TY - CONF TI - A novel method to construct genetic linkage maps in high autopolyploid species using hidden Markov models, with applications in sugarcane AU - Mollinari, M. AU - Marconi, T.G. AU - Mancini, M.C. AU - Costa, E.A. AU - Pinto, L.R. AU - Souza, A.P. AU - Garcia, A.A.F. T2 - International Plant & Animal Genome XX Conference C2 - 2012/// C3 - International Plant & Animal Genome XX Conference CY - San Diego, CA, USA DA - 2012/// PY - 2012/// ER - TY - JOUR TI - On ε-Optimality of the Pursuit Learning Algorithm AU - Martin, Ryan AU - Tilak, Omkar T2 - Journal of Applied Probability AB - Estimator algorithms in learning automata are useful tools for adaptive, real-time optimization in computer science and engineering applications. In this paper we investigate theoretical convergence properties for a special case of estimator algorithms - the pursuit learning algorithm. We identify and fill a gap in existing proofs of probabilistic convergence for pursuit learning. It is tradition to take the pursuit learning tuning parameter to be fixed in practical applications, but our proof sheds light on the importance of a vanishing sequence of tuning parameters in a theoretical convergence analysis. DA - 2012/9// PY - 2012/9// DO - 10.1017/S0021900200009542 VL - 49 IS - 03 SP - 795-805 J2 - J. Appl. Probab. LA - en OP - SN - 0021-9002 1475-6072 UR - http://dx.doi.org/10.1017/S0021900200009542 DB - Crossref ER - TY - JOUR TI - Convergence rate for predictive recursion estimation of finite mixtures AU - Martin, Ryan T2 - Statistics & Probability Letters AB - Predictive recursion (PR) is a fast stochastic algorithm for nonparametric estimation of mixing distributions in mixture models. It is known that the PR estimates of both the mixing and mixture densities are consistent under fairly mild conditions, but currently very little is known about the rate of convergence. Here I first investigate asymptotic convergence properties of the PR estimate under model misspecification in the special case of finite mixtures with known support. Tools from stochastic approximation theory are used to prove that the PR estimates converge, to the best Kullback--Leibler approximation, at a nearly root-$n$ rate. When the support is unknown, PR can be used to construct an objective function which, when optimized, yields an estimate the support. I apply the known-support results to derive a rate of convergence for this modified PR estimate in the unknown support case, which compares favorably to known optimal rates. DA - 2012/2// PY - 2012/2// DO - 10.1016/j.spl.2011.10.023 VL - 82 IS - 2 SP - 378-384 J2 - Statistics & Probability Letters LA - en OP - SN - 0167-7152 UR - http://dx.doi.org/10.1016/j.spl.2011.10.023 DB - Crossref KW - Density estimation KW - Kullback-Leibler divergence KW - Lyapunov function KW - Mixture model KW - Stochastic approximation ER - TY - JOUR TI - A Model for Overdispersion and Underdispersion using Latent Markov Processes AU - Thaithanan, J. AU - Ghosh, S.K. AU - Bumrungsup, C. T2 - Thailand Statistician DA - 2012/// PY - 2012/// VL - 10 SP - 183–197 ER - TY - RPRT TI - Shape Restricted Nonparametric Regression Based on Multivariate Bernstein Polynomials AU - Wang, J. AU - Ghosh, S.K. A3 - North Carolina State University DA - 2012/// PY - 2012/// M1 - 2640 M3 - Department of Statistics Technical Report PB - North Carolina State University SN - 2640 ER - TY - CONF TI - Bayesian Average Error Based Approach to Sample Size Calculations for Hypothesis Testing AU - Ghosh, S. T2 - Conference on Contemporary Issues and Applications of Statistics C2 - 2012/// CY - Kolkata, India DA - 2012/// PY - 2012/1/2/ ER - TY - CONF TI - Spatio-Temporal Analysis of Total Nitrate Concentrations Using Dynamic Statistical Models AU - Ghosh, S. T2 - TIES C2 - 2012/// CY - Hyderabad, India DA - 2012/// PY - 2012/1/4/ ER - TY - CONF TI - Nonparametric Bayes Applications in Biostatistics: A Discussion AU - Ghosh, S. T2 - ISBA 2012 World Meeting C2 - 2012/// CY - Kyoto, Japan DA - 2012/// PY - 2012/6/25/ ER - TY - CONF TI - A Comparative Study of the Estimation of the Maximum Tolerated Dose AU - Ghosh, S. T2 - Joint Statistical Meeting C2 - 2012/// CY - San Diego, CA, USA DA - 2012/// PY - 2012/7/29/ ER - TY - CONF TI - Novel Statistical Methods for Noninferiority/Equivalence Testing: A Discussion AU - Ghosh, S. T2 - FDA-Industry Statistics Workshop C2 - 2012/// CY - Washington, D.C., USA DA - 2012/// PY - 2012/9/12/ ER - TY - CONF TI - Shape Restricted Regression Models with Applications to Econometrics: A Short Course AU - Ghosh, S. T2 - Bocconi University C2 - 2012/// CY - Milano, Italy DA - 2012/// PY - 2012/10/1/ ER - TY - CONF TI - A Statistician's Journey Through the 'Bayesian' Path AU - Ghosh, S. T2 - 8th Annual UNCG Regional Mathematics and Statistics Conference C2 - 2012/11/3/ CY - Greensboro, NC DA - 2012/11/3/ PY - 2012/11/3/ ER - TY - CONF TI - A Flexible Class of Models for Longitudinal Data Subject to Data Irregularities AU - Ghosh, S. T2 - Eighth International Triennial Calcutta Symposium C2 - 2012/// CY - Kolkata, India DA - 2012/// PY - 2012/12/27/ ER - TY - JOUR TI - Potential of Potassium Hydroxide Pretreatment of Switchgrass for Fermentable Sugar Production AU - Sharma, Rajat AU - Palled, Vijaykumar AU - Sharma-Shivappa, Ratna R. AU - Osborne, Jason T2 - Applied Biochemistry and Biotechnology DA - 2012/12/29/ PY - 2012/12/29/ DO - 10.1007/S12010-012-0009-X VL - 169 IS - 3 SP - 761-772 J2 - Appl Biochem Biotechnol LA - en OP - SN - 0273-2289 1559-0291 UR - http://dx.doi.org/10.1007/S12010-012-0009-X DB - Crossref KW - Switchgrass KW - Lignocelluloses KW - KOH KW - Enzymatic hydrolysis KW - AIL KW - Fermentable sugars ER - TY - JOUR TI - Disease dynamics in wild populations: modeling and estimation: a review AU - Cooch, Evan G. AU - Conn, Paul B. AU - Ellner, Stephen P. AU - Dobson, Andrew P. AU - Pollock, Kenneth H. T2 - Journal of Ornithology DA - 2012/// PY - 2012/// DO - 10.1007/S10336-010-0636-3 VL - 152 IS - S2 SP - 485–509 SN - 2193-7192 1439-0361 UR - http://dx.doi.org/10.1007/S10336-010-0636-3 KW - Detection probability KW - Disease models KW - Mark-recapture KW - Multi-state models KW - Parameterization KW - Time series KW - Uncertain state ER - TY - JOUR TI - The distribution of the relative arc density of a family of interval catch digraph based on uniform data AU - Ceyhan, Elvan T2 - Metrika DA - 2012/8// PY - 2012/8// DO - 10.1007/S00184-011-0351-Y VL - 75 IS - 6 SP - 761–793 SN - 0026-1335 1435-926X UR - http://dx.doi.org/10.1007/S00184-011-0351-Y KW - Class cover catch digraph KW - Intersection digraph KW - Proximity catch digraph KW - Proximity map KW - Random graph KW - U-statistics ER - TY - JOUR TI - Bootstrapping for Significance of Compact Clusters in Multidimensional Datasets AU - Maitra, Ranjan AU - Melnykov, Volodymyr AU - Lahiri, Soumendra N. T2 - Journal of the American Statistical Association AB - This article proposes a bootstrap approach for assessing significance in the clustering of multidimensional datasets. The procedure compares two models and declares the more complicated model a better candidate if there is significant evidence in its favor. The performance of the procedure is illustrated on two well-known classification datasets and comprehensively evaluated in terms of its ability to estimate the number of components via extensive simulation studies, with excellent results. The methodology is also applied to the problem of k-means color quantization of several standard images in the literature and is demonstrated to be a viable approach for determining the minimal and optimal numbers of colors needed to display an image without significant loss in resolution. Additional illustrations and performance evaluations are provided in the online supplementary material. DA - 2012/3// PY - 2012/3// DO - 10.1080/01621459.2011.646935 VL - 107 IS - 497 SP - 378-392 J2 - Journal of the American Statistical Association LA - en OP - SN - 0162-1459 1537-274X UR - http://dx.doi.org/10.1080/01621459.2011.646935 DB - Crossref KW - Bootstrap KW - Hierarchical clustering KW - k-means algorithm KW - Overlap KW - Prohorov metric KW - p-value quantitation map KW - q-value quantitation map ER - TY - JOUR TI - Block Bootstraps for Time Series With Fixed Regressors AU - Nordman, Daniel J. AU - Lahiri, Soumendra N. T2 - Journal of the American Statistical Association AB - This article examines block bootstrap methods in linear regression models with weakly dependent error variables and nonstochastic regressors. Contrary to intuition, the tapered block bootstrap (TBB) with a smooth taper not only loses its superior bias properties but may also fail to be consistent in the regression problem. A similar problem, albeit at a smaller scale, is shown to exist for the moving and the circular block bootstrap (MBB and CBB, respectively). As a remedy, an additional block randomization step is introduced that balances out the effects of nonuniform regression weights, and restores the superiority of the (modified) TBB. The randomization step also improves the MBB or CBB. Interestingly, the stationary bootstrap (SB) automatically balances out regression weights through its probabilistic blocking mechanism, without requiring any modification, and enjoys a kind of robustness. Optimal block sizes are explicitly determined for block bootstrap variance estimators under regression. Finite sample performance and practical uses of the methods are illustrated through a simulation study and two data examples, respectively. Supplementary materials are available online. DA - 2012/3// PY - 2012/3// DO - 10.1080/01621459.2011.646929 VL - 107 IS - 497 SP - 233-246 J2 - Journal of the American Statistical Association LA - en OP - SN - 0162-1459 1537-274X UR - http://dx.doi.org/10.1080/01621459.2011.646929 DB - Crossref KW - MSE expansions KW - Optimal blocks KW - Simultaneous confidence bands KW - Tapers KW - Variance estimation ER - TY - CONF TI - From data to constraints AU - Mukhopadhyay, S. AU - Parzen, E. AU - Lahiri, S. N. T2 - Bayesian Inference and Maximum Entropy Methods in Science and Engineering: 31st International Workshop on Bayesian Inference and Maximum Entropy Methods in Science and Engineering AB - Jaynes' Maximum Entropy (MaxEnt) inference starts with the assumption that we have a set of known constraints over the distribution. In statistical physics, we have a good intuition about the conserved macroscopic variables. It should not be surprising that in a real world applications, we have no idea about which coordinates to use for specifying the state of the system. In other words, we only observe empirical data and we have to take a decision on the constraints from the data. In an effort to circumvent this limitation, we propose a nonparametric quantile based method to extract relevant and significant facts (sufficient statistics) for the maximum entropy exponential model. C2 - 2012/// C3 - AIP Conference Proceedings CY - Waterloo, Ontario, Canada DA - 2012/// PY - 2011/7/9/ DO - 10.1063/1.3703617 VL - 1443 SP - 32-39 M1 - 1 PB - AIP UR - http://dx.doi.org/10.1063/1.3703617 KW - Maximum entropy KW - mid-rank transformations KW - exponential model KW - quantile function KW - nonparametric Entropy estimation ER - TY - JOUR TI - Integrative Prescreening in Analysis of Multiple Cancer Genomic Studies AU - Song, R. AU - Huang, J. AU - Ma, S. T2 - BMC Bioinformatics AB - In high throughput cancer genomic studies, results from the analysis of single datasets often suffer from a lack of reproducibility because of small sample sizes. Integrative analysis can effectively pool and analyze multiple datasets and provides a cost effective way to improve reproducibility. In integrative analysis, simultaneously analyzing all genes profiled may incur high computational cost. A computationally affordable remedy is prescreening, which fits marginal models, can be conducted in a parallel manner, and has low computational cost. An integrative prescreening approach is developed for the analysis of multiple cancer genomic datasets. Simulation shows that the proposed integrative prescreening has better performance than alternatives, particularly including prescreening with individual datasets, an intensity approach and meta-analysis. We also analyze multiple microarray gene profiling studies on liver and pancreatic cancers using the proposed approach. The proposed integrative prescreening provides an effective way to reduce the dimensionality in cancer genomic studies. It can be coupled with existing analysis methods to identify cancer markers. DA - 2012/// PY - 2012/// DO - 10.1186/1471-2105-13-168 VL - 13 IS - 168 ER - TY - JOUR TI - Evaluating temporally weighted kernel density methods for predicting the next event location in a series AU - Porter, Michael D. AU - Reich, Brian J. T2 - Annals of GIS AB - One aspect of tactical crime or terrorism analysis is predicting the location of the next event in a series. The objective of this article is to present a methodology to identify the optimal parameters and to test the performance of temporally weighted kernel density estimation models for predicting the next event in a criminal or terrorist event series. By placing event series in a space–time point pattern framework, the next event prediction models are shown to be based on estimating a conditional spatial density function. We use temporal weights that indicate how much influence past events have toward predicting future event locations, which can also incorporate uncertainty in the event timing. Results of applying this methodology to crime series in Baltimore County, MD, indicate that performance can vary greatly by crime type and little by series length and is fairly robust to choice of bandwidth. DA - 2012/9// PY - 2012/9// DO - 10.1080/19475683.2012.691904 VL - 18 IS - 3 SP - 225-240 J2 - Annals of GIS LA - en OP - SN - 1947-5683 1947-5691 UR - http://dx.doi.org/10.1080/19475683.2012.691904 DB - Crossref ER - TY - JOUR TI - Functional data analysis of mandibular movement using third-degree b-spline basis functions and self-modeling regression AU - Hayashi, Kazuo AU - Hayashi, Meiri AU - Reich, Brian AU - Lee, Seung-Pyo AU - Sachdeva, Arjun U.C. AU - Mizoguchi, Itaru T2 - Orthodontic Waves AB - The purposes of this study were (1) to establish a new method for analyzing the movement of an incisor point on the mandible as mandibular movement and for analyzing noisy mandibular finite helical axis (FHA) parameters, and (2) to apply this new method in a clinical situation. The subjects were patients with anterior crossbite who were scheduled to receive orthognathic surgery. Chewing movement was measured by an opto-electronic motion-analysis system that can detect mandibular movement in space. The population average curves (trajectories) of the incisor point and the position vector of the FHA during chewing were calculated using third-degree b-spline basis functions and self-modeling regression (SEMOR). Although this study focused on the use of a new statistical model for assessing mandibular movement, the results demonstrated the effectiveness of the combination of the FHA and an additional, supplementary scientific expression of movement, the trajectory of an incisor point. Furthermore, the effectiveness of this new method was demonstrated in a clinical situation. The results of this study demonstrated that the calculation of population average curves is effective for clarifying the characteristics of functional data, such as in mandibular movement. DA - 2012/3/1/ PY - 2012/3/1/ DO - 10.1016/j.odw.2011.11.001 VL - 71 IS - 1 SP - 17-25 J2 - Orthodontic Waves LA - en OP - SN - 1344-0241 1878-1837 UR - http://dx.doi.org/10.1016/j.odw.2011.11.001 DB - Crossref KW - Mandibular movement KW - Functional data analysis KW - Spline function KW - Self-modeling regression KW - Finite helical axis ER - TY - JOUR TI - Macromol. Rapid Commun. 1/2012 AU - Vargantwar, Pruthesh H. AU - Roskov, Kristen E. AU - Ghosh, Tushar K. AU - Spontak, Richard J. T2 - Macromolecular Rapid Communications AB - Back Cover: Ionic polymer-metal composites which bend in response to electric potential are fabricated using selectively-solvated block ionomers possessing a sulfonated midblock and hydrophobic endblocks. The electroactuation performance is comparable or superior to existing systems. Further details can be found in the article by P. H. Vargantwar, K. E. Roskov, T. K. Ghosh, and R. J. Spontak* on page 61. DA - 2012/1/3/ PY - 2012/1/3/ DO - 10.1002/marc.201290003 VL - 33 IS - 1 SP - 100-100 J2 - Macromol. Rapid Commun. LA - en OP - SN - 1022-1336 UR - http://dx.doi.org/10.1002/marc.201290003 DB - Crossref ER - TY - JOUR TI - Prediction and control of number of cells in microdroplets by stochastic modeling AU - Ceyhan, Elvan AU - Xu, Feng AU - Gurkan, Umut Atakan AU - Emre, Ahmet Emrehan AU - Turali, Emine Sumeyra AU - El Assal, Rami AU - Acikgenc, Ali AU - Wu, Chung-an Max AU - Demirci, Utkan T2 - Lab on a Chip AB - Manipulation and encapsulation of cells in microdroplets has found many applications in various fields such as clinical diagnostics, pharmaceutical research, and regenerative medicine. The control over the number of cells in individual droplets is important especially for microfluidic and bioprinting applications. There is a growing need for modeling approaches that enable control over a number of cells within individual droplets. In this study, we developed statistical models based on negative binomial regression to determine the dependence of number of cells per droplet on three main factors: cell concentration in the ejection fluid, droplet size, and cell size. These models were based on experimental data obtained by using a microdroplet generator, where the presented statistical models estimated the number of cells encapsulated in droplets. We also propose a stochastic model for the total volume of cells per droplet. The statistical and stochastic models introduced in this study are adaptable to various cell types and cell encapsulation technologies such as microfluidic and acoustic methods that require reliable control over number of cells per droplet provided that settings and interaction of the variables is similar. DA - 2012/// PY - 2012/// DO - 10.1039/c2lc40523g VL - 12 IS - 22 SP - 4884 J2 - Lab Chip LA - en OP - SN - 1473-0197 1473-0189 UR - http://dx.doi.org/10.1039/c2lc40523g DB - Crossref ER - TY - JOUR TI - Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis AU - Emond, Mary J AU - Louie, Tin AU - Emerson, Julia AU - Zhao, Wei AU - Mathias, Rasika A AU - Knowles, Michael R AU - Wright, Fred A AU - Rieder, Mark J AU - Tabor, Holly K AU - Nickerson, Deborah A AU - Barnes, Kathleen C AU - Gibson, Ronald L AU - Bamshad, Michael J T2 - Nature Genetics AB - Exome sequencing has become a powerful and effective strategy for the discovery of genes underlying Mendelian disorders. However, use of exome sequencing to identify variants associated with complex traits has been more challenging, partly because the sample sizes needed for adequate power may be very large. One strategy to increase efficiency is to sequence individuals who are at both ends of a phenotype distribution (those with extreme phenotypes). Because the frequency of alleles that contribute to the trait are enriched in one or both phenotype extremes, a modest sample size can potentially be used to identify novel candidate genes and/or alleles. As part of the National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project (ESP), we used an extreme phenotype study design to discover that variants in DCTN4, encoding a dynactin protein, are associated with time to first P. aeruginosa airway infection, chronic P. aeruginosa infection and mucoid P. aeruginosa in individuals with cystic fibrosis. DA - 2012/7/8/ PY - 2012/7/8/ DO - 10.1038/ng.2344 VL - 44 IS - 8 SP - 886-889 J2 - Nat Genet LA - en OP - SN - 1061-4036 1546-1718 UR - http://dx.doi.org/10.1038/ng.2344 DB - Crossref ER - TY - JOUR TI - Multiple apical plasma membrane constituents are associated with susceptibility to meconium ileus in individuals with cystic fibrosis AU - Sun, Lei AU - Rommens, Johanna M AU - Corvol, Harriet AU - Li, Weili AU - Li, Xin AU - Chiang, Theodore A AU - Lin, Fan AU - Dorfman, Ruslan AU - Busson, Pierre-François AU - Parekh, Rashmi V AU - Zelenika, Diana AU - Blackman, Scott M AU - Corey, Mary AU - Doshi, Vishal K AU - Henderson, Lindsay AU - Naughton, Kathleen M AU - O'Neal, Wanda K AU - Pace, Rhonda G AU - Stonebraker, Jaclyn R AU - Wood, Sally D AU - Wright, Fred A AU - Zielenski, Julian AU - Clement, Annick AU - Drumm, Mitchell L AU - Boëlle, Pierre-Yves AU - Cutting, Garry R AU - Knowles, Michael R AU - Durie, Peter R AU - Strug, Lisa J T2 - Nature Genetics AB - Variants associated with meconium ileus in cystic fibrosis were identified in 3,763 affected individuals by genome-wide association study (GWAS). Five SNPs at two loci near SLC6A14 at Xq23-24 (minimum P = 1.28 × 10(-12) at rs3788766) and SLC26A9 at 1q32.1 (minimum P = 9.88 × 10(-9) at rs4077468) accounted for ~5% of phenotypic variability and were replicated in an independent sample of affected individuals (n = 2,372; P = 0.001 and 0.0001, respectively). By incorporating the knowledge that disease-causing mutations in CFTR alter electrolyte and fluid flux across surface epithelium into a hypothesis-driven GWAS (GWAS-HD), we identified associations with the same SNPs in SLC6A14 and SLC26A9 and established evidence for the involvement of SNPs in a third solute carrier gene, SLC9A3. In addition, GWAS-HD provided evidence of association between meconium ileus and multiple genes encoding constituents of the apical plasma membrane where CFTR resides (P = 0.0002; testing of 155 apical membrane genes jointly and in replication, P = 0.022). These findings suggest that modulating activities of apical membrane constituents could complement current therapeutic paradigms for cystic fibrosis. DA - 2012/4/1/ PY - 2012/4/1/ DO - 10.1038/ng.2221 VL - 44 IS - 5 SP - 562-569 J2 - Nat Genet LA - en OP - SN - 1061-4036 1546-1718 UR - http://dx.doi.org/10.1038/ng.2221 DB - Crossref ER - TY - JOUR TI - Predicting native plant landscaping preferences in urban areas AU - Peterson, M. Nils AU - Thurmond, Brandi AU - Mchale, Melissa AU - Rodriguez, Shari AU - Bondell, Howard D. AU - Cook, Merril T2 - Sustainable Cities and Society AB - The rapidly growing physical footprint of cities makes understanding residential landscaping preferences increasingly important for water quality, biodiversity conservation, and addressing climate change. In this paper we answer four interrelated questions about residential landscaping preferences with a case study in Raleigh, NC: (1) How are residents’ landscaping preferences influenced by what residents believe their neighbors prefer? (2) Do residents accurately assess their neighbors’ landscaping preferences? (3) How does ethnicity influence landscaping preferences? and (4) Do the socio-demographic and neighborhood norm based correlates of landscaping preferences persist when both are accounted for in multivariate models? Respondents (n = 179) in this study preferred a 50% native plant garden design over 100% turf grass or the 75% and 100% native plant garden designs, and inaccurately assumed that their neighbors preferred turf over the native plant garden based landscaping designs. These results suggest that correcting erroneous assumptions about neighborhood preferences may alleviate normative pressure against adopting alternatives to turf grass landscaping. Although landscaping choices were best predicted by what residents perceived their neighbors preferred, ethnicity, income, and home ownership were also related to landscape preferences. African American ethnicity and income were positively related to preference for turf grass coverage. Environmental justice concerns linked to urban vegetation should be considered in light of the finding that African Americans appeared to prefer turf grass dominated landscaping. Results from this study indicate that middle income neighborhoods with high levels of home ownership may prove most receptive to initiatives aimed at increasing the use of more sustainable landscaping. DA - 2012/12// PY - 2012/12// DO - 10.1016/j.scs.2012.05.007 VL - 5 SP - 70-76 J2 - Sustainable Cities and Society LA - en OP - SN - 2210-6707 UR - http://dx.doi.org/10.1016/j.scs.2012.05.007 DB - Crossref KW - Biodiversity KW - Ecosystem services KW - Ethnicity KW - Landscape design KW - Native plant garden KW - Norms ER - TY - JOUR TI - Estimating public willingness to fund nongame conservation through state tax initiatives AU - Dalrymple, C. Jane AU - Peterson, M. Nils AU - Cobb, David T. AU - Sills, Erin O. AU - Bondell, Howard D. AU - Dalrymple, D. Joseph T2 - Wildlife Society Bulletin AB - Abstract Nongame conservation is insufficiently funded at local, national, and global levels. Despite campaigns and reforms over the past 30 years in the United States, adequate and consistent federal funding has failed to materialize and shifted the focus to state‐level initiatives. We surveyed North Carolina residents during April–May 2010, to assess public willingness to fund nongame conservation, preferred nongame conservation funding mechanisms, and key predictors of support for nongame funding. We estimated a model of willingness‐to‐pay (WTP) using interval‐censored data modeling and compared models using the Akaike Information Criterion. The mean WTP was US$98.80/year/household when respondents were allowed to choose their own tax vehicle, thus removing any payment vehicle bias; an additional sales tax on outdoor recreation equipment was the most preferred funding mechanism. In a follow‐up question, respondents indicated a mean WTP of US$32.92/employed adult (equivalent to about $65/household) annually via a flat income tax. The importance of nongame conservation to respondents, frequency of watching and/or enjoying wildlife, and education were positively related to WTP, whereas age was negatively related to WTP. Prisons were the most popular source from which to reallocate funds to nongame conservation (48%), and respondents believed an average of US$545,000 should be reallocated. Our findings suggested that while the general public indicated that they valued nongame conservation and were amenable to tax increases or reallocations for nongame conservation, they believed that taxes should be user‐based and specialized (e.g., outdoor equipment taxes). These findings highlighted public WTP for nongame conservation even during an economic recession. © 2012 The Wildlife Society. DA - 2012/7/25/ PY - 2012/7/25/ DO - 10.1002/wsb.164 VL - 36 IS - 3 SP - 483-491 J2 - Wildlife Society Bulletin LA - en OP - SN - 1938-5463 UR - http://dx.doi.org/10.1002/wsb.164 DB - Crossref KW - contingent valuation method KW - funding KW - nongame conservation KW - North Carolina KW - willingness-to-pay ER - TY - JOUR TI - Private landowner interest in market-based incentive programs for endangered species habitat conservation AU - Rodriguez, Shari L. AU - Peterson, M. Nils AU - Cubbage, Frederick W. AU - Sills, Erin O. AU - Bondell, Howard D. T2 - Wildlife Society Bulletin AB - Abstract More than 75% of endangered species in the United States rely on private lands for habitat. Although this habitat has long been regulated under the Endangered Species Act, there is now broad agreement that economic incentives are also needed for effective protection on private land. Many different mechanisms for incentive programs have been proposed and tested. For example, recovery credit systems use term‐duration market‐based contracts to engage landowners in endangered species conservation. We examined how market‐mechanism design influences interest in endangered species habitat conservation using a survey of North Carolina Farm Bureau county advisory board members in 93 of the 100 North Carolina counties ( n = 735) in 2009. Respondents preferred contracts (57% were interested) over easements (39% were interested). Endangered species conservation ranked low in importance relative to other conservation issues, but 45% of respondents were interested in contracts to conserve endangered species habitat on their property. The preferred contract duration was 10 years, and respondents preferred state‐ and agricultural‐related organizations over federal and wildlife conservation‐related organizations for managing contracts. Younger respondents, respondents who had previously participated in conservation programs, respondents who perceived endangered species conservation as important, and respondents who had lower property‐rights orientation scores, were most likely to be interested in contracts to restore and maintain endangered species habitat on their lands. Our results suggest that market mechanisms could drive down costs and drive up durations for endangered species habitat conservation contracts. Further, term contracts may prove critical for endangered species conservation efforts that require high levels of landowner support and spatial flexibility within relatively short‐time frames. © 2012 The Wildlife Society. DA - 2012/7/9/ PY - 2012/7/9/ DO - 10.1002/wsb.159 VL - 36 IS - 3 SP - 469-476 J2 - Wildlife Society Bulletin LA - en OP - SN - 1938-5463 UR - http://dx.doi.org/10.1002/wsb.159 DB - Crossref KW - contracts KW - easements KW - endangered species KW - market-based incentives KW - North Carolina KW - participation KW - private land KW - recovery credit system ER - TY - JOUR TI - The interface of protein structure, protein biophysics, and molecular evolution AU - Liberles, David A. AU - Teichmann, Sarah A. AU - Bahar, Ivet AU - Bastolla, Ugo AU - Bloom, Jesse AU - Bornberg-Bauer, Erich AU - Colwell, Lucy J. AU - de Koning, A. P. Jason AU - Dokholyan, Nikolay V. AU - Echave, Julian AU - Elofsson, Arne AU - Gerloff, Dietlind L. AU - Goldstein, Richard A. AU - Grahnen, Johan A. AU - Holder, Mark T. AU - Lakner, Clemens AU - Lartillot, Nicholas AU - Lovell, Simon C. AU - Naylor, Gavin AU - Perica, Tina AU - Pollock, David D. AU - Pupko, Tal AU - Regan, Lynne AU - Roger, Andrew AU - Rubinstein, Nimrod AU - Shakhnovich, Eugene AU - Sjölander, Kimmen AU - Sunyaev, Shamil AU - Teufel, Ashley I. AU - Thorne, Jeffrey L. AU - Thornton, Joseph W. AU - Weinreich, Daniel M. AU - Whelan, Simon T2 - Protein Science AB - Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. DA - 2012/4/23/ PY - 2012/4/23/ DO - 10.1002/pro.2071 VL - 21 IS - 6 SP - 769-785 J2 - Protein Science LA - en OP - SN - 0961-8368 UR - http://dx.doi.org/10.1002/pro.2071 DB - Crossref KW - evolutionary modeling KW - domain evolution KW - sequence-structure-function relationships KW - protein dynamics KW - protein thermodynamics KW - gene duplication KW - protein expression KW - ancestral sequence reconstruction ER - TY - JOUR TI - A Semi-nonparametric Approach to Joint Modeling of A Primary Binary Outcome and Longitudinal Data Measured at Discrete Informative Times AU - Yan, Song AU - Zhang, Daowen AU - Lu, Wenbin AU - Grifo, James A. AU - Liu, Mengling T2 - Statistics in Biosciences AB - In a study conducted at the New York University Fertility Center, one of the scientific objectives is to investigate the relationship between the final pregnancy outcomes of participants receiving an in vitro fertilization (IVF) treatment and their β-human chorionic gonadotrophin (β-hCG) profiles. A common joint modeling approach to this objective is to use subject-specific normal random effects in a linear mixed model for longitudinal β-hCG data as predictors in a model (e.g., logistic model) for the final pregnancy outcome. Empirical data exploration indicates that the observation times for longitudinal β-hCG data may be informative and the distribution of random effects for longitudinal β-hCG data may not be normally distributed. We propose to introduce a third model in the joint model for the informative β-hCG observation times, and relax the normality distributional assumption of random effects using the semi-nonparametric (SNP) approach of Gallant and Nychka (Econometrica 55:363–390, 1987). An EM algorithm is developed for parameter estimation. Extensive simulation designed to evaluate the proposed method indicates that ignoring either informative observation times or distributional assumption of the random effects would lead to invalid and/or inefficient inference. Applying our new approach to the data reveals some interesting findings the traditional approach failed to discover. DA - 2012/1/10/ PY - 2012/1/10/ DO - 10.1007/S12561-011-9053-2 VL - 4 IS - 2 SP - 213-234 J2 - Stat Biosci LA - en OP - SN - 1867-1764 1867-1772 UR - http://dx.doi.org/10.1007/S12561-011-9053-2 DB - Crossref KW - EM algorithm KW - Informative observation times KW - IVF KW - Joint model KW - Longitudinal data KW - Maximum likelihood estimation KW - SNP density ER - TY - JOUR TI - Authors' Reply AU - Tamura, Roy N. AU - Huang, Xiaohong AU - Boos, Dennis T2 - Statistics in Medicine AB - Statistics in MedicineVolume 31, Issue 29 p. 4143-4144 Authors' Reply Authors' Reply Roy N. Tamura, Roy N. Tamura [email protected] Eli Lilly and Company, Indianapolis, IN, U.S.ASearch for more papers by this authorXiaohong Huang, Xiaohong Huang [email protected] Sanofi-Aventis, Biostatistics, Bridgewater, NJ, U.S.ASearch for more papers by this authorDennis Boos, Dennis Boos [email protected] Department of Statistics, North Carolina State University, Raleigh, NC, U.S.ASearch for more papers by this author Roy N. Tamura, Roy N. Tamura [email protected] Eli Lilly and Company, Indianapolis, IN, U.S.ASearch for more papers by this authorXiaohong Huang, Xiaohong Huang [email protected] Sanofi-Aventis, Biostatistics, Bridgewater, NJ, U.S.ASearch for more papers by this authorDennis Boos, Dennis Boos [email protected] Department of Statistics, North Carolina State University, Raleigh, NC, U.S.ASearch for more papers by this author First published: 23 November 2012 https://doi.org/10.1002/sim.5360Read 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. Volume31, Issue2920 December 2012Pages 4143-4144 RelatedInformation DA - 2012/11/23/ PY - 2012/11/23/ DO - 10.1002/sim.5360 VL - 31 IS - 29 SP - 4143-4144 J2 - Statist. Med. LA - en OP - SN - 0277-6715 UR - http://dx.doi.org/10.1002/sim.5360 DB - Crossref ER - TY - JOUR TI - Loss of Power in Two-Stage Residual-Outcome Regression Analysis in Genetic Association Studies AU - Che, Ronglin AU - Motsinger-Reif, Alison A. AU - Brown, Chad C. T2 - Genetic Epidemiology AB - Disclaimer: Supplementary materials have been peer-reviewed but not copyedited. