - 1573-7691
KW - Homogenization
KW - Maxwell's equations
KW - debye dielectric materials
KW - pulsed antenna source microwaves
ER -
TY - JOUR
TI - Estimating the abundance of mouse populations of known size: Promises and pitfalls of new methods
AU - Conn, PB
AU - Arthur, AD
AU - Bailey, LL
AU - Singleton, GR
T2 - ECOLOGICAL APPLICATIONS
AB - Knowledge of animal abundance is fundamental to many ecological studies. Frequently, researchers cannot determine true abundance, and so must estimate it using a method such as mark-recapture or distance sampling. Recent advances in abundance estimation allow one to model heterogeneity with individual covariates or mixture distributions and to derive multimodel abundance estimators that explicitly address uncertainty about which model parameterization best represents truth. Further, it is possible to borrow information on detection probability across several populations when data are sparse. While promising, these methods have not been evaluated using mark-recapture data from populations of known abundance, and thus far have largely been overlooked by ecologists. In this paper, we explored the utility of newly developed mark-recapture methods for estimating the abundance of 12 captive populations of wild house mice (Mus musculus). We found that mark-recapture methods employing individual covariates yielded satisfactory abundance estimates for most populations. In contrast, model sets with heterogeneity formulations consisting solely of mixture distributions did not perform well for several of the populations. We show through simulation that a higher number of trapping occasions would have been necessary to achieve good estimator performance in this case. Finally, we show that simultaneous analysis of data from low abundance populations can yield viable abundance estimates.
DA - 2006/4//
PY - 2006/4//
DO - 10.1890/1051-0761(2006)016[0829:ETAOMP]2.0.CO;2
VL - 16
IS - 2
SP - 829-837
SN - 1939-5582
KW - abundance estimation
KW - Huggins-Alho model
KW - MARK
KW - mark-recapture
KW - model averaging
KW - Mus musculus
KW - Pledger model
ER -
TY - JOUR
TI - Comprehensive trend analysis of nutrients and related variables in a large eutrophic estuary: A decadal study of anthropogenic and climatic influences
AU - Burkholder, JoAnn M.
AU - Dickey, David A.
AU - Kinder, Carol A.
AU - Reed, Robert E.
AU - Mallin, Michael A.
AU - McIver, Matthew R.
AU - Cahoon, Lawrence B.
AU - Melia, Greg
AU - Brownie, Cavell
AU - Smith, Joy
AU - Deamer, Nora
AU - Springer, Jeffrey
AU - Glasgow, Howard B.
AU - Toms, David
T2 - LIMNOLOGY AND OCEANOGRAPHY
AB - We used a decadal data set, with weekly to biweekly sampling in April—October and monthly sampling in November—March, to characterize climatic (hurricane‐level storms, a sustained 3‐yr drought) and anthropogenic influences on N and P concentrations and loadings to a large eutrophic, poorly flushed estuary, the Neuse Estuary of the Albemarle—Pamlico Estuarine System. Mass volume transport data were obtained with cross‐estuary transect flow measurements taken near the entrance to the estuary. Although trends were minimally influenced by hurricanes, analyses were significantly affected by the sustained drought near the end of the study. As examples, decreasing trends in total N (TN), total P (TP), and bottom‐water dissolved oxygen concentrations, and in TN loadings were significant considering all data, but these trends were not significant when the sustained drought was excluded from analysis. In addition, the trend in TN loading was especially sensitive to the initial sampling period. NH 4 + concentrations dramatically increased (overall by ~500%) as a persistent trend regardless of attempts to control for climatic events. An increasing trend in NH 4 + also was documented in an adjacent, rapidly flushed Coastal Plain estuary, the Cape Fear. The NH 4 + data suggest a regional‐scale effect of high inputs from inadequately controlled, increasing nonpoint sources. The fragility of TN loading trends, the striking increase in NH 4 + concentrations, and the lack of management emphasis on controlling nonpoint sources such as “new” industrialized swine production collectively do not support recent reports of achievement of a 30% reduction in TN loading to the Neuse. Nonpoint sources remain a critical target for reduction to alleviate the negative effects of cultural eutrophication in this system, as in many estuaries throughout the world.
DA - 2006/1//
PY - 2006/1//
DO - 10.4319/lo.2006.51.1_part_2.0463
VL - 51
IS - 1
SP - 463-487
SN - 1939-5590
ER -
TY - JOUR
TI - Comparing the potential effectiveness of conservation planning approaches in central North Carolina, USA
AU - Hess, GR
AU - Koch, FH
AU - Rubino, MJ
AU - Eschelbach, KA
AU - Drew, CA
AU - Favreau, JM
T2 - BIOLOGICAL CONSERVATION
AB - Abstract We compared four approaches to conservation site selection to protect forest biodiversity in the Triangle Region of North Carolina, USA. Using biological inventory data and an inventory-based conservation plan as benchmarks, we evaluated the potential effectiveness of a focal species plan and three “simple” plans (large forested patches, close to wetlands and riparian areas, diverse forest types). Effectiveness was measured in three ways: the number of inventory elements captured at least once by the plan (representation), the total number of inventory elements captured (completeness), and the proportion of land in the inventory-based plan included (overlap). We further examined the potential effectiveness of the simple plans by calculating their overlap with land identified by the focal species approach. The simple and focal species plans did not differ markedly in terms of representation, but diverged when completeness and overlap were considered. Although representation rates for all four plans were relatively high, lower rates for completeness and overlap raise concerns about long-term viability. The simple plans did not identify the same lands as the focal species plan, and are thus unlikely to provide appropriate habitat for the focal species. Each approach we tested failed to capture some subset of species and communities, highlighting the importance of explicit conservation targets and consideration of ecological processes. Forced to act quickly and with little data, our findings suggest using initially a set of complementary simple plans, each focused on a different habitat type. This should be considered a stopgap measure, however, while more sophisticated plans are constructed, defining explicit conservation targets and considering ecological processes.
DA - 2006/3//
PY - 2006/3//
DO - 10.1016/j.biocon.2005.10.003
VL - 128
IS - 3
SP - 358-368
SN - 1873-2917
KW - conservation planning
KW - focal species
KW - biological inventory data
KW - reserve design
KW - surrogate species
KW - conservation targets
ER -
TY - JOUR
TI - A state-dependent Riccati equation-based estimator approach for HIV feedback control
AU - Banks, HT
AU - Kwon, HD
AU - Toivanen, JA
AU - Tran, HT
T2 - OPTIMAL CONTROL APPLICATIONS & METHODS
AB - We consider optimal dynamic multidrug therapies for human immunodeficiency virus (HIV) type 1 infection. In this context, we describe an optimal tracking problem attempting to drive the states of the system to a stationary state in which the viral load is low and the immune response is strong. We consider optimal feedback control with full-state as well as with partial-state measurements. In the case of partial-state measurement, a state estimator is constructed based on viral load and T-cell count measurements. We demonstrate by numerical simulations that by anticipation of and response to the disease progression, the dynamic multidrug strategy reduces the viral load, increases the CD4+ T-cell count and improves the immune response. Copyright © 2006 John Wiley & Sons, Ltd.
DA - 2006///
PY - 2006///
DO - 10.1002/oca.773
VL - 27
IS - 2
SP - 93-121
SN - 1099-1514
KW - multidrug therapies
KW - feedback control
KW - estimator
KW - HIV model
KW - SDRE
ER -
TY - JOUR
TI - A spatial analysis of basketball shot chart data
AU - Reich, BJ
AU - Hodges, JS
AU - Carlin, BP
AU - Reich, AM
T2 - AMERICAN STATISTICIAN
AB - Basketball coaches at all levels use shot charts to study shot locations and outcomes for their own teams as well as upcoming opponents. Shot charts are simple plots of the location and result of each shot taken during a game. Although shot chart data are rapidly increasing in richness and availability, most coaches still use them purely as descriptive summaries. However, a team's ability to defend a certain player could potentially be improved by using shot data to make inferences about the player's tendencies and abilities. This article develops hierarchical spatial models for shot-chart data, which allow for spatially varying effects of covariates. Our spatial models permit differential smoothing of the fitted surface in two spatial directions, which naturally correspond to polar coordinates: distance to the basket and angle from the line connecting the two baskets. We illustrate our approach using the 2003–2004 shot chart data for Minnesota Timberwolves guard Sam Cassell.
DA - 2006/2//
PY - 2006/2//
DO - 10.1198/000313006X90305
VL - 60
IS - 1
SP - 3-12
SN - 1537-2731
KW - Bayesian
KW - conditionally autoregressive prior
KW - sports
ER -
TY - JOUR
TI - A likelihood ratio test for separability of covariances
AU - Mitchell, MW
AU - Genton, MG
AU - Gumpertz, ML
T2 - JOURNAL OF MULTIVARIATE ANALYSIS
AB - We propose a formal test of separability of covariance models based on a likelihood ratio statistic. The test is developed in the context of multivariate repeated measures (for example, several variables measured at multiple times on many subjects), but can also apply to a replicated spatio-temporal process and to problems in meteorology, where horizontal and vertical covariances are often assumed to be separable. Separable models are a common way to model spatio-temporal covariances because of the computational benefits resulting from the joint space–time covariance being factored into the product of a covariance function that depends only on space and a covariance function that depends only on time. We show that when the null hypothesis of separability holds, the distribution of the test statistic does not depend on the type of separable model. Thus, it is possible to develop reference distributions of the test statistic under the null hypothesis. These distributions are used to evaluate the power of the test for certain nonseparable models. The test does not require second-order stationarity, isotropy, or specification of a covariance model. We apply the test to a multivariate repeated measures problem.
DA - 2006/5//
PY - 2006/5//
DO - 10.1016/j.jmva.2005.07.005
VL - 97
IS - 5
SP - 1025-1043
SN - 0047-259X
KW - Kronecker product
KW - multivariate regression
KW - multivariate repeated measures
KW - nonstationary
KW - separable covariance
KW - spatio-temporal process
ER -
TY - JOUR
TI - A Multivariate two-sample mean test for small sample size and missing data
AU - Wu, Yujun
AU - Genton, Marc G.
AU - Stefanski, Leonard A.
T2 - BIOMETRICS
AB - Summary We develop a new statistic for testing the equality of two multivariate mean vectors. A scaled chi-squared distribution is proposed as an approximating null distribution. Because the test statistic is based on componentwise statistics, it has the advantage over Hotelling's T2 test of being applicable to the case where the dimension of an observation exceeds the number of observations. An appealing feature of the new test is its ability to handle missing data by relying on only componentwise sample moments. Monte Carlo studies indicate good power compared to Hotelling's T2 and a recently proposed test by Srivastava (2004, Technical Report, University of Toronto). The test is applied to drug discovery data.
DA - 2006/9//
PY - 2006/9//
DO - 10.1111/j.1541-0420.2006.00533.x
VL - 62
IS - 3
SP - 877-885
SN - 0006-341X
KW - drug discovery
KW - high-dimensional data
KW - Hotelling's T-2
KW - small n large p
ER -
TY - JOUR
TI - Spatio-temporal analysis of wildfire ignitions in the St Johns River Water Management District, Florida
AU - Genton, MG
AU - Butry, DT
AU - Gumpertz, ML
AU - Prestemon, JP
T2 - INTERNATIONAL JOURNAL OF WILDLAND FIRE
AB - We analyse the spatio-temporal structure of wildfire ignitions in the St Johns River Water Management District in north-eastern Florida. We show, using tools to analyse point patterns (e.g. the L-function), that wildfire events occur in clusters. Clustering of these events correlates with irregular distribution of fire ignitions, including lightning and human sources, and fuels on the landscape. In addition, we define a relative clustering index that summarizes the amount of clustering over various spatial scales. We carry our analysis in three steps: purely temporal, purely spatial, and spatio-temporal. Our results show that arson and lightning are the leading causes of wildfires in this region and that ignitions by railroad, lightning, and arson are spatially more clustered than ignitions by other accidental causes.
DA - 2006///
PY - 2006///
DO - 10.1071/WF04034
VL - 15
IS - 1
SP - 87-97
SN - 1448-5516
KW - clustering
KW - confidence envelope
KW - fire occurrence
KW - L-function
KW - point process
ER -
TY - JOUR
TI - Semiparametric efficient estimation of survival distributions in two-stage randomisation designs in clinical trials with censored data
AU - Wahed, AS
AU - Tsiatis, AA
T2 - BIOMETRIKA
AB - Two-stage randomisation designs are useful in the evaluation of combination therapies where patients are initially randomised to an induction therapy and then, depending upon their response and consent, are randomised to a maintenance therapy. In this paper we derive the best regular asymptotically linear estimator for the survival distribution and related quantities of treatment regimes. We propose an estimator which is easily computable and is more efficient than existing estimators. Large-sample properties of the proposed estimator are derived and comparisons with other estimators are made using simulation.
DA - 2006/3//
PY - 2006/3//
DO - 10.1093/biomet/93.1.163
VL - 93
IS - 1
SP - 163-177
SN - 0006-3444
KW - censoring
KW - influence function
KW - inverse probability weighted estimator
KW - potential outcome
KW - regular asymptotically linear estimator
KW - two-stage design
ER -
TY - JOUR
TI - Selecting among available, elite tropical maize inbreds for use in long-term temperate breeding
AU - Nelson, P. T.
AU - Jines, M. P.
AU - Goodman, M. M.
T2 - Maydica
DA - 2006///
PY - 2006///
VL - 51
IS - 2
SP - 255-262
ER -
TY - JOUR
TI - Sampling hazelnuts for aflatoxin: Uncertainty associated with sampling, sample preparation, and analysis
AU - Ozay, G.
AU - Seyhan, F.
AU - Yilmaz, A.
AU - Whitaker, T. B.
AU - Slate, A. B.
AU - Giesbrecht, F.
T2 - Journal of AOAC International
DA - 2006///
PY - 2006///
VL - 89
IS - 4
SP - 1004-1011
ER -
TY - JOUR
TI - Sampling almonds for aflatoxin, part I: Estimation of uncertainty associated with sampling, sample preparation, and analysis
AU - Whitaker, T. B.
