Matching Items (11)
Description
Many longitudinal studies, especially in clinical trials, suffer from missing data issues. Most estimation procedures assume that the missing values are ignorable or missing at random (MAR). However, this assumption leads to unrealistic simplification and is implausible for many cases. For example, an investigator is examining the effect of treatment on depression. Subjects are scheduled with doctors on a regular basis and asked questions about recent emotional situations. Patients who are experiencing severe depression are more likely to miss an appointment and leave the data missing for that particular visit. Data that are not missing at random may produce bias in results if the missing mechanism is not taken into account. In other words, the missing mechanism is related to the unobserved responses. Data are said to be non-ignorable missing if the probabilities of missingness depend on quantities that might not be included in the model. Classical pattern-mixture models for non-ignorable missing values are widely used for longitudinal data analysis because they do not require explicit specification of the missing mechanism, with the data stratified according to a variety of missing patterns and a model specified for each stratum. However, this usually results in under-identifiability, because of the need to estimate many stratum-specific parameters even though the eventual interest is usually on the marginal parameters. Pattern mixture models have the drawback that a large sample is usually required. In this thesis, two studies are presented. The first study is motivated by an open problem from pattern mixture models. Simulation studies from this part show that information in the missing data indicators can be well summarized by a simple continuous latent structure, indicating that a large number of missing data patterns may be accounted by a simple latent factor. Simulation findings that are obtained in the first study lead to a novel model, a continuous latent factor model (CLFM). The second study develops CLFM which is utilized for modeling the joint distribution of missing values and longitudinal outcomes. The proposed CLFM model is feasible even for small sample size applications. The detailed estimation theory, including estimating techniques from both frequentist and Bayesian perspectives is presented. Model performance and evaluation are studied through designed simulations and three applications. Simulation and application settings change from correctly-specified missing data mechanism to mis-specified mechanism and include different sample sizes from longitudinal studies. Among three applications, an AIDS study includes non-ignorable missing values; the Peabody Picture Vocabulary Test data have no indication on missing data mechanism and it will be applied to a sensitivity analysis; the Growth of Language and Early Literacy Skills in Preschoolers with Developmental Speech and Language Impairment study, however, has full complete data and will be used to conduct a robust analysis. The CLFM model is shown to provide more precise estimators, specifically on intercept and slope related parameters, compared with Roy's latent class model and the classic linear mixed model. This advantage will be more obvious when a small sample size is the case, where Roy's model experiences challenges on estimation convergence. The proposed CLFM model is also robust when missing data are ignorable as demonstrated through a study on Growth of Language and Early Literacy Skills in Preschoolers.
ContributorsZhang, Jun (Author) / Reiser, Mark R. (Thesis advisor) / Barber, Jarrett (Thesis advisor) / Kao, Ming-Hung (Committee member) / Wilson, Jeffrey (Committee member) / St Louis, Robert D. (Committee member) / Arizona State University (Publisher)
Created2013
Description
In this era of fast computational machines and new optimization algorithms, there have been great advances in Experimental Designs. We focus our research on design issues in generalized linear models (GLMs) and functional magnetic resonance imaging(fMRI). The first part of our research is on tackling the challenging problem of constructing
exact designs for GLMs, that are robust against parameter, link and model
uncertainties by improving an existing algorithm and providing a new one, based on using a continuous particle swarm optimization (PSO) and spectral clustering. The proposed algorithm is sufficiently versatile to accomodate most popular design selection criteria, and we concentrate on providing robust designs for GLMs, using the D and A optimality criterion. The second part of our research is on providing an algorithm
that is a faster alternative to a recently proposed genetic algorithm (GA) to construct optimal designs for fMRI studies. Our algorithm is built upon a discrete version of the PSO.
exact designs for GLMs, that are robust against parameter, link and model
uncertainties by improving an existing algorithm and providing a new one, based on using a continuous particle swarm optimization (PSO) and spectral clustering. The proposed algorithm is sufficiently versatile to accomodate most popular design selection criteria, and we concentrate on providing robust designs for GLMs, using the D and A optimality criterion. The second part of our research is on providing an algorithm
that is a faster alternative to a recently proposed genetic algorithm (GA) to construct optimal designs for fMRI studies. Our algorithm is built upon a discrete version of the PSO.