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article. DA - 2012/8// PY - 2012/8// DO - 10.1002/gepi.21671 SP - n/a-n/a J2 - Genet. Epidemiol. LA - en OP - SN - 0741-0395 UR - http://dx.doi.org/10.1002/gepi.21671 DB - Crossref KW - loss of power KW - two-stage regression KW - degrees of freedom ER - TY - JOUR TI - Mathematical Models of Dividing Cell Populations: Application to CFSE Data AU - Banks, H.T. AU - Clayton Thompson, W. T2 - Mathematical Modelling of Natural Phenomena AB - Flow cytometric analysis using intracellular dyes such as CFSE is a powerful experimental tool which can be used in conjunction with mathematical modeling to quantify the dynamic behavior of a population of lymphocytes. In this survey we begin by providing an overview of the mathematically relevant aspects of the data collection procedure. We then present an overview of the large body of mathematical models, along with their assumptions and uses, which have been proposed to describe the dynamics of proliferating cell populations. While much of this body of work has been aimed at modeling the generation structure (cells per generation) of the proliferating population, several recent models have considered the more fundamental task of modeling CFSE histogram data directly. Such models are analyzed and recent results are discussed. Finally, directions for future research are suggested. DA - 2012/// PY - 2012/// DO - 10.1051/mmnp/20127504 VL - 7 IS - 5 SP - 24-52 J2 - Math. Model. Nat. Phenom. OP - SN - 0973-5348 1760-6101 UR - http://dx.doi.org/10.1051/mmnp/20127504 DB - Crossref KW - cell proliferation KW - cell division number KW - CFSE KW - ordinary differential equations KW - cytons KW - label structured population dynamics KW - partial differential equations KW - inverse problems ER - TY - JOUR TI - Propagation of Growth Uncertainty in a Physiologically Structured Population AU - Banks, H.T. AU - Hu, S. T2 - Mathematical Modelling of Natural Phenomena AB - In this review paper we consider physiologically structured population models that have been widely studied and employed in the literature to model the dynamics of a wide variety of populations. However in a number of cases these have been found inadequate to describe some phenomena arising in certain real-world applications such as dispersion in the structure variables due to growth uncertainty/variability. Prompted by this, we described two recent approaches that have been investigated in the literature to describe this growth uncertainty/variability in a physiologically structured population. One involves formulating growth as a Markov diffusion process while the other entails imposing a probabilistic structure on the set of possible growth rates across the entire population. Both approaches lead to physiologically structured population models with nontrivial dispersion. Even though these two approaches are conceptually quite different, they were found in [17] to have a close relationship: in some cases with properly chosen parameters and coefficient functions, the resulting stochastic processes have the same probability density function at each time. DA - 2012/// PY - 2012/// DO - 10.1051/mmnp/20127503 VL - 7 IS - 5 SP - 7-23 J2 - Math. Model. Nat. Phenom. OP - SN - 0973-5348 1760-6101 UR - http://dx.doi.org/10.1051/mmnp/20127503 DB - Crossref ER - TY - JOUR TI - Preface. Distributed Parameter Systems in Immunology AU - Banks, H.T. AU - Bocharov, G. AU - Grossman, Z. AU - Meyerhans, A. T2 - Mathematical Modelling of Natural Phenomena DA - 2012/// PY - 2012/// DO - 10.1051/mmnp/20127501 VL - 7 IS - 5 SP - 1-3 J2 - Math. Model. Nat. Phenom. OP - SN - 0973-5348 1760-6101 UR - http://dx.doi.org/10.1051/mmnp/20127501 DB - Crossref KW - mathematical model KW - distributed parameter systems KW - immunophysiological systems KW - virus infections ER - TY - CONF TI - Rainwater Harvesting: Integrating Water Conservation and Stormwater Management through Innovative Technologies AU - DeBusk, K. AU - Hunt, W. AU - Quigley, M. AU - Jeray, J. AU - Bedig, A. T2 - World Environmental And Water Resources Congress 2012 AB - Recent droughts, population increases, and predicted climate change have emphasized the fragility of water resources and the need for water conservation within the state of North Carolina, USA. The necessity of stormwater management is another ever-present reality for the state due to increases in urban development and resulting declines in water quality. Rainwater harvesting (RWH) systems are unique in their ability to provide an alternate source of water and serve as detention/retention for roof runoff that would otherwise be discharged to the stormwater network. This study focuses on two RWH systems, each of which employ an innovative method of increasing the stormwater management potential of the system: an active release mechanism and a passive release mechanism. The purpose of this study is to document how well RWH systems serve as both water conservation practices and stormwater management practices when equipped with these innovative technologies. C2 - 2012/5/17/ C3 - World Environmental and Water Resources Congress 2012 DA - 2012/5/17/ DO - 10.1061/9780784412312.372 PB - American Society of Civil Engineers SN - 9780784412312 UR - http://dx.doi.org/10.1061/9780784412312.372 DB - Crossref ER - TY - CONF TI - Developing a Carbon Footprint of Urban Stormwater Infrastructure AU - Moore, Trisha L. C. AU - Hunt, William F. T2 - World Environmental And Water Resources Congress 2012 AB - Concerns over global climate change have spurred interest in accounting for carbon emissions from human activities. Most of this effort has focused on emissions from vehicles and energy use within buildings. However, relatively little is known about how the urban landscape, and particularly stormwater management, contributes to the carbon footprint of urban areas. The objective of this work was to present a method by which carbon emissions attributable to the construction and maintenance of stormwater control measures (SCMs) and conveyances could be predicted. This method was then applied to present a comparison of the carbon footprint of eight common SCMs and three conveyance practices. The carbon embodied in construction materials represented a prominent part of the carbon footprint for green roofs, permeable pavement, sand filters, rainwater harvesting systems, and reinforced concrete pipes while material transport and construction dominated that of bioretention systems, ponds, wetlands, level spreader-grassed filter strips and concrete-lined swales. Despite accounting for sequestration by vegetation in these systems, only stormwater wetlands and grassed swales were predicted to store more carbon than was released through construction and maintenance. C2 - 2012/5/17/ C3 - World Environmental and Water Resources Congress 2012 DA - 2012/5/17/ DO - 10.1061/9780784412312.089 PB - American Society of Civil Engineers SN - 9780784412312 UR - http://dx.doi.org/10.1061/9780784412312.089 DB - Crossref ER - TY - CONF TI - Water Quality Benefits of Harvesting Rooftop Runoff AU - DeBusk, K. M. AU - Hunt, W. F. T2 - World Environmental And Water Resources Congress 2012 AB - It is well documented that runoff from roof surfaces carries a wide variety of pollutants including sediment, heavy metals, nutrients and bacteria. Collecting and storing this roof runoff via rainwater harvesting systems could provide water quality benefits due to physical and chemical processes that occur within the storage tank. Four fire stations in Raleigh, North Carolina, USA, were equipped with rainwater harvesting systems. Samples of roof runoff were collected after each storm to determine pre-cistern water quality characteristics. Samples were also collected at the extraction spigot for the system. All samples were analyzed for total suspended solids (TSS), total nitrogen (TN), total Kjeldahl nitrogen (TKN), nitrite (NO2)+nitrate (NO3), ammonia (NH3), and total phosphorus (TP). Water quality data will be analyzed to determine if storing water within a cistern has a significant effect on pollutant concentrations. Water usage data collected during the study period will be compiled and pollutant loads will be computed. C2 - 2012/5/17/ C3 - World Environmental and Water Resources Congress 2012 DA - 2012/5/17/ DO - 10.1061/9780784412312.063 PB - American Society of Civil Engineers SN - 9780784412312 UR - http://dx.doi.org/10.1061/9780784412312.063 DB - Crossref ER - TY - CONF TI - Stormwater Monitoring of Innovative Street Retrofits in Urban Wilmington, NC AU - Page, J. L. AU - Winston, R. J. AU - Hunt, W. F. T2 - World Environmental And Water Resources Congress 2012 AB - Many urban watersheds suffer from degraded water quality caused by stormwater runoff from rooftops, parking lots, streets and other impervious surfaces. Low Impact Development (LID) is a design approach that utilizes stormwater control measures (SCMs) to maintain and restore the natural hydrologic features of a watershed by promoting infiltration of runoff into the soil, treating runoff at its source, and minimizing impervious surface coverage. Peer-reviewed literature is lacking on the application of bioretention, permeable pavement and tree filter boxes to treat urban street runoff on a catchment-scale. A pre- and post-retrofit study has been designed to evaluate the impacts of catchment-scale retrofits on hydrology and water quality. The project will be implemented on two midblock street sections in a residential neighborhood in Wilmington, North Carolina. It includes construction of permeable pavement parking stalls, tree filter boxes and bioretention areas that extend into the street right-of-way, thereby reducing impervious surface area and increasing pedestrian safety. Runoff volumes and pollutant concentrations of bacteria, heavy metals, nutrients, polycyclic aromatic hydrocarbons (PAHs) and suspended solids were monitored from June 2011 to October 2011 at the retrofit site and an additional control site located four blocks to the West. Preliminary results from the pre-retrofit monitoring show mean concentrations of total Kjeldahl nitrogen (TKN) from the control and retrofit watersheds were 2.02 mg/L and 1.52 mg/L, respectively. Total phosphorus (TP) mean concentrations from the control and retrofit watersheds were similar at 0.31 mg/L and 0.29 mg/L, respectively. TKN and TP concentrations observed in this study at both monitoring sites were less than TKN and TP mean concentrations from National Urban Runoff Program (NURP) urban sites and NURP streets. Copper (Cu), lead (Pb) and zinc (Zn) mean concentrations from the control and retrofit watersheds were less than those reported from NURP urban sites and NURP streets. Total nitrogen (TN) and TP yearly loads were greater in the control watershed, which may be due to the greater fraction of impervious surface coverage and fertilizer use in the control watershed. The results and conclusions from this study will help refine street retrofit design standards to meet runoff volume reduction, peak discharge mitigation and water quality goals while increasing pedestrian safety and improving aesthetics in the neighborhood. C2 - 2012/5/17/ C3 - World Environmental and Water Resources Congress 2012 DA - 2012/5/17/ DO - 10.1061/9780784412312.056 PB - American Society of Civil Engineers SN - 9780784412312 UR - http://dx.doi.org/10.1061/9780784412312.056 DB - Crossref ER - TY - CONF TI - Evaluation of Bridge Deck Runoff and Its Effects on In-Stream Health AU - Winston, R. J. AU - Hunt, W. F. AU - Lauffer, M. S. T2 - World Environmental And Water Resources Congress 2012 AB - Bridges typically drain through scuppers directly to streams or estuaries below, potentially resulting in degradation of surface water quality. The North Carolina General Assembly enacted Session Law 2008-107 in July 2008, which required the N.C. Department of Transportation to study the effects of stormwater runoff from bridges over waterways. The resulting study characterized 15 bridge decks across three ecoregions of N.C. for runoff quality and quantity. Monitoring sites were located across the Piedmont, Coastal Plain, and Mountain ecoregions of NC and had differences in wearing surface, annual average daily traffic, rural vs. urban watershed, bridge deck surface area, and stream drainage areas. The goals included characterizing bridge deck pollutants of concern and determining the effects of bridge deck runoff on in-stream health. Runoff water quality and quantity were measured at 15 bridges, instream water quality and quantity at 4 sites, streambed sediment quality at 30 sites, bioassay tests at 13 sites, and biosurvey tests at 15 sites. Median EMCs for TSS, TN, TP, total petroleum hydrocarbons (TPH), total copper, total lead, and total zinc were 39 mg/L, 0.97 mg/L, 0.17 mg/L, 3.1 mg/L, 9.6 μg/L, 5.3 μg/L, and 66 μg/L, respectively. Twenty-two parameters of concern, those with maximum observed concentrations above the strictest available state or federal threshold, were identified, including: pH, TSS, TN, TP, five total heavy metals, five dissolved heavy metals, and seven semi-volatiles. The best predictor of pollutant concentration was the land-use type of the watershed (urban vs. rural). Pollutant concentrations and loads observed from bridge decks were similar to or less than those from other highway and urban runoff studies. Pollutant loads from the bridge decks for all analytes studied were less than 0.25% of the pollutant load contributed by the whole watershed, since the ratio of bridge deck area to watershed area was always small (<2%). At the 30 bridge deck sites studied for stream bed sediment quality (organic and inorganic pollutants), no significant difference was observed between upstream vs. downstream sediment quality or between downstream sediment quality from direct vs. no-direct discharge bridges. Composite samples from bridge deck stormwater runoff, in-stream stormflow, and in-stream baseflow were utilized in Ceriodaphnia dubia bioassay tests. All samples were tested at 100% concentration, and bridge deck runoff samples also were tested at dilutions of 50%, 25%, 12.5%, and 6.25%. Of 25 bridge deck runoff samples, 3 exhibited toxicity at 100% concentration due to significantly reduced reproduction in the test organism. Potential reasons for this toxicity included elevated conductivity in one sample and low hardness and pH in another sample. No toxicity was observed at lower dilutions of the bridge deck runoff, indicating the potential for toxicity would be attenuated at instream concentrations. Of 20 instream stormflow and baseflow samples, no toxicity was observed. Instream mixing and large catchment area relative to bridge deck footprints (as much as 106 larger) resulted in substantial dilution of bridge deck runoff at these sites. Biosurveys (benthic macroinvertebrate sampling) were conducted upstream and downstream of 12 bridges. Samples were obtained using Qual 5 methodology, and bioclassification was determined using the EPT and N.C. biotic index metrics. One study site had a biotic index change large enough to suggest a decline in water quality downstream of the bridge deck. However, bioclassification rating was never different between upstream and downstream sampling areas. When the data were evaluated en masse, runoff concentrations and pollutant loads were similar to those from other urban and transportation runoff studies. Attempts to tie stormwater runoff to reduced in-stream health (sediment quality, benthic health, aquatic toxicity) were unsuccessful; this suggests that bridge deck runoff does not have widespread effects on receiving water quality. C2 - 2012/5/17/ C3 - World Environmental and Water Resources Congress 2012 DA - 2012/5/17/ DO - 10.1061/9780784412312.041 PB - American Society of Civil Engineers SN - 9780784412312 UR - http://dx.doi.org/10.1061/9780784412312.041 DB - Crossref ER - TY - CONF TI - Enhancement of Exfiltration and Thermal Load Reduction from Permeable Pavement with Internal Water Storage AU - Wardynski, B. J. AU - Winston, R. J. AU - Hunt, W. F. T2 - World Environmental And Water Resources Congress 2012 AB - Stream temperature spikes associated with urban runoff can have negative ecological impacts on coldwater streams. Several local and federal regulations now specifically target urban runoff temperature, which creates a need for practices that reduce thermal export from a catchment. Several stormwater control measures (SCMs) have been shown to buffer thermal impacts to waterways by passing water through cooler subsurface media or by reducing overall runoff volume. Because it performs these functions, permeable pavement is a promising practice for thermal mitigation. A parking lot was constructed with permeable interlocking concrete pavers (PICP) the Mountain region of North Carolina to investigate the thermal behavior of this SCM. The 239-m2 lot was divided into three cells with varying depths and drainage configurations to also test the hydrologic and thermal effects of including internal water storage (IWS) in permeable pavement. After one year of monitoring, results showed substantial stormwater volume reductions from all permeable pavement configurations, with the most pronounced reductions (99.6% and 100%) experienced in the shallow and deep IWS cells, respectively. Consequently, thermal load export from the site was reduced by a comparable amount. Median and maximum stormwater effluent temperatures from the conventionally drained cell (78% runoff reduction) exceeded the critical trout threshold temperature of 21°C, however, outflow only occurred during 8 storm events (out of the 54 recorded). Temperature differentials between the top and bottom the PICP profiles suggest that buffering of extreme runoff temperatures can occur. Additionally, the subsoil interface never reached freezing temperatures during the winter season. These results credit the use of PICP where thermal impact to streams is of concern, particularly with the incorporation of IWS. C2 - 2012/5/17/ C3 - World Environmental and Water Resources Congress 2012 DA - 2012/5/17/ DO - 10.1061/9780784412312.038 PB - American Society of Civil Engineers SN - 9780784412312 UR - http://dx.doi.org/10.1061/9780784412312.038 DB - Crossref ER - TY - CONF TI - Can Roadside Vegetation and Soil Act As a Carbon Sink? AU - Bouchard, N. B. AU - Hunt, W. F. AU - Moore, T. L. C. AU - Winston, R. J. T2 - World Environmental And Water Resources Congress 2012 AB - Stormwater Control Measures (SCMs) have long been understood to clean and treat runoff, but these systems may provide additional ecosystem benefits not currently quantified. The main goal of this project was to determine carbon (C) sequestration potential of common roadside SCMs within the Piedmont and Coastal Plain eco-regions of North Carolina. Along highways vegetated filter strips (VFS) and vegetated swales (VS) or wetland swales (WS) work in conjunction to trap sediment bound pollutants associated with runoff from the roadway. The VFS/VS systems work well in the roadside environment since they are linear and easily border the roadway, additionally they require little maintenance. Roadside VFS/VS systems (ranging in age from 1 to 38 years) within two physiographic regions of NC were sampled to evaluate C accumulation within the soil. Based upon ArcGIS analysis, each site was identified and systematically sampled from May to July 2011. Twenty VFS/VS sites were established in the Piedmont and Coastal Plain region, respectively. An additional 20 wetland swale sites were also sampled in the Coastal Plain region, which allows a comparison between the dry swales and the WSs within the Coastal Plain. Age, regional (i.e. Piedmont versus Coastal Plain), position (sampling distance from roadway), depth, and swale characteristics (i.e. WS versus VS) effects upon C accumulation are being examined in this study. C2 - 2012/5/17/ C3 - World Environmental and Water Resources Congress 2012 DA - 2012/5/17/ DO - 10.1061/9780784412312.031 PB - American Society of Civil Engineers SN - 9780784412312 UR - http://dx.doi.org/10.1061/9780784412312.031 DB - Crossref ER - TY - CONF TI - Evaluation of Floating Wetland Islands As a Retrofit to Existing Stormwater Detention Basins AU - Winston, R. J. AU - Hunt, W. F. AU - Kennedy, S. G. T2 - World Environmental And Water Resources Congress 2012 AB - Since the passage of the Clean Water Act, wet detention ponds have been installed across the United States primarily for peak flow mitigation and sediment reduction. However, there are surprisingly minimal data on water quality benefits of these systems. Additionally, tremendous retrofitting pressure is likely to accompany state of North Carolina-implemented watershed rules associated with the Jordan Lake and Fall Lake reservoirs. Municipalities in these watersheds will be required to meet nutrient load reduction targets, necessitating urban stormwater practice retrofits for existing development. Therefore, it is imperative for many cities in central North Carolina to identify cost effective retrofits. One potential retrofit, floating wetland islands, is particularly attractive because they (1) do not require earth moving, (2) eliminate the need for additional land to be dedicated to treatment, and (3) will not detract from the required storage volume required for wet ponds (because they float). Two wet ponds in Durham, NC, were retrofitted with floating wetland islands. Prior to retrofit, both ponds had little to no vegetation growing inside them. After retrofit, one pond's surface area was comprised of 8% floating wetland islands and the second pond had 19% coverage. The two ponds were monitored in a non-retrofitted state from November 2008 to March 2010. Floating wetland islands were then installed in March-April 2010. After vegetation had established on the islands, monitoring recommenced in July 2010. Area-velocity meters and Manning's equation were used to take flow-proportional, composite water quality samples. Sixteen water quality samples were taken prior to the floating island retrofit, and twelve have been collected thus far post-retrofit. Initial results show that mean effluent concentrations of total nitrogen (TN) were reduced at one pond from 1.05 mg/L to 0.61 mg/L from pre- to post-retrofit. The other pond had relatively low effluent concentrations (0.41 mg/L and 0.43 mg/L) both pre- and post-retrofit. Mean TP effluent concentrations were reduced at both wet ponds from pre- to post-retrofit (0.17 mg/L to 0.12 mg/L and 0.11 mg/L to 0.05 mg/L. Additionally, TSS effluent concentrations at both ponds were modestly lower post-retrofit, presumably due to additional hydraulic resistance provided by the floating islands and their hanging roots, which have been measured to be approximately 0.6 m (2 ft). Initial results show some modest nutrient and sediment removal benefits from the addition of floating islands to stormwater detention ponds. Additional benefits which will be determined in the future include wetland vegetation root mass and potential improvements in benthic macroinvertebrate habitat. C2 - 2012/5/17/ C3 - World Environmental and Water Resources Congress 2012 DA - 2012/5/17/ DO - 10.1061/9780784412312.030 PB - American Society of Civil Engineers SN - 9780784412312 UR - http://dx.doi.org/10.1061/9780784412312.030 DB - Crossref ER - TY - JOUR TI - Harvestable Nitrogen Accumulation for Five Storm Water Wetland Plant Species: Trigger for Storm Water Control Measure Maintenance? AU - Lenhart, H. A. AU - Hunt, W. F. AU - Burchell, M. R. T2 - Journal of Environmental Engineering AB - As the use of constructed storm water wetlands to treat storm water runoff becomes more frequent, strategies for maintaining or increasing their pollutant removal over time must be examined. One potential strategy is plant harvesting at the water surface to remove nutrients that would otherwise be deposited back into the wetland during senescence. This technical note presents a first look at this strategy from a storm water management perspective. Vegetation was harvested from two storm water wetlands located in Smithfield and Pactolus, North Carolina, to evaluate the ability of five wetland plant species to sequester nitrogen. Biomass samples were collected from the following species of emergent vegetation: Pontederia cordata (Pickerelweed), Saururus cernuus (Lizard Tail), Scirpus cyperinus (Wool Grass), Sagittaria latifolia (Arrowhead), and Schoenoplectus tabernaemontani (Softstem Bulrush). Samples were collected immediately prior to senescence in September and October 2007 and analyzed for nitrogen content on a percent of biomass basis. At the Pactolus wetland the Pontederia cordata, Scirpus cyperinus, and Schoenoplectus tabernaemontani biomass retained significantly (p<0.05) more nitrogen than Sagittaria latifolia and Saururus cernuus. At the Smithfield wetland, Pontederia cordata and Sagittaria latifolia biomass retained significantly more nitrogen than Scirpus cyperinus and Saururus cernuus. Wetland maturity appears to have a direct relationship to harvestable nitrogen, which could explain why the relative amount of nitrogen sequestered in Scirpus cyperinus and Sagittaria latifolia varied between the two wetlands. A positive relationship existed between the density of harvested biomass and nitrogen removal for two species. To estimate the relative amount of harvestable nitrogen, a model for estimating total nitrogen loading in Coastal Plain watersheds in North Carolina was used to compare estimated inflow nitrogen mass to that which could theoretically be harvested. The harvestable N mass was greater than 20% of inflow nitrogen on an annual basis. Storm water wetland plant harvesting as a maintenance activity has potential to supplement wetland nitrogen removal. DA - 2012/9// PY - 2012/9// DO - 10.1061/(ASCE)EE.1943-7870.0000550 VL - 138 IS - 9 SP - 972-978 J2 - J. Environ. Eng. LA - en OP - SN - 0733-9372 1943-7870 UR - http://dx.doi.org/10.1061/(ASCE)EE.1943-7870.0000550 DB - Crossref KW - Storm water control measure KW - Best management practice KW - Storm water KW - Runoff KW - Wetlands KW - Nitrogen KW - Uptake KW - Harvesting ER - TY - JOUR TI - Effectiveness of LID for Commercial Development in North Carolina AU - Line, D. E. AU - Brown, R. A. AU - Hunt, W. F. AU - Lord, W. G. T2 - Journal of Environmental Engineering AB - The purpose of this project was to characterize runoff and pollutant export from three commercial sites: one with no storm water control measures (NoTreat), one with a wet detention basin (WetBasin), and one with low impact development (LID) measures. The sites were located in the Piedmont and Coastal Plain physiographic regions of central North Carolina. Rainfall, runoff, and pollutant concentrations were monitored at each site for more than one year by using automated rain gauges and samplers. The storm event mean concentrations (EMCs) of total kjeldahl nitrogen (TKN), nitrate+nitrite nitrogen (NOx-N), and total phosphorus (TP) in runoff were generally less than corresponding EMCs for many other urban areas in the United States. Also, EMCs were similar to those found for eight parking lots in North Carolina. Storm runoff to rainfall ratio was greatest for the NoTreat site and least for the WetBasin site, which was anticipated because the NoTreat site had no detention/storage and the WetBasin site had the greatest detention/storage. Export of TKN, ammonia nitrogen (NH3-N), TP, and total suspended solids (TSS) was lowest for the LID site, whereas export of NOx-N and TN was lowest for the WetBasin site. Although by no means definitive, the monitoring data indicated that the LID site with its multiple LID measures was more effective at reducing export for most pollutants than the WetBasin site with its wet detention basin. DA - 2012/6// PY - 2012/6// DO - 10.1061/(ASCE)EE.1943-7870.0000515 VL - 138 IS - 6 SP - 680-688 J2 - J. Environ. Eng. LA - en OP - SN - 0733-9372 1943-7870 UR - http://dx.doi.org/10.1061/(ASCE)EE.1943-7870.0000515 DB - Crossref KW - Low impact development KW - Effectiveness KW - Storm water monitoring KW - Commercial sites ER - TY - JOUR TI - Abundance, survival and temporary emigration of bottlenose dolphins (Tursiops sp.) off Useless Loop in the western gulf of Shark Bay, Western Australia AU - Nicholson, Krista AU - Bejder, Lars AU - Allen, Simon J. AU - Krützen, Michael AU - Pollock, Kenneth H. T2 - Marine and Freshwater Research AB - Capture–recapture models were used to provide estimates of abundance, apparent survival and temporary emigration of Indo-Pacific bottlenose dolphins (Tursiops sp.) in a 226-km2 study area off Useless Loop in the western gulf of Shark Bay, Western Australia. Photo-identification data were collected during boat-based surveys in Austral autumn to early spring (April–September) from 2007 to 2011. Abundance estimates varied from 115 (s.e. 5.2, 95% CI 105–126) individuals in 2008 to 208 (s.e. 17.3, 95% CI 177–245) individuals in 2010. The variability in abundance estimates is likely to be a reflection of how individuals used the study area, rather than fluctuations in true population size. The best fitting capture–recapture model suggested a random temporary emigration pattern and, when coupled with relatively high temporary emigration rates (0.33 (s.e. 0.07) – 0.66 (s.e. 0.05)) indicated that the study area did not cover the entire ranges of the photo-identified dolphins. Apparent survival rate is a product of true survival and permanent emigration and was estimated annually at 0.95 (s.e. 0.02). Since permanent emigration from the study area is unlikely, true survival was estimated to be close to 0.95. This study provides a robust baseline for future comparisons of dolphin demographics, which may be of importance should climate change or increasing anthropogenic activity affect this population. DA - 2012/// PY - 2012/// DO - 10.1071/MF12210 VL - 63 IS - 11 SP - 1059 J2 - Mar. Freshwater Res. LA - en OP - SN - 1323-1650 UR - http://dx.doi.org/10.1071/MF12210 DB - Crossref KW - capture-recapture KW - demographic parameters KW - photo-identification KW - Pollock's closed robust design ER - TY - JOUR TI - Overcoming socio-economic barriers to conservation subdivisions: A case-study of four successful communities AU - Allen, Stephen C. AU - Moorman, Christopher E. AU - Peterson, M. Nils AU - Hess, George R. AU - Moore, Susan E. T2 - Landscape and Urban Planning AB - Conservation subdivisions have emerged as an option to conserve open space, protect water quality and wildlife habitat, and maintain scenic views without compromising property rights. Despite economic and ecological advantages over traditional subdivisions, conservation subdivisions remain rare. We used a mixed-method study combining a survey of 246 people who attended conservation subdivision workshops with a qualitative case study of four communities that successfully developed conservation subdivisions to identify potential barriers to conservation subdivisions and strategies to overcome those barriers. A principal component analysis based on survey respondent rankings grouped barriers into: resistance to change among stakeholders, concerns about differences between traditional subdivisions and conservation subdivisions, concerns about consumer demand, and misperceptions about construction costs. Survey respondents indicated the top barrier to completion of conservation subdivisions was lack of incentives for developers. The case study communities overcame resistance from developers and landowners through educational efforts including informal meetings, charrettes, and workshops focusing on the environmental and economic benefits of conservation subdivisions. The communities had support from elected officials, and planning staff devoted necessary resources to rewrite ordinances, review sketch plans, and perform site visits. To overcome barriers to conservation subdivisions, communities could provide incentives including density bonuses and expedited approval processes. Encouraging participation in workshops and design charrettes for proposed developments may alleviate concerns of landowners who perceive a loss of property rights from new regulations and aid in the acceptance of conservation subdivisions. DA - 2012/6// PY - 2012/6// DO - 10.1016/j.landurbplan.2012.03.012 VL - 106 IS - 3 SP - 244-252 J2 - Landscape and Urban Planning LA - en OP - SN - 0169-2046 UR - http://dx.doi.org/10.1016/j.landurbplan.2012.03.012 DB - Crossref KW - Open space KW - Residential development KW - Conservation subdivision ER - TY - JOUR TI - Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids AU - Serang, Oliver AU - Mollinari, Marcelo AU - Garcia, Antonio Augusto Franco T2 - PLoS ONE AB - The problem of genotyping polyploids is extremely important for the creation of genetic maps and assembly of complex plant genomes. Despite its significance, polyploid genotyping still remains largely unsolved and suffers from a lack of statistical formality. In this paper a graphical bayesian model for SNP genotyping data is introduced. This model can infer genotypes even when the ploidy of the population is unknown. We also introduce an algorithm for finding the exact maximum a posteriori genotype configuration with this model. This algorithm is implemented in a freely available web-based software package SuperMASSA. We demonstrate the utility, efficiency, and flexibility of the model and algorithm by applying them to two different platforms, each of which is applied to a polyploid data set: Illumina GoldenGate data from potato and Sequenom MassARRAY data from sugarcane. Our method achieves state-of-the-art performance on both data sets and can be trivially adapted to use models that utilize prior information about any platform or species. DA - 2012/2/17/ PY - 2012/2/17/ DO - 10.1371/journal.pone.0030906 VL - 7 IS - 2 SP - e30906 J2 - PLoS ONE LA - en OP - SN - 1932-6203 UR - http://dx.doi.org/10.1371/journal.pone.0030906 DB - Crossref ER - TY - JOUR TI - A mixed model QTL analysis for sugarcane multiple-harvest-location trial data AU - Pastina, M.M. AU - Malosetti, M. AU - Gazaffi, R. AU - Mollinari, M. AU - Margarido, G.R.A. AU - Oliveira, K.M. AU - Pinto, L.R. AU - Souza, A.P. AU - Eeuwijk, F.A. AU - Garcia, A.A.F. T2 - Theoretical and Applied Genetics AB - Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane. DA - 2012/3// PY - 2012/3// DO - 10.1007/s00122-011-1748-8 VL - 124 IS - 5 SP - 835-849 UR - http://dx.doi.org/10.1007/s00122-011-1748-8 KW - Polyploids KW - Outcrossing species KW - Integrated linkage map KW - QTL x E ER - TY - JOUR TI - Studying the genetic basis of drought tolerance in sorghum by managed stress trials and adjustments for phenological and plant height differences AU - Sabadin, P. K. AU - Malosetti, M. AU - Boer, M. P. AU - Tardin, F. D. AU - Santos, F. G. AU - Guimarães, C. T. AU - Gomide, R. L. AU - Andrade, C. L. T. AU - Albuquerque, P. E. P. AU - Caniato, F. F. AU - Mollinari, M. AU - Margarido, G. R. A. AU - Oliveira, B. F. AU - Schaffert, R. E. AU - Garcia, A. A. F. AU - van Eeuwijk, F. A. AU - Magalhaes, J. V. T2 - Theoretical and Applied Genetics AB - Managed environments in the form of well watered and water stressed trials were performed to study the genetic basis of grain yield and stay green in sorghum with the objective of validating previously detected QTL. As variations in phenology and plant height may influence QTL detection for the target traits, QTL for flowering time and plant height were introduced as cofactors in QTL analyses for yield and stay green. All but one of the flowering time QTL were detected near yield and stay green QTL. Similar co-localization was observed for two plant height QTL. QTL analysis for yield, using flowering time/plant height cofactors, led to yield QTL on chromosomes 2, 3, 6, 8 and 10. For stay green, QTL on chromosomes 3, 4, 8 and 10 were not related to differences in flowering time/plant height. The physical positions for markers in QTL regions projected on the sorghum genome suggest that the previously detected plant height QTL, Sb-HT9-1, and Dw2, in addition to the maturity gene, Ma5, had a major confounding impact on the expression of yield and stay green QTL. Co-localization between an apparently novel stay green QTL and a yield QTL on chromosome 3 suggests there is potential for indirect selection based on stay green to improve drought tolerance in sorghum. Our QTL study was carried out with a moderately sized population and spanned a limited geographic range, but still the results strongly emphasize the necessity of corrections for phenology in QTL mapping for drought tolerance traits in sorghum. DA - 2012/2/2/ PY - 2012/2/2/ DO - 10.1007/s00122-012-1795-9 VL - 124 IS - 8 SP - 1389-1402 J2 - Theor Appl Genet LA - en OP - SN - 0040-5752 1432-2242 UR - http://dx.doi.org/10.1007/s00122-012-1795-9 DB - Crossref ER - TY - JOUR TI - A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers AU - Palhares, Alessandra C AU - Rodrigues-Morais, Taislene B AU - Van Sluys, Marie-Anne AU - Domingues, Douglas S AU - Maccheroni, Walter, Jr AU - Jordão, Hamilton, Jr AU - Souza, Anete P AU - Marconi, Thiago G AU - Mollinari, Marcelo AU - Gazaffi, Rodrigo AU - Garcia, Antonio Augusto F AU - Vieira, Maria Lucia Carneiro T2 - BMC Genetics AB - The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily.The mapping population parents ('IAC66-6' and 'TUC71-7') contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization.Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60) copies in the sugarcane genome, confirming previously reported molecular results. In addition, this research possibly will have indirect implications in crop economics e.g., productivity enhancement via QTL studies, as the mapping population parents differ in response to an important fungal disease. DA - 2012/6/28/ PY - 2012/6/28/ DO - 10.1186/1471-2156-13-51 VL - 13 IS - 1 J2 - BMC Genet LA - en OP - SN - 1471-2156 UR - http://dx.doi.org/10.1186/1471-2156-13-51 DB - Crossref KW - Saccharum spp KW - AFLP KW - EST-SSR KW - Retrotransposon-based markers KW - Single-dose markers KW - Integrated genetic map KW - Marker distribution ER - TY - JOUR TI - Estimating optimal treatment regimes from a classification perspective AU - Zhang, Baqun AU - Tsiatis, Anastasios A. AU - Davidian, Marie AU - Zhang, Min AU - Laber, Eric T2 - Stat AB - A treatment regime maps observed patient characteristics to a recommended treatment. Recent technological advances have increased the quality, accessibility, and volume of patient-level data; consequently, there is a growing need for powerful and flexible estimators of an optimal treatment regime that can be used with either observational or randomized clinical trial data. We propose a novel and general framework that transforms the problem of estimating an optimal treatment regime into a classification problem wherein the optimal classifier corresponds to the optimal treatment regime. We show that commonly employed parametric and semi-parametric regression estimators, as well as recently proposed robust estimators of an optimal treatment regime can be represented as special cases within our framework. Furthermore, our approach allows any classification procedure that can accommodate case weights to be used without modification to estimate an optimal treatment regime. This introduces a wealth of new and powerful learning algorithms for use in estimating treatment regimes. We illustrate our approach using data from a breast cancer clinical trial. DA - 2012/10// PY - 2012/10// DO - 10.1002/sta.411 VL - 1 IS - 1 SP - 103-114 J2 - Stat LA - en OP - SN - 2049-1573 UR - http://dx.doi.org/10.1002/sta.411 DB - Crossref KW - classification KW - doubly robust estimator KW - inverse probability weighting KW - personalized medicine KW - potential outcomes KW - propensity score ER - TY - JOUR TI - Clustering Random Curves Under Spatial Interdependence With Application to Service Accessibility AU - Jiang, Huijing AU - Serban, Nicoleta T2 - Technometrics AB - Service accessibility is defined as the access of a community to the nearby site locations in a service network consisting of multiple geographically distributed service sites. Leveraging new statistical methods, this article estimates and classifies service accessibility patterns varying over a large geographic area (Georgia) and over a period of 16 years. The focus of this study is on financial services but it generally applies to any other service operation. To this end, we introduce a model-based method for clustering random time-varying functions that are spatially interdependent. The underlying clustering model is nonparametric with spatially correlated errors. We also assume that the clustering membership is a realization from a Markov random field. Under these model assumptions, we borrow information across functions corresponding to nearby spatial locations resulting in enhanced estimation accuracy of the cluster effects and of the cluster membership as shown in a simulation study. Supplementary materials including the estimation algorithm, additional maps of the data, and the C++ computer programs for analyzing the data in our case study are available online. DA - 2012/5// PY - 2012/5// DO - 10.1080/00401706.2012.657106 VL - 54 IS - 2 SP - 108-119 J2 - Technometrics LA - en OP - SN - 0040-1706 1537-2723 UR - http://dx.doi.org/10.1080/00401706.2012.657106 DB - Crossref KW - Functional data analysis KW - Markov random field KW - Model-based clustering KW - Semiparametric modeling KW - Service accessibility KW - Spatial dependence ER - TY - JOUR TI - A Bayesian approach to the analysis of gauge R&R data AU - Weaver, B.P. AU - Hamada, M.S. AU - Vardeman, S.B. AU - Wilson, A.G. T2 - Quality Engineering AB - ABSTRACT Gauge repeatability and reproducibility (R&R) studies are used to assess precision of measurement systems. In particular, they are used to quantify the importance of various sources of variability in a measurement system. We take a Bayesian approach to data analysis and show how to estimate variance components associated with the sources of variability and relevant functions of these using the gauge R&R data together with prior information. We then provide worked examples of gauge R&R data analysis for types of studies common in industrial applications. With each example we provide WinBUGS code to illustrate how easy it is to implement a Bayesian analysis of gauge R&R data. DA - 2012/// PY - 2012/// DO - 10.1080/08982112.2012.702381 VL - 24 IS - 4 SP - 486-500 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84867050766&partnerID=MN8TOARS KW - gauge studies KW - random effects KW - repeatability KW - reproducibility KW - variance components ER - TY - JOUR TI - Statistical engineering-roles for statisticians and the path forward AU - Anderson-Cook, C.M. AU - Lu, L. AU - Clark, G. AU - Dehart, S.P. AU - Hoerl, R. AU - Jones, B. AU - MacKay, R.J. AU - Montgomery, D. AU - Parker, P.A. AU - Simpson, J. AU - Snee, R. AU - Steiner, S.H. AU - Van Mullekom, J. AU - Vining, G.G. AU - Wilson, A.G. T2 - Quality Engineering AB - Experts from diverse areas of industry, government, and academia are asked about the changing roles for statisticians in the SE workplace and discuss some of the opportunities and challenges for the future. DA - 2012/// PY - 2012/// DO - 10.1080/08982112.2012.641151 VL - 24 IS - 2 SP - 133-152 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84859802152&partnerID=MN8TOARS ER - TY - JOUR TI - Statistical engineering-forming the foundations AU - Anderson-Cook, C.M. AU - Lu, L. AU - Clark, G. AU - Dehart, S.P. AU - Hoerl, R. AU - Jones, B. AU - MacKay, R.J. AU - Montgomery, D. AU - Parker, P.A. AU - Simpson, J. AU - Snee, R. AU - Steiner, S.H. AU - Van Mullekom, J. AU - Vining, G.G. AU - Wilson, A.G. T2 - Quality Engineering AB - Click to increase image sizeClick to decrease image size Additional informationNotes on contributorsChristine M. Anderson-CookChristine M. Anderson-Cook is a research scientist in the Statistical Sciences Group at Los Alamos National Laboratory. Her research interests include design of experiments, reliability, and response surface methodology. She is a Fellow of the American Statistical Association and the American Society for Quality.Lu LuLu Lu is a postdoctoral research associate with the Statistical Sciences Group at Los Alamos National Laboratory. Her statistical research interests include reliability, design and analysis of experiments, response surface methodology, survey sampling, and analysis. She is a member of the American Statistical Association and American Society for Quality.Gordon ClarkGordon Clark is the principal consultant at Clark Solutions and a professor emeritus at The Ohio State University. His recent research interests include strategies for quality and performance improvement, statistical analysis of data to improve quality, and the use of simulation to improve quality. He is a Fellow of the American Society for Quality.Stephanie P. DeHartStephanie P. DeHart is a consulting statistician and Master Black Belt in the Applied Statistics Group at DuPont. She received her bachelor's degree in mathematics from Roanoke College and master's and Ph.D. degrees in statistics from Virginia Polytechnic Institute & State University. Her interests include design and analysis of experiments, response surface methodology, statistical applications in the chemical and engineering sciences, and Six Sigma. She is a member of ASA and ASQ and has served as an officer for the ASA Section on Physical & Engineering Sciences since 2007.Roger HoerlRoger W. Hoerl leads the Applied Statistics Lab at GE Global Research, which supports new product and service development across the GE businesses. Dr. Hoerl has been named a Fellow of the American Statistical Association and the American Society for Quality and has been elected to the International Statistical Institute and the International Academy for Quality. He has received the Brumbaugh and Hunter Awards, as well as the Shewhart Medal from the American Society for Quality and the Founders Award from the American Statistical Association. In 2006 he received the Coolidge Fellowship from GE Global Research, honoring one scientist a year from among the four global GE Research and Development sites for lifetime technical achievement. He used his 6-month Coolidge sabbatical to study the global HIV/AIDS pandemic.Bradley JonesBradley Jones is a principal research fellow in the JMP Division of SAS where he develops tools for the statistical design of experiments. He is the winner of the 2009 Brumbaugh and 2010 Lloyd S. Nelson Awards. He is a Fellow of the American Statistical Association and the Editor-in-Chief of the Journal of Quality Technology.R. Jock MacKayR. Jock MacKay is an associate professor in statistics and actuarial science and past director of the Institute for Improvement of Quality and Productivity at the University of Waterloo.Douglas MontgomeryDouglas Montgomery is Regents' Professor of industrial engineering and statistics and Foundation Professor of Engineering at Arizona State University. His research and teaching interests are in industrial statistics. Professor Montgomery is a Fellow of the ASA, a Fellow of the ASQ, a Fellow of the RSS, a Fellow of IIE, a member of the ISI, an academician of the IAQ, and has received several teaching and research awards.Peter A. ParkerPeter A. Parker is a research scientist in the Aeronautics Systems Engineering Branch at the National Aeronautics and Space Administration's Langley Research Center. He holds a B.S. in engineering from Old Dominion University (1989), an M.S. in applied physics and computer science from Christopher Newport University (2000), and an M.S. (2003) and Ph.D. (2005) in statistics from Virginia Tech. He is a senior member of the American Society for Quality and the American Institute for Aeronautics and Astronautics and a member American Statistical Association. His research interests include experimental design and analysis, response surface methodology, statistical quality control and improvement, and the integration of computational and physical experimentation.James SimpsonJames Simpson is Chief Operations Analyst for the Air Force's 53rd Test Management Group at Eglin Air Force Base, Florida. He is chair of the ASQ Journal Editors' Committee, a member of the ASQ Publication Management Board, and the past Editor-in-Chief for Quality Engineering. He is a senior member of ASQ.Ronald SneeRonald D. Snee is founder and president of Snee Associates, LLC, a firm dedicated to the successful implementation of process and organizational improvement initiatives. He was employed at the DuPont Company for 24 years prior to pursuing a consulting career. Ron also serves as adjunct professor in the Temple University School of Pharmacy. He is an academician in the International Academy for Quality and Fellow of the American Society of Quality, American Statistical Association, and American Association for the Advancement of Science. Ron's work has been awarded ASQ's Shewhart and Grant Medals and ASA's Deming Lecture Award and has coauthored three books with Roger Hoerl on statistical thinking and Six Sigma.Stefan H. SteinerStefan H. Steiner is a professor in the Department of Statistics and Actuarial Science as well as the director of the Business and Industrial Statistics Research Group at the University of Waterloo.Jennifer Van MullekomJennifer Van Mullekom is a consulting statistician at DuPont. She received her Ph.D. degrees in statistics from Virginia Polytechnic Institute & State University. She is a member of ASA and has served as chair of the ASA Section on Physical & Engineering Sciences.G. Geoff ViningG. Geoff Vining is a professor in the Department of Statistics at Virginia Tech. He is a Fellow of the American Statistical Association and the American Society for Quality. He is the 2011 recipient of the ASQ Statistics Division Hunter Award and the ASQ Shewhart Medal.Alyson G. WilsonAlyson G. Wilson is a research staff Member at the IDA Science and Technology Policy Institute. Her research interests include Bayesian methods, reliability, and applying statistics to problems in defense and security. She is a Fellow of the American Statistical Association. DA - 2012/// PY - 2012/// DO - 10.1080/08982112.2012.641150 VL - 24 IS - 2 SP - 110-132 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84859806129&partnerID=MN8TOARS ER - TY - JOUR TI - On Tensors, Sparsity, and Nonnegative Factorizations AU - Chi, E. AU - Kolda, T. T2 - SIAM Journal of Matrix Analysis and Applications AB - Tensors have found application in a variety of fields, ranging from chemometrics to signal processing and beyond. In this paper, we consider the problem of multilinear modeling of sparse count data. Our goal is to develop a descriptive tensor factorization model of such data, along with appropriate algorithms and theory. To do so, we propose that the random variation is best described via a Poisson distribution, which better describes the zeros observed in the data as compared to the typical assumption of a Gaussian distribution. Under a Poisson assumption, we fit a model to observed data using the negative log-likelihood score. We present a new algorithm for Poisson tensor factorization called CANDECOMP--PARAFAC alternating Poisson regression (CP-APR) that is based on a majorization-minimization approach. It can be shown that CP-APR is a generalization of the Lee--Seung multiplicative updates. We show how to prevent the algorithm from converging to non-KKT points and prove convergence of CP-APR under mild conditions. We also explain how to implement CP-APR for large-scale sparse tensors and present results on several data sets, both real and simulated. DA - 2012/12// PY - 2012/12// DO - 10.1137/110859063 VL - 33 IS - 4 SP - 1272-1299 UR - http://epubs.siam.org/doi/abs/10.1137/110859063 KW - nonnegative tensor factorization KW - nonnegative CANDECOMP-PARAFAC KW - Poisson tensor factorization KW - Lee-Seung multiplicative updates KW - majorization-minimization algorithms ER - TY - JOUR TI - Supplementary material for: Empirical Pathway Analysis, Without Permutation AU - Zhou, Yi-Hui AU - Barry, William T AU - Wright, Fred A AU - Hill, Chapel DA - 2012/// PY - 2012/// ER - TY - JOUR TI - Simple and accurate trend tests using a permutation approximation AU - Zhou, Yi-Hui AU - Wright, Fred A DA - 2012/// PY - 2012/// ER - TY - JOUR TI - Quantitative high-throughput screening for chemical toxicity in a population-based in vitro model AU - Lock, Eric F AU - Abdo, Nour AU - Huang, Ruili AU - Xia, Menghang AU - Kosyk, Oksana AU - O’Shea, Shannon H AU - Zhou, Yi-Hui AU - Sedykh, Alexander AU - Tropsha, Alexander AU - Austin, Christopher P AU - others T2 - Toxicological Sciences DA - 2012/// PY - 2012/// ER - TY - JOUR TI - Single Nucleotide Polymorphism (SNP) Detection and Genotype Calling from Massively Parallel Sequencing (MPS) Data AU - Li, Yun AU - Chen, Wei AU - Liu, Eric Yi AU - Zhou, Yi-Hui T2 - Statistics in Biosciences DA - 2012/// PY - 2012/// SP - 1-23 ER - TY - JOUR TI - Testing for spatial isotropy under general designs AU - Maity, Arnab AU - Sherman, Michael T2 - Journal of Statistical Planning and Inference AB - Spatial modeling is typically composed of a specification of a mean function and a model for the correlation structure. A common assumption on the spatial correlation is that it is isotropic. This means that the correlation between any two observations depends only on the distance between those sites and not on their relative orientation. The assumption of isotropy is often made due to a simpler interpretation of correlation behavior and to an easier estimation problem under an assumed isotropy. The assumption of isotropy, however, can have serious deleterious effects when not appropriate. In this paper we formulate a test of isotropy for spatial observations located according to a general class of stochastic designs. Distribution theory of our test statistic is derived and we carry out extensive simulations which verify the efficacy of our approach. We apply our methodology to a data set on longleaf pine trees from an oldgrowth forest in the southern United States. DA - 2012/// PY - 2012/// DO - 10.1016/j.jspi.2011.11.013 VL - 142 IS - 5 SP - 1081–1091 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84856023088&partnerID=MN8TOARS KW - Anisotropy KW - Covariogram KW - Isotropy KW - Spatial bootstrap KW - Spatial statistics ER - TY - JOUR TI - Design and analysis issues in gene and environment studies AU - Liu, C.-Y. AU - Maity, A. AU - Lin, X. AU - Wright, R.O. AU - Christiani, D.C. T2 - Environmental Health: A Global Access Science Source AB - Both nurture (environmental) and nature (genetic factors) play an important role in human disease etiology. Traditionally, these effects have been thought of as independent. This perspective is ill informed for non-mendelian complex disorders which result as an interaction between genetics and environment. To understand health and disease we must study how nature and nurture interact. Recent advances in human genomics and high-throughput biotechnology make it possible to study large numbers of genetic markers and gene products simultaneously to explore their interactions with environment. The purpose of this review is to discuss design and analytic issues for gene-environment interaction studies in the "-omics" era, with a focus on environmental and genetic epidemiological studies. We present an expanded environmental genomic disease paradigm. We discuss several study design issues for gene-environmental interaction studies, including confounding and selection bias, measurement of exposures and genotypes. We discuss statistical issues in studying gene-environment interactions in different study designs, such as choices of statistical models, assumptions regarding biological factors, and power and sample size considerations, especially in genome-wide gene-environment studies. Future research directions are also discussed. DA - 2012/// PY - 2012/// DO - 10.1186/1476-069X-11-93 VL - 11 IS - 1 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84872769763&partnerID=MN8TOARS KW - Gene-environment KW - Interactions KW - Expanded environmental genomic disease paradigm KW - Critical developmental windows KW - Genome-wide KW - Epigenetics ER - TY - JOUR TI - Multivariate Gene Selection and Testing in Studying the Exposure Effects on a Gene Set AU - Sofer, T. AU - Maity, A. AU - Coull, B. AU - Baccarelli, A.A. AU - Schwartz, J. AU - Lin, X. T2 - Statistics in Biosciences AB - Studying the association between a gene set (e.g., pathway) and exposures using multivariate regression methods is of increasing importance in genomic studies. Such an analysis is often more powerful and interpretable than individual-gene analysis. Since many genes in a gene set are likely not affected by exposures, one is often interested in identifying a subset of genes in the gene set that are affected by exposures. This allows for better understanding of the underlying biological mechanism and for pursuing further biological investigation of these genes. The selected subset of “signal” genes also provides an attractive vehicle for a more powerful test for the association between the gene set and exposures. We propose two computationally simple Canonical Correlation Analysis (CCA) based variable selection methods: Sparse Outcome Selection (SOS) CCA and step CCA, to jointly select a subset of genes in a gene set that are associated with exposures. Several model selection criteria, such as BIC and the new Correlation Information Criterion (CIC), are proposed and compared. We also develop a global test procedure for testing the exposure effects on the whole gene set, accounting for gene selection. Through simulation studies, we show that the proposed methods improve upon an existing method when the genes are correlated and are more computationally efficient. We apply the proposed methods to the analysis of the Normative Aging DNA methylation Study to examine the effects of airborne particular matter exposures on DNA methylations in a genetic pathway. DA - 2012/// PY - 2012/// DO - 10.1007/s12561-012-9072-7 VL - 4 IS - 2 SP - 319-338 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84870393737&partnerID=MN8TOARS KW - Canonical correlation analysis KW - Epigenetics KW - Global test KW - Sparsity KW - Variable selection KW - Tuning parameter ER - TY - CHAP TI - Composite Interval Mapping and Multiple Interval Mapping: Procedures and Guidelines for Using Windows QTL Cartographer AU - Silva, Luciano Da Costa E. AU - Wang, Shengchu AU - Zeng, Zhao-Bang T2 - Methods in Molecular Biology AB - Tremendous progress has been made in recent years on developing statistical methods for mapping quantitative trait loci (QTL) from crosses of inbred lines. In this chapter, we provide an introduction of composite interval mapping and multiple interval mapping methods for mapping QTL from inbred line crosses and also detailed instructions to perform the analyses in Windows QTL Cartographer. For each method, we discuss the meaning of each option in the analysis procedures and how to understand and interpret the mapping results through a work-out example. PY - 2012/// DO - 10.1007/978-1-61779-785-9_6 SP - 75-119 OP - PB - Humana Press SN - 9781617797842 9781617797859 UR - http://dx.doi.org/10.1007/978-1-61779-785-9_6 DB - Crossref ER - TY - JOUR TI - Metabolomics Reveals Amino Acids Contribute to Variation in Response to Simvastatin Treatment AU - Trupp, Miles AU - Zhu, Hongjie AU - Wikoff, William R. AU - Baillie, Rebecca A. AU - Zeng, Zhao-Bang AU - Karp, Peter D. AU - Fiehn, Oliver AU - Krauss, Ronald M. AU - Kaddurah-Daouk, Rima T2 - PLoS ONE AB - Statins are widely prescribed for reducing LDL-cholesterol (C) and risk for cardiovascular disease (CVD), but there is considerable variation in therapeutic response. We used a gas chromatography-time-of-flight mass-spectrometry-based metabolomics platform to evaluate global effects of simvastatin on intermediary metabolism. Analyses were conducted in 148 participants in the Cholesterol and Pharmacogenetics study who were profiled pre and six weeks post treatment with 40 mg/day simvastatin: 100 randomly selected from the full range of the LDL-C response distribution and 24 each from the top and bottom 10% of this distribution (“good” and “poor” responders, respectively). The metabolic signature of drug exposure in the full range of responders included essential amino acids, lauric acid (p<0.0055, q<0.055), and alpha-tocopherol (p<0.0003, q<0.017). Using the HumanCyc database and pathway enrichment analysis, we observed that the metabolites of drug exposure were enriched for the pathway class amino acid degradation (p<0.0032). Metabolites whose change correlated with LDL-C lowering response to simvastatin in the full range responders included cystine, urea cycle intermediates, and the dibasic amino acids ornithine, citrulline and lysine. These dibasic amino acids share plasma membrane transporters with arginine, the rate-limiting substrate for nitric oxide synthase (NOS), a critical mediator of cardiovascular health. Baseline metabolic profiles of the good and poor responders were analyzed by orthogonal partial least square discriminant analysis so as to determine the metabolites that best separated the two response groups and could be predictive of LDL-C response. Among these were xanthine, 2-hydroxyvaleric acid, succinic acid, stearic acid, and fructose. Together, the findings from this study indicate that clusters of metabolites involved in multiple pathways not directly connected with cholesterol metabolism may play a role in modulating the response to simvastatin treatment. Trial Registration ClinicalTrials.gov NCT00451828 DA - 2012/7/9/ PY - 2012/7/9/ DO - 10.1371/journal.pone.0038386 VL - 7 IS - 7 SP - e38386 J2 - PLoS ONE LA - en OP - SN - 1932-6203 UR - http://dx.doi.org/10.1371/journal.pone.0038386 DB - Crossref ER - TY - BOOK TI - A functional analysis framework for modeling, estimation, and control in science and engineering AU - Banks, H. T. AB - A Modern Framework Based on Time-Tested MaterialA Functional Analysis Framework for Modeling, Estimation and Control in Science and Engineering presents functional analysis as a tool for understanding and treating distributed parameter systems. Drawing on his extensive research and teaching from the past 20 years, the author explains how functional DA - 2012/// PY - 2012/// DO - 10.1201/b12209 PB - Boca Raton: CRC Press ER - TY - CHAP TI - Design and analysis of tagging studies AU - Pine, W. AU - Hightower, J. AU - Coggins, L. AU - Lauretta, M. AU - Pollock, K. T2 - Fisheries techniques (3rd ed.) A2 - A. V. Zale, D. L. Parrish A2 - Sutton, T. M. PY - 2012/// SP - 521-572 PB - Bethesda, Md.: American Fisheries Society SN - 9781934874295 ER - TY - JOUR TI - Temporal analysis of stormwater control measure effluent based on windows of harmful algal bloom (HAB) sensitivity: Are annual nutrient EMCs appropriate during HAB-sensitive seasons? AU - Hathaway, Jon M. AU - Moore, Trisha L. C. AU - Burkholder, JoAnn M. AU - Hunt, William F. T2 - ECOLOGICAL ENGINEERING AB - Nutrient removal by stormwater control measures (SCMs) is typically reported in terms of an average annual percent removal or effluent concentration. However, when the performance of these systems is considered in light of downstream receiving aquatic ecosystems, which display seasonal sensitivities to nutrient loadings, the use of an annual-based metric seems arbitrary. To investigate the potential temporal mismatch between nutrient-sensitive periods in receiving water bodies and average annual reporting periods adopted for SCM performance metrics, a case study is presented for four SCM types (constructed stormwater wetlands, bioretention, vegetated filter strips, and swales) draining to the Neuse River Estuary (NRE) in North Carolina, USA. Outbreaks of harmful algal blooms (HABs) in the NRE have been related to different nutrient forms at different times of the year, resulting in a “window” of importance for a given nutrient. These windows were utilized herein to define seasons of interest for various pollutants, and thus how SCM effluent data should be grouped to evaluate seasonal differences in performance. Effluent SCM nutrient concentrations were analyzed on an annual and HAB-sensitive seasonal basis. Although the use of annual performance metrics was deemed either appropriate or conservative for total phosphorus and nitrate–nitrite, effluent concentrations of total ammonia–nitrogen were significantly higher during HAB-sensitive seasons from both bioretention areas and stormwater wetlands. In the case of the NRE, these data suggest SCMs such as bioretention and stormwater wetlands may perform less effectively during periods of HAB sensitivity and that the contribution of SCMs to HAB control in sensitive water bodies may be overstated using presently accepted annual evaluation metrics. Though the seasonal analysis presented is specific to HAB formation in the Neuse River Estuary, evaluation of SCM effluent nutrient concentrations on the basis of nutrient-sensitive periods in receiving water bodies has broad application to evaluation of SCMs in any nutrient-sensitive watershed. The present study suggests that evaluation of SCM performance with respect to nutrient-sensitive periods in receiving aquatic ecosystems warrants further study. DA - 2012/12// PY - 2012/12// DO - 10.1016/j.ecoleng.2012.08.014 VL - 49 SP - 41-47 SN - 1872-6992 KW - Harmful algal bloom KW - Stormwater KW - BMP KW - SCM KW - Performance KW - Metrics KW - Stormwater wetland KW - Bioretention KW - Filter strip KW - Swale ER - TY - JOUR TI - OPTIMAL TWO-STAGE PROCEDURES FOR ESTIMATING LOCATION AND SIZE OF THE MAXIMUM OF A MULTIVARIATE REGRESSION FUNCTION AU - Belitser, Eduard AU - Ghosal, Subhashis AU - Zanten, Harry T2 - ANNALS OF STATISTICS AB - We propose a two-stage procedure for estimating the location $\bolds{\mu}$ and size M of the maximum of a smooth d-variate regression function f. In the first stage, a preliminary estimator of $\bolds{\mu}$ obtained from a standard nonparametric smoothing method is used. At the second stage, we "zoom-in" near the vicinity of the preliminary estimator and make further observations at some design points in that vicinity. We fit an appropriate polynomial regression model to estimate the location and size of the maximum. We establish that, under suitable smoothness conditions and appropriate choice of the zooming, the second stage estimators have better convergence rates than the corresponding first