AU - Slate, A. B.
AU - Jacobs, M.
AU - Hurley, J. M.
AU - Adams, J. C.
AU - Giesbrecht, F. C.
T2 - Journal of AOAC International
DA - 2006///
PY - 2006///
VL - 89
IS - 4
SP - 1027-1034
ER -
TY - JOUR
TI - Responses of soil microbial biomass and N availability to transition strategies from conventional to organic farming systems
AU - Tu, C
AU - Louws, FJ
AU - Creamer, NG
AU - Mueller, JP
AU - Brownie, C
AU - Fager, K
AU - Bell, M
AU - Hu, SJ
T2 - AGRICULTURE ECOSYSTEMS & ENVIRONMENT
AB - Abstract Organic farming can enhance soil biodiversity, alleviate environmental concerns and improve food safety through eliminating the applications of synthetic chemicals. However, yield reduction due to nutrient limitation and pest incidence in the early stages of transition from conventional to organic systems is a major concern for organic farmers, and is thus a barrier to implementing the practice of organic farming. Therefore, identifying transition strategies that minimize yield loss is critical for facilitating the implementation of organic practices. Soil microorganisms play a dominant role in nutrient cycling and pest control in organic farming systems, and their responses to changes in soil management practices may critically impact crop growth and yield. Here we examined soil microbial biomass and N supply in response to several strategies for transitioning from conventional to organic farming systems in a long-term field experiment in Goldsboro, NC, USA. The transitional strategies included one fully organic strategy (ORG) and four reduced-input strategies (withdrawal of each or gradual reduction of major conventional inputs—synthetic fertilizers, pesticides (insecticides/fungicides), and herbicides), with a conventional practice (CNV) serving as a control. Microbial biomass and respiration rate were more sensitive to changes in soil management practices than total C and N. In the first 2 years, the ORG was most effective in enhancing soil microbial biomass C and N among the transition strategies, but was accompanied with high yield losses. By the third year, soil microbial biomass C and N in the reduced-input transition strategies were statistically significantly greater than those in the CNV (averaging 32 and 35% higher, respectively), although they were slightly lower than those in the ORG (averaging 13 and 17% lower, respectively). Soil microbial respiration rate and net N mineralization in all transitional systems were statistically significantly higher than those in the CNV (averagely 83 and 66% greater, respectively), with no differences among the various transition strategies. These findings suggest that the transitional strategies that partially or gradually reduce conventional inputs can serve as alternatives that could potentially minimize economic hardships as well as benefit microbial growth during the early stages of transition to organic farming systems.
DA - 2006/4//
PY - 2006/4//
DO - 10.1016/j.agee.2005.09.013
VL - 113
IS - 1-4
SP - 206-215
SN - 1873-2305
KW - conventional farming system
KW - microbial biomass
KW - nitrogen supply
KW - organic farming system
KW - reduced-input transition strategy
ER -
TY - JOUR
TI - Registration of nine high-yielding tropical by temperate maize germplasm lines adapted for the southern USA
AU - Carson, M. L.
AU - Balint-Kurti, P. J.
AU - Blanco, M.
AU - Millard, M.
AU - Duvick, S.
AU - Holley, R.
AU - Hudyncia, J.
AU - Goodman, M. M.
T2 - CROP SCIENCE
AB - Crop ScienceVolume 46, Issue 4 p. 1825-1826 Registrations of Germplasm Registration of Nine High-Yielding Tropical by Temperate Maize Germplasm Lines Adapted for the Southern USA M.L. Carson, M.L. Carson USDA-ARS Cereal Disease Lab, Univ. of Minnesota, Saint Paul, MN, 55108Search for more papers by this authorP.J. Balint-Kurti, Corresponding Author P.J. Balint-Kurti peter_balintkurti@ncsu.edu USDA-ARS, North Carolina State Univ., Dep. of Plant Pathology, Raleigh, NC, 27695-7616Corresponding author (peter_balintkurti@ncsu.edu)Search for more papers by this authorM. Blanco, M. Blanco USDA-ARS, Iowa State Univ., Ames, IA, 50011Search for more papers by this authorM. Millard, M. Millard USDA-ARS, North Central Regional Plant Introduction Station, Iowa State Univ., Ames, IA, 50011Search for more papers by this authorS. Duvick, S. Duvick USDA-ARS, Iowa State Univ., Ames, IA, 50011Search for more papers by this authorR. Holley, R. Holley Syngenta Seeds, Inc., Henderson, KY, 42420 Pioneer Hi-bred, DuPont Agriculture and Nutrition, RR1, Box 90a, Princeton, IN, 47670Search for more papers by this authorJ. Hudyncia, J. Hudyncia USDA-ARS, North Carolina State Univ., Dep. of Plant Pathology, Raleigh, NC, 27695-7616Search for more papers by this authorM.M. Goodman, M.M. Goodman Dep. of Crop Science, North Carolina State Univ., Raleigh, NC, 27695Search for more papers by this author M.L. Carson, M.L. Carson USDA-ARS Cereal Disease Lab, Univ. of Minnesota, Saint Paul, MN, 55108Search for more papers by this authorP.J. Balint-Kurti, Corresponding Author P.J. Balint-Kurti peter_balintkurti@ncsu.edu USDA-ARS, North Carolina State Univ., Dep. of Plant Pathology, Raleigh, NC, 27695-7616Corresponding author (peter_balintkurti@ncsu.edu)Search for more papers by this authorM. Blanco, M. Blanco USDA-ARS, Iowa State Univ., Ames, IA, 50011Search for more papers by this authorM. Millard, M. Millard USDA-ARS, North Central Regional Plant Introduction Station, Iowa State Univ., Ames, IA, 50011Search for more papers by this authorS. Duvick, S. Duvick USDA-ARS, Iowa State Univ., Ames, IA, 50011Search for more papers by this authorR. Holley, R. Holley Syngenta Seeds, Inc., Henderson, KY, 42420 Pioneer Hi-bred, DuPont Agriculture and Nutrition, RR1, Box 90a, Princeton, IN, 47670Search for more papers by this authorJ. Hudyncia, J. Hudyncia USDA-ARS, North Carolina State Univ., Dep. of Plant Pathology, Raleigh, NC, 27695-7616Search for more papers by this authorM.M. Goodman, M.M. Goodman Dep. of Crop Science, North Carolina State Univ., Raleigh, NC, 27695Search for more papers by this author First published: 01 July 2006 https://doi.org/10.2135/cropsci2005.08-0283Citations: 8 Registration by CSSA. Read the full textAboutPDF 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 No abstract is available for this article.Citing Literature Volume46, Issue4July–August 2006Pages 1825-1826 RelatedInformation
DA - 2006///
PY - 2006///
DO - 10.2135/cropsci2005.08-0283
VL - 46
IS - 4
SP - 1825-1826
SN - 1435-0653
ER -
TY - JOUR
TI - Registration of 20 GEM maize breeding germplasm lines adapted to the southern USA
AU - Balint-Kurti, PJ
AU - Blanco, M
AU - Millard, M
AU - Duvick, S
AU - Holland, J
AU - Clements, M
AU - Holley, R
AU - Carson, ML
AU - Goodman, MM
T2 - CROP SCIENCE
AB - Crop ScienceVolume 46, Issue 2 p. 996-998 Registrations of Germplasm Registration of 20 GEM Maize Breeding Germplasm Lines Adapted to the Southern USA P.J. Balint-Kurti, Corresponding Author P.J. Balint-Kurti [email protected] USDA-ARS, Plant Science Research Unit, North Carolina State University, Raleigh, N.C., 27695-7616Author for correspondence ([email protected])Search for more papers by this authorM. Blanco, M. Blanco USDA-ARS, Iowa State University, Ames, IA, 50011Search for more papers by this authorM. Millard, M. Millard North Central Regional Plant Introduction Station (NC7), USDA-ARS & Iowa State University, Ames, IA, 50011Search for more papers by this authorS. Duvick, S. Duvick USDA-ARS, Iowa State University, Ames, IA, 50011Search for more papers by this authorJ. Holland, J. Holland USDA-ARS, Plant Science Research Unit, North Carolina State University, Raleigh, N.C., 27695-7616Search for more papers by this authorM. Clements, M. Clements USDA-ARS Corn Host Plant Resistance Research Unit, Mississippi State, MS, 39762Search for more papers by this authorR. Holley, R. Holley Syngenta Seeds, Inc., Henderson, KY, 42420Search for more papers by this authorM.L. Carson, M.L. Carson USDA-ARS Cereal Disease Lab, Univ. of Minnesota, Saint Paul, MN, 55108Search for more papers by this authorM.M. Goodman, M.M. Goodman Department of Crop Science, North Carolina State University, Raleigh, NC, 27695 Pioneer Hibred, DuPont Agriculture and Nutrition, RR1, Box 90a, Princeton, IN, 47670Search for more papers by this author P.J. Balint-Kurti, Corresponding Author P.J. Balint-Kurti [email protected] USDA-ARS, Plant Science Research Unit, North Carolina State University, Raleigh, N.C., 27695-7616Author for correspondence ([email protected])Search for more papers by this authorM. Blanco, M. Blanco USDA-ARS, Iowa State University, Ames, IA, 50011Search for more papers by this authorM. Millard, M. Millard North Central Regional Plant Introduction Station (NC7), USDA-ARS & Iowa State University, Ames, IA, 50011Search for more papers by this authorS. Duvick, S. Duvick USDA-ARS, Iowa State University, Ames, IA, 50011Search for more papers by this authorJ. Holland, J. Holland USDA-ARS, Plant Science Research Unit, North Carolina State University, Raleigh, N.C., 27695-7616Search for more papers by this authorM. Clements, M. Clements USDA-ARS Corn Host Plant Resistance Research Unit, Mississippi State, MS, 39762Search for more papers by this authorR. Holley, R. Holley Syngenta Seeds, Inc., Henderson, KY, 42420Search for more papers by this authorM.L. Carson, M.L. Carson USDA-ARS Cereal Disease Lab, Univ. of Minnesota, Saint Paul, MN, 55108Search for more papers by this authorM.M. Goodman, M.M. Goodman Department of Crop Science, North Carolina State University, Raleigh, NC, 27695 Pioneer Hibred, DuPont Agriculture and Nutrition, RR1, Box 90a, Princeton, IN, 47670Search for more papers by this author First published: 01 March 2006 https://doi.org/10.2135/cropsci2005.04-0013Citations: 24 Registration by CSSA. Read the full textAboutPDF 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 No abstract is available for this article.Citing Literature Volume46, Issue2March–April 2006Pages 996-998 RelatedInformation
DA - 2006///
PY - 2006///
DO - 10.2135/cropsci2005.04-0013
VL - 46
IS - 2
SP - 996-998
SN - 0011-183X
ER -
TY - JOUR
TI - Quantifying a possible Miocene phyletic change in Hemipristis (Chondrichthyes) teeth
AU - Chandler, R. E.
AU - Chiswell, K. E.
AU - Faulkner, G. D.
T2 - Palaeontologia Electronica
DA - 2006///
PY - 2006///
VL - 9
IS - 1
ER -
TY - JOUR
TI - Latent-model robustness in structural measurement error models
AU - Huang, XZ
AU - Stefanski, LA
AU - Davidian, M
T2 - BIOMETRIKA
AB - SUMMARY We present methods for diagnosing the effects of model misspecification of the true predictor distribution in structural measurement error models. We first formulate latent model robustness theoretically. Then we provide practical techniques for examining the adequacy of an assumed latent predictor model. The methods are illustrated via analytical examples, application to simulated data and with data from a study of coronary heart disease.
DA - 2006/3//
PY - 2006/3//
DO - 10.1093/biomet/93.1.53
VL - 93
IS - 1
SP - 53-64
SN - 1464-3510
KW - bias
KW - latent variable
KW - measurement error
KW - remeasurement method
KW - simulation extrapolation
KW - structural modelling
ER -
TY - JOUR
TI - Genetics of sex pheromone blend differences between Heliothis virescens and Heliothis subflexa: a chromosome mapping approach
AU - Sheck, AL
AU - Groot, AT
AU - Ward, CM
AU - Gemeno, C
AU - Wang, J
AU - Brownie, C
AU - Schal, C
AU - Gould, F
T2 - JOURNAL OF EVOLUTIONARY BIOLOGY
AB - Males of the noctuid moths, Heliothis virescens and H. subflexa locate mates based on species-specific responses to female-emitted pheromones that are composed of distinct blends of volatile compounds. We conducted genetic crosses between these two species and used AFLP marker-based mapping of backcross families (H. subflexa direction) to determine which of the 30 autosomes in these moths contained quantitative trait loci (QTL) controlling the proportion of specific chemical components in the pheromone blends. Presence/absence of single H. virescens chromosomes accounted for 7-34% of the phenotypic variation among backcross females in seven pheromone components. For a set of three similar 16-carbon acetates, two H. virescens chromosomes interacted in determining their relative amounts within the pheromone gland and together accounted for 53% of the phenotypic variance. Our results are discussed relative to theories about population genetic processes and biochemical mechanisms involved in the evolution of new sexual communication systems.
DA - 2006/3//
PY - 2006/3//
DO - 10.1111/j.1420-9101.2005.00999.x
VL - 19
IS - 2
SP - 600-617
SN - 1420-9101
KW - evolution
KW - Lepidoptera
KW - mate recognition
KW - Noctuidae
KW - pheromones
KW - quantitative trait loci
KW - sexual isolation
ER -
TY - JOUR
TI - Effects of chronic avian malaria (Plasmodium relictum) infection on reproductive success of Hawaii Amakihi (Hemignathus virens)
AU - Kilpatrick, A. Marm
AU - LaPointe, Dennis A.
AU - Atkinson, Carter T.
AU - Woodworth, Bethany L.
AU - Lease, Julie K.
AU - Reiter, Matthew E.
