Search results

Title: PARTNERSHIP AND PREDATION IN PLANT-BIOTIC INTERACTIONS : THEORY, METHODS, AND EVIDENCE
Creator: Rowe, Shawna L.
Date: 2022
Collection: Electronic Theses & Dissertations
Description: As sessile organisms, plants face an endless series of encounters with other living organisms in their environment. Ranging from the beneficial to the harmful, the pressures of these biotic interactions force plants to rapidly adapt to survive and thrive. This dissertation is aimed at addressing questions about the metabolism of plant interactions with herbivores and nutritional symbionts in legumes. Despite spanning different systems and methods, these questions reflect my interest in...
Show moreAs sessile organisms, plants face an endless series of encounters with other living organisms in their environment. Ranging from the beneficial to the harmful, the pressures of these biotic interactions force plants to rapidly adapt to survive and thrive. This dissertation is aimed at addressing questions about the metabolism of plant interactions with herbivores and nutritional symbionts in legumes. Despite spanning different systems and methods, these questions reflect my interest in understanding the biochemistry underlying ecological and evolutionary function and my desire to develop tools that enable the investigation of such questions. To this end, the work in this dissertation is aimed at building conceptual and methodological tools to enable more thorough investigations of plant symbioses and, more broadly, plant-biotic interactions across levels of biological organization.First, I present a framework for making predictions on evolutionary trajectories and origins of plant--microbe communication systems. By highlighting the prevalence of coercive interactions in plant--microbe interactions, I demonstrate the plausibility of such interactions types to be an evolutionary precursor to seemingly stable signaling mechanisms. This work aims to provide useful evolutionary context for investigations concerning the evolutionary stability and exploitation of signaling mechanisms in established biological relationships. Second, I present collaborative work in which we developed and applied a cost-effective, high-throughput protocol for quantifying multiple biochemical defense responses from small quantities of plant tissue using spectrophotometric techniques. This protocol was then applied on two distinct populations of the legume Medicago polymorpha to investigate how changes defensive traits in responses to altered selective pressures have manifested over the course of novel range expansion. Our work demonstrated the feasibility and potential of assessing defense responses across plant populations. Further, the work documents a shift in herbivore preference of plants from familiar and unfamiliar ranges by demonstrating a herbivore preference for plant tissues with pre-induced defenses over uninduced tissues from an unfamiliar geographic range. Finally, I demonstrate the creation, construction, and validity of a novel microcosm system for assessing nutrient exchange in the symbiotic mutualism between plants and arbuscular mycorrhizal fungi (AMF). The novel system is reliable, biologically-relevant, durable, and sufficiently simple and cost-effective to deploy. I demonstrate the validity of the microcosm system and discuss in-progress work which demonstrates its potential to rigorously investigate unknown aspects of the plant-AMF mutualism. Taken together, these developments and suggestions contribute to the growing set of methods and frameworks developed for improving our understanding a various plant-biotic interactions.
Show less

Title: CLICKABLE POLY(PROPARGYL METHACRYLATE) PREPARED BY ATOM TRANSFER RADICAL POLYMERIZATION AND ITS DERIVATIVES AS ENZYME STABILIZERS
Creator: Hsiao, Po-Jen
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Enzymes are nearly perfect catalysts with excellent selectivity and high turnover frequencies. A long-standing goal has been enabling enzymes to operate ex vivo in non-aqueous solvents, but the structures of native enzymes are typically compromised under these conditions. Polymer-enzyme bioconjugates have shown some promise—albeit limited—in this regard. The clickable poly(propargyl methacrylate) (PPMA) was proposed as a platform to enhance different polymer structures versus the residual...