stage estimators of $\bolds{\mu}$ and M. More specifically, for $\alpha$-smooth regression functions, the optimal nonparametric rates $n^{-(\alpha-1)/(2\alpha+d)}$ and $n^{-\alpha/(2\alpha+d)}$ at the first stage can be improved to $n^{-(\alpha-1)/(2\alpha)}$ and $n^{-1/2}$, respectively, for $\alpha>1+\sqrt{1+d/2}$. These rates are optimal in the class of all possible sequential estimators. Interestingly, the two-stage procedure resolves "the curse of the dimensionality" problem to some extent, as the dimension d does not control the second stage convergence rates, provided that the function class is sufficiently smooth. We consider a multi-stage generalization of our procedure that attains the optimal rate for any smoothness level $\alpha>2$ starting with a preliminary estimator with any power-law rate at the first stage. DA - 2012/12// PY - 2012/12// DO - 10.1214/12-AOS1053 VL - 40 IS - 6 SP - 2850-2876 SN - 0090-5364 KW - Two-stage procedure KW - optimal rate KW - sequential design KW - multi-stage procedure KW - adaptive estimation ER - TY - JOUR TI - Multivariate methods and software for association mapping in dose-response genome-wide association studies AU - Brown, C. C. AU - Havener, T. M. AU - Medina, M. W. AU - Krauss, R. M. AU - McLeod, H. L. AU - Motsinger-Reif, A. A. T2 - Biodata Mining DA - 2012/// PY - 2012/// VL - 5 ER - TY - JOUR TI - Expanding Aerial-Roving Surveys to Include Counts of Shore-Based Recreational Fishers from Remotely Operated Cameras: Benefits, Limitations, and Cost Effectiveness AU - Smallwood, C. B. AU - Pollock, K. H. AU - Wise, B. S. AU - Hall, N. G. AU - Gaughan, D. J. T2 - NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT AB - Abstract Information on shore‐based recreational fishing is essential for the sustainable management of nearshore fish stocks. However, obtaining estimates of catch and effort from such fishing activity can be complex and expensive due to the large spatial scales over which surveys are typically conducted and the fine‐scale temporal resolution that is desired. Complementary surveys are one option for improving the accuracy of estimates. A pilot study was conducted in Perth, Western Australia, from April to June 2010 to test an expanded aerial–roving survey design that incorporated remotely operated cameras. Cameras recorded the distribution of shore‐based fishing activity across a 24‐h day, highlighting an afternoon peak as well as some nighttime activity, which is rarely captured in existing survey designs. This information was combined with instantaneous counts of shore fishers from aerial surveys and trip length data that were obtained from 1,194 incomplete trip interviews conducted during roving creel surveys; the resulting estimate of fishing effort was 213,460 angler‐hours (SE = 18,141; relative SE [RSE] = 8%). Catch rates, which were calculated from roving creel survey data on the numbers of retained fish, were combined with fishing effort to estimate a total retained catch of 355,801 fish (SE = 41,446; RSE = 12%). The Australian herring Arripis georgianus was the dominant species, with a retained catch of 229,779 fish (SE = 39,007; RSE = 17%). In comparison with other on‐site techniques, the incorporation of cameras into an aerial–roving survey design provides a generic, cost‐effective method for measuring the distribution of shore‐based fishing activity across a 24‐h day. Our findings improve the understanding of the exploitation of nearshore fish stocks along the Perth coast. Our method has broad application to many other recreational fisheries around the world, especially where nighttime fishing is popular. Received June 28, 2012; accepted August 24, 2012 DA - 2012/12/1/ PY - 2012/12/1/ DO - 10.1080/02755947.2012.728181 VL - 32 IS - 6 SP - 1265-1276 SN - 0275-5947 ER - TY - JOUR TI - Design and analysis issues in gene and environment studies AU - Liu, C. Y. AU - Maity, A. AU - Lin, X. H. AU - Wright, R. O. AU - Christiani, D. C. T2 - Environmental Health DA - 2012/// PY - 2012/// VL - 11 ER - TY - JOUR TI - A HIERARCHICAL MAX-STABLE SPATIAL MODEL FOR EXTREME PRECIPITATION AU - Reich, Brian J. AU - Shaby, Benjamin A. T2 - ANNALS OF APPLIED STATISTICS AB - Extreme environmental phenomena such as major precipitation events manifestly exhibit spatial dependence. Max-stable processes are a class of asymptotically-justified models that are capable of representing spatial dependence among extreme values. While these models satisfy modeling requirements, they are limited in their utility because their corresponding joint likelihoods are unknown for more than a trivial number of spatial locations, preventing, in particular, Bayesian analyses. In this paper, we propose a new random effects model to account for spatial dependence. We show that our specification of the random effect distribution leads to a max-stable process that has the popular Gaussian extreme value process (GEVP) as a limiting case. The proposed model is used to analyze the yearly maximum precipitation from a regional climate model. DA - 2012/12// PY - 2012/12// DO - 10.1214/12-aoas591 VL - 6 IS - 4 SP - 1430-1451 SN - 1932-6157 KW - Gaussian extreme value process KW - generalized extreme value distribution KW - positive stable distribution KW - regional climate model ER - TY - JOUR TI - Stormwater in urban areas AU - Rauch, Wolfgang AU - Ledin, Anna AU - Eriksson, Eva AU - Deletic, Ana AU - Hunt, William F., III T2 - WATER RESEARCH AB - Collection, storage and treatment of stormwater in urban areas has been one of the classical disciplines of sanitary and environmental engineering in the past. Waste and pollution transported by st ... DA - 2012/12/15/ PY - 2012/12/15/ DO - 10.1016/j.watres.2012.10.044 VL - 46 IS - 20 SP - 6588-6588 SN - 0043-1354 ER - TY - JOUR TI - Spatial-Temporal Modeling of the Association between Air Pollution Exposure and Preterm Birth: Identifying Critical Windows of Exposure AU - Warren, Joshua AU - Fuentes, Montserrat AU - Herring, Amy AU - Langlois, Peter T2 - BIOMETRICS AB - Summary Exposure to high levels of air pollution during the pregnancy is associated with increased probability of preterm birth (PTB), a major cause of infant morbidity and mortality. New statistical methodology is required to specifically determine when a particular pollutant impacts the PTB outcome, to determine the role of different pollutants, and to characterize the spatial variability in these results. We develop a new Bayesian spatial model for PTB which identifies susceptible windows throughout the pregnancy jointly for multiple pollutants (PM 2.5 , ozone) while allowing these windows to vary continuously across space and time. We geo‐code vital record birth data from Texas (2002–2004) and link them with standard pollution monitoring data and a newly introduced EPA product of calibrated air pollution model output. We apply the fully spatial model to a region of 13 counties in eastern Texas consisting of highly urban as well as rural areas. Our results indicate significant signal in the first two trimesters of pregnancy with different pollutants leading to different critical windows. Introducing the spatial aspect uncovers critical windows previously unidentified when space is ignored. A proper inference procedure is introduced to correctly analyze these windows. DA - 2012/12// PY - 2012/12// DO - 10.1111/j.1541-0420.2012.01774.x VL - 68 IS - 4 SP - 1157-1167 SN - 0006-341X KW - Air pollution KW - Bayesian analysis KW - MCMC KW - Preterm birth KW - Probit regression KW - Spatial model ER - TY - JOUR TI - Power of a reproducing kernel-based method for testing the joint effect of a set of single-nucleotide polymorphisms AU - He, Hong AU - Zhang, Hongmei AU - Maity, Arnab AU - Zou, Yubo AU - Hussey, James AU - Karmaus, Wilfried T2 - GENETICA AB - This study explored a semi-parametric method built upon reproducing kernels for estimating and testing the joint effect of a set of single nucleotide polymorphisms (SNPs). The kernel adopted is the identity-by-state kernel that measures SNP similarity between subjects. In this article, through simulations we first assessed its statistical power under different situations. It was found that in addition to the effect of sample size, the testing power was impacted by the strength of association between SNPs and the outcome of interest, and by the SNP similarity among the subjects. A quadratic relationship between SNP similarity and testing power was identified, and this relationship was further affected by sample sizes. Next we applied the method to a SNP-lung function data set to estimate and test the joint effect of a set of SNPs on forced vital capacity, one type of lung function measure. The findings were then connected to the patterns observed in simulation studies and further explored via variable importance indices of each SNP inferred from a variable selection procedure. DA - 2012/12// PY - 2012/12// DO - 10.1007/s10709-012-9690-5 VL - 140 IS - 10-12 SP - 421-427 SN - 1573-6857 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84873408116&partnerID=MN8TOARS KW - Reproducing kernels KW - SNP KW - Mixed linear models KW - Testing power KW - Variable selection ER - TY - JOUR TI - Intra-event variability of Escherichia coli and total suspended solids in urban stormwater runoff AU - McCarthy, D. T. AU - Hathaway, J. M. AU - Hunt, W. F. AU - Deletic, A. T2 - WATER RESEARCH AB - Sediment levels are important for environmental health risk assessments of surface water bodies, while faecal pollution can introduce significant public health risks for users of these systems. Urban stormwater is one of the largest sources of contaminants to surface waters, yet the fate and transport of these contaminants (especially those microbiological) have received little attention in the literature. Stormwater runoff from five urbanized catchments were monitored for pathogen indicator bacteria and total suspended solids in two developed countries. Multiple discrete samples were collected during each storm event, allowing an analysis of intra-event characteristics such as initial concentration, peak concentration, maximum rate of change, and relative confidence interval. The data suggest that a catchment’s area influences pollutant characteristics, as larger catchments have more complex stormwater infrastructure and more variable pollutant sources. The variability of total suspended solids for many characteristics was similar to Escherichia coli, indicating that the variability of E. coli may not be substantially higher than that of other pollutants as initially speculated. Further, variations in E. coli appeared to be more commonly correlated to antecedent climate, while total suspended solids were more highly correlated to rainfall/runoff characteristics. This emphasizes the importance of climate on microbial persistence and die off in urban systems. Discrete intra-event concentrations of total suspended solids and, to a lesser extent E. coli, were correlated to flow, velocity, and rainfall intensity (adjusted by time of concentrations). Concentration changes were found to be best described by adjusted rainfall intensity, as shown by other researchers. This study has resulted in an increased understanding of the magnitude of intra-event variations of total suspended solids and E. coli and what physical and climatic parameters influence these variations. DA - 2012/12/15/ PY - 2012/12/15/ DO - 10.1016/j.watres.2012.01.006 VL - 46 IS - 20 SP - 6661-6670 SN - 0043-1354 KW - Urban runoff KW - Stormwater KW - Pollutograph KW - Microorganism KW - Escherichia coli KW - Sediment KW - TSS ER - TY - JOUR TI - Estimation of High Conditional Quantiles for Heavy-Tailed Distributions AU - Wang, Huixia Judy AU - Li, Deyuan AU - He, Xuming T2 - JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION AB - Estimation of conditional quantiles at very high or low tails is of interest in numerous applications. Quantile regression provides a convenient and natural way of quantifying the impact of covariates at different quantiles of a response distribution. However, high tails are often associated with data sparsity, so quantile regression estimation can suffer from high variability at tails especially for heavy-tailed distributions. In this article, we develop new estimation methods for high conditional quantiles by first estimating the intermediate conditional quantiles in a conventional quantile regression framework and then extrapolating these estimates to the high tails based on reasonable assumptions on tail behaviors. We establish the asymptotic properties of the proposed estimators and demonstrate through simulation studies that the proposed methods enjoy higher accuracy than the conventional quantile regression estimates. In a real application involving statistical downscaling of daily precipitation in the Chicago area, the proposed methods provide more stable results quantifying the chance of heavy precipitation in the area. Supplementary materials for this article are available online. DA - 2012/12// PY - 2012/12// DO - 10.1080/01621459.2012.716382 VL - 107 IS - 500 SP - 1453-1464 SN - 1537-274X KW - Downscaling KW - Extrapolation KW - Extreme value KW - High quantile KW - Quantile regression ER - TY - JOUR TI - Ecosystem service provision by stormwater wetlands and ponds - A means for evaluation? AU - Moore, T. L. C. AU - Hunt, W. F. T2 - Water Research AB - Stormwater control measures (SCMs) such as constructed stormwater ponds and constructed stormwater wetlands (CSWs) are designed to regulate runoff hydrology and quality. However, these created ecosystems also provide a range of other benefits, or ecosystem services, which are often acknowledged but rarely quantified. In this study, additional ecosystem services, including carbon sequestration, biodiversity, and cultural services, were assessed and compared between 20 ponds and 20 CSWs in North Carolina, USA. Carbon sequestration was estimated through the carbon content of pond and wetland sediments across a gradient of system age. Biodiversity was quantified in terms of the richness and Shannon diversity index of vegetative and aquatic macroinvertebrate communities. Cultural services were qualitatively assessed based on the potential for recreational and educational opportunities at each site. Ponds and wetlands were found to support similar levels of macroinvertebrate diversity, though differences community composition arose between the two habitat types. CSWs demonstrated greater potential to provide carbon sequestration, vegetative diversity, and cultural ecosystem services. This assessment provides an initial framework upon which future assessments of ecosystem service provision by SCMs can build. DA - 2012/// PY - 2012/// DO - 10.1016/j.watres.2011.11.026 VL - 46 IS - 20 SP - 6811-6823 ER - TY - JOUR TI - Determining duration of HER2-targeted therapy using stem cell extinction models AU - Riley, L. AU - Zhou, H. AU - Lange, K. AU - Sinsheimer, J. S. AU - Sehl, M. E. T2 - PLoS One DA - 2012/// PY - 2012/// VL - 7 IS - 12 ER - TY - JOUR TI - Consistent High-Dimensional Bayesian Variable Selection via Penalized Credible Regions AU - Bondell, Howard D. AU - Reich, Brian J. T2 - JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION AB - For high-dimensional data, particularly when the number of predictors greatly exceeds the sample size, selection of relevant predictors for regression is a challenging problem. Methods such as sure screening, forward selection, or penalized regressions are commonly used. Bayesian variable selection methods place prior distributions on the parameters along with a prior over model space, or equivalently, a mixture prior on the parameters having mass at zero. Since exhaustive enumeration is not feasible, posterior model probabilities are often obtained via long MCMC runs. The chosen model can depend heavily on various choices for priors and also posterior thresholds. Alternatively, we propose a conjugate prior only on the full model parameters and use sparse solutions within posterior credible regions to perform selection. These posterior credible regions often have closed-form representations, and it is shown that these sparse solutions can be computed via existing algorithms. The approach is shown to outperform common methods in the high-dimensional setting, particularly under correlation. By searching for a sparse solution within a joint credible region, consistent model selection is established. Furthermore, it is shown that, under certain conditions, the use of marginal credible intervals can give consistent selection up to the case where the dimension grows exponentially in the sample size. The proposed approach successfully accomplishes variable selection in the high-dimensional setting, while avoiding pitfalls that plague typical Bayesian variable selection methods. DA - 2012/12// PY - 2012/12// DO - 10.1080/01621459.2012.716344 VL - 107 IS - 500 SP - 1610-1624 SN - 1537-274X KW - Consistency KW - Credible region KW - LASSO KW - Stochastic search ER - TY - JOUR TI - A Robust Method for Estimating Optimal Treatment Regimes AU - Zhang, Baqun AU - Tsiatis, Anastasios A. AU - Laber, Eric B. AU - Davidian, Marie T2 - BIOMETRICS AB - Summary A treatment regime is a rule that assigns a treatment, among a set of possible treatments, to a patient as a function of his/her observed characteristics, hence “personalizing” treatment to the patient. The goal is to identify the optimal treatment regime that, if followed by the entire population of patients, would lead to the best outcome on average. Given data from a clinical trial or observational study, for a single treatment decision, the optimal regime can be found by assuming a regression model for the expected outcome conditional on treatment and covariates, where, for a given set of covariates, the optimal treatment is the one that yields the most favorable expected outcome. However, treatment assignment via such a regime is suspect if the regression model is incorrectly specified. Recognizing that, even if misspecified, such a regression model defines a class of regimes, we instead consider finding the optimal regime within such a class by finding the regime that optimizes an estimator of overall population mean outcome. To take into account possible confounding in an observational study and to increase precision, we use a doubly robust augmented inverse probability weighted estimator for this purpose. Simulations and application to data from a breast cancer clinical trial demonstrate the performance of the method. DA - 2012/12// PY - 2012/12// DO - 10.1111/j.1541-0420.2012.01763.x VL - 68 IS - 4 SP - 1010-1018 SN - 1541-0420 KW - Doubly robust estimator KW - Inverse probability weighting KW - Outcome regression KW - Personalized medicine KW - Potential outcomes KW - Propensity score ER - TY - JOUR TI - Multiple trait multiple interval mapping of quantitative trait loci from inbred line crosses AU - Silva, L. D. E. AU - Wang, S. C. AU - Zeng, Z. B. T2 - BMC Genetics DA - 2012/// PY - 2012/// VL - 13 ER - TY - CONF TI - A "Looking Glass" into electrolyte properties: Cyclic carbonate and ester-LiClO4 mixtures AU - Seo, D. M. AU - Afroz, T. AU - Ly, Q. AU - O'Connell, M. AU - Boyle, P. D. AU - Henderson, W. A. C2 - 2012/// C3 - Rechargeable lithium and lithium ion batteries DA - 2012/// VL - 41 SP - 11-15 M1 - 41 ER - TY - PCOMM TI - Loss of power in two-stage residual-outcome regression analysis in genetic association studies AU - Che, R. L. AU - Motsinger-Reif, A. A. AU - Brown, C. C. DA - 2012/// PY - 2012/// SP - 890-894 ER - TY - JOUR TI - Time series analysis of personal exposure to ambient air pollution and mortality using an exposure simulator AU - Chang, Howard H. AU - Fuentes, Montserrat AU - Frey, H. Christopher T2 - JOURNAL OF EXPOSURE SCIENCE AND ENVIRONMENTAL EPIDEMIOLOGY AB - This paper describes a modeling framework for estimating the acute effects of personal exposure to ambient air pollution in a time series design. First, a spatial hierarchical model is used to relate Census tract-level daily ambient concentrations and simulated exposures for a subset of the study period. The complete exposure time series is then imputed for risk estimation. Modeling exposure via a statistical model reduces the computational burden associated with simulating personal exposures considerably. This allows us to consider personal exposures at a finer spatial resolution to improve exposure assessment and for a longer study period. The proposed approach is applied to an analysis of fine particulate matter of <2.5 μm in aerodynamic diameter (PM2.5) and daily mortality in the New York City metropolitan area during the period 2001–2005. Personal PM2.5 exposures were simulated from the Stochastic Human Exposure and Dose Simulation. Accounting for exposure uncertainty, the authors estimated a 2.32% (95% posterior interval: 0.68, 3.94) increase in mortality per a 10 μg/m3 increase in personal exposure to PM2.5 from outdoor sources on the previous day. The corresponding estimates per a 10 μg/m3 increase in PM2.5 ambient concentration was 1.13% (95% confidence interval: 0.27, 2.00). The risks of mortality associated with PM2.5 were also higher during the summer months. DA - 2012/// PY - 2012/// DO - 10.1038/jes.2012.53 VL - 22 IS - 5 SP - 483-488 SN - 1559-064X KW - exposure modeling KW - particulate matter KW - time series analysis ER - TY - JOUR TI - Testing of Novel Dengue Virus 2 Vaccines in African Green Monkeys: Safety, Immunogenicity, and Efficacy AU - Smith, Katherine M. AU - Nanda, Kavita AU - McCarl, Victoria AU - Spears, Carla J. AU - Piper, Amanda AU - Ribeiro, Mariana AU - Quiles, Michelle AU - Briggs, Caitlin M. AU - Thomas, Gwynneth S. AU - Thomas, Malcolm E. AU - Brown, Dennis T. AU - Hernandez, Raquel T2 - AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE AB - The immunogenicity and safety of three novel host-range vaccines containing deletions in the transmembrane domain of dengue virus serotype 2 (DV2) E glycoprotein were evaluated in African green monkeys. The shorter transmembrane domains are capable of functionally spanning an insect but not a mammalian cell membrane, resulting in production of viral mutants that have reduced infectivity in mammalian hosts but efficient growth in insect cells. Groups of four monkeys received one dose each of test vaccine candidate with no booster immunization. After immunization, levels of viremia produced by each vaccine were determined by infectious center assay. Vaccine recipient immune response to wild-type DV2 challenge was measured on Day 57 by enzyme-linked immunosorbent assay and plaque reduction neutralization test. Two vaccines, DV2ΔGVII and DV2G460P, generated neutralizing antibody in the range of 700–900 50% plaque reduction neutralization test units. All three vaccine strains decreased the length of viremia by at least two days. No safety concerns were identified. DA - 2012/10// PY - 2012/10// DO - 10.4269/ajtmh.2012.12-0004 VL - 87 IS - 4 SP - 743-753 SN - 1476-1645 ER - TY - JOUR TI - Partially linear varying coefficient models stratified by a functional covariate AU - Maity, Arnab AU - Huang, Jianhua Z. T2 - STATISTICS & PROBABILITY LETTERS AB - We consider the problem of estimation in semiparametric varying coefficient models where the covariate modifying the varying coefficients is functional and is modeled nonparametrically. We develop a kernel-based estimator of the nonparametric component and a profiling estimator of the parametric component of the model, and derive their asymptotic properties. Specifically, we show the consistency of the nonparametric functional estimates and derive the asymptotic expansion of the estimates of the parametric component. We illustrate the performance of our methodology using a simulation study and a real data application. DA - 2012/10// PY - 2012/10// DO - 10.1016/j.spl.2012.06.002 VL - 82 IS - 10 SP - 1807-1814 SN - 1879-2103 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84864042756&partnerID=MN8TOARS KW - Functional regression KW - Kernel smoothing KW - Profile method KW - Semi-varying coefficient model ER - TY - JOUR TI - Nonlinear dimension reduction with Wright-Fisher kernel for genotype aggregation and association mapping AU - Zhu, Hongjie AU - Li, Lexin AU - Zhou, Hua T2 - BIOINFORMATICS AB - Abstract Motivation: Association tests based on next-generation sequencing data are often under-powered due to the presence of rare variants and large amount of neutral or protective variants. A successful strategy is to aggregate genetic information within meaningful single-nucleotide polymorphism (SNP) sets, e.g. genes or pathways, and test association on SNP sets. Many existing methods for group-wise tests require specific assumptions about the direction of individual SNP effects and/or perform poorly in the presence of interactions. Results: We propose a joint association test strategy based on two key components: a nonlinear supervised dimension reduction approach for effective SNP information aggregation and a novel kernel specially designed for qualitative genotype data. The new test demonstrates superior performance in identifying causal genes over existing methods across a large variety of disease models simulated from sequence data of real genes. In general, the proposed method provides an association test strategy that can (i) detect both rare and common causal variants, (ii) deal with both additive and interaction effect, (iii) handle both quantitative traits and disease dichotomies and (iv) incorporate non-genetic covariates. In addition, the new kernel can potentially boost the power of the entire family of kernel-based methods for genetic data analysis. Availability: The method is implemented in MATLAB. Source code is available upon request. Contact: hongjie.zhu@duke.edu DA - 2012/9/15/ PY - 2012/9/15/ DO - 10.1093/bioinformatics/bts406 VL - 28 IS - 18 SP - I375-I381 SN - 1460-2059 ER - TY - JOUR TI - EM vs MM: A case study AU - Zhou, Hua AU - Zhang, Yiwen T2 - COMPUTATIONAL STATISTICS & DATA ANALYSIS AB - The celebrated expectation–maximization (EM) algorithm is one of the most widely used optimization methods in statistics. In recent years it has been realized that EM algorithm is a special case of the more general minorization–maximization (MM) principle. Both algorithms create a surrogate function in the first (E or M) step that is maximized in the second M step. This two step process always drives the objective function uphill and is iterated until the parameters converge. The two algorithms differ in the way the surrogate function is constructed. The expectation step of the EM algorithm relies on calculating conditional expectations, while the minorization step of the MM algorithm builds on crafty use of inequalities. For many problems, EM and MM derivations yield the same algorithm. This expository note walks through the construction of both algorithms for estimating the parameters of the Dirichlet-Multinomial distribution. This particular case is of interest because EM and MM derivations lead to two different algorithms with completely distinct operating characteristics. The EM algorithm converges quickly but involves solving a nontrivial maximization problem in the M step. In contrast the MM updates are extremely simple but converge slowly. An EM–MM hybrid algorithm is derived which shows faster convergence than the MM algorithm in certain parameter regimes. The local convergence rates of the three algorithms are studied theoretically from the unifying MM point of view and also compared on numerical examples. DA - 2012/12// PY - 2012/12// DO - 10.1016/j.csda.2012.05.018 VL - 56 IS - 12 SP - 3909-3920 SN - 1872-7352 KW - Convergence rate KW - Dirichlet-multinomial distribution KW - EM algorithm KW - MM algorithm ER - TY - JOUR TI - Discussion of "Statistical modeling of spatial extremes" by A. C. Davison, S. A. Padoan and M. Ribatet AU - Cooley, D. AU - Sain, S. R. AU - Gabda, D. AU - Towe, R. AU - Wadsworth, J. AU - Tawn, J. AU - Segers, J. AU - Shaby, B. AU - Reich, B. J. AU - Davison, A. C. AU - Padoan, S. A. AU - Ribatet, M. T2 - Statistical Science DA - 2012/// PY - 2012/// VL - 27 IS - 2 SP - 187-201 ER - TY - JOUR TI - Bayesian Analysis of a Reduced-Form Air Quality Model AU - Foley, Kristen M. AU - Reich, Brian J. AU - Napelenok, Sergey L. T2 - ENVIRONMENTAL SCIENCE & TECHNOLOGY AB - Numerical air quality models are being used for assessing emission control strategies for improving ambient pollution levels across the globe. This paper applies probabilistic modeling to evaluate the effectiveness of emission reduction scenarios aimed at lowering ground-level ozone concentrations. A Bayesian hierarchical model is used to combine air quality model output and monitoring data in order to characterize the impact of emissions reductions while accounting for different degrees of uncertainty in the modeled emissions inputs. The probabilistic model predictions are weighted based on population density in order to better quantify the societal benefits/disbenefits of four hypothetical emission reduction scenarios in which domain-wide NO(x) emissions from various sectors are reduced individually and then simultaneously. Cross validation analysis shows the statistical model performs well compared to observed ozone levels. Accounting for the variability and uncertainty in the emissions and atmospheric systems being modeled is shown to impact how emission reduction scenarios would be ranked, compared to standard methodology. DA - 2012/7/17/ PY - 2012/7/17/ DO - 10.1021/es300666e VL - 46 IS - 14 SP - 7604-7611 SN - 0013-936X ER - TY - JOUR TI - A powerful test for comparing multiple regression functions AU - Maity, Arnab T2 - JOURNAL OF NONPARAMETRIC STATISTICS AB - In this article, we address the important problem of comparison of two or more population regression functions. Recently, Pardo-Fernández, Van Keilegom and González-Manteiga (2007) developed test statistics for simple nonparametric regression models: Y(ij) = θ(j)(Z(ij)) + σ(j)(Z(ij))∊(ij), based on empirical distributions of the errors in each population j = 1, … , J. In this paper, we propose a test for equality of the θ(j)(·) based on the concept of generalized likelihood ratio type statistics. We also generalize our test for other nonparametric regression setups, e.g, nonparametric logistic regression, where the loglikelihood for population j is any general smooth function [Formula: see text]. We describe a resampling procedure to obtain the critical values of the test. In addition, we present a simulation study to evaluate the performance of the proposed test and compare our results to those in Pardo-Fernández et al. (2007). DA - 2012/// PY - 2012/// DO - 10.1080/10485252.2012.677842 VL - 24 IS - 3 SP - 563-576 SN - 1048-5252 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84865271146&partnerID=MN8TOARS KW - bootstrap KW - comparison of regression functions KW - generalised likelihood ratio KW - kernel regression KW - local likelihood KW - nonparametric regression ER - TY - JOUR TI - A genome-wide association analysis of temozolomide response using lymphoblastoid cell lines shows a clinically relevant association with MGMT AU - Brown, Chad C. AU - Havener, Tammy M. AU - Medina, Marisa W. AU - Auman, J. Todd AU - Mangravite, Lara M. AU - Krauss, Ronald M. AU - McLeod, Howard L. AU - Motsinger-Reif, Alison A. T2 - PHARMACOGENETICS AND GENOMICS AB - Recently, lymphoblastoid cell lines (LCLs) have emerged as an innovative model system for mapping gene variants that predict the dose response to chemotherapy drugs.In the current study, this strategy was expanded to the in-vitro genome-wide association approach, using 516 LCLs derived from a White cohort to assess the cytotoxic response to temozolomide.Genome-wide association analysis using ∼2.1 million quality-controlled single-nucleotide polymorphisms (SNPs) identified a statistically significant association (P<10(-8)) with SNPs in the O(6)-methylguanine-DNA methyltransferase (MGMT) gene. We also show that the primary SNP in this region is significantly associated with the differential gene expression of MGMT (P<10(-26)) in LCLs and differential methylation in glioblastoma samples from The Cancer Genome Atlas.The previously documented clinical and functional relationships between MGMT and temozolomide response highlight the potential of well-powered genome-wide association studies of the LCL model system to identify meaningful genetic associations. DA - 2012/11// PY - 2012/11// DO - 10.1097/fpc.0b013e3283589c50 VL - 22 IS - 11 SP - 796-802 SN - 1744-6872 KW - genome-wide association studies KW - lymphoblastoid cell lines KW - MGMT KW - pharmacogenetics KW - temozolomide ER - TY - JOUR TI - A DIVISION-DEPENDENT COMPARTMENTAL MODEL FOR COMPUTING CELL NUMBERS IN CFSE-BASED LYMPHOCYTE PROLIFERATION ASSAYS AU - Banks, H. T. AU - Tompson, W. Clayton AU - Peligero, Cristian AU - Giest, Sandra AU - Argilaguet, Jordi AU - Meyerhans, Andreas T2 - MATHEMATICAL BIOSCIENCES AND ENGINEERING AB - Some key features of a mathematical description of an immune response are an estimate of the number of responding cells and the manner in which those cells divide, differentiate, and die. The intracellular dye CFSE is a powerful experimental tool for the analysis of a population of dividing cells, and numerous mathematical treatments have been aimed at using CFSE data to describe an immune response [30,31,32,37,38,42,48,49]. Recently, partial differential equation structured population models, with measured CFSE fluorescence intensity as the structure variable, have been shown to accurately fit histogram data obtained from CFSE flow cytometry experiments [18,19,52,54]. In this report, the population of cells is mathematically