ContributorsTemkit, M'Hamed (Author) / Kao, Jason (Thesis advisor) / Reiser, Mark R. (Committee member) / Barber, Jarrett (Committee member) / Montgomery, Douglas C. (Committee member) / Pan, Rong (Committee member) / Arizona State University (Publisher)
Created2014
Description
Quadratic growth curves of 2nd degree polynomial are widely used in longitudinal studies. For a 2nd degree polynomial, the vertex represents the location of the curve in the XY plane. For a quadratic growth curve, we propose an approximate confidence region as well as the confidence interval for x and y-coordinates of the vertex using two methods, the gradient method and the delta method. Under some models, an indirect test on the location of the curve can be based on the intercept and slope parameters, but in other models, a direct test on the vertex is required. We present a quadratic-form statistic for a test of the null hypothesis that there is no shift in the location of the vertex in a linear mixed model. The statistic has an asymptotic chi-squared distribution. For 2nd degree polynomials of two independent samples, we present an approximate confidence region for the difference of vertices of two quadratic growth curves using the modified gradient method and delta method. Another chi-square test statistic is derived for a direct test on the vertex and is compared to an F test statistic for the indirect test. Power functions are derived for both the indirect F test and the direct chi-square test. We calculate the theoretical power and present a simulation study to investigate the power of the tests. We also present a simulation study to assess the influence of sample size, measurement occasions and nature of the random effects. The test statistics will be applied to the Tell Efficacy longitudinal study, in which sound identification scores and language protocol scores for children are modeled as quadratic growth curves for two independent groups, TELL and control curriculum. The interpretation of shift in the location of the vertices is also presented.
ContributorsYu, Wanchunzi (Author) / Reiser, Mark R. (Thesis advisor) / Barber, Jarrett (Committee member) / Kao, Ming-Hung (Committee member) / St Louis, Robert D (Committee member) / Wilson, Jeffrey (Committee member) / Arizona State University (Publisher)
Created2015
Description
Hydrological models in arid and semi-arid ecosystems can be subject to high uncertainties. Spatial variability in soil moisture and evapotranspiration, key components of the water cycle, can contribute to model uncertainty. In particular, an understudied source of spatial variation is the effect of plant-plant interactions on water fluxes. At patch scales (plant and associated soil), plant neighbors can either negatively or positively affect soil water availability via competition or hydraulic redistribution, respectively. The aboveground microclimate can also be altered via canopy shading effects by neighbors. Across longer timescales (years), plants may adjust their physiological (water-use) traits in response to the neighbor-altered microclimate, which subsequently affects transpiration rates. The influence of physiological adjustments and neighbor-altered microclimate on water fluxes was assessed around Larrea tridentata in the Sonoran Desert. Field measurements of Larrea’s stomatal behavior and vertical root distributions were used to examine the effects of neighbors on Larrea’s physiological controls on transpiration. A modeling based approach was implemented to explore the sensitivity of evapotranspiration and soil moisture to neighbor effects. Neighbors significantly altered both above- and belowground physiological controls on evapotranspiration. Compared to Larrea growing alone, neighbors increased Larrea’s annual transpiration by up to 75% and 30% at the patch and stand scales, respectively. Estimates of annual transpiration were highly sensitive to the presence/absence of competition for water, and on seasonal timescales, physiological adjustments significantly influenced transpiration estimates. Plant-plant interactions can be a significant source of spatial variation in ecohydrological models, and both physiological adjustments to neighbors and neighbor effects on microclimate affect small scale (patch to ecosystem) water fluxes.