AU - Gross, Kevin
T2 - AUK
AB - We studied the effects of chronic avian malaria (Plasmodium relictum) infections on the reproductive success of a native Hawaiian honeycreeper, Hawaii Amakihi (Hemignathus virens). Chronic malaria infections in male and female parents did not significantly reduce reproductive success as measured by clutch size, hatching success, fledging mass, number of nestlings fledged, nesting success (daily survival rate), and minimum fledgling survival. In fact, nesting success of pairs with chronically infected males was significantly higher than those with uninfected males (76% vs. 38%), and offspring that had at least one parent that had survived the acute phase of malaria infection had a significantly greater chance of being resighted the following year (25% vs. 10%). The reproduction and survival of infected birds were sufficient for a per-capita population growth rate >1, which suggests that chronically infected Hawaii Amakihi could support a growing population.
DA - 2006/7//
PY - 2006/7//
DO - 10.1642/0004-8038(2006)123[764:EOCAMP]2.0.CO;2
VL - 123
IS - 3
SP - 764-774
SN - 1938-4254
KW - disease
KW - Drepanidini
KW - evolution
KW - fitness
KW - fledgling survival
KW - Hawaii Amakihi
KW - Hemignathus virens
KW - Plasmodium relictum
ER -
TY - JOUR
TI - Combining multistate capture-recapture data with tag recoveries to estimate demographic parameters
AU - Kendall, W. L.
AU - Conn, P. B.
AU - Hines, J. E.
T2 - Ecology (Brooklyn, New York, N.Y.)
DA - 2006///
PY - 2006///
VL - 87
IS - 1
SP - 169-177
ER -
TY - JOUR
TI - A population-based latent variable approach for association mapping of quantitative trait loci
AU - Wang, T
AU - Weir, B
AU - Zeng, ZB
T2 - ANNALS OF HUMAN GENETICS
AB - A population-based latent variable approach is proposed for association mapping of quantitative trait loci (QTL), using multiple closely linked genetic markers within a small candidate region in the genome. By incorporating QTL as latent variables into a penetrance model, the QTL are flexible to characterize either alleles at putative trait loci or potential risk haplotypes/sub-haplotypes of the markers. Under a general likelihood framework, we develop an EM-based algorithm to estimate genetic effects of the QTL and haplotype frequencies of the QTL and markers jointly. Closed form solutions derived in the maximization step of the EM procedure for updating the joint haplotype frequencies of QTL and markers can effectively reduce the computational intensity. Various association measures between QTL and markers can then be derived from the haplotype frequencies of markers and used to infer QTL positions. The likelihood ratio statistic also provides a joint test for association between a quantitative trait and marker genotypes without requiring adjustment for the multiple testing. Extensive simulation studies are performed to evaluate the approach.
DA - 2006/7//
PY - 2006/7//
DO - 10.1111/j.1469-1809.2006.00264.x
VL - 70
SP - 506-523
SN - 0003-4800
KW - association mapping
KW - maximum likelihood
KW - haplotype
KW - latent variable
KW - EM algorithm
ER -
TY - JOUR
TI - A macroarray expression analysis of novel cDNAs vital for growth initiation and primary metabolism during development of Heterobasidion parviporum conidiospores
AU - Li, Guosheng
AU - Osborne, Jason
AU - Asiegbu, Fred O.
T2 - ENVIRONMENTAL MICROBIOLOGY
AB - The pathogen Heterobasidion parviporum causes significant losses to forest industries in Europe and North America. The fungus is spread by basidiospores on fresh stumps where it differentiates into a specialized infection hyphae to colonize its host. This differentiation is driven by recognition and its strategic success lies in its ability to do this rapidly and efficiently. To investigate gene expression pattern during the spore germination stages, mRNA of germinated and ungerminated conidiospores of H. parviporum harvested at distinct developmental time points (18, 36, 72 and 120 h) corresponding to periods of isotropic/germ tube emergence, polarized apical, early and late mycelial lateral branching growth stages was hybridized to macroarrays containing 338 cDNAs from H. parviporum. The results of the statistical analysis identified a total of 24, 39, 38 and 30 genes that were differentially upregulated at 18, 36, 72 and 120 h, respectively, relative to time 0. The number of the downregulated genes was 4, 6, 8 and 13 genes respectively. During isotropic, polarized and mycelial growth stages, majority of the differentially expressed genes belonged to functional categories metabolism (21-32%) and protein formation (21-30%). Real-time polymerase chain reaction (real-time-PCR) data essentially confirmed the macroarray analyses. The real-time-PCR result showed that transcript levels of genes involved in glucose metabolism (phosphoglucomutase), amino acid metabolism (arginase, delta-1-pyrroline-5-carboxylate reductase, sulfur metabolism-negative regulator, imidazoleglycerol phosphate dehydratase) and protein synthesis (40S ribosomal protein S15) were significantly increased during polarized growth (36 h) stage but decreased at early and late stages of mycelial growth (72-120 h). An understanding of the various molecular and physiological processes during the development of H. parviporum spores is an important step towards the goal of identifying novel antifungal strategies.
DA - 2006/8//
PY - 2006/8//
DO - 10.1111/j.1462-2920.2006.01027.x
VL - 8
IS - 8
SP - 1340-1350
SN - 1462-2920
ER -
TY - JOUR
TI - Some algorithms for the conditional mean vector and covariance matrix
AU - Monahan, J. F.
T2 - Journal of Statistical Software
DA - 2006///
PY - 2006///
VL - 16
IS - 8
ER -
TY - BOOK
TI - Semiparametric theory and missing data
AU - Tsiatis, A. A.
DA - 2006///
PY - 2006///
PB - New York: Springer
SN - 0387324488
ER -
TY - JOUR
TI - Multiple-interval mapping for ordinal traits
AU - Li, Jian
AU - Wang, Shengchu
AU - Zeng, Zhao-Bang
T2 - GENETICS
AB - Abstract Many statistical methods have been developed to map multiple quantitative trait loci (QTL) in experimental cross populations. Among these methods, multiple-interval mapping (MIM) can map QTL with epistasis simultaneously. However, the previous implementation of MIM is for continuously distributed traits. In this study we extend MIM to ordinal traits on the basis of a threshold model. The method inherits the properties and advantages of MIM and can fit a model of multiple QTL effects and epistasis on the underlying liability score. We study a number of statistical issues associated with the method, such as the efficiency and stability of maximization and model selection. We also use computer simulation to study the performance of the method and compare it to other alternative approaches. The method has been implemented in QTL Cartographer to facilitate its general usage for QTL mapping data analysis on binary and ordinal traits.
DA - 2006/7//
PY - 2006/7//
DO - 10.1534/genetics.105.054619
VL - 173
IS - 3
SP - 1649-1663
SN - 0016-6731
ER -
TY - JOUR
TI - Likelihood-based inference on haplotype effects in genetic association studies - Comment
AU - Tzeng, J. Y.
AU - Roeder, K.
T2 - Journal of the American Statistical Association
DA - 2006///
PY - 2006///
VL - 101
IS - 473
SP - 111-114
ER -
TY - JOUR
TI - Interrelationships between p-coumaric acid, evapotranspiration, soil water content, and leaf expansion
AU - Blum, Udo
AU - Gerig, Thomas M.
T2 - JOURNAL OF CHEMICAL ECOLOGY
DA - 2006/8//
PY - 2006/8//
DO - 10.1007/s10886-006-9111-2
VL - 32
IS - 8
SP - 1817-1834
SN - 1573-1561
KW - cucumber seedlings
KW - p-coumaric acid
KW - evaporation
KW - evapotranspiration leaf area expansion
KW - soil water content
KW - soil solution concentrations inhibition and recovery
KW - negative feedback regulation
KW - allelopathy
KW - competition
ER -
TY - JOUR
TI - Information-based monitoring of clinical trials
AU - Tsiatis, Anastasios A.
T2 - STATISTICS IN MEDICINE
AB - When designing a clinical trial to compare the effect of different treatments on response, a key issue facing the statistician is to determine how large a study is necessary to detect a clinically important difference with sufficient power. This is the case whether the study will be analysed only once (single-analysis) or whether it will be monitored periodically with the possibility of early stopping (group-sequential). Standard sample size calculations are based on both the magnitude of difference that is considered clinically important as well as values for the nuisance parameters in the statistical model. For planning purposes, best guesses are made for the value of the nuisance parameters and these are used to determine the sample size. However, if these guesses are incorrect this will affect the subsequent power to detect the clinically important difference. It is argued in this paper that statistical precision is directly related to Statistical Information and that the study should continue until the requisite statistical information is obtained. This is referred to as information-based design and analysis of clinical trials. We also argue that this type of methodology is best suited with group-sequential trials which monitor the data periodically and allow for estimation of the statistical information as the study progresses.
DA - 2006/10/15/
PY - 2006/10/15/
DO - 10.1002/sim.2625
VL - 25
IS - 19
SP - 3236-3244
SN - 0277-6715
KW - group-sequential test
KW - statistical information
ER -
TY - JOUR
TI - Genome architecture drives protein evolution in ciliates
AU - Zufall, Rebecca A.
AU - McGrath, Casey L.
AU - Muse, Spencer V.
AU - Katz, Laura A.
T2 - MOLECULAR BIOLOGY AND EVOLUTION
AB - Studies of microbial eukaryotes have been pivotal in the discovery of biological phenomena, including RNA editing, self-splicing RNA, and telomere addition. Here we extend this list by demonstrating that genome architecture, namely the extensive processing of somatic (macronuclear) genomes in some ciliate lineages, is associated with elevated rates of protein evolution. Using newly developed likelihood-based procedures for studying molecular evolution, we investigate 6 genes to compare 1) ciliate protein evolution to that of 3 other clades of eukaryotes (plants, animals, and fungi) and 2) protein evolution in ciliates with extensively processed macronuclear genomes to that of other ciliate lineages. In 5 of the 6 genes, ciliates are estimated to have a higher ratio of nonsynonymous/synonymous substitution rates, consistent with an increase in the rate of protein diversification in ciliates relative to other eukaryotes. Even more striking, there is a significant effect of genome architecture within ciliates as the most divergent proteins are consistently found in those lineages with the most highly processed macronuclear genomes. We propose a model whereby genome architecture-specifically chromosomal processing, amitosis within macronuclei, and epigenetics-allows ciliates to explore protein space in a novel manner. Further, we predict that examination of diverse eukaryotes will reveal additional evidence of the impact of genome architecture on molecular evolution.
DA - 2006/9//
PY - 2006/9//
DO - 10.1093/molbev/msl032
VL - 23
IS - 9
SP - 1681-1687
SN - 1537-1719
KW - genome evolution
KW - genome architecture
KW - protein evolution
KW - ciliate evolution
ER -
TY - JOUR
TI - Empirical likelihood inference for linear transformation models
AU - Lu, WB
AU - Liang, Y
T2 - JOURNAL OF MULTIVARIATE ANALYSIS
AB - Empirical likelihood inference is developed for censored survival data under the linear transformation models, which generalize Cox's [Regression models and life tables (with Discussion), J. Roy. Statist. Soc. Ser. B 34 (1972) 187–220] proportional hazards model. We show that the limiting distribution of the empirical likelihood ratio is a weighted sum of standard chi-squared distribution. Empirical likelihood ratio tests for the regression parameters with and without covariate adjustments are also derived. Simulation studies suggest that the empirical likelihood ratio tests are more accurate (under the null hypothesis) and powerful (under the alternative hypothesis) than the normal approximation based tests of Chen et al. [Semiparametric of transformation models with censored data, Biometrika 89 (2002) 659–668] when the model is different from the proportional hazards model and the proportion of censoring is high.
DA - 2006/8//
PY - 2006/8//
DO - 10.1016/j.jmva.2005.09.007
VL - 97
IS - 7
SP - 1586-1599
SN - 0047-259X
KW - censored survival data
KW - empirical likelihood
KW - limiting distribution
KW - linear transformation models
KW - normal approximation
ER -
TY - JOUR
TI - Effectiveness of biodiversity indicators varies with extent, grain, and region
AU - Hess, George R.
AU - Bartel, Rebecca A.
AU - Leidner, Allison K.
AU - Rosenfeld, Kristen M.
AU - Rubino, Matthew J.
AU - Snider, Sunny B.
AU - Ricketts, Taylor H.
T2 - BIOLOGICAL CONSERVATION
AB - Abstract The use of indicator taxa for conservation planning is common, despite inconsistent evidence regarding their effectiveness. These inconsistencies may be the result of differences among species and taxonomic groups studied, geographic location, or scale of analysis. The scale of analysis can be defined by grain and extent, which are often confounded. Grain is the size of each observational unit and extent is the size of the entire study area. Using species occurrence records compiled by NatureServe from survey data, range maps, and expert opinion, we examined correlations in species richness between each of seven taxa (amphibians, birds, butterflies, freshwater fish, mammals, freshwater mussels, and reptiles) and total richness of the remaining six taxa at varying grains and extents in two regions of the US (Mid-Atlantic and Pacific Northwest). We examined four different spatial units of interest: hexagon (∼649 km 2 ), subecoregion (3800–34,000 km 2 ), ecoregion (8300–79,000 km 2 ), and geographic region (315,000–426,000 km 2 ). We analyzed the correlations with varying extent of analysis (grain held constant at the hexagon) and varying grain (extent held constant at the region). The strength of correlation among taxa was context dependent, varying widely with grain, extent, region, and taxon. This suggests that (1) taxon, grain, extent, and study location explain, in part, inconsistent results of previous studies; (2) planning based on indicator relationships developed at other grains or extents should be undertaken cautiously; and (3) planning based on indicator relationships developed in other geographic locations is risky, even if planning occurs at an equivalent grain and extent.
DA - 2006/10//
PY - 2006/10//
DO - 10.1016/j.biocon.2006.04.037
VL - 132
IS - 4
SP - 448-457
SN - 1873-2917
KW - indicator taxa
KW - scale
KW - grain
KW - extent
KW - biodiversity hotspots
ER -
TY - JOUR
TI - Determination of interrogating frequencies to maximize electromagnetic backscatter from objects with material coatings
AU - Banks, H. T.