Show moreEnzymes are nearly perfect catalysts with excellent selectivity and high turnover frequencies. A long-standing goal has been enabling enzymes to operate ex vivo in non-aqueous solvents, but the structures of native enzymes are typically compromised under these conditions. Polymer-enzyme bioconjugates have shown some promise—albeit limited—in this regard. The clickable poly(propargyl methacrylate) (PPMA) was proposed as a platform to enhance different polymer structures versus the residual enzymatic activities. The degree of polymerization and polydispersity are two factors that affect the polymer properties and can affect the enzymatic activities of the polymer-enzyme bioconjugates. The literature examples of PPMA with degree of polymerization greater than 200 are limited. In the atom transfer radical polymerization (ATRP) conditions we discovered, the degree of polymerization and the polydispersity of poly(trimethylsilylpropargyl methacrylate) (PTMSPMA) can be precisely adjusted by the initiator and monomer ratio, the copper catalyst loading, and the reducing agent loading (copper wire). After deprotection, PPMA is further reacted with different mole fraction compositions of hydrophilic triethylene glycol monomethyl ether (mDEG) azide and hydrophobic dodecyl azide to prepare amphiphilic polymers as enzyme stabilizers. The activities of the model enzyme, Subtilisin Carlsberg (SC), and polymer-SC bioconjugates were determined by 4-nitrophenolate and 4-thiopyridone assays, and the polymer-enzyme bioconjugate SC@82%mDEG-PPMA was found to be more active than SC alone in toluene. The SC@82%mDEG-PPMA is also more active than SC@100%mDEG-PPMA in 4-nitrophenolate assay, proving that the side chain structure of the polymer micelles can affect the polymer-enzyme bioconjugates. The micelle 80%mDEG-PPMA may isolate the enzyme from the bulk toluene better than 100%mDEG-PPMA. Deprotonated amino acid salts are great alternatives to the synthesized alkylamines as post-combustion CO2 absorbents due to their non-toxic and low volatile nature. For CO2 capture, gas uptake was measured when solutions of monodeprotonated amino acids were sparged with CO2. The speciation between dissolved CO32–, HCO3– , and CO2(aq), and CO2 captured as carbamates of the deprotonated amino acids, was quantified by 13C{1H} and 1H NMR spectroscopy. Less hindered amino acids like glycine tend to have faster CO2 absorption kinetic and higher carbamate concentrations due to the formation of relatively stable carbamates. One equivalent of carbamate forms requires one equivalent of amino acid as sacrificial base. Therefore, the formation of carbamate decreases the total CO2 absorption capacity and is an unfavorable pathway for CO2 capture. While the amino acids containing substituents at the α carbon atom adjacent to the amino group, like alanine and proline, destabilize their carbamates by unfavorable steric interaction and lead to carbamate hydrolysis to CO32–/HCO3– and enhance the CO2 capture capacity. Therefore, mixing different amino acids can have the fast absorption kinetics and higher absorption capacity. Based on the results, the mixture amino acid solutions were observed to have higher CO2 absorption capacity than the single amino acid counterparts.
Show less

Title: UNDERSTANDING THE GENETIC BASIS OF HUMAN DISEASES BY COMPUTATIONALLY MODELING THE LARGE-SCALE GENE REGULATORY NETWORKS
Creator: Wang, Hao
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Many severe diseases are known to be caused by the genetic disorder of the human genome, including breast cancer and Alzheimer's disease. Understanding the genetic basis of human diseases plays a vital role in personalized medicine and precision therapy. However, the pervasive spatial correlations between the disease-associated SNPs have hindered the ability of traditional GWAS studies to discover causal SNPs and obscured the underlying mechanisms of disease-associated SNPs. Recently, diverse...