ContributorsKropp, Heather (Author) / Ogle, Kiona (Thesis advisor) / Hultine, Kevin (Committee member) / Sala, Osvaldo (Committee member) / Vivoni, Enrique (Committee member) / Wojciechowski, Martin (Committee member) / Arizona State University (Publisher)
Created2015
Description
Functional traits research has improved our understanding of how plants respond to their environments, identifying key trade-offs among traits. These studies primarily rely on correlative methods to infer trade-offs and often overlook traits that are difficult to measure (e.g., root traits, tissue senescence rates), limiting their predictive ability under novel conditions. I aimed to address these limitations and develop a better understanding of the trait space occupied by trees by integrating data and process models, spanning leaves to whole-trees, via modern statistical and computational methods. My first research chapter (Chapter 2) simultaneously fits a photosynthesis model to measurements of fluorescence and photosynthetic response curves, improving estimates of mesophyll conductance (gm) and other photosynthetic traits. I assessed how gm varies across environmental gradients and relates to other photosynthetic traits for 4 woody species in Arizona. I found that gm was lower at high aridity sites, varied little within a site, and is an important trait for obtaining accurate estimates of photosynthesis and related traits under dry conditions. Chapter 3 evaluates the importance of functional traits for whole-tree performance by fitting an individual-based model of tree growth and mortality to millions of measurements of tree heights and diameters to assess the theoretical trait space (TTS) of “healthy” North American trees. The TTS contained complicated, multi-variate structure indicative of potential trade-offs leading to successful growth. In Chapter 4, I applied an environmental filter (light stress) to the TTS, leading to simulated stand-level mortality rates up to 50%. Tree-level mortality was explained by 6 of the 32 traits explored, with the most important being radiation-use efficiency. The multidimentional space comprising these 6 traits differed in volume and location between trees that survived and died, indicating that selective mortality alters the TTS.
ContributorsFell, Michael (Author) / Ogle, Kiona (Thesis advisor) / Barber, Jarrett (Committee member) / Hultine, Kevin (Committee member) / Franklin, Janet (Committee member) / Day, Thomas (Committee member) / Arizona State University (Publisher)
Created2017
Climate Sensitivity in Mature Versus Pre-Reproductive Saguaro Determined from Spine Isotopic Signals
Description
The saguaro cactus is vital to the unique biodiversity of the Sonoran Desert. Many animals rely on it for survival and shelter. Due to its thick waxy exterior, it is able to retain a massive amount of water in its succulent stems, making it an ideal habitat for many birds that are native to the region. It also holds a large cultural significance for many native tribes of this region. Thus, it is important to understand how these magnificent plants are affected by changing environmental conditions in order to protect them in the future. Measurements of carbon isotope (13C) signals in saguaros spine tissues have been shown to be a robust approach for evaluating plant responses to climate variation over multiple seasons and years. This study investigated growth and 13C signals in young saguaros (< 2.5 m tall) at a location north of Phoenix to compare with large saguaros (> 4 m tall) that actively flower in the spring. Adolescent saguaros were examined to determine how they responded to variation in moisture between the years 2012 through 2016. As with a previous study by Hultine et al. (2018), this research demonstrated a strong relationship between height growth and precipitation. Stem growth was also highly correlated with the number of areoles produced across both young and old plants. Winter and late summer moisture from the previous year had a significant effect on stem growth, and a legacy effect could be seen in the low growth rates in 2014 which may be a result of low precipitation during the previous fall and winter. This study also established that the adolescent saguaro may be less sensitive to seasonal changes than the mature saguaro. When comparing the large plants with the adolescent plants, spine 13C values were similar between mature and adolescent plants, indicating that perhaps flower does not impose a significant added cost to saguaro water budgets. However, identifying the cost of flowering requires more investigation than that from only spine carbon isotope measurements and coarse measurements of plant productivity.
