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Poythress JC, Park C, Ahn J. Dimension-wise sparse low-rank approximation of a matrix with application to variable selection in high-dimensional integrative analyzes of association. J Appl Stat 2021; 49:3889-3907. [DOI: 10.1080/02664763.2021.1967892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- J. C. Poythress
- Department of Mathematics and Statistics, University of New Hampshire, Durham, NH, USA
| | - Cheolwoo Park
- Department of Mathematical Sciences, KAIST, Daejeon, The Republic of Korea
| | - Jeongyoun Ahn
- Department of Industrial and Systems Engineering, KAIST, Daejeon, The Republic of Korea
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Poythress JC, Ahn J, Park C. Low-rank, Orthogonally Decomposable Tensor Regression With Application to Visual Stimulus Decoding of fMRI Data. J Comput Graph Stat 2021. [DOI: 10.1080/10618600.2021.1951741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- J. C. Poythress
- Department of Mathematics and Statistics, University of New Hampshire, Durham, NC
| | - Jeongyoun Ahn
- Department of Industrial and Systems Engineering, KAIST, Daejeon, South Korea
| | - Cheolwoo Park
- Department of Mathematical Sciences, KAIST, Daejeon, South Korea
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Kaiser EE, Poythress JC, Scheulin KM, Jurgielewicz BJ, Lazar NA, Park C, Stice SL, Ahn J, West FD. An integrative multivariate approach for predicting functional recovery using magnetic resonance imaging parameters in a translational pig ischemic stroke model. Neural Regen Res 2021; 16:842-850. [PMID: 33229718 PMCID: PMC8178783 DOI: 10.4103/1673-5374.297079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Magnetic resonance imaging (MRI) is a clinically relevant, real-time imaging modality that is frequently utilized to assess stroke type and severity. However, specific MRI biomarkers that can be used to predict long-term functional recovery are still a critical need. Consequently, the present study sought to examine the prognostic value of commonly utilized MRI parameters to predict functional outcomes in a porcine model of ischemic stroke. Stroke was induced via permanent middle cerebral artery occlusion. At 24 hours post-stroke, MRI analysis revealed focal ischemic lesions, decreased diffusivity, hemispheric swelling, and white matter degradation. Functional deficits including behavioral abnormalities in open field and novel object exploration as well as spatiotemporal gait impairments were observed at 4 weeks post-stroke. Gaussian graphical models identified specific MRI outputs and functional recovery variables, including white matter integrity and gait performance, that exhibited strong conditional dependencies. Canonical correlation analysis revealed a prognostic relationship between lesion volume and white matter integrity and novel object exploration and gait performance. Consequently, these analyses may also have the potential of predicting patient recovery at chronic time points as pigs and humans share many anatomical similarities (e.g., white matter composition) that have proven to be critical in ischemic stroke pathophysiology. The study was approved by the University of Georgia (UGA) Institutional Animal Care and Use Committee (IACUC; Protocol Number: A2014-07-021-Y3-A11 and 2018-01-029-Y1-A5) on November 22, 2017.