organized into compartments, with all cells in a single compartment having undergone the same number of divisions. A system of structured partial differential equations is derived which can be fit directly to CFSE histogram data. From such a model, cell counts (in terms of the number of divisions undergone) can be directly computed and thus key biological parameters such as population doubling time and precursor viability can be determined. Mathematical aspects of this compartmental model are discussed, and the model is fit to a data set. As in [18,19], we find temporal and division dependence in the rates of proliferation and death to be essential features of a structured population model for CFSE data. Variability in cellular autofluorescence is found to play a significant role in the data, as well. Finally, the compartmental model is compared to previous work, and statistical aspects of the experimental data are discussed. DA - 2012/10// PY - 2012/10// DO - 10.3934/mbe.2012.9.699 VL - 9 IS - 4 SP - 699-736 SN - 1551-0018 KW - Cell proliferation KW - cell division number KW - CFSE KW - label structured population dynamics KW - partial differential equations KW - inverse problems ER - TY - JOUR TI - Pollination biology and seed production of a federally endangered perennial, Echinacea laevigata (Asteraceae:Heliantheae) AU - Stucky, J. M. AU - Gadd, L. E. AU - Arellano, C. T2 - American Midland Naturalist AB - Pollination biology and factors affecting reproductive success of the federally endangered Echinacea laevigata (coneflower) were studied in one large and five small populations. Insect visitor exclusion from flowering heads and pollination treatments showed that seed production was 10x higher in open-pollinated treatments compared to bagged flowers that were not pollinated and 20x higher than flower heads receiving self pollen suggesting that cross-pollination was responsible for most seed production. Peak flowering occurred the 2nd–4th wk of Jun. 2004 and the large population contributed 50–68% of the flowering individuals in its plant community. During this period, Bombus (Apidae, bumblebees), Hesperiidae (skippers), and Megachile (Megachilidae, leaf-cutter bees) accounted for 73%, 12%, and 11% of the observed visits to coneflower, respectively. Species richness of coneflower flower visitors and number of flower visits was lower in each small population than in the large population. However, comparison of seed production between heads receiving supplemental pollen and open-pollination heads indicated that seed production was not pollen limited. In addition, over 93% of pollen grains stained normally in cotton blue-lactophenol in all six populations suggesting that pollen viability was high in small and large populations. However, seed production in the large population exceeded that in each of three small populations during 2005, and seedling size was larger in the large population compared to seedlings from one of the small populations. Comparison of soil cation concentrations among populations suggested that cations did not limit seed production. We suggest that genetic factors, such as inbreeding or low S allele variation, may limit seed production in the small populations. DA - 2012/// PY - 2012/// DO - 10.1674/0003-0031-168.1.93 VL - 168 IS - 1 SP - 93-111 ER - TY - JOUR TI - Increasing Stream Geomorphic Stability Using Storm Water Control Measures in a Densely Urbanized Watershed AU - Tillinghast, E. D. AU - Hunt, W. F. AU - Jennings, G. D. AU - D'Arconte, Patricia T2 - JOURNAL OF HYDROLOGIC ENGINEERING AB - This study used previously established unit critical discharges, annual allowable erosional hours, and annual allowable volume of eroded bed-load standards to evaluate two types of storm water control measures (SCMs): low-impact development (LID) practices and a large detention SCM (wet pond). Nine initial scenarios modeled in PCSWMM incorporated different combinations of wet ponds, green roofs, rainwater harvesting systems, permeable pavement, and rain gardens to determine the best scenario for reducing stream erosion potential within a highly urbanized watershed in Chapel Hill, NC. The best-case scenario to reduce annual erosional hours and eroded bed load within the stream consisted of an aggressive utilization of LID practices in combination with an undersized wet pond. Although this scenario did not meet the annual erosional hour standard for rural reference streams, 0.35 h/ha/year, it did reduce erosional hours and eroded bed-load sediment by factors of 2.4 and 2.5, respectively, improving the existing condition. An alternative wet pond outlet structure that used two elevations of small drawdown orifices was explored to determine if current wet pond design practices could be improved to include stream stability. The new configuration provided a modest reduction in the number of erosional hours, a factor of 1.3, but increased the volume of eroded bed load by a factor of 1.2 when compared with the normal wet pond. However, adding widespread LID practices to the alternative outlet design reduced erosional hours and bed load transport by factors of 1.8 and 1.2, respectively, when compared with the normally configured wet pond. The failure to meet the erosional standards in all scenarios demonstrated the difficulty of requiring highly urbanized watersheds (60% impervious) to meet such strict stream protection measures. DA - 2012/12// PY - 2012/12// DO - 10.1061/(asce)he.1943-5584.0000577 VL - 17 IS - 12 SP - 1381-1388 SN - 1943-5584 KW - Low-Impact development practices KW - SWMM KW - Stream stability KW - Erosional hours KW - Sediment transport KW - Wet detention ponds ER - TY - JOUR TI - Evaluation of Polymorphisms in the Sulfonamide Detoxification Genes CYB5A and CYB5R3 in Dogs with Sulfonamide Hypersensitivity AU - Funk-Keenan, J. AU - Sacco, J. AU - Wong, Y. Y. AU - Rasmussen, S. AU - Motsinger-Reif, A. AU - Trepanier, L. A. T2 - JOURNAL OF VETERINARY INTERNAL MEDICINE AB - Background Delayed hypersensitivity ( HS ) reactions to potentiated sulfonamide antimicrobials occur in both dogs and humans, and involve an intermediate hydroxylamine metabolite that is detoxified by cytochrome b 5 and NADH cytochrome b 5 reductase. Hypothesis/Objectives We hypothesized that polymorphisms in the genes ( CYB 5A and CYB 5R3) encoding these 2 enzymes would be associated with risk of sulfonamide HS in dogs. Animals A total of 18 dogs with delayed HS to potentiated sulfonamide antimicrobials and 16 dogs that tolerated ( TOL ) a therapeutic course of these drugs without adverse effect. Methods CYB 5A and CYB 5R3 were sequenced from canine liver, and the promoter, exons, and 3′ untranslated regions of both genes were resequenced from genomic DNA obtained from all dogs. Results Multiple polymorphisms were found in both genes. When controlled for multiple comparisons, the 729 GG variant in CYB 5R3 was significantly overrepresented in dogs with sulfonamide HS (78% of dogs), compared to TOL dogs (31%; P = .003). Conclusions and Clinical Importance The CYB 5R3 729 GG variant may contribute to the risk of sulfonamide HS in dogs. Functional characterization of this polymorphism, as well as genotyping in a larger number of HS and TOL dogs, is warranted. DA - 2012/// PY - 2012/// DO - 10.1111/j.1939-1676.2012.00965.x VL - 26 IS - 5 SP - 1126-1133 SN - 1939-1676 KW - Genotype KW - Idiosyncratic KW - Potentiated sulfonamide KW - Predisposition ER - TY - JOUR TI - Assessing the utility of whole genome amplified DNA as a template for DMET Plus array AU - He, Y. J. AU - Misher, A. D. AU - Irvin, W. AU - Motsinger-Reif, A. AU - McLeod, H. L. AU - Hoskins, J. M. T2 - Clinical Chemistry and Laboratory Medicine DA - 2012/// PY - 2012/// VL - 50 IS - 8 SP - 1329-1334 ER - TY - JOUR TI - A COMPARISON OF COMPUTATIONAL EFFICIENCIES OF STOCHASTIC ALGORITHMS IN TERMS OF TWO INFECTION MODELS AU - Banks, H. Thomas AU - Hu, Shuhua AU - Joyner, Michele AU - Broido, Anna AU - Canter, Brandi AU - Gayvert, Kaitlyn AU - Link, Kathryn T2 - MATHEMATICAL BIOSCIENCES AND ENGINEERING AB - In this paper, we investigate three particular algorithms: a stochastic simulation algorithm (SSA), and explicit and implicit tau-leaping algorithms. To compare these methods, we used them to analyze two infection models: a Vancomycin-resistant enterococcus (VRE) infection model at the population level, and a Human Immunodeficiency Virus (HIV) within host infection model. While the first has a low species count and few transitions, the second is more complex with a comparable number of species involved. The relative efficiency of each algorithm is determined based on computational time and degree of precision required. The numerical results suggest that all three algorithms have the similar computational efficiency for the simpler VRE model, and the SSA is the best choice due to its simplicity and accuracy. In addition, we have found that with the larger and more complex HIV model, implementation and modification of tau-Leaping methods are preferred. DA - 2012/7// PY - 2012/7// DO - 10.3934/mbe.2012.9.487 VL - 9 IS - 3 SP - 487-526 SN - 1551-0018 KW - Dynamical models KW - continuous time Markov chain models KW - stochastic simulation algorithms KW - Gillespie KW - tau-leaping KW - bacterial and viral infection models ER - TY - JOUR TI - Thermal Mitigation of Urban Storm Water by Level Spreader-Vegetative Filter Strips (vol 137, pg 707, 2011) AU - Winston, R. J. AU - Hunt, W. F. AU - Lord, W. G. T2 - JOURNAL OF ENVIRONMENTAL ENGINEERING-ASCE AB - During composition, an error was introduced on p. 711 of the original paper. The text incorrectly indicates that an afternoon storm “occurred between 12 p.m. and 7 a.m.” This should have read “7 p.m.” The complete sentence is as follows: “Overnight storms were defined as those with rainfall occurring between 9 p.m. and 6 a.m., and afternoon storms occurred between 12 p.m. and 7 p.m.” ASCE regrets this error. DA - 2012/11// PY - 2012/11// DO - 10.1061/(asce)ee.1943-7870.0000587 VL - 138 IS - 11 SP - 1165-1165 SN - 0733-9372 ER - TY - JOUR TI - Response of the modern lactating sow and progeny to source and level of supplemental dietary fat during high ambient temperatures AU - Rosero, D. S. AU - Heugten, E. AU - Odle, J. AU - Arellano, C. AU - Boyd, R. D. T2 - Journal of Animal Science AB - The objective of this study was to determine the response to increments of 2 sources of dietary fat on lactating sow and progeny performance during high ambient temperatures. Data were collected from 391 sows (PIC Camborough) from June to September in a 2,600-sow commercial unit in Oklahoma. Sows were randomly assigned to a 2 × 3 factorial arrangement of treatments and a control diet. Factors included 1) fat sources, animal-vegetable blend (A-V) and choice white grease (CWG), and 2) fat levels (2%, 4%, and 6%). The A-V blend contained 14.5% FFA with an iodine value of 89, peroxide value of 4.2 mEq/kg, and anisidine value of 23, whereas CWG contained 3.7% FFA with an iodine value of 62, peroxide value of 9.8 mEq/kg, and anisidine value of 5. Diets were corn-soybean meal based, with 8.0% distillers dried grains with solubles and 6.0% wheat middlings, and contained 3.56-g standardized ileal digestible Lys/Mcal ME. Sows were balanced by parity, with 192 and 199 sows representing parity 1 and parity 3 to 5, respectively. Feed refusal increased linearly (P < 0.001) with the addition of supplemental fat, but feed and energy intake increased linearly (P < 0.01) with increasing dietary fat. Sows fed CWG diets had reduced (linear, P < 0.05) BW loss during lactation. Litter growth rate was not affected by additional dietary fat. Addition of CWG to the diets improved G:F (sow and litter gain relative to feed intake) compared with the G:F of sows fed the control diet or the diets containing the A-V blend (0.50, 0.43, and 0.44, respectively; P < 0.05). Gain:ME (kg/Mcal ME) was greater (P < 0.05) for CWG (0.146) than A-V blend (0.129) but was not different from that of the control diet (0.131). Addition of A-V blend and CWG both improved (P < 0.05) conception and farrowing rates and subsequent litter size compared with the control diet. In conclusion, energy intake increased with the addition of fat. The A-V blend contained a greater amount of aldehydes (quantified by anisidine value) and was more susceptible to oxidation, resulting in reduced feed efficiency than CWG. Subsequent litter size and reproductive performance was improved by inclusion of both sources of fat in diets fed to lactating sows. DA - 2012/// PY - 2012/// DO - 10.2527/jas.2012-4242 VL - 90 IS - 8 SP - 2609-2619 ER - TY - JOUR TI - On the robustness of the adaptive lasso to model misspecification AU - Lu, W. AU - Goldberg, Y. AU - Fine, J. P. T2 - BIOMETRIKA AB - Journal Article On the robustness of the adaptive lasso to model misspecification Get access W. Lu, W. Lu Department of Statistics, North Carolina State University, 2311 Stinson Drive, 5212 SAS Hall, Raleigh, North Carolina 27695-8203, U.S.A., lu@stat.ncsu.edu Search for other works by this author on: Oxford Academic Google Scholar Y. Goldberg, Y. Goldberg Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7420, U.S.A.yair.goldy@gmail.com Search for other works by this author on: Oxford Academic Google Scholar J. P. Fine J. P. Fine Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7420, U.S.A., jfine@email.unc.edu Search for other works by this author on: Oxford Academic Google Scholar Biometrika, Volume 99, Issue 3, September 2012, Pages 717–731, https://doi.org/10.1093/biomet/ass027 Published: 11 July 2012 Article history Received: 01 April 2011 Revision received: 01 February 2012 Published: 11 July 2012 DA - 2012/9// PY - 2012/9// DO - 10.1093/biomet/ass027 VL - 99 IS - 3 SP - 717-731 SN - 1464-3510 KW - Least false parameter KW - Model misspecification KW - Oracle property KW - Penalization KW - Selection consistency KW - Shrinkage estimation KW - Variable selection ER - TY - JOUR TI - Multivariate Phenotype Association Analysis by Marker-Set Kernel Machine Regression AU - Maity, Arnab AU - Sullivan, Patrick E. AU - Tzeng, Jung-Ying T2 - GENETIC EPIDEMIOLOGY AB - Genetic studies of complex diseases often collect multiple phenotypes relevant to the disorders. As these phenotypes can be correlated and share common genetic mechanisms, jointly analyzing these traits may bring more power to detect genes influencing individual or multiple phenotypes. Given the advancement brought by the multivariate phenotype approaches and the multimarker kernel machine regression, we construct a multivariate regression based on kernel machine to facilitate the joint evaluation of multimarker effects on multiple phenotypes. The kernel machine serves as a powerful dimension-reduction tool to capture complex effects among markers. The multivariate framework incorporates the potentially correlated multidimensional phenotypic information and accommodates common or different environmental covariates for each trait. We derive the multivariate kernel machine test based on a score-like statistic, and conduct simulations to evaluate the validity and efficacy of the method. We also study the performance of the commonly adapted strategies for kernel machine analysis on multiple phenotypes, including the multiple univariate kernel machine tests with original phenotypes or with their principal components. Our results suggest that none of these approaches has the uniformly best power, and the optimal test depends on the magnitude of the phenotype correlation and the effect patterns. However, the multivariate test retains to be a reasonable approach when the multiple phenotypes have none or mild correlations, and gives the best power once the correlation becomes stronger or when there exist genes that affect more than one phenotype. We illustrate the utility of the multivariate kernel machine method through the Clinical Antipsychotic Trails of Intervention Effectiveness antibody study. DA - 2012/11// PY - 2012/11// DO - 10.1002/gepi.21663 VL - 36 IS - 7 SP - 686-695 SN - 1098-2272 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84867539542&partnerID=MN8TOARS KW - kernel machine regression KW - multivariate regression KW - multivariate phenotypes KW - score-based test ER - TY - CONF TI - Fast genome-wide QTL association mapping with pedigrees AU - Zhou, H. AU - Sobel, E. AU - Lange, K. C2 - 2012/// C3 - Genetic Epidemiology DA - 2012/// VL - 36 SP - 771-772 M1 - 7 ER - TY - JOUR TI - Comparison of venous sampling methods for thromboelastography in clinically normal dogs AU - Walker, Julie M. AU - Hanel, Rita M. AU - Hansen, Bernard D. AU - Motsinger-Reif, Alison A. T2 - AMERICAN JOURNAL OF VETERINARY RESEARCH AB - Abstract Objective —To evaluate effects of blood collection method and site on results of thromboelastography in healthy dogs. Animals —8 clinically normal purpose-bred dogs. Procedures —Blood was collected from the external jugular vein by syringe aspiration via direct venipuncture with a 20-gauge needle, through a central venous catheter, or into an evacuated tube with a 21-gauge winged needle catheter. Blood was collected from the lateral saphenous vein by syringe aspiration via direct venipuncture with a 20-gauge needle or into an evacuated tube with a 21-gauge winged needle catheter. Kaolin-activated thromboelastographic analyses were performed, and R (reaction time), K (clot formation time), α angle, maximal amplitude, and G (global clot strength) were analyzed. Results —No significant differences were observed with regard to sampling site. Sample collection method had no effect on thromboelastographic results for saphenous vein samples. Blood samples collected from the jugular vein by syringe aspiration had a lower R and K and higher α angle than did blood samples collected from the jugular vein by evacuated tube collection. Significant differences were observed between blood samples collected from the jugular vein by syringe aspiration and samples collected from the saphenous vein by evacuated tube collection and between samples collected from the saphenous vein by evacuated tube collection and samples collected from the jugular vein through a central venous catheter. Conclusions and Clinical Relevance —Different sampling methods resulted in small but significant differences in thromboelastographic values. Results justify the use of standardized techniques for research purposes, but all of these sampling methods were acceptable for 1-time clinical use. DA - 2012/12// PY - 2012/12// DO - 10.2460/ajvr.73.12.1864 VL - 73 IS - 12 SP - 1864-1870 SN - 1943-5681 ER - TY - JOUR TI - Bootstrap-based inference on the difference in the means of two correlated functional processes AU - Crainiceanu, Ciprian M. AU - Staicu, Ana-Maria AU - Ray, Shubankar AU - Punjabi, Naresh T2 - STATISTICS IN MEDICINE AB - We propose nonparametric inference methods on the mean difference between two correlated functional processes. We compare methods that (1) incorporate different levels of smoothing of the mean and covariance; (2) preserve the sampling design; and (3) use parametric and nonparametric estimation of the mean functions. We apply our method to estimating the mean difference between average normalized δ power of sleep electroencephalograms for 51 subjects with severe sleep apnea and 51 matched controls in the first 4 h after sleep onset. We obtain data from the Sleep Heart Health Study, the largest community cohort study of sleep. Although methods are applied to a single case study, they can be applied to a large number of studies that have correlated functional data. DA - 2012/11/20/ PY - 2012/11/20/ DO - 10.1002/sim.5439 VL - 31 IS - 26 SP - 3223-3240 SN - 1097-0258 KW - EEG KW - sleep KW - penalized splines KW - measurement error KW - spectrogram ER - TY - JOUR TI - Bayesian spatial-temporal model for cardiac congenital anomalies and ambient air pollution risk assessment AU - Warren, Joshua AU - Fuentes, Montserrat AU - Herring, Amy AU - Langlois, Peter T2 - ENVIRONMETRICS AB - We introduce a Bayesian spatial–temporal hierarchical multivariate probit regression model that identifies weeks during the first trimester of pregnancy, which are impactful in terms of cardiac congenital anomaly development. The model is able to consider multiple pollutants and a multivariate cardiac anomaly grouping outcome jointly while allowing the critical windows to vary in a continuous manner across time and space. We utilize a dataset of numerical chemical model output that contains information regarding multiple species of PM 2.5 . Our introduction of an innovative spatial–temporal semiparametric prior distribution for the pollution risk effects allows for greater flexibility to identify critical weeks during pregnancy, which are missed when more standard models are applied. The multivariate kernel stick‐breaking prior is extended to include space and time simultaneously in both the locations and the masses in order to accommodate complex data settings. Simulation study results suggest that our prior distribution has the flexibility to outperform competitor models in a number of data settings. When applied to the geo‐coded Texas birth data, weeks 3, 7 and 8 of the pregnancy are identified as being impactful in terms of cardiac defect development for multiple pollutants across the spatial domain. Copyright © 2012 John Wiley & Sons, Ltd. DA - 2012/12// PY - 2012/12// DO - 10.1002/env.2174 VL - 23 IS - 8 SP - 673-684 SN - 1099-095X KW - environmental health KW - multivariate statistics KW - nonparametric Bayes KW - spatial statistics KW - stick-breaking prior ER - TY - JOUR TI - Bayesian spatial extreme value analysis to assess the changing risk of concurrent high temperatures across large portions of European cropland AU - Shaby, Benjamin A. AU - Reich, Brian J. T2 - ENVIRONMETRICS AB - There is strong evidence that extremely high temperatures are detrimental to the yield and quality of many economically and socially critical crops. Fortunately, the most deleterious conditions for agriculture occur rarely. We wish to assess the risk of the catastrophic scenario in which large areas of croplands experience extreme heat stress during the same growing season. Applying a hierarchical Bayesian spatial extreme value model that allows the distribution of extreme temperatures to change in time both marginally and in spatial coherence, we examine whether the risk of widespread extremely high temperatures across agricultural land in Europe has increased over the last century. Copyright © 2012 John Wiley & Sons, Ltd. DA - 2012/12// PY - 2012/12// DO - 10.1002/env.2178 VL - 23 IS - 8 SP - 638-648 SN - 1099-095X KW - max-stable process KW - agriculture KW - climate change ER - TY - JOUR TI - A Traditional Analysis of the First Flush Effect for Nutrients in Stormwater Runoff from Two Small Urban Catchments AU - Hathaway, J. M. AU - Tucker, R. S. AU - Spooner, J. M. AU - Hunt, W. F. T2 - WATER AIR AND SOIL POLLUTION DA - 2012/11// PY - 2012/11// DO - 10.1007/s11270-012-1327-x VL - 223 IS - 9 SP - 5903-5915 SN - 1573-2932 KW - Stormwater KW - Runoff KW - First flush KW - Watershed KW - Catchment KW - TSS KW - Nutrients KW - Nitrogen KW - Phosphorus ER - TY - JOUR TI - Variable selection for covariate-adjusted semiparametric inference in randomized clinical trials AU - Yuan, Shuai AU - Zhang, Hao Helen AU - Davidian, Marie T2 - STATISTICS IN MEDICINE AB - Extensive baseline covariate information is routinely collected on participants in randomized clinical trials, and it is well recognized that a proper covariate‐adjusted analysis can improve the efficiency of inference on the treatment effect. However, such covariate adjustment has engendered considerable controversy, as post hoc selection of covariates may involve subjectivity and may lead to biased inference, whereas prior specification of the adjustment may exclude important variables from consideration. Accordingly, how to select covariates objectively to gain maximal efficiency is of broad interest. We propose and study the use of modern variable selection methods for this purpose in the context of a semiparametric framework, under which variable selection in modeling the relationship between outcome and covariates is separated from estimation of the treatment effect, circumventing the potential for selection bias associated with standard analysis of covariance methods. We demonstrate that such objective variable selection techniques combined with this framework can identify key variables and lead to unbiased and efficient inference on the treatment effect. A critical issue in finite samples is validity of estimators of uncertainty, such as standard errors and confidence intervals for the treatment effect. We propose an approach to estimation of sampling variation of estimated treatment effect and show its superior performance relative to that of existing methods. Copyright © 2012 John Wiley & Sons, Ltd. DA - 2012/12/20/ PY - 2012/12/20/ DO - 10.1002/sim.5433 VL - 31 IS - 29 SP - 3789-3804 SN - 1097-0258 KW - covariate adjustment KW - false selection rate control KW - oracle property KW - semiparametric treatment effect estimation KW - shrinkage methods KW - variable selection ER - TY - PCOMM TI - Two-stage randomized trials: Outstanding issues Authors' Reply AU - Tamura, R. N. AU - Huang, X. H. AU - Boos, D. DA - 2012/// PY - 2012/// SP - 4143-4144 ER - TY - JOUR TI - Sample size calculation for the proportional hazards cure model AU - Wang, Songfeng AU - Zhang, Jiajia AU - Lu, Wenbin T2 - STATISTICS IN MEDICINE AB - In clinical trials with time‐to‐event endpoints, it is not uncommon to see a significant proportion of patients being cured (or long‐term survivors), such as trials for the non‐Hodgkins lymphoma disease. The popularly used sample size formula derived under the proportional hazards (PH) model may not be proper to design a survival trial with a cure fraction, because the PH model assumption may be violated. To account for a cure fraction, the PH cure model is widely used in practice, where a PH model is used for survival times of uncured patients and a logistic distribution is used for the probability of patients being cured. In this paper, we develop a sample size formula on the basis of the PH cure model by investigating the asymptotic distributions of the standard weighted log‐rank statistics under the null and local alternative hypotheses. The derived sample size formula under the PH cure model is more flexible because it can be used to test the differences in the short‐term survival and/or cure fraction. Furthermore, we also investigate as numerical examples the impacts of accrual methods and durations of accrual and follow‐up periods on sample size calculation. The results show that ignoring the cure rate in sample size calculation can lead to either underpowered or overpowered studies. We evaluate the performance of the proposed formula by simulation studies and provide an example to illustrate its application with the use of data from a melanoma trial. Copyright © 2012 John Wiley & Sons, Ltd. DA - 2012/12/20/ PY - 2012/12/20/ DO - 10.1002/sim.5465 VL - 31 IS - 29 SP - 3959-3971 SN - 1097-0258 KW - clinical trial KW - proportional hazards cure model KW - power KW - sample size KW - weighted log-rank test ER - TY - JOUR TI - QUANTIFYING SHEAR EFFECTS ON A MODEL EMULSION SYSTEM AU - Yurgec, M. J. AU - Osborne, J. AU - Steffe, J. F. AU - Daubert, C. R. T2 - JOURNAL OF FOOD PROCESS ENGINEERING AB - ABSTRACT A model corn oil‐in‐water emulsion, stabilized by Tween 20 (0.2–0.6%), was subjected to homogenization conditions of time, number of homogenization cycles and pressure (100–800 bar), which corresponded to predetermined shear work and shear power intensity values. This project investigated the roles that shear work and intensity have on the development and destabilization of a sensitive emulsion system. Samples with the same shear work level produced an emulsion with any identical median particle size (MPS). Particle size data were modeled (MPS is a function of shear work and surfactant concentration). The data revealed a critical shear limit, where an increase in shear work no longer reduced the particle size that was directly related to surfactant concentration. A statistical model was adapted to determine the critical shear work value, resulting in the lowest MPS for each surfactant concentration tested. PRACTICAL APPLICATIONS Shear work and shear power intensity are rheological tools that can be used to design processing systems to yield optimum product quality. A process technologist can understand the shear limitations of a fluid system simply by understanding the affects that increasing levels of shear work and shear power intensity have on that system. By understanding the shear input that is occurring within a fluid system caused by various unit operations, a process technologist would be able to correlate this to the known shear limitations and make a determination if the process is too severe or not intense enough. Knowledge of this information would enable a process technologist to better select equipment, piping schematics and settings on devices that cause shear, which could lead to more optimum product quality and less product loss caused by over‐ or under‐shearing. DA - 2012/12// PY - 2012/12// DO - 10.1111/j.1745-4530.2011.00640.x VL - 35 IS - 6 SP - 905-914 SN - 1745-4530 ER - TY - JOUR TI - Modelling and optimal control of immune response of renal transplant recipients AU - Banks, H. T. AU - Hu, Shuhua AU - Jang, Taesoo AU - Kwon, Hee-Dae T2 - JOURNAL OF BIOLOGICAL DYNAMICS AB - We consider the increasingly important and highly complex immunological control problem: control of the dynamics of immunosuppression for organ transplant recipients. The goal in this problem is to maintain the delicate balance between over-suppression (where opportunistic latent viruses threaten the patient) and under-suppression (where rejection of the transplanted organ is probable). First, a mathematical model is formulated to describe the immune response to both viral infection and introduction of a donor kidney in a renal transplant recipient. Some numerical results are given to qualitatively validate and demonstrate that this initial model exhibits appropriate characteristics of primary infection and reactivation for immunosuppressed transplant recipients. In addition, we develop a computational framework for designing adaptive optimal treatment regimes with partial observations and low-frequency sampling, where the state estimates are obtained by solving a second deterministic optimal tracking problem. Numerical results are given to illustrate the feasibility of this method in obtaining optimal treatment regimes with a balance between under-suppression and over-suppression of the immune system. DA - 2012/// PY - 2012/// DO - 10.1080/17513758.2012.655328 VL - 6 IS - 2 SP - 539-567 SN - 1751-3766 KW - renal transplant KW - human cytomegalovirus KW - mathematical model KW - optimal feedback control KW - state estimation KW - model predictive control ER - TY - JOUR TI - Cerebrospinal Fluid Metabolome in Mood Disorders-Remission State has a Unique Metabolic Profile AU - Kaddurah-Daouk, Rima AU - Yuan, Peixiong AU - Boyle, Stephen H. AU - Matson, Wayne AU - Wang, Zhi AU - Zeng, Zhao Bang AU - Zhu, Hongjie AU - Dougherty, George G. AU - Yao, Jeffrey K. AU - Chen, Guang AU - Guitart, Xavier AU - Carlson, Paul J. AU - Neumeister, Alexander AU - Zarate, Carlos AU - Krishnan, Ranga R. AU - Manji, Husseini K. AU - Drevets, Wayne T2 - Scientific Reports AB - Targeted metabolomics provides an approach to quantify metabolites involved in specific molecular pathways. We applied an electrochemistry-based, targeted metabolomics platform to define changes in tryptophan, tyrosine, purine and related pathways in the depressed and remitted phases of major depressive disorder (MDD). Biochemical profiles in the cerebrospinal fluid of unmedicated depressed (n = 14; dMDD) or remitted MDD subjects (n = 14; rMDD) were compared against those in healthy controls (n = 18; HC). The rMDD group showed differences in tryptophan and tyrosine metabolism relative to the other groups. The rMDD group also had higher methionine levels and larger methionine-to-glutathione ratios than the other groups, implicating methylation and oxidative stress pathways. The dMDD sample showed nonsignificant differences in the same direction in several of the metabolic branches assessed. The reductions in metabolites associated with tryptophan and tyrosine pathways in rMDD may relate to the vulnerability this population shows for developing depressive symptoms under tryptophan or catecholamine depletion. DA - 2012/9/19/ PY - 2012/9/19/ DO - 10.1038/srep00667 VL - 2 IS - 1 J2 - Sci Rep LA - en OP - SN - 2045-2322 UR - http://dx.doi.org/10.1038/srep00667 DB - Crossref ER - TY - JOUR TI - Analysis of sliver thickness variation from process perturbations in roller drafting AU - Kim, Jong S. AU - Suh, Moon W. AU - Huh, You T2 - JOURNAL OF THE TEXTILE INSTITUTE AB - In processing fiber bundles in staple yarn manufacturing, the bundles are doubled and attenuated to an appropriate thickness via drafting. The process conditions are optimized with respect to the fiber and bundle properties. Otherwise, the output fiber bundle becomes non-uniform in its linear density. This research deals with finding the changes in linear density of the output bundle when perturbations are applied to the drafting conditions. Perturbations with specific autocorrelation functions were generated by the random phase spectral method. Along with the stochastically generated test signals, the transient linear density profiles of the fiber bundle in the drafting zone were simulated by using a mathematical model