ContributorsDe Leon, Isabella (Author) / Hultine, Kevin (Thesis advisor) / Pigg, Kathleen (Thesis advisor) / Maienschein, Jane (Committee member) / Arizona State University (Publisher)
Created2021
Description
Xylem conduits, a primary feature of most terrestrial plant taxa, deliver water to photosynthetic tissues and play a critical role in plant water relations and drought tolerance. Non-succulent woody taxa generally follow a universal rate of tip-to-base conduit widening such that hydraulic resistance remains constant throughout the plant stem. Giant cacti inhabit arid regions throughout the Americas and thrive in water-limited environments by complimenting water-storing succulent tissues with resource-efficient Crassulacean Acid Metabolism. Considering these adaptations, the objectives of this study were threefold: 1) determine whether xylem conduits in columnar cacti follow universal scaling theory as observed in woody taxa; 2) evaluate whether xylem hydraulic diameter is inversely correlated with xylem vessel density; and 3) determine whether xylem double-wall thickness-to-span ratio and other hydraulic architectural traits are convergent among phylogenetically diverse cactus species. This thesis investigates the xylem anatomy of nine cactus species native to the Sonoran Desert of Arizona and Mexico, the tropical dry forests of southern Mexico, and the Alto Plano region of Argentina. Soft xylem tissues closest to the stem apex underwent a modified polyethylene glycol treatment to stabilize for sectioning with a sledge microtome. Across all species: hydraulic diameter followed a basipetal widening rate of 0.21 (p < 0.001), closely matching the universal rate of 0.20 for woody taxa; and xylem vessel density was inversely correlated with both length from stem apex (p < 0.001) and hydraulic diameter (p < 0.001). Double-wall thickness-to-span ratio had little to no significant correlation with either length from stem apex or hydraulic diameter. There was no significant difference in hydraulic architectural trait patterns between phylogenetically diverse species with various stem morphologies, nor was there a significant correlation between conduit widening rates and volume-to-surface-area ratios.
This study demonstrates that giant cacti follow similar internal anatomical constraints as non-succulent woody taxa, yet stem succulence and water storage behavior in cacti remain separate from internal hydraulic architecture, allowing cacti to thrive in arid environments. Understanding how cacti cope with severe water limitations provides new insights on evolutionary constraints of stem succulents as they functionally diverged from other life forms.
ContributorsCaspeta, Ivanna (Author) / Hultine, Kevin (Thesis advisor) / Throop, Heather (Thesis advisor) / Hernandez, Tania (Committee member) / Arizona State University (Publisher)
Created2023
Description
As climate change continues, understanding the water use strategies and water relations of cacti becomes even more important in conservation. Cacti are not only one of the most threatened taxonomic groups but also ecologically important to desert ecosystems. Water conservation strategies vary among species of columnar cacti as a tradeoff between photosynthetic and water storage capacities, such as the different volume-to-surface-area ratios in Carnegiea gigantea and Stenocereus thurberi. These variations in water and growth relations could be associated with the basipetal xylem vessel widening pattern that has been observed in many woody plant species, and most recently in cacti as well. This phenomenon provides a buffer to the accumulation of hydrodynamic resistance in xylem vessels as the plant stem elongates, and in cacti, stem water storage tissues (cortex and pith) also provide a buffer. This thesis investigates the rate of basipetal xylem conduit widening in Carnegiea gigantea and Stenocereus thurberi, with the expectation that columnar cacti will show similar rates of widening as other plants. I found that while the xylem conduits in both species widened at significantly different rates, the rate of widening was much lower than expected. While there are a few possible explanations, such as buffering from the succulent cortex tissue, more research on cactus xylem anatomy and its reflection in plant water conduction strategies is needed.