AU - Ito, K.
AU - Toivanen, J.
T2 - Communications in Computational Physics
DA - 2006///
PY - 2006///
VL - 1
IS - 2
SP - 362-382
ER -
TY - JOUR
TI - Comparative analysis and integrative classification of NC160 cell lines and primary tumors using gene expression profiling data
AU - Wang, H. X.
AU - Huang, S. G.
AU - Shou, J. Y.
AU - Su, E. W.
AU - Onyia, J. E.
AU - Liao, B. R.
AU - Li, S. Y.
T2 - BMC Genomics
DA - 2006///
PY - 2006///
VL - 7
ER -
TY - JOUR
TI - Adaptive two-stage designs in phase II clinical trials
AU - Banerjee, Anindita
AU - Tsiatis, Anastasios A.
T2 - STATISTICS IN MEDICINE
AB - Two-stage designs have been widely used in phase II clinical trials. Such designs are desirable because they allow a decision to be made on whether a treatment is effective or not after the accumulation of the data at the end of each stage. Optimal fixed two-stage designs, where the sample size at each stage is fixed in advance, were proposed by Simon when the primary outcome is a binary response. This paper proposes an adaptive two-stage design which allows the sample size at the second stage to depend on the results at the first stage. Using a Bayesian decision-theoretic construct, we derive optimal adaptive two-stage designs; the optimality criterion being minimum expected sample size under the null hypothesis. Comparisons are made between Simon's two-stage fixed design and the new design with respect to this optimality criterion. Copyright © 2006 John Wiley & Sons, Ltd.
DA - 2006/10/15/
PY - 2006/10/15/
DO - 10.1002/sim.2501
VL - 25
IS - 19
SP - 3382-3395
SN - 1097-0258
KW - two-stage adaptive design
KW - backward induction
KW - Bayesian decision theory
KW - simulated annealing
ER -
TY - JOUR
TI - Survival prediction of diffuse large-B-cell lymphoma based on both clinical and gene expression information
AU - Li, LX
T2 - BIOINFORMATICS
AB - Abstract Motivation: It is important to predict the outcome of patients with diffuse large-B-cell lymphoma after chemotherapy, since the survival rate after treatment of this common lymphoma disease is <50%. Both clinically based outcome predictors and the gene expression-based molecular factors have been proposed independently in disease prognosis. However combining the high-dimensional genomic data and the clinically relevant information to predict disease outcome is challenging. Results: We describe an integrated clinicogenomic modeling approach that combines gene expression profiles and the clinically based International Prognostic Index (IPI) for personalized prediction in disease outcome. Dimension reduction methods are proposed to produce linear combinations of gene expressions, while taking into account clinical IPI information. The extracted summary measures capture all the regression information of the censored survival phenotype given both genomic and clinical data, and are employed as covariates in the subsequent survival model formulation. A case study of diffuse large-B-cell lymphoma data, as well as Monte Carlo simulations, both demonstrate that the proposed integrative modeling improves the prediction accuracy, delivering predictions more accurate than those achieved by using either clinical data or molecular predictors alone. Availability: R programs are available at Contact: li@stat.ncsu.edu Supplementary information: Supplementary data are available at
DA - 2006/2/15/
PY - 2006/2/15/
DO - 10.1093/bioinformatics/bti824
VL - 22
IS - 4
SP - 466-471
SN - 1460-2059
ER -
TY - JOUR
TI - Statistical design of pools using optimal coverage and minimal collision
AU - Remlinger, KS
AU - Hughes-Oliver, JM
AU - Young, SS
AU - Lam, RL
T2 - TECHNOMETRICS
AB - Discovery of a new drug involves screening large chemical libraries to identify new and diverse active compounds. Screening efficiency can be improved by testing compounds in pools. We consider two criteria for designing pools: optimal coverage of the chemical space and minimal collision between compounds. We apply four pooling designs to a public dataset. We evaluate each method by determining how well the design criteria are met and whether the methods are able to find many diverse active compounds. One pooling design emerges as a winner, but all designed pools clearly outperform randomly created pools.
DA - 2006/2//
PY - 2006/2//
DO - 10.1198/004017005000000481
VL - 48
IS - 1
SP - 133-143
SN - 0040-1706
KW - drug discovery
KW - high-throughput screening
KW - molecular descriptor
KW - pooling experiment
KW - Tanimoto similarity
KW - uniform cell coverage design
ER -
TY - JOUR
TI - A unified mixed-model method for association mapping that accounts for multiple levels of relatedness
AU - Yu, JM
AU - Pressoir, G
AU - Briggs, WH
AU - Bi, , IV
AU - Yamasaki, M
AU - Doebley, JF
AU - McMullen, MD
AU - Gaut, BS
AU - Nielsen, DM
AU - Holland, JB
AU - Kresovich, S
AU - Buckler, ES
T2 - NATURE GENETICS
DA - 2006/2//
PY - 2006/2//
DO - 10.1038/ng1702
VL - 38
IS - 2
SP - 203-208
SN - 1546-1718
ER -
TY - JOUR
TI - Validation of two major quantitative trait loci for fusarium head blight resistance in Chinese wheat line W14
AU - Chen, J
AU - Griffey, CA
AU - Maroof, MAS
AU - Stromberg, EL
AU - Biyashev, RM
AU - Zhao, W
AU - Chappell, MR
AU - Pridgen, TH
AU - Dong, Y
AU - Zeng, Z
T2 - PLANT BREEDING
AB - Identity of quantitative trait loci (QTL) governing resistance to fusarium head blight (FHB) initial infection (type I), spread (type II), kernel infection, and deoxynivalenol (DON) accumulation was characterized in Chinese wheat line W14. Ninety-six double-haploid lines derived from a cross of W14 × ’Pion2684’ were evaluated for FHB resistance in two greenhouse and one field experiment. Two known major QTL were validated on chromosomes 3BS and 5AS in W14 using the composite interval mapping method. The 3BS QTL had a larger effect on resistance than the 5AS QTL in the greenhouse experiments, whereas, the 5AS QTL had a larger effect in the field experiment. These two QTL together explained 33%, 35%, and 31% of the total phenotypic variation for disease spread, kernel infection, and DON concentration in the greenhouse experiments, respectively. In the field experiment, the two QTL explained 34% and 26% of the total phenotypic variation for FHB incidence and severity, respectively. W14 has both QTL, which confer reduced initial infection, disease spread, kernel infection, and DON accumulation. Therefore, marker-assisted selection (MAS) for both QTL should be implemented in incorporating W14 resistance into adapted backgrounds. Flanking markers Xbarc133 and Xgwm493 on 3BS and Xbarc117 and Xbarc56 on 5AS are suggested for MAS.
DA - 2006/2//
PY - 2006/2//
DO - 10.1111/j.1439-0523.2006.01182.x
VL - 125
IS - 1
SP - 99-101
SN - 1439-0523
KW - Triticum aestivum
KW - Fusarium head blight
KW - microsatellite
KW - QTL mapping
ER -
TY - JOUR
TI - Real-time identification of the draft system using neural network
AU - Chun, SY
AU - Bae, HJ
AU - Kim, SM
AU - Suh, MW
AU - Grady, P
AU - Lyoo, WS
AU - Yoon, WS
AU - Han, SS
T2 - FIBERS AND POLYMERS
DA - 2006/3//
PY - 2006/3//
DO - 10.1007/BF02933604
VL - 7
IS - 1
SP - 62-65
SN - 1875-0052
KW - draft system
KW - sliver
KW - control
KW - neural network
KW - modeling
ER -
TY - JOUR
TI - On closed form semiparametric estimators for measurement error models
AU - Ma, Y. Y.
AU - Tsiatis, A. A.
T2 - Statistica Sinica
DA - 2006///
PY - 2006///
VL - 16
IS - 1
SP - 183-193
ER -
TY - JOUR
TI - An automated statistical process control study of inline mixing using spectrophotometric detection
AU - Dickey, M. D.
AU - Stewart, M. D.
AU - Willson, C. G.
AU - Dickey, D. A.
T2 - Journal of Chemical Education
AB - Statistical process control (SPC) charts are used to distinguish natural, random variations in a process parameter from fluctuations associated with an assignable cause, such as equipment malfunction or operator error. SPC charts are widely used in industry for quality and process control. In fact, feedback from recent graduates of the undergraduate chemical engineering program indicates that familiarity with SPC charts is one of the most valuable skills for newly hired process engineers. In the following experiment, students are introduced to the concept of SPC through a simple inline mixing experiment. Students learn to create SPC control charts and, more importantly, to understand their function.
DA - 2006///
PY - 2006///
DO - 10.1021/ed083p110
VL - 83
IS - 1
SP - 110-113
ER -
TY - JOUR
TI - Void detection in foam with knit lines using THz pulse interrogation
AU - Banks, H. T.
AU - Gibson, N. L.
T2 - MATHEMATICAL AND COMPUTER MODELLING
AB - We model the electromagnetic interrogation of a polyurethane foam using the transverse electric (TE) mode of the two-dimensional (2D) Maxwell’s equations reduced to the wave equation for a fixed frequency in the terahertz (THz) regime. The foam block target contains knit lines which are modeled by modifying the speed of propagation, i.e., by altering the index of refraction. We describe our efforts to estimate the dielectric constant in the knit lines, as well as in the surrounding foam, by use of the classical Clausius–Mossotti equation, assuming only a change in density. We compare the numerical simulations accounting for knit lines to those in which knit lines are neglected, each in the context of modeling reflections of plane waves in foam with voids.
DA - 2006/11//
PY - 2006/11//
DO - 10.1016/j.mcm.2006.02.014
VL - 44
IS - 9-10
SP - 807-815
SN - 0895-7177
KW - terahertz electromagnetic waves
KW - heterogeneous materials
KW - numerical simulations
ER -
TY - JOUR
TI - Time-dependent instantaneous mortality rates from multiple tagging experiments with exact times of release and recovery
AU - Leigh, GM
AU - Hearn, WS
AU - Pollock, KH
T2 - ENVIRONMENTAL AND ECOLOGICAL STATISTICS
DA - 2006/3//
PY - 2006/3//
DO - 10.1007/s10651-005-5693-z
VL - 13
IS - 1
SP - 89-108
SN - 1573-3009
KW - fishing mortality
KW - hunting mortality
KW - natural mortality
KW - nonparametric estimation
KW - tag shedding
KW - tuna
ER -
TY - JOUR
TI - Spatial analysis of Aedes albopictus (Diptera : Culicidae) oviposition in suburban neighborhoods of a piedmont community in North Carolina
AU - Richards, Stephanie L.
AU - Apperson, Charles S.
AU - Ghosh, Sujit K.
AU - Cheshire, Heather M.
AU - Zeichner, Brian C.
T2 - JOURNAL OF MEDICAL ENTOMOLOGY
AB - Temporal and spatial distribution of egg-laying by Aedes albopictus (Skuse) (Diptera: Culicidae) was investigated in suburban neighborhoods in Raleigh, NC, by using oviposition traps (ovitraps) at fixed sampling stations during the 2002 and 2003 mosquito seasons. Variations in the phenology of oviposition between the two mosquito seasons resulted from differences in the patterns and amounts of rainfall early in the season. Aerial images of each study neighborhood were digitized, and the proportions of specific types of land cover within buffer zones encompassing ovitraps were estimated. Retrospective analyses showed that in some neighborhoods, oviposition intensity was significantly associated with specific types of land cover. However, in general, it seemed that gravid Ae. albopictus searched throughout the landscape for water-filled containers in which to lay eggs. Peridomestic surveys were carried out concurrently with ovitrap collections to estimate production of Ae. albopictus pupae in discarded water-filled containers and the abundance of females in vegetation that made up the resting habitat. Results of linear regression analyses indicated that the mean standing crop of pupae (total and per container) per residence was not a significant predictor of mean egg densities in ovitraps. However, the mean standing crop of adult females was a significant but weak predictor variable, because the magnitude and sign of regression coefficients varied between neighborhoods. Linear spatial regression analyses revealed that oviposition intensity was not spatially dependent on pupal standing crop or the numbers of pupae-positive containers distributed peridomestically. However, a weak spatial dependence on the standing crop of adult females was found in some neighborhoods. Based on spherical variogram models, kriging was carried out to predict the spatial patterns of oviposition in suburban neighborhoods. Focal areas of high and low oviposition intensity were evident in most neighborhoods; however, the spatial patterns of oviposition changed between mosquito seasons. Kriging predictions were evaluated, using cross-validation, by systematically removing each data point from our data set and predicting the removed point by using the remaining points. The root mean square (standardized) error values of best fitting variogram models approximated 1, and plots of standardized PRESS residuals showed no distinct pattern for most neighborhoods, indicating that predictions of the spatial distribution of oviposition intensity were valid. Spherical variogram models are a satisfactory method for describing the spatial distribution of Ae. albopictus oviposition, and kriging can be a useful technique for predicting oviposition intensity at locations that have not been sampled.
DA - 2006/9//
PY - 2006/9//
DO - 10.1603/0022-2585(2006)43[976:SAOAAD]2.0.CO;2
VL - 43
IS - 5
SP - 976-989
SN - 0022-2585
UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-33750941447&partnerID=MN8TOARS
KW - Aedes albopictus
KW - oviposition
KW - spatial analysis
KW - kriging
ER -
TY - JOUR
TI - Sensitivity of dynamical systems to Banach space parameters
AU - Banks, H. T.
AU - Nguyen, Hoan K.
T2 - JOURNAL OF MATHEMATICAL ANALYSIS AND APPLICATIONS
AB - We consider general nonlinear dynamical systems in a Banach space with dependence on parameters in a second Banach space. An abstract theoretical framework for sensitivity equations is developed. An application to measure dependent delay differential systems arising in a class of HIV models is presented.