describing the dynamics of the roller drafting, and thus, the linear density of the output bundle could be predicted. Our results showed that the disturbances in input linear density affected the transient profiles of the linear density of the fiber bundle inside the draft zone. It was also shown that the output irregularities were strongly influenced by the perturbation in the input bundle thickness. During drafting, the perturbations in the draft ratio perturbations were not shown to have influenced the transient profiles of the bundle linear density inside the draft zone. However, the variation in the linear density appeared again in the output bundle following exactly the changes in the daft ratio. Disturbances in the process speed, however, were not shown to have influenced the output variation. DA - 2012/// PY - 2012/// DO - 10.1080/00405000.2012.660754 VL - 103 IS - 10 SP - 1055-1062 SN - 0040-5000 KW - random phase spectral method KW - autocorrelation KW - stochastic signals KW - draft dynamics KW - disturbances KW - linear density of fiber bundle KW - draft ratio KW - process speed ER - TY - JOUR TI - An informative subset-based estimator for censored quantile regression AU - Tang, Yanlin AU - Wang, Huixia Judy AU - He, Xuming AU - Zhu, Zhongyi T2 - TEST DA - 2012/12// PY - 2012/12// DO - 10.1007/s11749-011-0266-y VL - 21 IS - 4 SP - 635-655 SN - 1133-0686 KW - Asymptotic efficiency KW - Censoring probability KW - Fixed censoring KW - Informative subset KW - Nonparametric KW - Quantile regression ER - TY - JOUR TI - Twice-Daily Application of HIV Microbicides Alters the Vaginal Microbiota AU - Ravel, Jacques AU - Gajer, Pawel AU - Fu, Li AU - Mauck, Christine K. AU - Koenig, Sara S. K. AU - Sakamoto, Joyce AU - Motsinger-Reif, Alison A. AU - Doncel, Gustavo F. AU - Zeichner, Steven L. T2 - MBIO AB - Vaginal HIV microbicides offer great promise in preventing HIV transmission, but failures of phase 3 clinical trials, in which microbicide-treated subjects had an increased risk of HIV transmission, raised concerns about endpoints used to evaluate microbicide safety. A possible explanation for the increased transmission risk is that the agents shifted the vaginal bacterial community, resulting in loss of natural protection and enhanced HIV transmission susceptibility. We characterized vaginal microbiota, using pyrosequencing of bar-coded 16S rRNA gene fragments, in samples from 35 healthy, sexually abstinent female volunteer subjects (ages 18 to 50 years) with regular menses in a repeat phase 1 study of twice-daily application over 13.5 days of 1 of 3 gel products: a hydroxyethylcellulose (HEC)-based "universal" placebo (10 subjects), 6% cellulose sulfate (CS; 13 subjects), and 4% nonoxynol-9 (N-9; 12 subjects). We used mixed effects models inferred using Bayesian Markov chain Monte Carlo methods, which showed that treatment with active agents shifted the microbiota toward a community type lacking significant numbers of Lactobacillus spp. and dominated by strict anaerobes. This state of the vaginal microbiota was associated with a low or intermediate Nugent score and was not identical to bacterial vaginosis, an HIV transmission risk factor. The placebo arm contained a higher proportion of communities dominated by Lactobacillus spp., particularly L. crispatus, throughout treatment. The data suggest that molecular evaluation of microbicide effects on vaginal microbiota may be a critical endpoint that should be incorporated in early clinical assessment of microbicide candidates.Despite large prevention efforts, HIV transmission and acquisition rates remain unacceptably high. In developing countries, transmission mainly occurs through heterosexual intercourse, where women are significantly more vulnerable to infection than men. Vaginal microbicides are considered to be one of the most promising female-controlled products, in that women themselves insert the microbicides into the vagina to prevent HIV transmission during sexual intercourse. The failure of several microbicides in clinical trials has raised questions concerning the low in vivo efficacy of such anti-HIV molecules. This study was designed to gain insights into the failures of two microbicides by testing the hypothesis that the microbicides negatively affect a critical line of defense against HIV, the vaginal microbiota. The results suggest that in the early assessment of candidate microbicides, culture-independent evaluation of their effect on the vaginal microbiota should be considered and may constitute a critical endpoint. DA - 2012/// PY - 2012/// DO - 10.1128/mbio.00370-12 VL - 3 IS - 6 SP - SN - 2150-7511 ER - TY - JOUR TI - Trajectory Analyses in Alcohol Treatment Research AU - Chen, Jinsong AU - Johnson, Bankole A. AU - Wang, Xin-Qun AU - O'Quigley, John AU - Isaac, Maria AU - Zhang, Daowen AU - Liu, Lei T2 - ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH AB - Background Various statistical methods have been used for data analysis in alcohol treatment studies. Trajectory analyses can better capture differences in treatment effects and may provide insight on the optimal duration of future clinical trials and grace periods. This improves on the limitation of commonly used parametric (e.g., linear) methods that cannot capture nonlinear temporal trends in the data. Methods We propose an exploratory approach, using more flexible smoothing mixed effects models, more accurately to characterize the temporal patterns of the drinking data. We estimated the trajectories of the treatment arms for data sets from 2 sources: a multisite topiramate study, and the Combined Pharmacotherapies (acamprosate and naltrexone) and Behavioral Interventions study. Results Our methods illustrate that drinking outcomes of both the topiramate and placebo arms declined over the entire course of the trial but with a greater rate of decline for the topiramate arm. By the point‐wise confidence intervals, the heavy drinking probabilities for the topiramate arm might differ from those of the placebo arm as early as week 2. Furthermore, the heavy drinking probabilities of both arms seemed to stabilize at the end of the study. Overall, naltrexone was better than placebo in reducing drinking over time yet was not different from placebo for subjects receiving the combination of a brief medical management and an intensive combined behavioral intervention. Conclusions The estimated trajectory plots clearly showed nonlinear temporal trends of the treatment with different medications on drinking outcomes and offered more detailed interpretation of the results. This trajectory analysis approach is proposed as a valid exploratory method for evaluating efficacy in pharmacotherapy trials in alcoholism. DA - 2012/8// PY - 2012/8// DO - 10.1111/j.1530-0277.2012.01748.x VL - 36 IS - 8 SP - 1442-1448 SN - 0145-6008 KW - Alcohol Research KW - Clinical Trial KW - Grace Periods KW - Splines KW - Mixed Model ER - TY - JOUR TI - Thermal Biology of Sea Snakes and Sea Kraits AU - Heatwole, Harold AU - Grech, Alana AU - Monahan, John F. AU - King, Susan AU - Marsh, Helene T2 - INTEGRATIVE AND COMPARATIVE BIOLOGY AB - Temperature probably had no direct effect on the evolution of sea kraits within their center of origin, a geologically stable thermal zone straddling the equator, but may have indirectly affected expansions and contractions in distributions beyond that zone through global fluctuations that caused alternation of higher and lower sea levels. The northern limit of the Laticauda colubrina complex seems to be the 20°C isotherm; in the south, the range does not reach that isotherm because there is no land (also a habitat requirement of sea kraits) within the zone of suitable temperature. The relationship of temperature to the pattern of geographic variation in morphology supports either the hypothesis of peripheral convergence or the developmental hypothesis but does not distinguish between them. Quadratic surfaces relating cumulative scores for coloration and morphological characters to global position showed a strong latitudinal component and an even stronger longitudinal one in which the direction of the latitudinal effect was reversed between east and west. A multivariate analysis revealed that while morphological characters vary significantly by location and climate when tested separately, when the influence of location on morphology is taken into account, no residual relationship between climate and morphology remains. Most marine snakes have mean upper temperature tolerances between 39°C and 40°C and operate at temperatures much nearer their upper thermal limits than their lower limits but still avoid deleterious extremes by diving from excessively hot water to deeper, cooler strata, and by surfacing when water is cold. At the surface in still water in sunlight, Pelamis can maintain its body temperature slightly above that of the water, but whether this is significant in nature is questionable. As temperature falls below 18-20°C, survival time is progressively reduced, accompanied by the successive occurrence of cessation of feeding, cessation of swimming, and failure to orient. Acclimation does not seem to be in this species' repertoire. In the water column, marine snakes track water temperature; on land, sea kraits can thermoregulate by basking, selecting favorable locations, and by kleptothermy. Laticauda colubrina adjusts its reproductive cycle geographically in ways that avoid breeding in the coldest months. Mean voluntary diving time is not temperature-dependent within the normal range of temperatures experienced by marine snakes in the field, but is reduced in water colder than 20°C. On land, much as while diving in the sea, sea kraits maintain long periods of apnea; intervals between breaths are inversely related to temperature. DA - 2012/8// PY - 2012/8// DO - 10.1093/icb/ics080 VL - 52 IS - 2 SP - 257-273 SN - 1557-7023 ER - TY - JOUR TI - Spatiotemporal quantile regression for detecting distributional changes in environmental processes AU - Reich, B. J. T2 - Journal of the Royal Statistical Society. Series C, Applied Statistics DA - 2012/// PY - 2012/// VL - 61 SP - 535-553 ER - TY - JOUR TI - Recommendations for Catch-Curve Analysis AU - Smith, Matthew W. AU - Then, Amy Y. AU - Wor, Catarina AU - Ralph, Gina AU - Pollock, Kenneth H. AU - Hoenig, John M. T2 - NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT AB - Abstract Three common cross‐sectional catch‐curve methods for estimating total mortality rate ( Z ) are the Chapman–Robson, regression, and Heincke estimators. There are five unresolved methodological issues: (1) which is the best estimator, (2) how one should determine the first age‐group to use in the analysis, (3) how the variance estimators perform; and, for regression estimators, (4) how the observations should be weighted, including (5) whether and how the oldest ages should be truncated. We used analytical methods and Monte Carlo simulation to evaluate the three catch‐curve methods, including unweighted and weighted versions of the regression estimator. We evaluated four criteria for specifying the first age‐class used. Regression estimators were evaluated with four different methods of right data truncation. Heincke's method performed poorly and is generally not recommended. The two‐tailed χ 2 test and one‐tailed z ‐test for full selectivity described by Chapman and Robson did not perform as well as simpler criteria and are not recommended. Estimates with the lowest mean square error were generally provided by (1) the Chapman–Robson estimator with the age of full recruitment being the age of maximum catch plus 1 year and (2) the weighted regression estimator with the age of full recruitment being the age of maximum catch and with no right truncation. Differences in performance between the two methods were small (<6% of Z ). The Chapman–Robson estimator of the variance of had large negative bias when not corrected for overdispersion; once corrected, it performed as well as or better than all other variance estimators evaluated. The regression variance estimator is generally precise and slightly negatively biased. We recommend that the traditional Chapman–Robson approach be corrected for overdispersion and used routinely to estimate Z . Weighted linear regression may work slightly better but is completely ad hoc. Unweighted linear regression should no longer be used for analyzing catch‐curve data. Received November 30, 2011; accepted July 4, 2012 DA - 2012/// PY - 2012/// DO - 10.1080/02755947.2012.711270 VL - 32 IS - 5 SP - 956-967 SN - 1548-8675 ER - TY - JOUR TI - Effect of Urban Catchment Composition on Runoff Temperature AU - Jones, Matthew P. AU - Hunt, William F. AU - Winston, Ryan J. T2 - JOURNAL OF ENVIRONMENTAL ENGINEERING AB - Urban runoff adversely impacts cold-water stream environments due to sporadic fluxes of thermally enriched runoff. This adversely impacts tourism in regions that support trout and salmon streams. Research on storm water control measures (SCMs) has shown that meeting the 21°C trout threshold is not consistently feasible with current SCM technologies. Thus, it is important to consider other factors in storm water temperature management, such as catchment characteristics. Median and maximum runoff temperatures from a shaded parking lot were consistently lower than those from a nearby unshaded lot. This suggests the need to implement a tree canopy cover in trout-sensitive catchments. A light-colored chip seal pavement was compared to a traditional hot-mix asphalt pavement; the light-colored chip seal produced median storm water temperatures that were 1.4°C lower than the standard hot-mix asphalt. It was shown that runoff temperature measurement location is critical when evaluating SCM performance, and that underground conveyances can substantially reduce runoff temperature. DA - 2012/12// PY - 2012/12// DO - 10.1061/(asce)ee.1943-7870.0000577 VL - 138 IS - 12 SP - 1231-1236 SN - 1943-7870 KW - Storm water KW - Trout KW - Salmon KW - Watershed KW - Thermal load ER - TY - CONF TI - Disease dynamics in wild populations: modeling and estimation: a review AU - Cooch, E. G. AU - Conn, P. B. AU - Ellner, S. P. AU - Dobson, A. P. AU - Pollock, K. H. C2 - 2012/// C3 - Journal of Ornithology DA - 2012/// VL - 152 SP - S485-509 ER - TY - JOUR TI - CYP2C8*3 predicts benefit/risk profile in breast cancer patients receiving neoadjuvant paclitaxel AU - Hertz, Daniel L. AU - Motsinger-Reif, Alison A. AU - Drobish, Amy AU - Winham, Stacey J. AU - McLeod, Howard L. AU - Carey, Lisa A. AU - Dees, E. Claire T2 - BREAST CANCER RESEARCH AND TREATMENT AB - Paclitaxel is one of the most frequently used chemotherapeutic agents for the treatment of breast cancer patients. Using a candidate gene approach, we hypothesized that polymorphisms in genes relevant to the metabolism and transport of paclitaxel are associated with treatment efficacy and toxicity. Patient and tumor characteristics and treatment outcomes were collected prospectively for breast cancer patients treated with paclitaxel-containing regimens in the neoadjuvant setting. Treatment response was measured before and after each phase of treatment by clinical tumor measurement and categorized according to RECIST criteria, while toxicity data were collected from physician notes. The primary endpoint was achievement of clinical complete response (cCR) and secondary endpoints included clinical response rate (complete response+partial response) and grade 3+ peripheral neuropathy. The genotypes and haplotypes assessed were CYP1B1*3, CYP2C8*3, CYP3A4*1B/CYP3A5*3C, and ABCB1*2. A total of 111 patients were included in this study. Overall, cCR was 30.1% to the paclitaxel component. CYP2C8*3 carriers (23/111, 20.7%) had higher rates of cCR (55% vs. 23%; OR=3.92 [95% CI: 1.46-10.48], corrected p=0.046). In the secondary toxicity analysis, we observed a trend toward greater risk of severe neuropathy (22% vs. 8%; OR=3.13 [95% CI: 0.89-11.01], uncorrected p=0.075) in subjects carrying the CYP2C8*3 variant. Other polymorphisms interrogated were not significantly associated with response or toxicity. Patients carrying CYP2C8*3 are more likely to achieve clinical complete response from neoadjuvant paclitaxel treatment, but may also be at increased risk of experiencing severe peripheral neurotoxicity. DA - 2012/7// PY - 2012/7// DO - 10.1007/s10549-012-2054-0 VL - 134 IS - 1 SP - 401-410 SN - 1573-7217 KW - Paclitaxel KW - CYP2C8*3 KW - Pharmacogenetics KW - Neoadjuvant breast cancer therapy KW - Clinical complete response ER - TY - JOUR TI - Are Bioretention Cells Being Installed Per Design Standards in North Carolina? A Field Study AU - Wardynski, Brad J. AU - Hunt, William F., III T2 - JOURNAL OF ENVIRONMENTAL ENGINEERING-ASCE AB - Forty-three bioretention cells (BRCs) throughout North Carolina were assessed for maintenance needs, soil media composition, and as-built surface storage volume to determine whether BRCs are typically constructed per their intended design specifications. Visual inspections identified hydric soils and redoximorphic features (indicators of prolonged anaerobic conditions) and quantified the occurrence of issues requiring maintenance. Particle-size distribution and permeability of soil media were measured at multiple locations within each cell, and topographic surveys were performed to calculate as-built surface storage volumes. Field drawdown tests were used to verify permeability measurements and assess overall BRC function. Of the studied cells, 22% contained redoximorphic features in the upper 30 cm, and 53% were in need of maintenance due to one or more factors. Although 71% of assessed cells failed to meet soil media particle-size distribution specifications, 98% of BRCs contained media with adequate or high permeability. Over half (65%) of cells were undersized vis-à-vis intended design, with 53% exhibiting moderately or severely undersized surface storage capacity. Discrepancies in average ponding depth and incorporation of inspection/maintenance programs significantly influenced the accuracy of as-built BRC storage volume; therefore, it is important for inspectors to verify that the bed elevations of BRCs have been accurately graded. Despite being typically undersized, it was concluded that most observed bioretention cells are meeting the hydrologic goals of North Carolina standards. DA - 2012/12// PY - 2012/12// DO - 10.1061/(asce)ee.1943-7870.0000575 VL - 138 IS - 12 SP - 1210-1217 SN - 0733-9372 KW - Bioretention KW - Rain garden KW - Best management practice (BMP) KW - Storm water control measure (SCM) KW - Inspection KW - Construction KW - Storm water KW - Survey KW - Maintenance ER - TY - JOUR TI - Advanced oxidation of toluene using Ni-olivine catalysts: Part 1. syntheses, characterization, and evaluation of Ni-olivine catalysts for toluene oxidation AU - Smith, V. M. AU - Kolar, P. AU - Boyette, M. D. AU - Chinn, M. AU - Smith, C. AU - Gangadharan, R. AU - Zhang, G. T2 - Transactions of the ASABE DA - 2012/// PY - 2012/// VL - 55 IS - 3 SP - 1013-1024 ER - TY - JOUR TI - A review of selected techniques in inverse problem nonparametric probability distribution estimation AU - Banks, H. T. AU - Kenz, Z. R. AU - Thompson, W. C. T2 - Journal of Inverse and Ill-Posed Problems DA - 2012/// PY - 2012/// VL - 20 IS - 4 SP - 429-460 ER - TY - JOUR TI - A Dataflow Framework for DSP Algorithm Refinement AU - Kim, Youngsoo AU - Alexander, Winser E. AU - Edmonson, William W. T2 - 2012 IEEE COMPUTER SOCIETY ANNUAL SYMPOSIUM ON VLSI (ISVLSI) AB - Current video compression algorithms are increasingly complicated and difficult to analyze and profile. Design tools and system level languages often prove to be inefficient and incapable of providing complexity analysis as a first step directed toward at the implementation of video compression algorithms. This paper proposes framework that will help to develop a methodology that facilitates the derivation of analytical dataflow models. The framework proposes dataflow models for quantifying the underlying algorithm's memory complexity, related timing considerations, and verification of the correctness of the video compression algorithm. DA - 2012/// PY - 2012/// DO - 10.1109/isvlsi.2012.74 SP - 1-+ KW - refinement KW - DSP KW - dataflow KW - framework ER - TY - JOUR TI - Variance estimation in censored quantile regression via induced smoothing AU - Pang, Lei AU - Lu, Wenbin AU - Wang, Huixia Judy T2 - COMPUTATIONAL STATISTICS & DATA ANALYSIS AB - Statistical inference in censored quantile regression is challenging, partly due to the unsmoothness of the quantile score function. A new procedure is developed to estimate the variance of the Bang and Tsiatis inverse-censoring-probability weighted estimator for censored quantile regression by employing the idea of induced smoothing. The proposed variance estimator is shown to be asymptotically consistent. In addition, a numerical study suggests that the proposed procedure performs well in finite samples, and it is computationally more efficient than the commonly used bootstrap method. DA - 2012/4/1/ PY - 2012/4/1/ DO - 10.1016/j.csda.2010.10.018 VL - 56 IS - 4 SP - 785-796 SN - 1872-7352 KW - Censored quantile regression KW - Smoothing KW - Survival analysis KW - Variance estimation ER - TY - JOUR TI - Thermal based methods for damage detection and characterization in porous materials AU - Banks, H T AU - Criner, Amanda Keck T2 - Inverse Problems AB - In this effort we consider damage detection algorithms using thermal probes. The techniques proposed employ models derived from homogenization theory as the model solution in parameter estimation procedures for simulated data for heat flow in a porous medium. We consider data simulated from a model on a perforated domain with isotropic flow and data simulated from a model on a homogeneous domain with anisotropic flow. We report on ordinary least squares methods combined with the method of mappings to detect the presence of damage and to characterize the geometry of the damage. DA - 2012/5/31/ PY - 2012/5/31/ DO - 10.1088/0266-5611/28/6/065021 VL - 28 IS - 6 SP - 065021 J2 - Inverse Problems OP - SN - 0266-5611 1361-6420 UR - http://dx.doi.org/10.1088/0266-5611/28/6/065021 DB - Crossref ER - TY - JOUR TI - The interface of protein structure, protein biophysics, and molecular evolution AU - Liberles, D. A. AU - Teichmann, S. A. AU - Bahar, I. AU - Bastolla, U. AU - Bloom, J. AU - Bornberg-Bauer, E. AU - Colwell, L. J. AU - Koning, A. P. J. AU - Dokholyan, N. V. AU - Echave, J. AU - Elofsson, A. AU - Gerloff, D. L. AU - Goldstein, R. A. AU - Grahnen, J. A. AU - Holder, M. T. AU - Lakner, C. T2 - Protein Science DA - 2012/// PY - 2012/// VL - 21 IS - 6 SP - 769-785 ER - TY - JOUR TI - Shape restricted nonparametric regression with Bernstein polynomials AU - Wang, J. AU - Ghosh, S. K. T2 - COMPUTATIONAL STATISTICS & DATA ANALYSIS AB - The objective of this article is to develop a computationally efficient estimator of the regression function subject to various shape constraints. In particular, nonparametric estimators of monotone and/or convex (concave) regression functions are obtained by using a nested sequence of Bernstein polynomials. One of the key distinguishing features of the proposed estimator is that a given shape constraint (e.g., monotonicity and/or convexity) is maintained for any finite sample size and satisfied over the entire support of the predictor space. Moreover, it is shown that the Bernstein polynomial based regression estimator can be obtained as a solution of a constrained least squares method and hence the estimator can be computed efficiently using a quadratic programming algorithm. Finally, the asymptotic properties (e.g., strong uniform consistency) of the estimator are established under very mild conditions, and finite sample properties are explored using several simulation studies and real data analysis. The predictive performances are compared with some of the existing methods. DA - 2012/9// PY - 2012/9// DO - 10.1016/j.csda.2012.02.018 VL - 56 IS - 9 SP - 2729-2741 SN - 1872-7352 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84862822817&partnerID=MN8TOARS KW - Bernstein polynomials KW - Convex KW - Monotone KW - Nonparametric regression KW - Shape restriction ER - TY - JOUR TI - Quantile regression for competing risks data with missing cause of failure AU - Sun, Y. Q. AU - Wang, H. J. AU - Gilbert, P. B. T2 - Statistica Sinica DA - 2012/// PY - 2012/// VL - 22 IS - 2 SP - 703-728 ER - TY - JOUR TI - Prestrain-Free Dielectric Elastomers Based on Acrylic Thermoplastic Elastomer Gels: A Morphological and (Electro)Mechanical Property Study AU - Vargantwar, Pruthesh H. AU - Oezcam, A. Evren AU - Ghosh, Tushar K. AU - Spontak, Richard J. T2 - ADVANCED FUNCTIONAL MATERIALS AB - Abstract Recent efforts have established that thermoplastic elastomer gels (TPEGs) composed of styrenic triblock copolymers swollen with a midblock‐selective solvent exhibit remarkable electromechanical properties as high‐performance dielectric elastomers. This class of electroactive polymers typically requires high electric fields for actuation, and a shortcoming that continues to thwart the widespread commercialization of such materials in general is the need to apply mechanical prestrain prior to electroactuation to decrease film thickness and, thus, the electric potential required to promote actuation. To alleviate this requirement, TPEGs consisting of acrylic triblock copolymers differing in molecular weight and composition, and swollen with a high dielectric, midblock‐selective solvent are investigated. Synchrotron small‐angle x‐ray scattering is used to probe the nanoscale morphologies of the resultant materials, and analysis of quasi‐static and cyclic tensile properties provides additional insight into both blend morphologies and electroactuation efficacy. Actuation strains measured in the absence of mechanical prestrain exceed 100% on an area basis, and electric fields capable of inducing actuation are as low as ∼20 kV/mm. Failure occurs by either electromechanical instability or dielectric breakdown, depending on the copolymer and TPEG composition employed. The electromechanical properties of these acrylic‐based TPEGs match or exceed those of skeletal muscle, in which case they constitute an attractive and unexplored alternative to existing dielectric elastomers. DA - 2012/5/23/ PY - 2012/5/23/ DO - 10.1002/adfm.201101985 VL - 22 IS - 10 SP - 2100-2113 SN - 1616-301X ER - TY - JOUR TI - Multiple Loci Mapping via Model-free Variable Selection AU - Sun, Wei AU - Li, Lexin T2 - BIOMETRICS AB - Summary Despite recent flourish of proposals on variable selection, genome‐wide multiple loci mapping remains to be challenging. The majority of existing variable selection methods impose a model, and often the homoscedastic linear model, prior to selection. However, the true association between the phenotypical trait and the genetic markers is rarely known a priori, and the presence of epistatic interactions makes the association more complex than a linear relation. Model‐free variable selection offers a useful alternative in this context, but the fact that the number of markers p often far exceeds the number of experimental units n renders all the existing model‐free solutions that require n > p inapplicable. In this article, we examine a number of model‐free variable selection methods for small‐ n ‐large‐ p regressions in the context of genome‐wide multiple loci mapping. We propose and advocate a multivariate group‐wise adaptive penalization solution, which requires no model prespecification and thus works for complex trait‐marker association, and handles one variable at a time so that works for n < p . Effectiveness of the new method is demonstrated through both intensive simulations and a comprehensive real data analysis across 6100 gene expression traits. DA - 2012/3// PY - 2012/3// DO - 10.1111/j.1541-0420.2011.01650.x VL - 68 IS - 1 SP - 12-22 SN - 1541-0420 KW - Adaptive Lasso KW - Epistatic interaction KW - Grouped Lasso KW - Iterative adaptive Lasso KW - Model-free variable selection KW - Multiple loci mapping KW - Multivariate group-wise adaptive penalization KW - Sliced inverse regression ER - TY - JOUR TI - KI-impregnated oyster shell as a solid catalyst for soybean oil transesterification AU - Jairam, Suguna AU - Kolar, Praveen AU - Sharma-Shivappa, Ratna AU - Osborne, Jason A. AU - Davis, Jack P. T2 - BIORESOURCE TECHNOLOGY AB - Research on inexpensive and green catalysts is needed for economical production of biodiesel. The goal of the research was to test KI-impregnated calcined oyster shell as a solid catalyst for transesterification of soybean oil. Specific objectives were to characterize KI-impregnated oyster shell, determine the effect of reaction variables and reaction kinetics. The catalyst was synthesized by impregnating KI on calcined oyster shells. X-ray diffraction analysis indicated the presence of portlandite and potassium iodide on the surface and a 31-fold increase in surface as a result of calcination and KI impregnation. Under the conditions tested, ideal reaction variables were 1 mmol g−1 for catalyst loading, 50 °C for temperature, 10:1 for methanol/oil, and 4 h for reaction time. The transesterification followed a first-order reaction (k = 0.4385 h−1). The option of using oyster shell for the production of transesterification catalysts could have economic benefits to the aquaculture industry in the US. DA - 2012/1// PY - 2012/1// DO - 10.1016/j.biortech.2011.10.039 VL - 104 SP - 329-335 SN - 1873-2976 KW - Biodiesel KW - Fatty acid methyl esters KW - Solid catalysts KW - KI-impregnated oyster shells ER - TY - JOUR TI - Heavy Metal and Disinfectant Resistance of Listeria monocytogenes from Foods and Food Processing Plants AU - Ratani, Shakir S. AU - Siletzky, Robin M. AU - Dutta, Vikrant AU - Yildirim, Suleyman AU - Osborne, Jason A. AU - Lin, Wen AU - Hitchins, Anthony D. AU - Ward, Todd J. AU - Kathariou, Sophia T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - ABSTRACT The persistence of Listeria monocytogenes in food processing plants and other ecosystems reflects its ability to adapt to numerous stresses. In this study, we investigated 138 isolates from foods and food processing plants for resistance to the quaternary ammonium disinfectant benzalkonium chloride (BC) and to heavy metals (cadmium and arsenic). We also determined the prevalence of distinct cadmium resistance determinants ( cadA1 , cadA2 , and cadA3 ) among cadmium-resistant isolates. Most BC-resistant isolates were resistant to cadmium as well. Arsenic resistance was encountered primarily in serotype 4b and was an attribute of most isolates of the serotype 4b epidemic clonal group ECIa. Prevalence of the known cadmium resistance determinants was serotype associated: cadA1 was more common in isolates of serotypes 1/2a and 1/2b than 4b, while cadA2 was more common in those of serotype 4b. A subset (15/77 [19%]) of the cadmium-resistant isolates lacked the known cadmium resistance determinants. Most of these isolates were of serotype 4b and were also resistant to arsenic, suggesting novel determinants that may confer resistance to both cadmium and arsenic in these serotype 4b strains. The findings may reflect previously unrecognized components of the ecological history of different serotypes and clonal groups of L. monocytogenes , including exposures to heavy metals and disinfectants. DA - 2012/10// PY - 2012/10// DO - 10.1128/aem.01553-12 VL - 78 IS - 19 SP - 6938-6945 SN - 0099-2240 ER - TY - JOUR TI - Experimental design and inverse problems in plant biological modeling AU - Avery, M. AU - Banks, H. T. AU - Basu, K. AU - Cheng, Y. S. AU - Eager, E. AU - Khasawinah, S. AU - Potter, L. AU - Rehm, K. L. T2 - Journal of Inverse and Ill-Posed Problems DA - 2012/// PY - 2012/// VL - 20 IS - 2 SP - 169-191 ER - TY - JOUR TI - Evaluation of polymorphisms in the sulfonamide detoxification genes NAT2, CYB5A, and CYB5R3 in patients with sulfonamide hypersensitivity AU - Sacco, James C. AU - Abouraya, Mahmoud AU - Motsinger-Reif, Alison AU - Yale, Steven H. AU - McCarty, Catherine A. AU - Trepanier, Lauren A. T2 - PHARMACOGENETICS AND GENOMICS AB - Objective To determine whether polymorphisms in the sulfonamide detoxification genes, CYB5A (encoding cytochrome b5), CYB5R3 (encoding cytochrome b5 reductase), or NAT2 (encoding N-acetyltransferase 2) were over-represented in patients with delayed sulfonamide drug hypersensitivity, compared with control patients who tolerated a therapeutic course of trimethoprim–sulfamethoxazole without adverse event. Methods DNA from 99 nonimmunocompromised patients with sulfonamide hypersensitivity who were identified from the Personalized Medicine Research Project at the Marshfield Clinic, and from 99 age-matched, race-matched, and sex-matched drug-tolerant controls, were genotyped for four CYB5A and five CYB5R3 polymorphisms, and for all coding NAT2 SNPs. Results CYB5A and CYB5R3 SNPs were found at low allele frequencies (<3–4%), which did not differ between hypersensitive and tolerant patients. NAT2 allele and haplotype frequencies, as well as inferred NAT2 phenotypes, also did not differ between groups (60 vs. 59% slow acetylators). Finally, no difference in NAT2 status was found in a subset of patients with more severe hypersensitivity signs (drug reaction with eosinophilia and systemic symptoms) compared with tolerant patients. Conclusion We found no evidence of a substantial involvement of these nine CYB5A or CYB5R3 polymorphisms in sulfonamide hypersensitivity risk, although minor effects cannot be completely ruled out. Despite careful medical record review and full resequencing of the NAT2 coding region, we found no