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Affiliation(s)
- Erin E Kaiser
- Regenerative Bioscience Center; Neuroscience, Biomedical and Health Sciences Institute; Department of Animal and Dairy Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, USA
| | - J C Poythress
- Department of Statistics, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA
| | - Kelly M Scheulin
- Regenerative Bioscience Center; Neuroscience, Biomedical and Health Sciences Institute; Department of Animal and Dairy Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, USA
| | - Brian J Jurgielewicz
- Regenerative Bioscience Center; Neuroscience, Biomedical and Health Sciences Institute; Department of Animal and Dairy Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, USA
| | - Nicole A Lazar
- Department of Statistics, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA
| | - Cheolwoo Park
- Department of Statistics, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA
| | - Steven L Stice
- Regenerative Bioscience Center; Neuroscience, Biomedical and Health Sciences Institute; Department of Animal and Dairy Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, USA
| | - Jeongyoun Ahn
- Department of Statistics, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA
| | - Franklin D West
- Regenerative Bioscience Center; Neuroscience, Biomedical and Health Sciences Institute; Department of Animal and Dairy Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, USA
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Poythress JC, Lee MY, Young J. Planning and analyzing clinical trials with competing risks: Recommendations for choosing appropriate statistical methodology. Pharm Stat 2019; 19:4-21. [PMID: 31625290 DOI: 10.1002/pst.1966] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 04/15/2019] [Accepted: 06/05/2019] [Indexed: 12/14/2022]
Abstract
In the analysis of time-to-event data, competing risks occur when multiple event types are possible, and the occurrence of a competing event precludes the occurrence of the event of interest. In this situation, statistical methods that ignore competing risks can result in biased inference regarding the event of interest. We review the mechanisms that lead to bias and describe several statistical methods that have been proposed to avoid bias by formally accounting for competing risks in the analyses of the event of interest. Through simulation, we illustrate that Gray's test should be used in lieu of the logrank test for nonparametric hypothesis testing. We also compare the two most popular models for semiparametric modelling: the cause-specific hazards (CSH) model and Fine-Gray (F-G) model. We explain how to interpret estimates obtained from each model and identify conditions under which the estimates of the hazard ratio and subhazard ratio differ numerically. Finally, we evaluate several model diagnostic methods with respect to their sensitivity to detect lack of fit when the CSH model holds, but the F-G model is misspecified and vice versa. Our results illustrate that adequacy of model fit can strongly impact the validity of statistical inference. We recommend analysts incorporate a model diagnostic procedure and contingency to explore other appropriate models when designing trials in which competing risks are anticipated.
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Affiliation(s)
- J C Poythress
- Department of Statistics, University of Georgia, Athens, Georgia
| | - Misun Yu Lee
- Data Science, Astellas Pharma Inc., Northbrook, Illinois
| | - James Young
- Data Science, Astellas Pharma Inc., Northbrook, Illinois
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Affiliation(s)
- Hosik Choi
- Department of Applied Statistics, Kyonggi University, Suwon, Korea
| | - J. C. Poythress
- Department of Statistics, University of Georgia, Athens, GA, Georgia
| | - Cheolwoo Park
- Department of Statistics, University of Georgia, Athens, GA, Georgia
| | - Jong-June Jeon
- Department of Statistics, University of Seoul, Dongdaemun-gu, Seoul Korea
- Natural Science Research Institute, University of Seoul, Dongdaemun-gu, Seoul, Korea
| | - Changyi Park
- Department of Statistics, University of Seoul, Dongdaemun-gu, Seoul Korea
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Poythress JC, Affolter JM. Ecological Value of Native Plant Cultivars Versus Wild-Type Native Plants for Promoting Hemipteran Diversity in Suburban Areas. Environ Entomol 2018; 47:890-901. [PMID: 29668938 DOI: 10.1093/ee/nvy057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Indexed: 06/08/2023]
Abstract
Because of concerns over recent declines in overall biodiversity in suburban areas, homeowners are attempting to improve the ecological functioning of their landscapes by incorporating native plants. Native plants are important for supporting native herbivorous insects, but it is unknown whether the native plants that are commercially available, typically cultivated varieties (cultivars) of a single genotype, are equally effective as food sources as the local, wild-type plants. We compared the hemipteran communities feeding on cultivars and wild-propagated plants for four species of native perennials commonly used as ornamentals. Of 65 hemipteran species collected, 35 exhibited a preference for some plant species over others, indicating a high degree of host-plant specialization. Moreover, the insect community associated with cultivars was distinct from the insect community associated with wild-type plants for each plant species, with three to four insect species accounting for most of the observed difference. Total insect abundance and insect biomass differed between cultivars and wild-propagated plants, but the direction of the difference changed over time and was not consistent among plant species. Species richness and a diversity index (the Q statistic) did not differ between cultivars and wild-type plants. These data suggest that abundance and diversity of hemipteran insects does not depend on the source of the plant material per se, but rather on the particular characteristics of cultivars that distinguish them from the wild type.
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Affiliation(s)
- J C Poythress
- Department of Horticulture, University of Georgia, Athens, GA
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