DA - 2006/11/1/
PY - 2006/11/1/
DO - 10.1016/j.jmaa.2005.09.084
VL - 323
IS - 1
SP - 146-161
SN - 0022-247X
KW - sensitivity equations
KW - delay differential equations
KW - approximation
ER -
TY - JOUR
TI - Modeling vital rates improves estimation of population projection matrices
AU - Gross, K
AU - Morris, WF
AU - Wolosin, MS
AU - Doak, DF
T2 - POPULATION ECOLOGY
AB - Population projection matrices are commonly used by ecologists and managers to analyze the dynamics of stage-structured populations. Building projection matrices from data requires estimating transition rates among stages, a task that often entails estimating many parameters with few data. Consequently, large sampling variability in the estimated transition rates increases the uncertainty in the estimated matrix and quantities derived from it, such as the population multiplication rate and sensitivities of matrix elements. Here, we propose a strategy to avoid overparameterized matrix models. This strategy involves fitting models to the vital rates that determine matrix elements, evaluating both these models and ones that estimate matrix elements individually with model selection via information criteria, and averaging competing models with multimodel averaging. We illustrate this idea with data from a population of Silene acaulis (Caryophyllaceae), and conduct a simulation to investigate the statistical properties of the matrices estimated in this way. The simulation shows that compared with estimating matrix elements individually, building population projection matrices by fitting and averaging models of vital-rate estimates can reduce the statistical error in the population projection matrix and quantities derived from it.
DA - 2006/1//
PY - 2006/1//
DO - 10.1007/s10144-005-0238-8
VL - 48
IS - 1
SP - 79-89
SN - 1438-390X
KW - information criteria
KW - model selection
KW - multimodel averaging
KW - vital rates
ER -
TY - JOUR
TI - Major gene detection for fusiform rust resistance using Bayesian complex segregation analysis in loblolly pine
AU - Li, Hua
AU - Ghosh, Sujit
AU - Amerson, Henry
AU - Li, Bailian
T2 - THEORETICAL AND APPLIED GENETICS
AB - The presence of major genes affecting rust resistance of loblolly pine was investigated in a progeny population that was generated with a half-diallel mating of six parents. A Bayesian complex segregation analysis was used to make inference about a mixed inheritance model (MIM) that included polygenic effects and a single major gene effect. Marginalizations were achieved by using Gibbs sampler. A parent block sampling by which genotypes of a parent and its offspring were sampled jointly was implemented to improve mixing. The MIM was compared with a pure polygenic model (PM) using Bayes factor. Results showed that the MIM was a better model to explain the inheritance of rust resistance than the pure PM in the diallel population. A large major gene variance component estimate (> 50% of total variance), indicated the existence of major genes for rust resistance in the studied loblolly pine population. Based on estimations of parental genotypes, it appears that there may be two or more major genes affecting disease phenotypes in this diallel population.
DA - 2006/9//
PY - 2006/9//
DO - 10.1007/s00122-006-0351-x
VL - 113
IS - 5
SP - 921-929
SN - 0040-5752
UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-33747640613&partnerID=MN8TOARS
ER -
TY - JOUR
TI - Gene selection using support vector machines with non-convex penalty
AU - Zhang, HH
AU - Ahn, J
AU - Lin, XD
AU - Park, C
T2 - BIOINFORMATICS
AB - With the development of DNA microarray technology, scientists can now measure the expression levels of thousands of genes simultaneously in one single experiment. One current difficulty in interpreting microarray data comes from their innate nature of 'high-dimensional low sample size'. Therefore, robust and accurate gene selection methods are required to identify differentially expressed group of genes across different samples, e.g. between cancerous and normal cells. Successful gene selection will help to classify different cancer types, lead to a better understanding of genetic signatures in cancers and improve treatment strategies. Although gene selection and cancer classification are two closely related problems, most existing approaches handle them separately by selecting genes prior to classification. We provide a unified procedure for simultaneous gene selection and cancer classification, achieving high accuracy in both aspects.In this paper we develop a novel type of regularization in support vector machines (SVMs) to identify important genes for cancer classification. A special nonconvex penalty, called the smoothly clipped absolute deviation penalty, is imposed on the hinge loss function in the SVM. By systematically thresholding small estimates to zeros, the new procedure eliminates redundant genes automatically and yields a compact and accurate classifier. A successive quadratic algorithm is proposed to convert the non-differentiable and non-convex optimization problem into easily solved linear equation systems. The method is applied to two real datasets and has produced very promising results.MATLAB codes are available upon request from the authors.
DA - 2006/1/1/
PY - 2006/1/1/
DO - 10.1093/bioinformatics/bti736
VL - 22
IS - 1
SP - 88-95
SN - 1460-2059
ER -
TY - JOUR
TI - Exact sample sizes needed to detect dependence in 2 x 3 tables
AU - Sanchez, MS
AU - Basten, CJ
AU - Ferrenberg, AM
AU - Asmussen, MA
AU - Arnold, J
T2 - THEORETICAL POPULATION BIOLOGY
AB - Many medical and biological studies entail classifying a number of observations according to two factors, where one has two and the other three possible categories. This is the case of, for example, genetic association studies of complex traits with single-nucleotide polymorphisms (SNPs), where the a priori statistical planning, analysis, and interpretation of results are of critical importance. Here, we present methodology to determine the minimum sample size required to detect dependence in 2 x 3 tables based on Fisher's exact test, assuming that neither of the two margins is fixed and only the grand total N is known in advance. We provide the numerical tools necessary to determine these sample sizes for desired power, significance level, and effect size, where only the computational time can be a limitation for extreme parameter values. These programs can be accessed at . This solution of the sample size problem for an exact test will permit experimentalists to plan efficient sampling designs, determine the extent of statistical support for their hypotheses, and gain insight into the repeatability of their results. We apply this solution to the sample size problem to three empirical studies, and discuss the results with specified power and nominal significance levels.
DA - 2006/3//
PY - 2006/3//
DO - 10.1016/j.tpb.2005.11.001
VL - 69
IS - 2
SP - 111-120
SN - 1096-0325
KW - disease status
KW - disequilibrium
KW - exact test
KW - genetic association
KW - heterozygosity
KW - mitochondrial and nuclear DNA
KW - nonrandom associations
KW - power
KW - sample size
KW - 2 x 3 table
ER -
TY - JOUR
TI - Component selection and smoothing for nonparametric regression in exponential families
AU - Zhang, H. H.
AU - Lin, Y.
T2 - Statistica Sinica
DA - 2006///
PY - 2006///
VL - 16
IS - 3
SP - 1021-1041
ER -
TY - JOUR
TI - Effect of testing temperature on internal egg quality measurements
AU - Keener, KM
AU - McAvoy, KC
AU - Foegeding, JB
AU - Curtis, PA
AU - Anderson, KE
AU - Osborne, JA
AU - Bush, DJ
T2 - POULTRY SCIENCE
AB - The objective of this study was to determine the effect of egg testing temperature on quality measurements of shell eggs. The quality measurements compared included 3 Haugh unit (HU) devices (electronic Haugh, tripod Haugh, and Haugh meter), egg weight, albumen height, albumen width, albumen index, yolk width, yolk height, yolk index, percentage of thin albumen, and vitelline membrane strength at 3 temperatures of 5, 13, and 23 degrees C from 2 strains of laying hens (Hyline W36 and Bovans White) at 2 storage times. The HU measurements averaged 72.44 at time zero and 59.99 at 7 wk. At 7 wk for all devices, HU values decreased 6 units with increased temperature (P < 0.05). The electronic Haugh and tripod Haugh devices gave equal measurements for all testing conditions. The Haugh meter gave equal values at 5 degrees C for fresh eggs but lower HU at higher temperatures and 7 wk storage. Thus, it is recommended that egg testing temperature be reported when HU are measured. Coefficient of variation generally increased for all HU methods with increasing temperature. Although there was a proportionately different amount of thin albumen detected between the strains of laying hens, no significant difference was seen in HU. From the evaluated methods for measuring quality, the electronic Haugh, which electronically measures albumen height and calculates HU, provided the lowest coefficient of variation, was sensitive to quality loss, and gave the highest quality measurement (5 degrees C).
DA - 2006/3//
PY - 2006/3//
DO - 10.1093/ps/85.3.550
VL - 85
IS - 3
SP - 550-555
SN - 0032-5791
KW - egg quality
KW - testing temperature
KW - Haugh unit
KW - albumen quality
ER -
TY - JOUR
TI - Regression-based association analysis with clustered haplotypes through use of genotypes
AU - Tzeng, JY
AU - Wang, CH
AU - Kao, JT
AU - Hsiao, CK
T2 - AMERICAN JOURNAL OF HUMAN GENETICS
AB - Haplotype-based association analysis has been recognized as a tool with high resolution and potentially great power for identifying modest etiological effects of genes. However, in practice, its efficacy has not been as successfully reproduced as expected in theory. One primary cause is that such analysis tends to require a large number of parameters to capture the abundant haplotype varieties, and many of those are expended on rare haplotypes for which studies would have insufficient power to detect association even if it existed. To concentrate statistical power on more-relevant inferences, in this study, we developed a regression-based approach using clustered haplotypes to assess haplotype-phenotype association. Specifically, we generalized the probabilistic clustering methods of Tzeng to the generalized linear model (GLM) framework established by Schaid et al. The proposed method uses unphased genotypes and incorporates both phase uncertainty and clustering uncertainty. Its GLM framework allows adjustment of covariates and can model qualitative and quantitative traits. It can also evaluate the overall haplotype association or the individual haplotype effects. We applied the proposed approach to study the association between hypertriglyceridemia and the apolipoprotein A5 gene. Through simulation studies, we assessed the performance of the proposed approach and demonstrate its validity and power in testing for haplotype-trait association. Haplotype-based association analysis has been recognized as a tool with high resolution and potentially great power for identifying modest etiological effects of genes. However, in practice, its efficacy has not been as successfully reproduced as expected in theory. One primary cause is that such analysis tends to require a large number of parameters to capture the abundant haplotype varieties, and many of those are expended on rare haplotypes for which studies would have insufficient power to detect association even if it existed. To concentrate statistical power on more-relevant inferences, in this study, we developed a regression-based approach using clustered haplotypes to assess haplotype-phenotype association. Specifically, we generalized the probabilistic clustering methods of Tzeng to the generalized linear model (GLM) framework established by Schaid et al. The proposed method uses unphased genotypes and incorporates both phase uncertainty and clustering uncertainty. Its GLM framework allows adjustment of covariates and can model qualitative and quantitative traits. It can also evaluate the overall haplotype association or the individual haplotype effects. We applied the proposed approach to study the association between hypertriglyceridemia and the apolipoprotein A5 gene. Through simulation studies, we assessed the performance of the proposed approach and demonstrate its validity and power in testing for haplotype-trait association. In the search for genes underlying human complex diseases, one crucial step is to detect the association between the genetic variants and the disease phenotypes. Since a high density of SNPs is being identified and used in genetic studies, jointly analyzing all variants within a gene or chromosomal region for association can be more informative and effective (Stephens et al. Stephens et al., 2001Stephens J Schneider J Tanguay D Choi J Acharya T Stanley S Jiang R et al.Haplotype variation and linkage disequilibrium in 313 human genes.Science. 2001; 293: 489-493Crossref PubMed Scopus (690) Google Scholar). The haplotype, the ordered allele sequences on a chromosome, provides a natural framework for performing joint analysis of multiple markers and is predominantly considered the unit of analysis in association studies. Haplotype analyses are believed to provide high resolution and potentially great power for identifying modest etiological effects of genes (International HapMap Consortium International HapMap Consortium, 2003International HapMap Consortium The International HapMap Project.Nature. 2003; 426: 789-796Crossref PubMed Scopus (4684) Google Scholar). Following this viewpoint, many statistical methods have been proposed to evaluate haplotype-disease association for case-control samples, including likelihood ratio tests for testing equality of haplotype frequencies between cases and controls (e.g., Sham Sham, 1998Sham P Statistics in human genetics. 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Seltman et al., 2001Seltman H Roeder K Devlin B Transmission/disequilibrium test meets measured haplotype analysis: family-based association analysis guided by evolution of haplotypes.Am J Hum Genet. 2001; 68: 1250-1263Abstract Full Text Full Text PDF PubMed Scopus (83) Google Scholar, Seltman et al., 2003Seltman H Roeder K Devlin B Evolutionary-based association analysis using haplotype data.Genet Epidemiol. 2003; 25: 48-58Crossref PubMed Scopus (93) Google Scholar; Molitor et al. Molitor et al., 2003aMolitor 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, Molitor et al., 2003bMolitor J Marjoram P Thomas D Fine-scale mapping of disease genes with multiple mutations via spatial clustering techniques.Am J Hum Genet. 2003; 73: 1368-1384Abstract Full Text Full Text PDF PubMed Scopus (76) Google Scholar; Durrant et al. Durrant et al., 2004Durrant 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; Tzeng Tzeng, 2005Tzeng JY Evolutionary-based grouping of haplotypes in association analysis.Genet Epidemiol. 2005; 28: 220-231Crossref PubMed Scopus (35) Google Scholar). Whereas the progress in both data availability and data analyses increases the feasibility of haplotype-based association studies, practical implementation indicates that the study findings of such types are not consistently reproducible (Lohmueller et al. Lohmueller et al., 2003Lohmueller KE Pearce CL Pike M Lander ES Hirschhorn JN Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease.Nat Genet. 