association of NAT2 coding alleles with sulfonamide hypersensitivity (predominantly cutaneous eruptions) in this adult Caucasian population. DA - 2012/10// PY - 2012/10// DO - 10.1097/fpc.0b013e328357a735 VL - 22 IS - 10 SP - 733-740 SN - 1744-6872 KW - cytochrome b(5) KW - drug hypersensitivity KW - hydroxylamine KW - N-acetyltransferase KW - potentiated sulfonamides KW - sulfamethoxazole ER - TY - JOUR TI - Estimating the Health Impact of Climate Change With Calibrated Climate Model Output AU - Zhou, Jingwen AU - Chang, Howard H. AU - Fuentes, Montserrat T2 - JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS AB - Studies on the health impacts of climate change routinely use climate model output as future exposure projection. Uncertainty quantification, usually in the form of sensitivity analysis, has focused predominantly on the variability arise from different emission scenarios or multi-model ensembles. This paper describes a Bayesian spatial quantile regression approach to calibrate climate model output for examining to the risks of future temperature on adverse health outcomes. Specifically, we first estimate the spatial quantile process for climate model output using nonlinear monotonic regression during a historical period. The quantile process is then calibrated using the quantile functions estimated from the observed monitoring data. Our model also down-scales the gridded climate model output to the point-level for projecting future exposure over a specific geographical region. The quantile regression approach is motivated by the need to better characterize the tails of future temperature distribution where the greatest health impacts are likely to occur. We applied the methodology to calibrate temperature projections from a regional climate model for the period 2041 to 2050. Accounting for calibration uncertainty, we calculated the number of of excess deaths attributed to future temperature for three cities in the US state of Alabama. DA - 2012/9// PY - 2012/9// DO - 10.1007/s13253-012-0105-y VL - 17 IS - 3 SP - 377-394 SN - 1537-2693 KW - Bayesian spatial quantile regression KW - Model calibration ER - TY - JOUR TI - Effects of acepromazine maleate on platelet function assessed by use of adenosine diphosphate activated- and arachidonic acid-activated modified thromboelastography in healthy dogs AU - Conner, Bobbi J. AU - Hanel, Rita M. AU - Hansen, Bernard D. AU - Motsinger-Reif, Alison A. AU - Asakawa, Makoto AU - Swanson, Clifford R. T2 - AMERICAN JOURNAL OF VETERINARY RESEARCH AB - Abstract Objective —To evaluate the effect of acepromazine maleate administered IV on platelet function assessed in healthy dogs by use of a modified thromboelastography assay. Animals —6 healthy adult mixed-breed dogs. Procedures —Dogs received each of 3 treatments (saline [0.9% NaCl] solution [1 to 2 mL, IV] and acepromazine maleate [0.05 and 0.1 mg/kg, IV]) in a randomized crossover study with a minimum 3-day washout period between treatments. From each dog, blood samples were collected via jugular venipuncture immediately before and 30 and 240 minutes after administration of each treatment. A modified thromboelastography assay, consisting of citrated kaolin–activated (baseline assessment), reptilase-ADP–activated (ADP-activated), and reptilase-arachidonic acid (AA)–activated (AA-activated) thromboelastography, was performed for each sample. Platelet inhibition was evaluated by assessing the percentage change in maximum amplitude for ADP-activated or AA-activated samples, compared with baseline values. Percentage change in maximum amplitude was analyzed by use of Skillings-Mack tests with significance accepted at a family-wise error rate of P < 0.05 by use of Bonferroni corrections for multiple comparisons. Results —No significant differences were found in the percentage change of maximum amplitude from baseline for ADP-activated or AA-activated samples among treatments at any time. Conclusions and Clinical Relevance —Platelet function in dogs, as assessed by use of a modified thromboelastography assay, was not inhibited by acepromazine at doses of 0.05 or 0.1 mg/kg, IV. This was in contrast to previous reports in which it was suggested that acepromazine may alter platelet function via inhibition of ADP and AA. DA - 2012/5// PY - 2012/5// DO - 10.2460/ajvr.73.5.595 VL - 73 IS - 5 SP - 595-601 SN - 1943-5681 ER - TY - JOUR TI - Editorial for the special issue on quantile regression and semiparametric methods AU - Fung, Wing-Kam AU - He, Xuming AU - Hubert, Mia AU - Portnoy, Stephen AU - Wang, Huixia Judy T2 - COMPUTATIONAL STATISTICS & DATA ANALYSIS DA - 2012/4/1/ PY - 2012/4/1/ DO - 10.1016/j.csda.2011.12.012 VL - 56 IS - 4 SP - 753-754 SN - 0167-9473 ER - TY - JOUR TI - A unified variable selection approach for varying coefficient models AU - Tang, Y. L. AU - Wang, H. J. AU - Zhu, Z. Y. AU - Song, X. Y. T2 - Statistica Sinica DA - 2012/// PY - 2012/// VL - 22 IS - 2 SP - 601-628 ER - TY - JOUR TI - A novel N-terminal domain may dictate the glucose response of Mondo proteins AU - McFerrin, L. G. AU - Atchley, W. R. T2 - PLoS One DA - 2012/// PY - 2012/// VL - 7 IS - 4 ER - TY - JOUR TI - A compact dielectric elastomer tubular actuator for refreshable Braille displays AU - Chakraborti, P. AU - Toprakci, H. A. Karahan AU - Yang, P. AU - Di Spigna, N. AU - Franzon, P. AU - Ghosh, T. T2 - SENSORS AND ACTUATORS A-PHYSICAL AB - Electroactive polymer actuators stimulated by appropriate levels of electric field are particularly attractive for human-assist devices such as Braille. The development of a full page refreshable Braille display is very important for the integration of the visually impaired into the new era of communication. In this paper, development of a compact dielectric elastomer actuator suitable for Braille application is reported. The actuators are fabricated from commercially available silicone tubes. The tube has been rendered mechanically anisotropic through asymmetric levels of applied pretension in circumferential and axial directions in order to direct the actuation strain in the axial direction of the actuator. Key performance parameters, such as displacement, force, and response time of the actuator are investigated. The test results demonstrate the potential of the compact, lightweight, and low cost dielectric elastomer as actuators for a refreshable full page Braille display. DA - 2012/6// PY - 2012/6// DO - 10.1016/j.sna.2012.02.004 VL - 179 SP - 151-157 SN - 0924-4247 KW - Electroactive polymers KW - Dielectric elastomer actuator KW - Braille display actuators KW - Refreshable Braille display ER - TY - JOUR TI - A Confidence Region Approach to Tuning for Variable Selection AU - Gunes, Funda AU - Bondell, Howard D. T2 - JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS AB - We develop an approach to tuning of penalized regression variable selection methods by calculating the sparsest estimator contained in a confidence region of a specified level. Because confidence intervals/regions are generally understood, tuning penalized regression methods in this way is intuitive and more easily understood by scientists and practitioners. More importantly, our work shows that tuning to a fixed confidence level often performs better than tuning via the common methods based on Akaike information criterion (AIC), Bayesian information criterion (BIC), or cross-validation (CV) over a wide range of sample sizes and levels of sparsity. Additionally, we prove that by tuning with a sequence of confidence levels converging to one, asymptotic selection consistency is obtained, and with a simple two-stage procedure, an oracle property is achieved. The confidence-region-based tuning parameter is easily calculated using output from existing penalized regression computer packages. Our work also shows how to map any penalty parameter to a corresponding confidence coefficient. This mapping facilitates comparisons of tuning parameter selection methods such as AIC, BIC, and CV, and reveals that the resulting tuning parameters correspond to confidence levels that are extremely low, and can vary greatly across datasets. Supplemental materials for the article are available online. DA - 2012/6// PY - 2012/6// DO - 10.1080/10618600.2012.679890 VL - 21 IS - 2 SP - 295-314 SN - 1061-8600 KW - Adaptive LASSO KW - Penalized regression KW - Tuning parameter ER - TY - JOUR TI - Water Quality of Drainage from Permeable Friction Course AU - Eck, Bradley J. AU - Winston, Ryan J. AU - Hunt, William F. AU - Barrett, Michael E. T2 - JOURNAL OF ENVIRONMENTAL ENGINEERING-ASCE AB - An overlay of porous asphalt known as permeable friction course (PFC) is an innovative roadway material that improves both driving conditions in wet weather and water quality. Placed in a layer 25–50 mm thick on top of regular impermeable pavement, PFC allows rainfall to drain within the porous layer rather than on top of the pavement. This paper presents water quality measurements for PFC and conventional pavement collected over six years near Austin, TX and two years in eastern North Carolina. The data show that concentrations of total suspended solids from PFC are more than 90% lower than from conventional pavement. Lower effluent concentrations are also observed for total amounts of phosphorus, copper, lead, and zinc. The combined data sets show that PFC’s benefits last through the design life of the pavement, that results in Texas are consistent with those from North Carolina, and that both are consistent with earlier studies from France, the Netherlands, and Germany. DA - 2012/2// PY - 2012/2// DO - 10.1061/(asce)ee.1943-7870.0000476 VL - 138 IS - 2 SP - 174-181 SN - 0733-9372 KW - Highway runoff KW - Field monitoring KW - Permeable friction course KW - Stormwater ER - TY - JOUR TI - Using Stated Preference and Prior Purchase Intention in the Estimation of Willingness to Pay a Premium for Genetically Modified Foods AU - Chiang, Jeng-Tung AU - Lin, Chen-Yen AU - Fu, Tsu-Tan AU - Chen, Chen-Hsin T2 - AGRIBUSINESS AB - ABSTRACT This study provides an appropriate analytical approach using stated preference analysis and the contingent valuation method to investigate consumers’ willingness to pay a premium for genetically modified ( GM ) foods together with their prior purchase intentions. Although most analyses treat consumers’ attitudes and willingness to pay as separate issues, we introduce the idea of prior purchase intention to analyze these two issues as a whole. To achieve this purpose, a modeling technique invoking the multinomial logistic model and the accelerated failure time model is presented. Based on the data collected from an essential double‐bounded design, our empirical results suggest that Taiwanese consumers are willing to pay a premium of about 11 NT dollars (7% of the given average market price of 150 NT dollars for the non‐ GM salmon) to avoid GM ‐soybean‐fed salmon. In addition, the results of this study provide evidence that our stated‐preference double‐bounded design has a better‐off statistical efficiency than the single‐bounded one. DA - 2012/// PY - 2012/// DO - 10.1002/agr.20291 VL - 28 IS - 1 SP - 103-117 SN - 0742-4477 ER - TY - JOUR TI - Quantification of emission factor uncertainty AU - Pouliot, George AU - Wisner, Emily AU - Mobley, David AU - Hunt, William, Jr. T2 - JOURNAL OF THE AIR & WASTE MANAGEMENT ASSOCIATION AB - Emissions factors are important for estimating and characterizing emissions from sources of air pollution. There is no quantitative indication of uncertainty for these emission factors, most factors do not have an adequate data set to compute uncertainty, and it is very difficult to locate the data for those that do. The objectives are to compare the current emission factors of Electric Generating Unit NOX sources with currently available continuous emission monitoring data, develop quantitative uncertainty indicators for the Environmental Protection Agency (EPA) data quality rated emission factors, and determine the possible ranges of uncertainty associated with EPA's data quality rating of emission factors. EPA's data letter rating represents a general indication of the robustness of the emission factor and is assigned based on the estimated reliability of the tests used to develop the factor and on the quantity and representativeness of the data. Different sources and pollutants that have the same robustness in the measured emission factor and in the representativeness of the measured values are assumed to have a similar quantifiable uncertainty. For the purposes of comparison, we assume that the emission factor estimates from source categories with the same letter rating have enough robustness and consistency that we can quantify the uncertainty of these common emission factors based on the qualitative indication of data quality which is known for almost all factors. The results showed that EPA's current emission factor values for NOX emissions from combustion sources were found to be reasonably representative for some sources; however, AP-42 values should be updated for over half of the sources to reflect current data. The quantified uncertainty ranges were found to be 25–62% for A rated emission factors, 45–75% for B rated emission factors, 60–82% for C rated emission factors, and 69–86% for D rated emission factors, and 82–92% for E rated emission factors. Implications Currently, a letter grade indicates the data quality uncertainty of emission factors in EPA's Compilation of Emission Factors (AP-42). However, a quantitative characterization would be much preferred. If the uncertainty of emission factors is quantified, scientists may be able to more accurately characterize the uncertainty associated with air quality modeling and emission data. A quantitative measure of uncertainty will also give decision makers the ability to determine the confidence that should be placed in the analysis of the data being used for policy decisions. DA - 2012/3// PY - 2012/3// DO - 10.1080/10473289.2011.649155 VL - 62 IS - 3 SP - 287-298 SN - 2162-2906 ER - TY - JOUR TI - On estimation of linear transformation models with nested case-control sampling AU - Lu, Wenbin AU - Liu, Mengling T2 - LIFETIME DATA ANALYSIS AB - Nested case-control (NCC) sampling is widely used in large epidemiological cohort studies for its cost effectiveness, but its data analysis primarily relies on the Cox proportional hazards model. In this paper, we consider a family of linear transformation models for analyzing NCC data and propose an inverse selection probability weighted estimating equation method for inference. Consistency and asymptotic normality of our estimators for regression coefficients are established. We show that the asymptotic variance has a closed analytic form and can be easily estimated. Numerical studies are conducted to support the theory and an application to the Wilms' Tumor Study is also given to illustrate the methodology. DA - 2012/1// PY - 2012/1// DO - 10.1007/s10985-011-9203-3 VL - 18 IS - 1 SP - 80-93 SN - 1380-7870 KW - Linear transformation models KW - Nested case-control sampling KW - Weighted estimating equation ER - TY - JOUR TI - Merging pharmacometabolomics with pharmacogenomics using ‘1000 Genomes’ single-nucleotide polymorphism imputation AU - Abo, Ryan AU - Hebbring, Scott AU - Ji, Yuan AU - Zhu, Hongjie AU - Zeng, Zhao-Bang AU - Batzler, Anthony AU - Jenkins, Gregory D. AU - Biernacka, Joanna AU - Snyder, Karen AU - Drews, Maureen AU - Fiehn, Oliver AU - Fridley, Brooke AU - Schaid, Daniel AU - Kamatani, Naoyuki AU - Nakamura, Yusuke AU - Kubo, Michiaki AU - Mushiroda, Taisei AU - Kaddurah-Daouk, Rima AU - Mrazek, David A. AU - Weinshilboum, Richard M. T2 - Pharmacogenetics and Genomics AB - Objective We set out to test the hypothesis that pharmacometabolomic data could be efficiently merged with pharmacogenomic data by single-nucleotide polymorphism (SNP) imputation of metabolomic-derived pathway data on a ‘scaffolding’ of genome-wide association (GWAS) SNP data to broaden and accelerate ‘pharmacometabolomics-informed pharmacogenomic’ studies by eliminating the need for initial genotyping and by making broader SNP association testing possible. Methods We previously genotyped 131 tag SNPs for six genes encoding enzymes in the glycine synthesis and degradation pathway using DNA from 529 depressed patients treated with citalopram/escitalopram to pursue a glycine metabolomics ‘signal’ associated with selective serotonine reuptake inhibitor response. We identified a significant SNP in the glycine dehydrogenase gene. Subsequently, GWAS SNP data were generated for the same patients. In this study, we compared SNP imputation within 200 kb of these same six genes with the results of the previous tag SNP strategy as a rapid strategy for merging pharmacometabolomic and pharmacogenomic data. Results Imputed genotype data provided greater coverage and higher resolution than did tag SNP genotyping, with a higher average genotype concordance between genotyped and imputed SNP data for ‘1000 Genomes’ (96.4%) than HapMap 2 (93.2%) imputation. Many low P-value SNPs with novel locations within genes were observed for imputed compared with tag SNPs, thus altering the focus for subsequent functional genomic studies. Conclusion These results indicate that the use of GWAS data to impute SNPs for genes in pathways identified by other ‘omics’ approaches makes it possible to rapidly and cost efficiently identify SNP markers to ‘broaden’ and accelerate pharmacogenomic studies. DA - 2012/4// PY - 2012/4// DO - 10.1097/fpc.0b013e32835001c9 VL - 22 IS - 4 SP - 247-253 J2 - Pharmacogenetics and Genomics LA - en OP - SN - 1744-6872 UR - http://dx.doi.org/10.1097/FPC.0b013e32835001c9 DB - Crossref KW - 1000 Genomes KW - HapMap KW - imputation KW - major depressive disorder KW - pharmacometabolomics KW - pharmacogenomics KW - selective serotonin reuptake inhibitors KW - tag single-nucleotide polymorphisms ER - TY - JOUR TI - Meeting Hydrologic and Water Quality Goals through Targeted Bioretention Design AU - Hunt, William F. AU - Davis, Allen P. AU - Traver, Robert G. T2 - JOURNAL OF ENVIRONMENTAL ENGINEERING AB - Bioretention is one of the most commonly used stormwater control measures (SCMs) in North America and Australasia. However, current design is not targeted to regulatory need, often reflecting an outdated understanding of how and why bioretention works. The purpose of this manuscript is to synthesize research to recommend a suite of design standards focused on the purpose of bioretention SCM. Both hydrologic (peak flow mitigation, infiltration, annual hydrology, and stream stability) and water quality [total suspended solids (TSS) and particulates, pathogen-indicator species, metals, hydrocarbons, phosphorus, nitrogen, and temperature] regulatory and stream ecology needs are addressed. Bioretention cells designed to meet a prioritized subset of those measures would be substantially different than cells that are designed for a different subset of needs. Designers have the ability to adjust bowl volume, media composition, media depth, underdrainage configuration, and vegetation type. This study examines how each of those design parameters can be adjusted such that a “one size fits all” approach is no longer the norm. DA - 2012/6// PY - 2012/6// DO - 10.1061/(asce)ee.1943-7870.0000504 VL - 138 IS - 6 SP - 698-707 SN - 1943-7870 KW - Stormwater KW - Infiltration KW - Bioretention KW - Hydrology KW - Water quality KW - Design KW - Pathogens KW - Temperature KW - Nutrients KW - Bioinfiltration ER - TY - JOUR TI - LID Treatment Train: Pervious Concrete with Subsurface Storage in Series with Bioretention and Care with Seasonal High Water Tables AU - Brown, R. A. AU - Line, D. E. AU - Hunt, W. F. T2 - JOURNAL OF ENVIRONMENTAL ENGINEERING AB - Two infiltrating low-impact development (LID) practices configured in-series, pervious concrete and bioretention (PC-B), were monitored for 17 months to examine the hydrologic and water quality response of this LID treatment train design. For the first LID practice, 0.53 ha of pervious concrete was installed to treat direct rainfall and run-on from 0.36 ha of asphalt parking lot. The pervious concrete was installed over a gravel subsurface storage basin, which was designed to store 25 mm (1 in.) of runoff from the parking lot before draining into the second LID practice, which was a 0.05 ha bioretention cell. The bioretention cell was conventionally drained, had a media depth of 0.5 m (1.6 ft), and was constructed at a location with a high water table. Outflow was only generated in 33 out of 80 monitored events, and over the course of the entire monitoring period, the total outflow volume reduction was 69%. The large outflow reduction subsequently led to high pollutant load reductions for total nitrogen (49%), total phosphorus (51%), and total suspended solids (89%). However, when the contribution of base flow was included in the calculation, the total nitrogen load discharged from the bioretention cell was 64% higher than that of the runoff load because of nitrite and nitrate, NO2- and NO3-(NO2,3-N), which were present in the base flow. The total nitrogen (TN) loads of runoff, storm flow (total outflow minus base flow), base flow, and outflow (total) were 7.70, 3.94, 8.69, and 12.64 kg/ha·year, respectively. Of the 8.69 kg/ha·year TN in the base flow, 92% was in the form of NO2,3-N. This study demonstrated the hydrologic benefits (peak flow and outflow reduction) gained by having two infiltration LID practices in-series. When compared with a single treatment practice (bioretention) that was monitored at the same site, the two LID practices in-series treated an additional 10% of annual runoff volume, discharged approximately one-half as much outflow volume, and discharged significantly lower peak outflow rates. However, the water quality results were not as promising because of the influx of groundwater in the bioretention cell and the lack of denitrifying conditions in either the bioretention cell or pervious concrete system. This study also quantified increased TN and NO2,3-N export to surface waters from a bioretention cell that was situated in an area with a high water table. DA - 2012/6// PY - 2012/6// DO - 10.1061/(asce)ee.1943-7870.0000506 VL - 138 IS - 6 SP - 689-697 SN - 1943-7870 KW - Storm water management KW - Low-impact development KW - Storm water control measure KW - Permeable pavement KW - Water quality KW - Hydrology KW - Peak flow reduction KW - Intercepted water table ER - TY - JOUR TI - Why Statistics? AU - Davidian, Marie AU - Louis, Thomas A. T2 - SCIENCE AB - Popular media and science publications sound the drum: “Big Data” will drive our future, from translating genomic information into new therapies, to harnessing the Web to untangle complex social interactions, to detecting infectious disease outbreaks. Statistics is the science of learning from data, and of measuring, controlling, and communicating uncertainty; and it thereby provides the navigation essential for controlling the course of scientific and societal advances. This field will become ever more critical as academia, businesses, and governments rely increasingly on data-driven decisions, expanding the demand for statistics expertise. DA - 2012/4/6/ PY - 2012/4/6/ DO - 10.1126/science.1218685 VL - 336 IS - 6077 SP - 12-12 SN - 0036-8075 ER - TY - JOUR TI - Redispersal of seeds by a keystone ant augments the spread of common wildflowers AU - Canner, Judith E. AU - Dunn, Robert R. AU - Giladi, Itamar AU - Gross, Kevin T2 - ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY AB - Myrmecochory (dispersal of seeds by ants) is an evolutionarily and ecologically common mutualism. Most of the research on the costs and benefits of myrmecochory in North America assumes that ant-dispersed seeds are taken to, and left in, the ant nest. Here, we use a novel seed-tracking technique to quantify secondary dispersal of seeds from the nest into the surrounding leaf litter by the keystone seed-dispersing ant, Aphaenogaster rudis. We found that A. rudis redispersed >90% of the seeds it took into its nest an average distance of 51.5 cm. A mathematical model shows redispersal increases the rate of population spread of the myrmecochores Hexastylis arifolia and Asarum canadense by 22.5%, and increases the expected cumulative dispersal distance away from the parent plant by 24%. Our results suggest myrmecochory benefits plants in eastern North American forests by increasing the distance between the seed and parent plant and reducing competition among siblings. DA - 2012/4// PY - 2012/4// DO - 10.1016/j.actao.2012.02.004 VL - 40 SP - 31-39 SN - 1873-6238 KW - Redispersal KW - Myrmecochory KW - Aphaenogaster rudis KW - Population spread rate KW - Plant benefits KW - Temperate forest ER - TY - JOUR TI - Quantile Regression for Analyzing Heterogeneity in Ultra-High Dimension AU - Wang, Lan AU - Wu, Yichao AU - Li, Runze T2 - JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION AB - Ultra-high dimensional data often display heterogeneity due to either heteroscedastic variance or other forms of non-location-scale covariate effects. To accommodate heterogeneity, we advocate a more general interpretation of sparsity, which assumes that only a small number of covariates influence the conditional distribution of the response variable, given all candidate covariates; however, the sets of relevant covariates may differ when we consider different segments of the conditional distribution. In this framework, we investigate the methodology and theory of nonconvex, penalized quantile regression in ultra-high dimension. The proposed approach has two distinctive features: (1) It enables us to explore the entire conditional distribution of the response variable, given the ultra-high-dimensional covariates, and provides a more realistic picture of the sparsity pattern; (2) it requires substantially weaker conditions compared with alternative methods in the literature; thus, it greatly alleviates the difficulty of model checking in the ultra-high dimension. In theoretic development, it is challenging to deal with both the nonsmooth loss function and the nonconvex penalty function in ultra-high-dimensional parameter space. We introduce a novel, sufficient optimality condition that relies on a convex differencing representation of the penalized loss function and the subdifferential calculus. Exploring this optimality condition enables us to establish the oracle property for sparse quantile regression in the ultra-high dimension under relaxed conditions. The proposed method greatly enhances existing tools for ultra-high-dimensional data analysis. Monte Carlo simulations demonstrate the usefulness of the proposed procedure. The real data example we analyzed demonstrates that the new approach reveals substantially more information as compared with alternative methods. This article has online supplementary material. DA - 2012/3// PY - 2012/3// DO - 10.1080/01621459.2012.656014 VL - 107 IS - 497 SP - 214-222 SN - 1537-274X KW - Penalized quantile regression KW - SCAD KW - Sparsity KW - Ultra-high-dimensional data ER - TY - JOUR TI - Multiple Imputation for M-Regression With Censored Covariates AU - Wang, Huixia Judy AU - Feng, Xingdong T2 - JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION AB - Abstract We develop a new multiple imputation approach for M-regression models with censored covariates. Instead of specifying parametric likelihoods, our method imputes the censored covariates by their conditional quantiles given the observed data, where the conditional quantiles are estimated through fitting a censored quantile regression process. The resulting estimator is shown to be consistent and asymptotically normal, and it improves the estimation efficiency by using information from cases with censored covariates. Compared with existing methods, the proposed method is more flexible as it does not require stringent parametric assumptions on the distributions of either the regression errors or the covariates. The finite sample performance of the proposed method is assessed through a simulation study and the analysis of a c-reactive protein dataset in the 2007–2008 National Health and Nutrition Examination Survey. This article has supplementary material online. KEY WORDS: Censored predictorCensored quantile regressionDetection limitImputationLinear regression M-estimatorNonignorable missingness Acknowledgments The research is partially supported by the NSF Award DMS-1007420 and the NSFC grant 11101254. The authors thank two anonymous reviewers, the associate editor, and the editor for constructive comments and helpful suggestions that led to a major improvement of the article. DA - 2012/3// PY - 2012/3// DO - 10.1080/01621459.2011.643198 VL - 107 IS - 497 SP - 194-204 SN - 1537-274X KW - Censored predictor KW - Censored quantile regression KW - Detection limit KW - Imputation KW - Linear regression KW - M-estimator KW - Nonignorable missingness ER - TY - JOUR TI - Hydrologic Performance of Bioretention Storm-Water Control Measures AU - Davis, Allen P. AU - Traver, Robert G. AU - Hunt, William F. AU - Lee, Ryan AU - Brown, Robert A. AU - Olszewski, Jennifer M. T2 - JOURNAL OF HYDROLOGIC ENGINEERING AB - The transportation and urban infrastructure relies heavily on impervious surfaces. Unmitigated rainfall runoff from impervious surfaces can lead to a myriad of environmental problems in downgradient areas. To address this issue, novel stormwater control measures (SCMs) are being emphasized and implemented widely to mitigate some of the impacts of impervious surface. Bioretention is a soil/media-based SCM that is often used for this purpose, but current design practices are highly empirical. This study compiles work from three research sites in three states to provide some fundamental underpinnings to bioretention design. Although all sites demonstrate different levels of performance, water volumetric performance trends are common to all. These trends are based on the available storage in the bioretention cell, termed herein as the Bioretention Abstraction Volume (BAV). The BAV is directly related to available media porosity and storage in the surface bowl. A finite capacity to completely store all runoff from smaller events is defined by the BAV. Normalization for this storage provides prediction for volumetric performance. Recommendations for bioretention design are provided. DA - 2012/5// PY - 2012/5// DO - 10.1061/(asce)he.1943-5584.0000467 VL - 17 IS - 5 SP - 604-614 SN - 1084-0699 KW - Stormwater KW - Runoff KW - Urban KW - Hydrology. ER - TY - JOUR TI - Comment AU - Crainiceanu, Ciprian M. AU - Staicu, Ana-Maria T2 - TECHNOMETRICS DA - 2012/5// PY - 2012/5// DO - 10.1080/00401706.2011.649821 VL - 54 IS - 2 SP - 120-122 SN - 0040-1706 ER - TY - JOUR TI - Autolytic Degradation of Skipjack Tuna during Heating As Affected by Initial Quality and Processing Conditions AU - Stagg, Nicola J. AU - Amato, Penny M. AU - Giesbrecht, Francis AU - Lanier, Tyre C. T2 - JOURNAL OF FOOD SCIENCE AB - Abstract: Several factors were studied as affecting protein degradation and texture of skipjack tuna muscle following ambient pressure thermal processing (precooking). These included degree of mushy tuna syndrome (MTS) evidenced in the raw meat, raw meat pH, abusive thawing/holding, and precooking temperature/time. Slurries and intact pieces from frozen skipjack tuna, either tempered for 2 h or thawed and held at 25 °C for 22 h (abusive treatment) were heated at temperatures ranging from 40 to 80 °C for up to 2 h, and also at 90 °C for 1 h, with or without prior adjustment of pH to 5 or 7 to favor cathepsin or calpain activity, respectively. Proteolysis of precooked samples was monitored by Lowry assay and SDS–PAGE; cooked texture of intact meat was measured using a Kramer shear press and by sensory profile analysis. Proteolysis maximally occurred in slurries of skipjack tuna muscle that had been abusively stored (22 h at 25 °C) and adjusted to pH 5 prior to heating at 55 °C. Intact pieces of tuna abusively thawed/held for 22 h with subsequent heating at 55 °C also evidenced the most proteolysis and were the least firm in texture. Raw fish that evidenced higher severity of MTS when raw displayed higher levels of proteolysis prior to cooking, which were further increased after cooking at 55 °C. Practical Application: The kinetic data presented here can be used to optimize processing conditions for skipjack tuna canning to minimize textural degradation and optimize quality. DA - 2012/2// PY - 2012/2// DO - 10.1111/j.1750-3841.2011.02543.x VL - 77 IS - 2 SP - C149-C155 SN - 1750-3841 KW - fish KW - meat KW - myosin KW - proteolysis KW - texture ER - TY - JOUR TI - A Monte Carlo based analysis of optimal design criteria AU - Banks, H. T. AU - Holm, Kathleen J. AU - Kappel, Franz T2 - JOURNAL OF INVERSE AND ILL-POSED PROBLEMS AB - Abstract. Optimal design methods (designed to choose optimal sampling distributions through minimization of a specific cost function related to the resulting error in parameter estimates) for inverse or parameter estimation problems are considered. We compare a recent design criteria, SE-optimal design (standard error optimal design) with the more traditional D-optimal and E-optimal designs. The optimal sampling distributions from each design are used to compute and compare standard errors; here the standard errors for parameters are computed using the optimal mesh along with Monte Carlo simulations as compared to asymptotic theory based standard errors. We illustrate ideas with two examples: the Verhulst–Pearl logistic population model and the standard harmonic oscillator model. DA - 2012/3// PY - 2012/3// DO - 10.1515/jip-2012-0201 VL - 20 IS - 1 SP - 1-37 SN - 