ContributorsCaspeta, Ivanna (Author) / Hultine, Kevin (Thesis director) / Throop, Heather (Thesis director) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2021-05
Description
Flowering phenology offers a sensitive and reliable biological indicator of climate change because plants use climatic and other environmental cues to initiate flower production. Drylands are the largest terrestrial biome, but with unpredictable precipitation patterns and infertile soils, they are particularly vulnerable to climate change. There is a need to increase our comprehension of how dryland plants might respond and adapt to environmental changes. I conducted a meta-analysis on the flowering phenology of dryland plants and showed that some species responded to climate change through accelerated flowering, while others delayed their flowering dates. Dryland plants advanced their mean flowering dates by 2.12 days decade-1, 2.83 days °C-1 and 2.91 days mm-1, respectively, responding to time series, temperature, and precipitation. Flowering phenology responses varied across taxonomic and functional groups, with the grass family Poaceae (-3.91 days decade1) and bulb forming Amaryllidaceae (-0.82 days decade1) showing the highest and lowest time series responses respectively, while Brassicaceae was not responsive. Analysis from herbarium specimens collected across Namibian drylands, spanning 26 species and six families, revealed that plants in hyper-arid to arid regions have lower phenological sensitivity to temperature (-9 days °C-1) and greater phenological responsiveness to precipitation (-0.56 days mm-1) than those in arid to semi-arid regions (-17 days °C-1, -0.35 days mm-1). The flowering phenology of serotinous plants showed greater sensitivity to both temperature and precipitation than that of non-serotinous plants. I used rainout shelters to reduce rainfall in a field experiment and showed that drought treatment advanced the vegetative and reproductive phenology of Cleome gynandra, a highly nutritional and medicinal semi-wild vegetable species. The peak leaf length date, peak number of leaves date, and peak flowering date of Cleome gynandra advanced by six, 10 and seven days, respectively. Lastly, I simulated drought and flood in a greenhouse experiment and found that flooding conditions resulted in higher germination percentage of C. gynandra than drought. My study found that the vegetative, and flowering phenology of dryland plants is responsive to climate change, with differential responses across taxonomic and functional groups, and aridity zones, which could alter the structure and function of these systems.
ContributorsKangombe, Fransiska Ndiiteela (Author) / Throop, Heather (Thesis advisor) / Sala, Osvaldo (Committee member) / Vivoni, Enrique (Committee member) / Pigg, Kathleen (Committee member) / Hultine, Kevin (Committee member) / Kwembeya, Ezekeil (Committee member) / Arizona State University (Publisher)
Created2023
Description
The southwestern US will experience more frequent heat waves, prolonged droughts, and declining water supply. Riparian ecosystems are particularly at-risk under climate change predictions, but little is known about the thermal tolerance of plant species inhabiting these ecosystems. Populus fremontii, a pioneer and foundation tree species in riparian ecosystems throughout the southwest, is of concern given its importance in driving community structure and influencing ecosystem processes. This study compared leaf thermal tolerance across populations of P. fremontii to determine if local adaptation affects leaf thermal tolerance. I hypothesized that warm-adapted (low-elevation) populations would have larger leaf thermal tolerance thresholds, thermal safety margins, and thermal time constants than cool-adapted (high-elevation) populations. I expected warm-adapted populations to maintain lower maximum leaf temperatures due to local adaptation affecting leaf thermal regulation. Using a common garden at the warm edge of this species’ range, I measured leaf thermal tolerance metrics in eight populations spanning a 1,200 m elevational gradient. Data collection occurred in May, during mild air temperatures, and in August, during high air temperatures. The first two metrics were leaf thermal tolerance thresholds. The critical temperature (Tcrit) is the temperature at which the electron transport capacity of PSII is disrupted. T50 is the temperature at which the electron transport capacity decreases to 50%. The next metric was thermal safety margins (TSMs), which reflect a leaf’s vulnerability to reaching thermal tolerance thresholds. TSMs are the difference between either Tcrit or T50 and an experienced environmental variable such as leaf or air temperature. The last metric was the thermal time constant (?), which is a trait that represents how quickly leaf temperatures respond to changes in air temperatures. Tcrit, T50, and ? were not correlated with elevation regardless of season, suggesting that acclimation or phenotypic plasticity is affecting these metrics. Conversely, TSMs using maximum leaf temperature were negatively correlated with elevation in August because warm-adapted populations maintained lower maximum leaf temperatures. These findings suggest that warm-adapted populations are locally adapted to maintain cooler leaf temperatures, which is critical for their future survival since they do not maintain higher leaf thermal tolerance thresholds than cool-adapted populations.
ContributorsMoran, Madeline (Author) / Hultine, Kevin (Thesis advisor) / Throop, Heather (Thesis advisor) / Butterfield, Bradley (Committee member) / Arizona State University (Publisher)
Created2022