2003; 33: 177-182Crossref PubMed Scopus (1583) Google Scholar; Neale and Sham Neale and Sham, 2004Neale BM Sham PC The future of association studies: gene-based analysis and replication.Am J Hum Genet. 2004; 75: 353-362Abstract Full Text Full Text PDF PubMed Scopus (505) Google Scholar). Lohmueller et al. (Lohmueller et al., 2003Lohmueller KE Pearce CL Pike M Lander ES Hirschhorn JN Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease.Nat Genet. 2003; 33: 177-182Crossref PubMed Scopus (1583) Google Scholar) concluded that the inconsistency could be explained largely by a high rate of false-negative results or, equivalently, lack of power. Recently, Chapman and colleagues (Chapman et al. Chapman et al., 2003Chapman JM Cooper JD Todd JA Clayton DG Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power.Hum Hered. 2003; 56: 18-31Crossref PubMed Scopus (347) Google Scholar; Clayton et al. Clayton et al., 2004Clayton D Chapman J Cooper J Use of unphased multilocus genotype data in indirect association studies.Genet Epidemiol. 2004; 27: 415-428Crossref PubMed Scopus (165) Google Scholar) further revealed that analyses-based locus models that regress phenotypes on multiple SNP loci can sometimes be more powerful than haplotype analyses, such as when tag SNPs are used. The main reason is that the locus model uses fewer parameters than does a haplotype model; by modeling only the main effect and low-order interactions of SNPs, the locus model does not spend degrees of freedom on rare haplotypes for which studies would have insufficient power to detect association even if it were present (Clayton et al. Clayton et al., 2004Clayton D Chapman J Cooper J Use of unphased multilocus genotype data in indirect association studies.Genet Epidemiol. 2004; 27: 415-428Crossref PubMed Scopus (165) Google Scholar). In contrast to a locus model, haplotype analysis requires a larger number of parameters to capture the abundant haplotype varieties, and the test power is limited by the many degrees of freedom that they use. The power is worsened by the need to adjust for multiple testing when many genes are evaluated. Further difficulties emerge from the fact that complex diseases are derived from intricate genetic and environmental factors (see, e.g., Peltonen and McKusick Peltonen and McKusick, 2001Peltonen L McKusick VA Genomics and medicine: dissecting human disease in the postgenomic era.Science. 2001; 291: 1224-1229Crossref PubMed Scopus (314) Google Scholar). Understanding the genetic etiology of complex diseases requires a joint consideration of all potential attributes and sometimes even other auxiliary covariates. The vast quantities of covariates from environmental effects and gene-gene and gene-environment interactions further exacerbate the degrees-of-freedom problem. Model-based association methods, which incorporate covariate information in association analysis, play an increasingly important role in modern association studies. They facilitate the study of complex gene-disease association. Besides the ability to accommodate polygenic effects, environmental covariates, and interactions among them, model-based analyses can evaluate haplotype effects at either the global level (i.e., evaluating overall haplotype association) or the individual level (i.e., evaluating haplotype-specific association). They also allow modeling of diseases through a variety of clinical phenotypes, from dichotomous to ordinal to quantitative traits. These flexibilities and advantages again reflect the need for efficient usage of haplotype information in a model-based framework for studying association. Haplotype grouping offers one promising avenue for controlling the issue of degrees of freedom that is encountered in haplotypes-based multiple-marker analysis. It enhances the efficiency of haplotype analysis by using a small number of degrees of freedom to study haplotypes and concentrates statistical power on more-relevant inference. In an earlier study (Tzeng Tzeng, 2005Tzeng JY Evolutionary-based grouping of haplotypes in association analysis.Genet Epidemiol. 2005; 28: 220-231Crossref PubMed Scopus (35) Google Scholar), we introduced an algorithm to cluster related haplotypes to improve the power of association tests. This algorithm adapts the same evolutionary concepts of cladistic analyses and groups rare haplotypes with their closest major haplotypes according to the evolutionary relationships summarized in a haplotype tree. Since many haplotype trees are often virtually likely given the observed data, one key feature of the proposed algorithm is the incorporation of the tree uncertainty in association testing. The algorithm is motivated by and relies on the common disease/common variants assumption (Collins et al. Collins et al., 1997Collins FS Guyer MS Charkravarti A Variations on a theme: cataloging human DNA sequence variation.Science. 1997; 278: 1580-1581Crossref PubMed Scopus (822) Google Scholar), which conjectures that common modest-risk variants may contribute more to the development of common complex disease than do rare high-risk variants. The algorithm is also built on the recent discovery of the human genome structure that the majority of haplotype diversities are concentrated on a few major categories because of the correlations among proximate SNPs (e.g., Daly et al. Daly et al., 2001Daly MJ Rioux JD Schaffner SF Hudson TJ Lander ES High-resolution haplotype structure in the human genome.Nat Genet. 2001; 29: 229-232Crossref PubMed Scopus (1383) Google Scholar; Johnson et al. Johnson et al., 2001Johnson GC Esposito L Barratt BJ Smith AN Heward J Di Genova G Ueda H Cordell HJ Eaves IA Dudbridge F Twells RC Payne F Hughes W Nutland S Stevens H Carr P Tuomilehto-Wolf E Tuomilehto J Gough SC Clayton DG Todd JA Haplotype tagging for the identification of common disease genes.Nat Genet. 2001; 29: 233-237Crossref PubMed Scopus (999) Google Scholar). Therefore, instead of spending degrees of freedom on rare haplotypes that would result in unstable statistical inference and insufficient testing power, the algorithm reduces the observed haplotype space, in a probabilistic manner, to a core haplotype set that contains fewer polymorphisms but possesses the essential information for studying haplotype-disease association. Such core haplotype diversity presumably mimics the diversity before the occurrence of other events that are not directly related to the evolution of disease mutation—for example, recent marker mutation, gene conversion, genotyping error, and even missing data. The grouping analysis of Tzeng (Tzeng, 2005Tzeng JY Evolutionary-based grouping of haplotypes in association analysis.Genet Epidemiol. 2005; 28: 220-231Crossref PubMed Scopus (35) Google Scholar) is limited to assessing global association between haplotypes and traits. It cannot evaluate the effect of individual haplotypes or accommodate for covariates. Its implementation requires phased haplotypes and empirical evaluation of the significance level. In the present study, we generalized the clustering approach of Tzeng (Tzeng, 2005Tzeng JY Evolutionary-based grouping of haplotypes in association analysis.Genet Epidemiol. 2005; 28: 220-231Crossref PubMed Scopus (35) Google Scholar) to a generalized linear model framework and allowed for unphased genotypes. We constructed tests that are based on clustered haplotypes, for assessing association at both global and haplotype-specific levels. The test incorporates two major sources of uncertainties in haplotype analysis—clustering uncertainty and phase uncertainty. Among the many promising regression-based approaches that evaluate individual effects of haplotypes through use of genotypes, we established our work on the score tests developed by Schaid et al. (Schaid et al., 2002Schaid DJ Rowland CM Tines DE Jacobson RM Poland GA Score tests for association between traits and haplotypes when linkage phase is ambiguous.Am J Hum Genet. 2002; 70: 425-434Abstract Full Text Full Text PDF PubMed Scopus (1538) Google Scholar). Their method has been shown to be robust to departure from the Hardy-Weinberg equilibrium and to possess comparable power with retrospective approaches for case-control data that are sampled retrospectively (Satten and Epstein Satten and Epstein, 2004Satten GA Epstein MP Comparison of prospective and retrospective methods for haplotype inference in case-control studies.Genet Epidemiol. 2004; 27: 192-201Crossref PubMed Scopus (71) Google Scholar). Through simulation studies, we assessed the performance of the proposed approach and demonstrated its validity and power in testing for haplotype-trait association. We also illustrated the proposed approach through an application to a hypertriglyceridemia study, in which we tested the apolipoprotein A5 gene (APOA5), a confirmed risk factor of hypertriglyceridemia. We begin this section by reviewing the clustering methods of Tzeng (Tzeng, 2005Tzeng JY Evolutionary-based grouping of haplotypes in association analysis.Genet Epidemiol. 2005; 28: 220-231Crossref PubMed Scopus (35) Google Scholar). We then integrate the clustering algorithm into a regression framework. Finally, we construct the score test for association that incorporates phase ambiguity and clustering uncertainty on the basis of the work of Schaid et al. (Schaid et al., 2002Schaid DJ Rowland CM Tines DE Jacobson RM Poland GA Score tests for association between traits and haplotypes when linkage phase is ambiguous.Am J Hum Genet. 2002; 70: 425-434Abstract Full Text Full Text PDF PubMed Scopus (1538) Google Scholar) and Tzeng (Tzeng, 2005Tzeng JY Evolutionary-based grouping of haplotypes in association analysis.Genet Epidemiol. 2005; 28: 220-231Crossref PubMed Scopus (35) Google Scholar). The fundamental purpose of the clustering algorithm is to group rare haplotypes with their corresponding ancestral haplotypes. Given an evolutionary tree of haplotypes, the algorithm sequentially combines “rare” haplotypes into their one-step neighboring haplotypes, from the tips of the tree toward the major nodes. Each of the resulting clusters is represented by the most common haplotype, and haplotypes within a cluster are assumed to have the same effect on the disease trait. Determining “rare” haplotypes requires a trade-off between information and dimensionality, and the algorithm uses an information criterion to find the optimal balance between the two. The information criterion is defined as “the cumulative Shannon information content” (Shannon Shannon, 1948Shannon CE A mathematical theory of communication.Bell System Tech J. 1948; 27 (623-656): 379-423Crossref Scopus (20636) Google Scholar), with penalty function determined by the number of dimensions and the sample size involved. Denote HF as the full set of observed haplotypes and HC as the set of clustered haplotypes. The algorithm obtains HC by preserving high-frequency haplotypes—that is, to set HC as the ℓ most frequent haplotypes, where ℓ maximizes the information criterion. In reality, the evolutionary tree is often unknown and needs to be inferred. Instead of inferring the most-likely tree relationship and performing grouping accordingly, the algorithm assigns each relationship branch a probability. It then clusters haplotypes by considering all relationships according to the probability weights. The branch probability is determined by two factors that were commonly considered in reconstructing a haplotype tree (Crandall and Templeton Crandall and Templeton, 1993Crandall KA Templeton AR Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction.Genetics. 1993; 134: 959-969PubMed Google Scholar; Slatkin and Rannala Slatkin and Rannala, 1997Slatkin M Rannala B Estimating the age of alleles by use of intraallelic variability.Am J Hum Genet. 1997; 60: 447-458PubMed Google Scholar): (1) the relatedness of haplotypes and (2) the age of haplotypes. The algorithm uses haplotype frequencies to indicate the haplotype age. To measure the relatedness of haplotypes, a certain metric of haplotype similarity is used, such as counting the number of matching loci between two haplotypes. When the evolutionary relationships are known, the branch probability is reduced to an indicator function of whether two haplotypes u and v are one-step related. For further detail, see Tzeng (Tzeng, 2005Tzeng JY Evolutionary-based grouping of haplotypes in association analysis.Genet Epidemiol. 2005; 28: 220-231Crossref PubMed Scopus (35) Google Scholar). The general algorithm can be described as follows: first, partition the list HF into (1) H(0)=HC, the core category, (2) H(1), the one-step neighbors of H(0) that consist of haplotypes different from the core haplotypes by one step of mutation, and (3) H(2), the two-step neighbors of H(0) that consist of haplotypes different from the core haplotypes by two steps of mutation, and continue until the entire space of HF is exhausted. Let ΠF denote the haplotype frequencies of HF; correspondingly, ΠF is also decomposed into Π(0),Π(1),…,Π(j),…,Π(J). Starting from j=J to j=1, group each element of H(j) to its one-step ancestor in H(j-1) and combine the frequencies. The grouping rule is specified according to the branch probabilities that are stored in the allocation matrix B(j); each row of B(j) describes to whom and how a certain haplotype of H(j) is allocated among H(j-1). As illustrated by Tzeng (Tzeng, 2005Tzeng JY Evolutionary-based grouping of haplotypes in association analysis.Genet Epidemiol. 2005; 28: 220-231Crossref PubMed Scopus (35) Google Scholar), this one-step grouping process is equivalent to the matrix operation Π(j)′B(j), and the overall process can be described as Π′C(=Π(0)*′)=Π(0)′+Π(1)′B(1)+Π(2)′B(2)B(1)+⋯+Π(J)′B(J)B(J-1)⋯B(2)B(1) . Or, equivalently, ΠC′=ΠF′B ,(1) where ΠF=[Π(0)_Π(1)_Π(2)_⋮] B=[I_B(1)_B(2)B(1)_⋮] . Suppose there are (L+1) distinct haplotypes in the population and they are clustered into (L*+1) groups. The dimension of B is (L+1)×(L*+1). Given that the clustering procedure can be implemented via the matrix multiplication in equation (1), it is straightforward to integrate this dimension reduction procedure into a regression framework. Under the regression model, probabilistic clustering of haplotypes can be done by replacing the vector of the haplotype frequencies Π in equation (1) with the data matrix of haplotypes. That is, denote XF as the haplotype matrix of the full dimension with use of a certain scoring rule; its (h,i) entry, for example, can be the number of copies of haplotype h that individual i possesses. The matrix XF has dimension (L+1)×n, where n is the sample size. Then the data matrix of clustered haplotypes, XC, can be obtained by XC′=XF′B(Π) .