1569-3945 KW - Optimal design methods KW - least squares inverse problems KW - Fisher information matrix KW - D-optimal KW - E-optimal KW - SE-optimal KW - Monte Carlo analysis ER - TY - JOUR TI - The Scientific Grand Challenges of the 21st Century for the Crop Science Society of America AU - Lauer, Joseph G. AU - Bijl, Caron Gala AU - Grusak, Michael A. AU - Baenziger, P. Stephen AU - Boote, Ken AU - Lingle, Sarah AU - Carter, Thomas AU - Kaeppler, Shawn AU - Boerma, Roger AU - Eizenga, Georgia AU - Carter, Paul AU - Goodman, Major AU - Nafziger, Emerson AU - Kidwell, Kimberlee AU - Mitchell, Rob AU - Edgerton, Michael D. AU - Quesenberry, Ken AU - Willcox, Martha C. T2 - CROP SCIENCE AB - ABSTRACT Crop science is a highly integrative science employing expertise from multiple disciplines to broaden our understanding of agronomic, turf, and forage crops. A major goal of crop science is to ensure an adequate and sustainable production of food, feed, fuel, and fiber for our world's growing population. The Crop Science Society of America (CSSA) identified key Grand Challenges which, when addressed, will provide the tools, technologies, and solutions required to meet these challenges. The Grand Challenges are: (i) Crop adaptation to climate change: Increase the speed with which agriculture can adapt to climate change by using crop science to address abiotic stresses such as drought and heat. (ii) Resistance to biotic stresses: Increase durability of resistance to biotic stresses that threaten yield and quality of major crops. (iii) Management for resource limited systems: Create novel crop cultivars and management approaches designed for problem soils and low‐input farming to increase economic prosperity for farmers and overcome world hunger. (iv) Crop management systems: Create novel crop management systems that are resilient in the face of changes in climate and rural demographics. (v) Biofuels: Develop sustainable biofuel feedstock cropping systems that require minimal land area, optimize production, and improve the environment. (vi) Bioresources: Genotyping the major crop germplasm collections to facilitate identification of gene treasures for breeding and genetics research and deployment of superior genes into adapted germplasm around the globe. These challenges are intended to be dynamic and change as societal needs evolve. Available funding and national prioritization will determine the rate that they will be addressed. DA - 2012/// PY - 2012/// DO - 10.2135/cropsci2011.12.0668 VL - 52 IS - 3 SP - 1003-1010 SN - 1435-0653 ER - TY - JOUR TI - Indicator Bacteria Performance of Storm Water Control Measures in Wilmington, North Carolina AU - Hathaway, J. M. AU - Hunt, W. F. T2 - JOURNAL OF IRRIGATION AND DRAINAGE ENGINEERING AB - Indicator bacteria are a common source of impairment in surface waters in the United States. Urban storm water runoff has been identified as a contributor to elevated indicator bacteria concentrations. Six storm water control measures (SCMs) were monitored in Wilmington, North Carolina, for E. coli and enterococci. Monitored SCMs included two storm water wet ponds, two bioretention cells, and two storm water wetlands. Sandier watersheds in Wilmington potentially lead to differences in SCM performance for indicator bacteria compared to SCMs implemented in clayey watersheds. Results showed E. coli and enterococci concentration reductions between 70 and 98% for the two wet ponds and a bioretention cell with a 60-cm-deep fill media. Other SCMs showed poor removal of indicator bacteria, in some cases negative, with storm water wetlands performing the poorest overall for the three SCM types. Further analysis showed that SCMs with high concentration reductions tended to have geometric mean effluent concentrations lower than the U.S. EPA’s target surface-water concentration for E. coli. Conversely, no SCM had a geometric mean effluent enterococci concentration lower than the U.S. EPA target value. SCM geometric mean effluent concentrations were typically higher during North Carolina’s swimming season between the beginning of April and the end of October, although no statistically significant relationship could be found (p<0.05). Despite a lack of statistically significant relationships, the potential for higher effluent indicator bacteria concentrations from SCMs during the peak recreational season may have implications for both public health and watershed management and should be further evaluated by the scientific community. DA - 2012/2// PY - 2012/2// DO - 10.1061/(asce)ir.1943-4774.0000378 VL - 138 IS - 2 SP - 185-197 SN - 1943-4774 KW - Storm water KW - Best management practice (BMP) KW - Indicator bacteria KW - Fecal coliform KW - E. coli KW - Enterococci KW - Storm water control measure (SCM) ER - TY - JOUR TI - Short-term response of small mammals following oak regeneration silviculture treatments AU - Raybuck, Amy L. AU - Moorman, Christopher E. AU - Greenberg, Cathryn H. AU - DePerno, Christopher S. AU - Gross, Kevin AU - Simon, Dean M. AU - Warburton, Gordon S. T2 - FOREST ECOLOGY AND MANAGEMENT AB - Upland, mixed-oak forests in the eastern United States have experienced widespread oak regeneration failure, largely due to cessation of anthropogenic disturbance. Silvicultural practices used to promote advance oak regeneration may affect ground-dwelling mammals. From May to August 2008 (pre-treatment), 2010 (first year post-treatment), and 2011 (second year post-treatment), we trapped small mammals to assess changes in species richness and abundance following experimental tests of three silvicultural treatments (prescribed burns, midstory herbicide applications, and shelterwood harvests) used to promote oak regeneration. We trapped small mammals in five replicates of each treatment and controls using Sherman live traps (2008 and 2010) and drift fences (2008, 2010, and 2011). From pre- to post-treatment, we evaluated the change in estimated peromyscid abundance and relative abundance of masked shrews (Sorex cinereus), smoky shrews (Sorex fumeus), and northern short-tailed shrews (Blarina brevicauda). Additionally, we evaluated the change in species richness across treatments for both sampling techniques. For all measures analyzed (i.e., species richness, peromyscid abundance, and relative abundance of shrews), the change from pre- to post-treatment did not differ among treatments. However, more masked shrews, smoky shrews, and northern short-tailed shrews were captured in 2011 (i.e., second year post-treatment) than in 2010 (i.e., first year post-treatment). Our research indicates that, in the short-term, small mammals (e.g., mice and shrews) can tolerate a wide range of forest disturbance following oak regeneration treatments. However, delayed treatment effects (e.g., additional post-herbicide midstory dieback) or additive changes following future treatments (e.g., prescribed burns following shelterwood harvests or multiple prescribed burns) may compound effects on small mammal populations, and should be assessed with long-term research (>2 years post-treatment). DA - 2012/6/15/ PY - 2012/6/15/ DO - 10.1016/j.foreco.2012.02.012 VL - 274 SP - 10-16 SN - 1872-7042 KW - Herbicide KW - Mice KW - Prescribed fire KW - Shelterwood harvest KW - Shrew KW - Southern Appalachians ER - TY - JOUR TI - Nonparametric Bayesian models for a spatial covariance AU - Reich, Brian J. AU - Fuentes, Montserrat T2 - STATISTICAL METHODOLOGY AB - A crucial step in the analysis of spatial data is to estimate the spatial correlation function that determines the relationship between a spatial process at two locations. The standard approach to selecting the appropriate correlation function is to use prior knowledge or exploratory analysis, such as a variogram analysis, to select the correct parametric correlation function. Rather that selecting a particular parametric correlation function, we treat the covariance function as an unknown function to be estimated from the data. We propose a flexible prior for the correlation function to provide robustness to the choice of correlation function. We specify the prior for the correlation function using spectral methods and the Dirichlet process prior, which is a common prior for an unknown distribution function. Our model does not require Gaussian data or spatial locations on a regular grid. The approach is demonstrated using a simulation study as well as an analysis of California air pollution data. DA - 2012/// PY - 2012/// DO - 10.1016/j.stamet.2011.01.007 VL - 9 IS - 1-2 SP - 265-274 SN - 1572-3127 KW - Covariance estimation KW - Dirichlet process prior KW - Particulate matter KW - Spectral density ER - TY - JOUR TI - Implied distributions in multiple change point problems AU - Aston, J. A. D. AU - Peng, J. Y. AU - Martin, D. E. K. T2 - STATISTICS AND COMPUTING AB - A method for efficiently calculating exact marginal, conditional and joint distributions for change points defined by general finite state Hidden Markov Models is proposed. The distributions are not subject to any approximation or sampling error once parameters of the model have been estimated. It is shown that, in contrast to sampling methods, very little computation is needed. The method provides probabilities associated with change points within an interval, as well as at specific points. DA - 2012/7// PY - 2012/7// DO - 10.1007/s11222-011-9268-6 VL - 22 IS - 4 SP - 981-993 SN - 1573-1375 KW - Finite Markov chain imbedding KW - Hidden Markov models KW - Change point probability KW - Run length distributions KW - Generalised change points KW - Waiting time distributions ER - TY - JOUR TI - Corrected-loss estimation for quantile regression with covariate measurement errors AU - Wang, Huixia Judy AU - Stefanski, Leonard A. AU - Zhu, Zhongyi T2 - BIOMETRIKA AB - We study estimation in quantile regression when covariates are measured with errors. Existing methods require stringent assumptions, such as spherically symmetric joint distribution of the regression and measurement error variables, or linearity of all quantile functions, which restrict model flexibility and complicate computation. In this paper, we develop a new estimation approach based on corrected scores to account for a class of covariate measurement errors in quantile regression. The proposed method is simple to implement. Its validity requires only linearity of the particular quantile function of interest, and it requires no parametric assumptions on the regression error distributions. Finite-sample results demonstrate that the proposed estimators are more efficient than the existing methods in various models considered. DA - 2012/6// PY - 2012/6// DO - 10.1093/biomet/ass005 VL - 99 IS - 2 SP - 405-421 SN - 0006-3444 KW - Corrected loss function KW - Laplace distribution KW - Measurement error KW - Normal distribution KW - Quantile regression KW - Smoothing ER - TY - JOUR TI - A zero-sum electromagnetic evader-interrogator differential game with uncertainty AU - Banks, H. T. AU - Hu, Shuhua T2 - APPLICABLE ANALYSIS AB - We consider dynamic electromagnetic evasion-interrogation games in which the evader can use ferroelectric material coatings to attempt to avoid detection while the interrogator can manipulate the interrogating frequencies to enhance detection. The resulting problem is formulated as a two-player zero-sum dynamic differential game in which the cost functional is based on the expected value of the intensity of the reflected signal. We show that there exists a saddle point for the relaxed form of this dynamic differential game in which the relaxed controls appear bilinearly in the dynamics governed by a partial differential equation. We also present a computational framework for construction of approximate saddle point strategies in feedback form for a special case of this relaxed differential game with strategies and payoff in the sense of Berkovitz. DA - 2012/// PY - 2012/// DO - 10.1080/00036811.2012.667081 VL - 91 IS - 4 SP - 645-674 SN - 1563-504X KW - electromagnetic evasion pursuit KW - uncertainty KW - differential games KW - theory and approximation KW - backward Kolmogorov equations ER - TY - JOUR TI - Variable selection for high dimensional Bayesian density estimation: application to human exposure simulation AU - Reich, B. J. AU - Kalendra, E. AU - Storlie, C. B. AU - Bondell, H. D. AU - Fuentes, M. T2 - Journal of the Royal Statistical Society. Series C, Applied Statistics DA - 2012/// PY - 2012/// VL - 61 SP - 47-66 ER - TY - JOUR TI - Field Evaluation of Storm-Water Control Measures for Highway Runoff Treatment AU - Winston, Ryan J. AU - Hunt, William F. AU - Kennedy, Shawn G. AU - Wright, Jason D. AU - Lauffer, Matthew S. T2 - JOURNAL OF ENVIRONMENTAL ENGINEERING AB - The thousands of kilometers of highways in North Carolina have the potential to generate large amounts of storm-water runoff. Thus, investigation of storm-water control measures (SCMs) for these somewhat unique linear catchments, where space is limited for SCM implementation, was needed. This study examined the quantity and quality of highway runoff at four sites over a 48-km stretch of Interstate 40 in the coastal plain of North Carolina. The highway had a 4-cm overlay of permeable asphalt, known as permeable friction course (PFC), which influenced the export of sediment-bound pollutants and produced median effluent concentrations of total suspended solids (TSS) of 8 mg/L, 8 mg/L, 9 mg/L, and 17 mg/L at the four sites, well below concentrations observed from standard asphalt highway runoff. Two vegetative filter strips (VFSs), two traditional dry swales, and two wetland swales were also tested for pollutant removal efficacy at the four highway research sites. The filter strips generally produced higher pollutant concentrations than the edge of pavement due to a lack of vegetative cover, substantial soil compaction, and high slopes. Total nitrogen (TN) median effluent concentrations were significantly lower for wetland swales (1.02 mg/L and 1.03 mg/L) than for dry swales (1.50 mg/L and 1.63 mg/L). TN load export appeared lower from wetland swales when compared with dry swales, potentially due to the greater number of nutrient removal mechanisms that are present in wetland swales. Maintenance of highway SCMs was shown to be extremely important, as one of the dry swales produced an effluent TSS concentration of 70 mg/L due to a head cut in the thalweg of the channel. As noted in other scientific literature, vegetative SCMs did not further reduce pollutant concentrations released by the PFC because TSS and sediment-bound pollutant concentrations seemingly were at or near irreducible concentrations. This study showed that incorporating wetland elements in the design of swales and the use of PFC should be considered by roadway designers. DA - 2012/1// PY - 2012/1// DO - 10.1061/(asce)ee.1943-7870.0000454 VL - 138 IS - 1 SP - 101-111 SN - 1943-7870 KW - Storm water KW - Highway runoff KW - Permeable friction course KW - Dry swale KW - Wetland swale KW - Filter strip KW - Nitrogen KW - Phosphorus KW - Sediment ER - TY - JOUR TI - Elastic net for Cox's proportional hazards model with a solution path algorithm AU - Wu, Y. C. T2 - Statistica Sinica DA - 2012/// PY - 2012/// VL - 22 IS - 1 SP - 271-294 ER - TY - JOUR TI - A predictive model for Efavirenz dosing AU - Brown, C. AU - Oki, N. O. AU - Hariani, G. AU - Motsinger-Reif, A. A. T2 - Pharmacogenomics DA - 2012/// PY - 2012/// VL - 13 IS - 2 SP - 137-138 ER - TY - JOUR TI - Nonparametric regression models for right-censored data using Bernstein polynomials AU - Osman, M. AU - Ghosh, Sujit K. T2 - Computational Statistics and Data Analysis AB - In some applications of survival analysis with covariates, the commonly used semiparametric assumptions (e.g., proportional hazards) may turn out to be stringent and unrealistic, particularly when there is scientific background to believe that survival curves under different covariate combinations will cross during the study period. We present a new nonparametric regression model for the conditional hazard rate using a suitable sieve of Bernstein polynomials. The proposed nonparametric methodology has three key features: (i) the smooth estimator of the conditional hazard rate is shown to be a unique solution of a strictly convex optimization problem for a wide range of applications; making it computationally attractive, (ii) the model is shown to encompass a proportional hazards structure, and (iii) large sample properties including consistency and convergence rates are established under a set of mild regularity conditions. Empirical results based on several simulated data scenarios indicate that the proposed model has reasonably robust performance compared to other semiparametric models particularly when such semiparametric modeling assumptions are violated. The proposed method is further illustrated on the gastric cancer data and the Veterans Administration lung cancer data. DA - 2012/// PY - 2012/// DO - 10.1016/j.csda.2011.08.019 VL - 56 IS - 3 SP - 559-573 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-80455143671&partnerID=MN8TOARS KW - Bernstein polynomials KW - Censored data KW - Nonparametric regression KW - Nonproportional hazards KW - Sieve ER - TY - JOUR TI - Modelling semi-continuous data using mixture regression models with an application to cattle production yields AU - Belasco, E.J. AU - Ghosh, Sujit K. T2 - Journal of Agricultural Science AB - SUMMARY The present paper develops a mixture regression model that allows for distributional flexibility in modelling the likelihood of a semi-continuous outcome that takes on zero value with positive probability while continuous on the positive half of the real line. A multivariate extension is also developed that builds on past multivariate models by systematically capturing the relationship between continuous and semi-continuous variables, while allowing for the semi-continuous variable to be characterized by a mixture model. The flexibility associated with this model provides potential applications in many production system studies. The empirical model is shown to provide a more accurate measure of mortality rates in cattle feedlots, both independently and within a system including other performance and health factors. DA - 2012/// PY - 2012/// DO - 10.1017/S0021859611000608 VL - 150 IS - 1 SP - 109-121 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84255178409&partnerID=MN8TOARS ER - TY - JOUR TI - Improving bioretention/biofiltration performance with restorative maintenance AU - Brown, Robert A. AU - Hunt, William F. T2 - WATER SCIENCE AND TECHNOLOGY AB - One of the most popular Stormwater Control Measures is bioretention, or biofiltration. Anecdotal evidence suggests that well-designed bioretention cells are often not adequately installed and that maintenance is lacking, leading to less-than-adequate water storage volume and/or surface infiltration rates post-construction. In March 2009, two sets of bioretention cells were repaired by excavating the top 75 mm of fill media, increasing the bioretention surface storage volume by nearly 90% and the infiltration rate by up to a factor of 10. Overflow volume decreased from 35 and 37% in the pre-repair state for two different sets of cells, respectively, to 11 and 12%. Nearly all effluent pollutant loads exiting the post-repair cells were lower than their pre-repair conditions. The bioretention systems employed two different media depths (0.6 and 0.9 m). The deeper media cells discharged less outflow volume than the shallower cells, with 10-11% more runoff volume leaving as exfiltration from the 0.9-m than from the 0.6-m media depth cells. This study showed that maintenance is both critical and beneficial to restore otherwise poorly performing bioretention. Moreover, while deeper media cells did outperform the shallower systems, the improvement in this case was somewhat modest vis-à-vis additional construction costs. DA - 2012/// PY - 2012/// DO - 10.2166/wst.2012.860 VL - 65 IS - 2 SP - 361-367 SN - 1996-9732 KW - bioretention KW - construction KW - LID KW - maintenance KW - media depth KW - runoff KW - stormwater KW - SUDS KW - WSUD ER - TY - JOUR TI - Enhanced Biomimetic Performance of Ionic Polymer-Metal Composite Actuators Prepared with Nanostructured Block Ionomers AU - Vargantwar, Pruthesh H. AU - Roskov, Kristen E. AU - Ghosh, Tushar K. AU - Spontak, Richard J. T2 - MACROMOLECULAR RAPID COMMUNICATIONS AB - Abstract Ionic polymer–metal composites (IPMCs) represent an important class of stimuli‐responsive polymers that are capable of bending upon application of an electric potential. Conventional IPMCs, prepared with Nafion and related polyelectrolytes, often suffer from processing challenges, relatively low actuation levels and back relaxation during actuation. In this study, we examine and compare the effects of fabrication and solvent on the actuation behavior of a block ionomer with a sulfonated midblock and glassy endblocks that are capable of self‐organizing and thus stabilizing a molecular network in the presence of a polar solvent. Unlike Nafion, this material can be readily dissolved and cast from solution to yield films that vary in thickness and exhibit enormous solvent uptake. Cycling the initial chemical deposition of Pt on the surfaces of swollen films (the compositing process) increases the extent to which the electrodes penetrate the films, thereby improving contact along the polymer/electrode interface. The maximum bending actuation measured from IPMCs prepared with different solvents is at least comparable, but is often superior, to that reported for conventional IPMCs, without evidence of back relaxation. An unexpected characteristic observed here is that the actuation direction can be solvent regulated. Our results confirm that this block ionomer constitutes an attractive alternative for use in IPMCs and their associated applications. DA - 2012/1/16/ PY - 2012/1/16/ DO - 10.1002/marc.201100535 VL - 33 IS - 1 SP - 61-68 SN - 1022-1336 KW - block ionomer KW - electroactive polymer KW - ionic polymer-metal composite KW - ion transport KW - polyelectrolyte KW - stimulti-responsive polymer ER - TY - JOUR TI - Circular conditional autoregressive modeling of vector fields AU - Modlin, Danny AU - Fuentes, Montserrat AU - Reich, Brian T2 - ENVIRONMETRICS AB - As hurricanes approach landfall, there are several hazards for which coastal populations must be prepared. Damaging winds, torrential rains, and tornadoes play havoc with both the coast and inland areas; but, the biggest seaside menace to life and property is the storm surge. Wind fields are used as the primary forcing for the numerical forecasts of the coastal ocean response to hurricane force winds, such as the height of the storm surge and the degree of coastal flooding. Unfortunately, developments in deterministic modeling of these forcings have been hindered by computational expenses. In this paper, we present a multivariate spatial model for vector fields, that we apply to hurricane winds. We parameterize the wind vector at each site in polar coordinates and specify a circular conditional autoregressive model for the vector direction, and a spatial CAR model for speed. We apply our framework for vector fields to hurricane surface wind fields for Hurricane Floyd of 1999 and compare our circular conditional autoregressive model to prior methods that decompose wind speed and direction into its N‐S and W‐E cardinal components. Copyright © 2011 John Wiley & Sons, Ltd. DA - 2012/2// PY - 2012/2// DO - 10.1002/env.1133 VL - 23 IS - 1 SP - 46-53 SN - 1180-4009 KW - CAR KW - circular statistics KW - cross-covariance KW - hurricane winds KW - spatial statistics ER - TY - JOUR TI - Analysis of quantitative disease resistance to southern leaf blight and of multiple disease resistance in maize, using near-isogenic lines AU - Belcher, Araby R. AU - Zwonitzer, John C. AU - Cruz, Jose Santa AU - Krakowsky, Mathew D. AU - Chung, Chia-Lin AU - Nelson, Rebecca AU - Arellano, Consuelo AU - Balint-Kurti, Peter J. T2 - THEORETICAL AND APPLIED GENETICS DA - 2012/2// PY - 2012/2// DO - 10.1007/s00122-011-1718-1 VL - 124 IS - 3 SP - 433-445 SN - 1432-2242 ER - TY - JOUR TI - Mixed model analysis of censored longitudinal data with flexible random-effects density AU - Vock, David M. AU - Davidian, Marie AU - Tsiatis, Anastasios A. AU - Muir, Andrew J. T2 - BIOSTATISTICS AB - Mixed models are commonly used to represent longitudinal or repeated measures data. An additional complication arises when the response is censored, for example, due to limits of quantification of the assay used. While Gaussian random effects are routinely assumed, little work has characterized the consequences of misspecifying the random-effects distribution nor has a more flexible distribution been studied for censored longitudinal data. We show that, in general, maximum likelihood estimators will not be consistent when the random-effects density is misspecified, and the effect of misspecification is likely to be greatest when the true random-effects density deviates substantially from normality and the number of noncensored observations on each subject is small. We develop a mixed model framework for censored longitudinal data in which the random effects are represented by the flexible seminonparametric density and show how to obtain estimates in SAS procedure NLMIXED. Simulations show that this approach can lead to reduction in bias and increase in efficiency relative to assuming Gaussian random effects. The methods are demonstrated on data from a study of hepatitis C virus. DA - 2012/1// PY - 2012/1// DO - 10.1093/biostatistics/kxr026 VL - 13 IS - 1 SP - 61-73 SN - 1468-4357 KW - Censoring KW - HCV KW - HIV KW - Limit of quantification KW - Longitudinal data KW - Random effects ER - TY - JOUR TI - Identifying damage locations under ambient vibrations utilizing vector autoregressive models and Mahalanobis distances AU - Mosavi, A. A. AU - Dickey, D. AU - Seracino, R. AU - Rizkalla, S. T2 - MECHANICAL SYSTEMS AND SIGNAL PROCESSING AB - This paper presents a study for identifying damage locations in an idealized steel bridge girder using the ambient vibration measurements. A sensitive damage feature is proposed in the context of statistical pattern recognition to address the damage detection problem. The study utilizes an experimental program that consists of a two-span continuous steel beam subjected to ambient vibrations. The vibration responses of the beam are measured along its length under simulated ambient vibrations and different healthy/damage conditions of the beam. The ambient vibration is simulated using a hydraulic actuator, and damages are induced by cutting portions of the flange at two locations. Multivariate vector autoregressive models were fitted to the vibration response time histories measured at the multiple sensor locations. A sensitive damage feature is proposed for identifying the damage location by applying Mahalanobis distances to the coefficients of the vector autoregressive models. A linear discriminant criterion was used to evaluate the amount of variations in the damage features obtained for different sensor locations with respect to the healthy condition of the beam. The analyses indicate that the highest variations in the damage features were coincident with the sensors closely located to the damages. The presented method showed a promising sensitivity to identify the damage location even when the induced damage was very small. DA - 2012/1// PY - 2012/1// DO - 10.1016/j.ymssp.2011.06.009 VL - 26 SP - 254-267 SN - 0888-3270 KW - Damage location KW - Ambient vibration KW - Vector Autoregressive model KW - Statistical pattern recognition KW - Bridges KW - Structural health monitoring ER - TY - JOUR TI - Sow and litter response to supplemental dietary fat in lactation diets during high ambient temperatures AU - Rosero, D. S. AU - Heugten, E. AU - Odle, J. AU - Cabrera, R. AU - Arellano, C. AU - Boyd, R. D. T2 - JOURNAL OF ANIMAL SCIENCE AB - The objective of this experiment was to determine the impact of supplemental dietary fat on total lactation energy intake and sow and litter performance during high ambient temperatures (27 ± 3°C). Data were collected from 337 mixed-parity sows from July to September in a 2,600-sow commercial unit in Oklahoma. Diets were corn-soybean meal-based with 7.5% corn distillers dried grains with solubles and 6.0% wheat middlings and contained 3.24 g of standardized ileal digestible Lys/Mcal of ME. Animal-vegetable fat blend (A-V) was supplemented at 0, 2, 4, or 6%. Sows were balanced by parity, with 113, 109, and 115 sows representing parity 1, 2, and 3 to 7 (P3+), respectively. Feed disappearance (subset of 190 sows; 4.08, 4.18, 4.44, and 4.34 kg/d, for 0, 2, 4, and 6%, respectively; P < 0.05) and apparent caloric intake (12.83, 13.54, 14.78, and 14.89 Mcal of ME/d, respectively; P < 0.001) increased linearly with increasing dietary fat. Gain:feed (sow and litter BW gain relative to feed intake) was not affected (P = 0.56), but gain:Mcal ME declined linearly with the addition of A-V (0.16, 0.15, 0.15, and 0.14 for 0, 2, 4, and 6%, respectively; P < 0.01). Parity 1 sows (3.95 kg/d) had less (P < 0.05) feed disappearance than P2 (4.48 kg/d) and P3+ (4.34 kg/d) sows. Body weight change in P1 sows was greater (P < 0.01) than either P2 or P3+ sows (-0.32 vs. -0.07 and 0.12 kg/d), whereas backfat loss was less (P < 0.05) and loin depth gain was greater (P < 0.05) in P3+ sows compared with P1 and P2 sows. Dietary A-V improved litter ADG (P < 0.05; 1.95, 2.13, 2.07, and 2.31 kg/d for 0, 2, 4, and 6% fat, respectively) only in P3+ sows. Sows bred within 8 d after weaning (58.3, 72.0, 70.2, and 74.7% for 0, 2, 4, and 6%, respectively); conception rate (78.5, 89.5, 89.2, and 85.7%) and farrowing rate (71.4, 81.4, 85.5, and 78.6%) were improved (P < 0.01) by additional A-V, but weaning-to-breeding interval was not affected. Rectal and skin temperature and respiration rate of sows were greater (P < 0.002) when measured at wk 3 compared with wk 1 of lactation, but were not affected by A-V addition. Parity 3+ sows had lower (P < 0.05) rectal temperature than P1 and P2 sows, and respiration rate was reduced (P < 0.001) in P1 sows compared with P2 and P3+ sows. In conclusion, A-V improved feed disappearance and caloric intake, resulting in improved litter weight gain and subsequent reproductive performance of sows; however, feed and caloric efficiency were negatively affected. DA - 2012/2// PY - 2012/2// DO - 10.2527/jas.2011-4049 VL - 90 IS - 2 SP - 550-559 SN - 0021-8812 KW - fat KW - heat stress KW - lactation KW - sow ER - TY - JOUR TI - Relative effects of fertilizer nitrogen form and phosphate level on control of bedding plant seedling growth AU - Nelson, P. V. AU - Song, C. Y. AU - Huang, J. S. AU - Niedziela, C. E. AU - Swallow, W. H. T2 - HortScience DA - 2012/// PY - 2012/// VL - 47 IS - 2 SP - 249-253 ER - TY - JOUR TI - Chang et al. Respond to "Environmental Exposures and Preterm Birth" AU - Chang, Howard H. AU - Reich, Brian J. AU - Miranda, Marie Lynn T2 - AMERICAN JOURNAL OF EPIDEMIOLOGY DA - 2012/1/15/ PY - 2012/1/15/ DO - 10.1093/aje/kwr406 VL - 175 IS - 2 SP - 111-112 SN - 1476-6256 ER - TY - JOUR TI - Association of Hexachlorobenzene (HCB), Dichlorodiphenyltrichloroethane (DDT), and Dichlorodiphenyldichloroethylene (DDE) with in Vitro Fertilization (IVF) Outcomes AU - Mahalingaiah, Shruthi AU - Missmer, Stacey A. AU - Maity, Arnab AU - Williams, Paige L. AU - Meeker, John D. AU - Berry, Katharine AU - Ehrlich, Shelley AU - Perry, Melissa J. AU - Cramer, Daniel W. AU - Hauser, Russ T2 - ENVIRONMENTAL HEALTH PERSPECTIVES AB - Background: Hexachlorobenzene (HCB), dichlorodiphenyltrichloroethane (DDT), and dichlorodiphenyldichloroethylene (DDE) are persistent chlorinated pesticides with endocrine activity that may adversely affect the early stages of human reproduction.Objective: Our goal was to determine the association of serum levels of HCB, DDT, and DDE with implantation failure, chemical pregnancy, and spontaneous abortion in women undergoing in vitro fertilization (IVF) from 1994 to 2003.Methods: Levels of HCB and congeners of DDT and DDE were measured in serum collected during the follicular phase. Multivariable-adjusted statistical models accommodating multiple outcomes and multiple cycles per woman were used to estimate the relation between serum pesticide levels and IVF outcomes.Results: A total of 720 women with a mean ± SD age 35.4 ± 4.2 years at enrollment contributed 774 IVF cycles. All samples had detectable levels of HCB, DDT, and DDE, with median levels of 0.087 ng/g serum for HCB, 1.12 ng/g serum for total DDT, and 1.04 ng/g serum for p,p´-DDE. Compared with the lowest quartile (Q1) of HCB, the lipid- and multivariable-adjusted odds ratio (OR) for failed implantation was significantly elevated for those with higher HCB quartiles [Q2–Q4; adjusted ORs: for Q2, 1.71; 95% confidence interval (CI): 1.03, 2.82; for Q3, 2.30; 95% CI: 1.39, 3.81; for Q4, 2.32; 95% CI: 1.38, 3.90] and showed a significantly increasing trend (p = 0.001). No statistically significant associations were observed between DDT/DDE and IVF outcomes or between HCB and chemical pregnancy or spontaneous abortion.Conclusions: Serum HCB concentrations were on average lower than that of the general U.S. population and associated with failed implantation among women undergoing IVF. DA - 2012/2// PY - 2012/2// DO - 10.1289/ehp.1103696 VL - 120 IS - 2 SP - 316-320 SN - 1552-9924 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84856736612&partnerID=MN8TOARS KW - assisted reproduction KW - dichlorodiphenyldichloroethylene KW - dichlorodiphenyltrichloroethane KW - hexachlorobenzene KW - prospective cohort ER -