(2) Here, we rewrite the allocation matrix B as B(Π) to emphasize the fact that the allocation matrix B is a function of the haplotype frequency Π. Let Y denote an n×1 vector of the disease trait values, and let Z denote a P×n matrix of the P environmental covariates. With the original haplotype data of full dimension, the effects of the genetic and environmental covariates can be modeled by the generalized linear model (GLM): g(EY)≡η=XF′βF+Z′γ , where β′F=(βF(0),βF(1),˙,βF(L)) is an (L+1)×1 vector. The association of haplotypes with the disease traits can be detected by testing H0:βF(0)=βF(1)=˙=βF(L). To reduce the degrees of freedom, we performed an analysis on groups of homogeneous haplotypes, using the following model: g(EY)≡η=XC′βC+Z′γ , where X′C is obtained by the clustering algorithm of equation (2) and β′C=(βC(0), βC(1), ˙, βC(L*)) with L*≤L. The association test is now performed through the (L*+1) parameters of the clustered haplotypes, H0:βC(0)=βC(1)=⋯=βC(L*) .(3) Here, we derive the score test for association in the clustered haplotype space. We first calculate the score function, which is the partial derivative of the log likelihood function, and then use it to construct the score test. To facilitate derivation, we reparameterize βC via a linear transformation βC≡[μμ+α1⋮μ+αL*]=A[μα] with A=[10⋯01⋮IL*×L*1] . Consequently, the global null hypothesis (3) is equivalent to H0:α1=α2=˙=αL*=0, and the effect of haplotype h can be examined by H0:αh=0. Consider observed data (Y,G,Z) in which G is the data matrix of unphased genotypes. For each individual i, we treat the observed genotype gi as an incomplete version of haplotype count xF,i, which is the ith column of the design matrix XF. Without losing generality, here we assume that the vector xF,i is normed so that its entries sum to 1. Under the assumption of Hardy-Weinberg equilibrium, xF,i∼½×multinomial(2,ΠF). The GLM density of trait yi, given covariates xF,i and zi, is f(yi|xF,i,zi;α,μ,ϕ,γ,Π)=exp[yiηi-b(ηi)a(ϕ)+c(yi,ϕ)] , where ηi=xC,i′βC+zi′γ=xF,i′ B(Π)A [μα]+zi′γ , and ϕ is the dispersion parameter (see table 1 of Schaid et al. [Schaid et al., 2002Schaid DJ Rowland CM Tines DE Jacobson RM Poland GA Score tests for association between traits and haplotypes when linkage phase is ambiguous.Am J Hum Genet. 2002; 70: 425-434Abstract Full Text Full Text PDF PubMed Scopus (1538) Google Scholar]). Let ζ denote the vector of the nuisance parameters (μ,γ,ϕ,Π). The likelihood function for (α,ζ) on the basis of the data (Y,G,Z) is L(α,ζ;Y,G,Z)=Πi=1n{∑xF,if(yi,xF,i,gi|zi; α,β)}=Πi=1n{∑xF,if(yi|xF,i,zi;α,ζ)×P(gi|xF,i)×P(xF,i;Π)} .(4) Because P(gi|xF,i) is an indicator function of whether the haplotype count xF,i is compatible with the observed genotype gi, likelihood (4) can be further simplified as L(α,ζ;Y,G,Z)=Πi=1n{∑xF,i∈gif(yi|xF,i,zi;α,ζ)×P(xF,i;Π)} .(5) The score function for α is the partial derivative of likelihood (5), with respect to α. The resulting score statistic, denoted by Sα, is the score function evaluated at the restricted maximum-likelihood estimates under the null hypothesis. Sα is the statistic we use to test haplotype effect; in appendix A, we show the following result: Sα=∑i=1nyi-y¯a(ϕ)B(Π)′-0E(Xi|gi)|α=α˜=0ζ=ζ˜ , where α˜ and ζ˜ are the restricted maximum-likelihood estimates under the null hypothesis, B(Π)′-0 is the matrix B(Π) with the first column (i.e., the baseline haplotype) removed, and E(Xi|gi) is the same as that defined by Schaid et al. (Schaid et al., 2002Schaid DJ Rowland CM Tines DE Jacobson RM Poland GA Score tests for association between traits and haplotypes when linkage phase is ambiguous.Am J Hum Genet. 2002; 70: 425-434Abstract Full Text Full Text PDF PubMed Scopus (1538) Google Scholar), the expected haplotype counts given the observed genotypes. We see that the proposed score statistic that accounts for phase and clustering ambiguities is the original score test of Schaid et al. (Schaid et al., 2002Schaid DJ Rowland CM Tines DE Jacobson RM Poland GA Score tests for association between traits and haplot
DA - 2006/2//
PY - 2006/2//
DO - 10.1086/500025
VL - 78
IS - 2
SP - 231-242
SN - 1537-6605
ER -
TY - JOUR
TI - Pleiotropic quantitative trait loci contribute to population divergence in traits associated with life-history variation in Mimulus guttatus
AU - Hall, MC
AU - Basten, CJ
AU - Willis, JH
T2 - GENETICS
AB - Abstract Evolutionary biologists seek to understand the genetic basis for multivariate phenotypic divergence. We constructed an F2 mapping population (N = 539) between two distinct populations of Mimulus guttatus. We measured 20 floral, vegetative, and life-history characters on parents and F1 and F2 hybrids in a common garden experiment. We employed multitrait composite interval mapping to determine the number, effect, and degree of pleiotropy in quantitative trait loci (QTL) affecting divergence in floral, vegetative, and life-history characters. We detected 16 QTL affecting floral traits; 7 affecting vegetative traits; and 5 affecting selected floral, vegetative, and life-history traits. Floral and vegetative traits are clearly polygenic. We detected a few major QTL, with all remaining QTL of small effect. Most detected QTL are pleiotropic, implying that the evolutionary shift between these annual and perennial populations is constrained. We also compared the genetic architecture controlling floral trait divergence both within (our intraspecific study) and between species, on the basis of a previously published analysis of M. guttatus and M. nasutus. Eleven of our 16 floral QTL map to approximately the same location in the interspecific map based on shared, collinear markers, implying that there may be a shared genetic basis for floral divergence within and among species of Mimulus.
DA - 2006/3//
PY - 2006/3//
DO - 10.1534/genetics.105.051227
VL - 172
IS - 3
SP - 1829-1844
SN - 0016-6731
ER -
TY - JOUR
TI - Sensitivity of ecological models to their climate drivers: Statistical ensembles for forcing
AU - Fuentes, M
AU - Kittel, TGF
AU - Nychka, D
T2 - ECOLOGICAL APPLICATIONS
AB - Global and regional numerical models for terrestrial ecosystem dynamics require fine spatial resolution and temporally complete historical climate fields as input variables. However, because climate observations are unevenly spaced and have incomplete records, such fields need to be estimated. In addition, uncertainty in these fields associated with their estimation are rarely assessed. Ecological models are usually driven with a geostatistical model's mean estimate (kriging) of these fields without accounting for this uncertainty, much less evaluating such errors in terms of their propagation in ecological simulations. We introduce a Bayesian statistical framework to model climate observations to create spatially uniform and temporally complete fields, taking into account correlation in time and space, spatial heterogeneity, lack of normality, and uncertainty about all these factors. A key benefit of the Bayesian model is that it generates uncertainty measures for the generated fields. To demonstrate this method, we reconstruct historical monthly precipitation fields (a driver for ecological models) on a fine resolution grid for a climatically heterogeneous region in the western United States. The main goal of this work is to evaluate the sensitivity of ecological models to the uncertainty associated with prediction of their climate drivers. To assess their numerical sensitivity to predicted input variables, we generate a set of ecological model simulations run using an ensemble of different versions of the reconstructed fields. We construct such an ensemble by sampling from the posterior predictive distribution of the climate field. We demonstrate that the estimated prediction error of the climate field can be very high. We evaluate the importance of such errors in ecological model experiments using an ensemble of historical precipitation time series in simulations of grassland biogeochemical dynamics with an ecological numerical model, Century. We show how uncertainty in predicted precipitation fields is propagated into ecological model results and that this propagation had different modes. Depending on output variable, the response of model dynamics to uncertainty in inputs ranged from uncertainty in outputs that matched that of inputs to those that were muted or that were biased, as well as uncertainty that was persistent in time after input errors dropped.
DA - 2006/2//
PY - 2006/2//
DO - 10.1890/04-1157
VL - 16
IS - 1
SP - 99-116
SN - 1939-5582
KW - Bayesian inference
KW - ecological numerical models
KW - kriging
KW - nonstationary process
KW - spatial statistics
KW - variogram
ER -
TY - JOUR
TI - Tuning variable selection procedures by adding noise
AU - Luo, X. H.
AU - Stefanski, L. A.
AU - Boos, D. D.
T2 - Technometrics
AB - Many variable selection methods for linear regression depend critically on tuning parameters that control the performance of the method, for example, “entry” and “stay” significance levels in forward and backward selection. However, most methods do not adapt the tuning parameters to particular datasets. We propose a general strategy for adapting variable selection tuning parameters that effectively estimates the tuning parameters so that the selection method avoids overfitting and underfitting. The strategy is based on the principle that overfitting and underfitting can be directly observed in estimates of the error variance after adding controlled amounts of additional independent noise to the response variable, then running a variable selection method. It is related to the simulation technique SIMEX found in the measurement error literature. We focus on forward selection because of its simplicity and ability to handle large numbers of explanatory variables. Monte Carlo studies show that the new method compares favorably with established methods.
DA - 2006///
PY - 2006///
DO - 10.1198/004017005000000319
VL - 48
IS - 2
SP - 165-175
ER -
TY - JOUR
TI - Isozyme and morphological variation in maize of five Andean countries
AU - Sanchez, J. J.
AU - Goodman, M. M.
AU - Bird, R. M.
AU - Stuber, C. W.
T2 - Maydica
DA - 2006///
PY - 2006///
VL - 51
IS - 1
SP - 25-42
ER -
TY - JOUR
TI - A real-time hurricane surface wind forecasting model: Formulation and verification
AU - Xie, L
AU - Bao, SW
AU - Pietrafesa, LJ
AU - Foley, K
AU - Fuentes, M
T2 - MONTHLY WEATHER REVIEW
AB - Abstract A real-time hurricane wind forecast model is developed by 1) incorporating an asymmetric effect into the Holland hurricane wind model; 2) using the National Oceanic and Atmospheric Administration (NOAA)/National Hurricane Center’s (NHC) hurricane forecast guidance for prognostic modeling; and 3) assimilating the National Data Buoy Center (NDBC) real-time buoy data into the model’s initial wind field. The method is validated using all 2003 and 2004 Atlantic and Gulf of Mexico hurricanes. The results show that 6- and 12-h forecast winds using the asymmetric hurricane wind model are statistically more accurate than using a symmetric wind model. Detailed case studies were conducted for four historical hurricanes, namely, Floyd (1999), Gordon (2000), Lily (2002), and Isabel (2003). Although the asymmetric model performed generally better than the symmetric model, the improvement in hurricane wind forecasts produced by the asymmetric model varied significantly for different storms. In some cases, optimizing the symmetric model using observations available at initial time and forecast mean radius of maximum wind can produce comparable wind accuracy measured in terms of rms error of wind speed. However, in order to describe the asymmetric structure of hurricane winds, an asymmetric model is needed.
DA - 2006/5//
PY - 2006/5//
DO - 10.1175/MWR3126.1
VL - 134
IS - 5
SP - 1355-1370
SN - 0027-0644
ER -
TY - JOUR
TI - Resistance of temperately adapted tropical inbred lines and testcrosses to three important maize pathogens
AU - Hawbaker, M. S.
AU - Goodman, M. M.
T2 - Maydica
DA - 2006///
PY - 2006///
VL - 51
IS - 1
SP - 135-139
ER -
TY - JOUR
TI - Phylogeography of the wild subspecies of Zea mays
AU - Buckler, E. S.
AU - Goodman, M. M.
AU - Holtsford, T. P.
AU - Doebley, J. F.
AU - Sanchez, J.
T2 - Maydica
DA - 2006///
PY - 2006///
VL - 51
IS - 1
SP - 123-134
ER -
TY - JOUR
TI - Variation in volume production through clonal deployment: Results from a simulation model to minimize risk for both a currently known and unknown future pest
AU - Yanchuk, A. D.
AU - Bishir, J.
AU - Russell, J. H.
AU - Polsson, K. R.
T2 - SILVAE GENETICA
AB - Abstract A simulation model was developed to examine optimum patterns of deploying selected clones in the hypothetical situations of both a currently known pest and an unknown future pest. We modelled the interactions between Sitka spruce (Picea sitchensis (Bong.) Carr.), an economically important forest tree in British Columbia and the northwestern U.S., and the spruce terminal weevil (Pissodes strobi (Peck)), a major pest in western spruces. The model is combined with the Province of British Columbia’s Tree and Stand Simulator (TASS) model to drive individual tree growth and stand establishment and development. Two clonal-sampling strategies are examined: a randomly drawn set of genotypes or clones, to depict the potential consequences of a new (e.g., exotic) or a previously unimportant natural pest attacking a ‘random’ set of genotypes, and a ‘fixed’ set of clones, emulating a ‘commercial’ or known set of clones for growth and resistance mechanisms. Simulations use a range of numbers of genotypes or clones (2, 6, 18 and 30), and three deployment patterns (a random mixture of ramets, single- clone blocks, and a mosaic of smaller clonal blocks), in one and five hectare (Ha) stands. Total merchantable timber volume on a per Ha basis at harvest age 80 is used to compare the various combinations and schemes. With both random and fixed chosen sets of clones, the random planting pattern (i.e., random mixture of ramets from the clonal set) produced the most volume. Eighteen randomly chosen clones generally produced more volume, than 2, 6 and 30 clones, but differences among 6, 18 and 30 clones were small in most cases, irrespective of planting pattern. For fixed clones, the use of more resistant clones with higher growth potential produced more volume; however, pure clonal blocks of the best clone were not better than a mixture of that clone and an inferior one. Reducing the effects of insect activity and attack on trees, by lowering the average annual temperature in the model, or turning off all insect ‘activity’, increased merchantable volume but did not change the optimum number of clones (~18) or deployment pattern (random mixture). Forestry agencies can weigh these findings against economic advantages of block plantings of similar genotypes, in the choice of an appropriate number of clones and a deployment strategy.
DA - 2006///
PY - 2006///
DO - 10.1515/sg-2006-0005
VL - 55
IS - 1
SP - 25-37
SN - 2509-8934
KW - clonal forestry
KW - genetic diversity
KW - risk
KW - merchantable volume loss
KW - insect resistance
ER -
TY - JOUR
TI - Variable selection for support vector machines via smoothing spline ANOVA
AU - Zhang, H. H.
T2 - Statistica Sinica
DA - 2006///
PY - 2006///
VL - 16
IS - 2
SP - 659-674
ER -
TY - JOUR
TI - Pathogenicity, aggressiveness, and virulence of three species of Cercospora associated with gray leaf spot of maize
AU - Carson, M. L.
AU - Goodman, M. M.
T2 - Maydica
DA - 2006///
PY - 2006///
VL - 51
IS - 1
SP - 89-92
ER -
TY - JOUR
TI - Estimating animal abundance in heterogeneous environments: An application to aerial surveys for Dugongs
AU - Pollock, KH
AU - Marsh, HD
AU - Lawler, IR
AU - Alldredge, MW
T2 - JOURNAL OF WILDLIFE MANAGEMENT
AB - The probability of detecting an animal in a sampled area during a survey consists of 2 components: 1) the probability of an animal being available for detection (availability), which can be highly variable in heterogeneous environments; and 2) the probability of an animal being detected, conditional on its being available for detection (perception). Many surveys only estimate the latter probability because modeling the availability process requires information collected external to the survey. We illustrate estimation of both probabilities in an application to aerial surveys of dugongs (Dugong dugon) in Northern Australian coastal waters where water clarity varies greatly over relatively small spatial scales. Using artificial dugong models and timed depth recorders deployed on 15 wild dugongs to obtain dive profiles, we carried out experiments to determine zones of detectability for dugongs at the range of depths, turbidities, and sea states that spanned the environmental heterogeneity encountered on dugong surveys. Resulting probability estimates were heterogeneous and dependent on the measured conditions. To estimate perception probability, we used a tandem team of 2 observers on either side of the aircraft. This permitted fitting generalized Lincoln–Petersen models with Program MARK. We then used the generalized Horvitz–Thompson estimator, based on the overall detection probability for each individual dugong, to generate population estimates. We also developed a new simulation-based method for estimating standard errors and confidence intervals. We contrast absolute abundance estimates of dugongs in the Torres Strait and Northern Great Barrier Reef regions using both the new and original approaches (Marsh and Sinclair 1989a). For Torres Strait, the new method produced a substantially smaller estimate (11,956 vs. 14,106 dugongs) and a very much smaller standard error (1,189 vs. 2,314 dugongs), whereas the new method produced slightly larger estimates (mean 9,855 vs. 9,193 dugongs, standard error 1,184 vs. 917 dugongs) for the Northern Great Barrier Reef survey.
DA - 2006///
PY - 2006///
DO - 10.2193/0022-541X(2006)70[255:EAAIHE]2.0.CO;2
VL - 70
IS - 1
SP - 255-262
SN - 1937-2817
KW - aerial surveys
KW - availability bias
KW - capture-recapture methods
KW - heterogeneous sighting probabilities
KW - line transects
KW - multiple observer methods
KW - perception bias
KW - sampling
KW - strip transects
KW - visibility bias
ER -
TY - JOUR
TI - Models and partition of variance for quantitative trait loci with epistasis and linkage disequilibrium
AU - Wang, T.
AU - Zeng, Z. B.
T2 - BMC Genetics
DA - 2006///
PY - 2006///
VL - 7
ER -
TY - JOUR
TI - Integrating catch-at-age and multiyear tagging data: a combined Brownie and Petersen estimation approach in a fishery context
AU - Polacheck, T
AU - Eveson, JP
AU - Laslett, GM
AU - Pollock, KH
AU - Hearn, WS
T2 - CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES
AB - A comprehensive framework for modelling data from multiyear tagging experiments in a fishery context is presented that incorporates catch data into the traditional Brownie tagrecapture model. Incorporation of catch data not only allows for improved estimation of natural and fishing mortality rates, but also for direct estimation of population size at the time of tagging. These are the primary quantities required to be estimated in stock assessments having an approach for directly estimating them that does not require catch rates provides a potentially powerful alternative for augmenting traditional stock assessment methods. Simulations are used to demonstrate the value of directly incorporating catch data in the model. Results from the range of scenarios considered suggest that in addition to providing a precise estimate of population size (coefficients of variation ranging from ~15% to 30%), including catch data can decrease biases in the mortality rate estimates (natural mortality especially) and improve precision of fishing mortality rate estimates (by as much as 60% at age 1). The model is applied to southern bluefin tuna (Thunnus maccoyii) tagrecapture and catch data collected in the 1990s to provide estimates of natural mortality, fishing mortality, and abundance for five cohorts of fish.
DA - 2006/3//
PY - 2006/3//
DO - 10.1139/f05-232
VL - 63
IS - 3
SP - 534-548
SN - 1205-7533
ER -
TY - JOUR
TI - Unit roots: Periodogram ordinate
AU - Bhattacharyya, BB
AU - Richardson, GD
AU - Flores, PV
T2 - STATISTICS & PROBABILITY LETTERS
AB - The periodogram ordinate is used to define an asymptotic test for the testing problem H0:α=1 vs. HA:|α|<1 under appropriate assumptions on the model Yt=αYt-1+εt-θεt-1, where θ is near one. A drift term is also included in the model. An independent and identically distributed error structure as well as one exhibiting long memory are studied.
DA - 2006/3/15/
PY - 2006/3/15/
DO - 10.1016/j.spl.2005.09.011
VL - 76
IS - 6
SP - 641-651
SN - 1879-2103
KW - autoregressive moving average processes
KW - unit roots
KW - periodograrn ordinate
KW - limiting distributions
ER -
TY - JOUR
TI - The relation of stroke admissions to recent weather, airborne allergens, air pollution, seasons, upper respiratory infections, and asthma incidence, September 11, 2001, and day of the week
AU - Low, RB
AU - Bielory, L
AU - Qureshi, AI
AU - Dunn, V
AU - Stuhlmiller, DFE
AU - Dickey, DA
T2 - STROKE
AB - Some previous research links stroke incidence to weather, some links strokes to air pollution, and some report seasonal effects. Alveolar inflammation was proposed as the mechanistic link. We present a unified model of time, weather, pollution, and upper respiratory infection (URI) incidence.We combined existing databases: US Environmental Protection Agency pollution levels, National Weather Service data, counts of airborne allergens, and New York City Health and Hospitals Corporation counts of stroke, asthma, and URI patients. We used autoregressive integrated moving average modeling (a statistical time series modeling technique) with stroke admissions as the response variable and day of week, holidays, September 11th, and other counts and levels as explanatory variables.Using a broad definition of stroke, there were 5.1+/-2.3 stroke admissions per day: narrowly defined, 4.2+/-2.1 strokes per day. There are relatively fewer strokes on Sundays (0.50 strokes; P=0.0011), Saturdays (0.62; P<0.0001), Fridays (0.38; P=0.0009) and holidays (0.875; P=0.0016). We found relatively small, independent exacerbating effects of higher air temperature (P=0.0211), dry air (P=0.0187), URIs, (P<0.0001), grass pollen (P=0.0341), sulfur dioxide (SO2; P=0.0471), and suspended particles <10 microm in size (P=0.0404). These effects are modest: < or =0.6, 0.6, 2.4, 1, 0.9, and 0.7 strokes per day, respectively. We did not find statistically significant exacerbating effects of other variables.We found statistically significant, independent exacerbating effects of warmer, drier air, URIs, grass pollen, SO2, and particulate air pollution. The model supports the theory that links pulmonary inflammation to stroke.
DA - 2006/4//
PY - 2006/4//
DO - 10.1161/01.STR.0000214681.94680.66
VL - 37
IS - 4
SP - 951-957
SN - 0039-2499
KW - air pollution
KW - cerebrovascular accident
KW - fungal spores
KW - influenza, human
KW - pollen
KW - respiratory infections
KW - weather
ER -
TY - JOUR
TI - Testing for spatial clustering of amino acid replacements within protein tertiary structure
AU - Yu, Jiaye
AU - Thorne, Jeffrey L.
T2 - JOURNAL OF MOLECULAR EVOLUTION
DA - 2006/6//
PY - 2006/6//
DO - 10.1007/s00239-005-0107-2
VL - 62
IS - 6
SP - 682-692
SN - 1432-1432
KW - protein tertiary structure
KW - protein evolution
KW - spatial clustering
ER -
TY - JOUR
TI - Multiclass proximal support vector machines
AU - Tang, Yongqiang
AU - Zhang, Hao Helen
T2 - JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS
AB - This article proposes the multiclass proximal support vector machine (MPSVM) classifier, which extends the binary PSVM to the multiclass case. Unlike the one-versus-rest approach that constructs the decision rule based on multiple binary classification tasks, the proposed method considers all classes simultaneously and has better theoretical properties and empirical performance. We formulate the MPSVM as a regularization problem in the reproducing kernel Hilbert space and show that it implements the Bayes rule for classification. In addition, the MPSVM can handle equal and unequal misclassification costs in a unified framework. We suggest an efficient algorithm to implement the MPSVM by solving a system of linear equations. This algorithm requires much less computational effort than solving the standard SVM, which often requires quadratic programming and can be slow for large problems. We also provide an alternative and more robust algorithm for ill-posed problems. The effectiveness of the MPSVM is demonstrated by both simulation studies and applications to cancer classifications using microarray data.
DA - 2006/6//
PY - 2006/6//
DO - 10.1198/106186006X113647
VL - 15
IS - 2
SP - 339-355
SN - 1537-2715
KW - Bayes rule
KW - nonstandard classifications
KW - reproducing kernel Hilbert space.
ER -
TY - JOUR
TI - The multivariate skew-slash distribution
AU - Wang, J
AU - Genton, MG
T2 - JOURNAL OF STATISTICAL PLANNING AND INFERENCE
AB - The slash distribution is often used as a challenging distribution for a statistical procedure. In this article, we define a skewed version of the slash distribution in the multivariate setting and derive several of its properties. The multivariate skew-slash distribution is shown to be easy to simulate from and can therefore be used in simulation studies. We provide various examples for illustration.
DA - 2006/1/1/
PY - 2006/1/1/
DO - 10.1016/j.jspi.2004.06.023
VL - 136
IS - 1
SP - 209-220
SN - 1873-1171
KW - cauchy
KW - configural polysampling
KW - kurtosis
KW - multivariate distributions
KW - skewness
KW - skew-normal
KW - slash
ER -
TY - JOUR
TI - Testing for separability of spatial-temporal covariance functions
AU - Fuentes, M
T2 - JOURNAL OF STATISTICAL PLANNING AND INFERENCE
AB - Most applications in spatial statistics involve modeling of complex spatial–temporal dependency structures, and many of the problems of space and time modeling can be overcome by using separable processes. This subclass of spatial–temporal processes has several advantages, including rapid fitting and simple extensions of many techniques developed and successfully used in time series and classical geostatistics. In particular, a major advantage of these processes is that the covariance matrix for a realization can be expressed as the Kronecker product of two smaller matrices that arise separately from the temporal and purely spatial processes, and hence its determinant and inverse are easily determinable. However, these separable models are not always realistic, and there are no formal tests for separability of general spatial–temporal processes. We present here a formal method to test for separability. Our approach can be also used to test for lack of stationarity of the process. The beauty of our approach is that by using spectral methods the mechanics of the test can be reduced to a simple two-factor analysis of variance (ANOVA) procedure. The approach we propose is based on only one realization of the spatial–temporal process. We apply the statistical methods proposed here to test for separability and stationarity of spatial–temporal ozone fields using data provided by the US Environmental Protection Agency (EPA).
DA - 2006/2/1/
PY - 2006/2/1/
DO - 10.1016/j.jspi.2004.07.004
VL - 136
IS - 2
SP - 447-466
SN - 1873-1171
KW - covariance
KW - Fourier transform
KW - periodogram
KW - spectral density
KW - weakly stationarity
ER -
TY - JOUR
TI - Quasi-lilkelihood estimation for GLM with random scales
AU - Lu, JC
AU - Chen, D
AU - Zhou, WX
T2 - JOURNAL OF STATISTICAL PLANNING AND INFERENCE
AB - This paper uses random scales similar to random effects used in the generalized linear mixed models to describe “inter-location” population variation in variance components for modeling complicated data obtained from applications such as antenna manufacturing. Our distribution studies lead to a complicated integrated extended quasi-likelihood (IEQL) for parameter estimations and large sample inference derivations. Laplace's expansion and several approximation methods are employed to simplify the IEQL estimation procedures. Asymptotic properties of the approximate IEQL estimates are derived for general structures of the covariance matrix of random scales. Focusing on a few special covariance structures in simpler forms, the authors further simplify IEQL estimates such that typically used software tools such as weighted regression can compute the estimates easily. Moreover, these special cases allow us to derive interesting asymptotic results in much more compact expressions. Finally, numerical simulation results show that IEQL estimates perform very well in several special cases studied.
DA - 2006/2/1/
PY - 2006/2/1/
DO - 10.1016/j.jspi.2004.06.028
VL - 136
IS - 2
SP - 401-429
SN - 1873-1171
KW - generalized linear model
KW - integrated extended quasi-likelihood
KW - random scale
KW - multi-normality
KW - consistent estimate
KW - unbiasedness
ER -
TY - JOUR
TI - Bayesian analysis of zero-inflated regression models
AU - Ghosh, SK
AU - Mukhopadhyay, P
AU - Lu, JC
T2 - JOURNAL OF STATISTICAL PLANNING AND INFERENCE
AB - In modeling defect counts collected from an established manufacturing processes, there are usually a relatively large number of zeros (non-defects). The commonly used models such as Poisson or Geometric distributions can underestimate the zero-defect probability and hence make it difficult to identify significant covariate effects to improve production quality. This article introduces a flexible class of zero inflated models which includes other familiar models such as the Zero Inflated Poisson (ZIP) models, as special cases. A Bayesian estimation method is developed as an alternative to traditionally used maximum likelihood based methods to analyze such data. Simulation studies show that the proposed method has better finite sample performance than the classical method with tighter interval estimates and better coverage probabilities. A real-life data set is analyzed to illustrate the practicability of the proposed method easily implemented using WinBUGS.
DA - 2006/4/1/
PY - 2006/4/1/
DO - 10.1016/j.jspi.2004.10.008
VL - 136
IS - 4
SP - 1360-1375
SN - 0378-3758
UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-29444448265&partnerID=MN8TOARS
KW - Bayesian inference
KW - data augmentation
KW - Gibbs sampling
KW - Markov chain Monte Carlo
KW - WinBUGS
KW - zero-inflated power series models
ER -