Show moreMany severe diseases are known to be caused by the genetic disorder of the human genome, including breast cancer and Alzheimer's disease. Understanding the genetic basis of human diseases plays a vital role in personalized medicine and precision therapy. However, the pervasive spatial correlations between the disease-associated SNPs have hindered the ability of traditional GWAS studies to discover causal SNPs and obscured the underlying mechanisms of disease-associated SNPs. Recently, diverse biological datasets generated by large data consortia provide a unique opportunity to fill the gap between genotypes and phenotypes using biological networks, representing the complex interplay between genes, enhancers, and transcription factors (TF) in the 3D space. The comprehensive delineation of the regulatory landscape calls for highly scalable computational algorithms to reconstruct the 3D chromosome structures and mechanistically predict the enhancer-gene links. In this dissertation, I first developed two algorithms, FLAMINGO and tFLAMINGO, to reconstruct the high-resolution 3D chromosome structures. The algorithmic advancements of FLAMINGO and tFLAMINGO lead to the reconstruction of the 3D chromosome structures in an unprecedented resolution from the highly sparse chromatin contact maps. I further developed two integrative algorithms, ComMUTE and ProTECT, to mechanistically predict the long-range enhancer-gene links by modeling the TF profiles. Based on the extensive evaluations, these two algorithms demonstrate superior performance in predicting enhancer-gene links and decoding TF regulatory grammars over existing algorithms. The successful application of ComMUTE and ProTECT in 127 cell types not only provide a rich resource of gene regulatory networks but also shed light on the mechanistic understanding of QTLs, disease-associated genetic variants, and high-order chromatin interactions.
Show less

Title: RECREATIONAL CANNABIS LEGALIZATION : PREDICTING LOCAL POLICY ADOPTION AND ESTIMATING THE ASSOCIATED EFFECTS ON POPULATION CANNABIS USE
Creator: Montgomery, Barrett Wallace
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Cannabis is undergoing a remarkable transformation from a regulated drug to a recreationally legal one in the United States (U.S.). Yet, in states that have legalized recreational cannabis, there is substantial geographic variability in actual cannabis policies and the effects of cannabis legalization are still being debated. This dissertation addresses these modern scientific issues of the recreational cannabis landscape. The population under study primarily includes non-institutionalized U...
Show moreCannabis is undergoing a remarkable transformation from a regulated drug to a recreationally legal one in the United States (U.S.). Yet, in states that have legalized recreational cannabis, there is substantial geographic variability in actual cannabis policies and the effects of cannabis legalization are still being debated. This dissertation addresses these modern scientific issues of the recreational cannabis landscape. The population under study primarily includes non-institutionalized U.S. civilian residents, sampled and assessed in successive waves of the National Survey on Drug Use and Health (NSDUH) starting in 2008 through 2019. Estimates on drug use and mental illness prevalences are aggregated to the county level for the first aim, and to the state level for the second and third aims. In the first aim, the county-level data are linked to several other publicly available sources of information on all 3,142 U.S. counties including the 2010 Census, 2012 presidential election, and recreational cannabis sales policies. I then used these data to train a machine learning algorithm to predict which counties allowed for the recreational sale of cannabis in 2014. In the second aim, I used state-level estimates of cannabis incidence in an event study model to estimate the effects of legalizing recreational cannabis on cannabis use onsets for persons under and over the legal minimum age of 21. The final aim focuses specifically on 21 year-olds to better understand the implications for setting a legal minimum age drug policy on age-specific patterns of incidence and proposes a theoretical framework that may help understand these findings. For the first aim, the model-averaging predictions classified almost 94% of the U.S. counties correctly. The main factors associated with county-level recreational cannabis laws were the prevalences of past-month cannabis use and past-year cocaine use. In the second aim, I found that for those who were legally able to purchase cannabis (21 and older), cannabis legalization did not appear to affect incidence in the first year following legalization. Even so, between two and four years after legalization, the difference in differences modeling disclosed statistically robust increases of 0.6% for this sub-population of adults. After four years, the estimated increase is 1.3%. The corresponding estimates for underage persons who were ineligible to legally purchase cannabis show no appreciable differences in the occurrence in past-year cannabis use incidence. Finally, the age-specific incidence estimates for 21-year-olds show a rise after the passage of recreational cannabis laws (RCL) and are suggestive of the arrival of a new pattern of age-specific incidence. Taken together, the work and results of this dissertation point toward four potential conclusions. First, cannabis legalization might depend on a predictable process driven in part by prior drug use in each jurisdiction. Second, once implemented, recreational cannabis legalization might not have effects on adolescent onset newly incident cannabis use. Third, for adults permitted to buy cannabis without penalty, the occurrence of newly incident cannabis use might increase. Fourth, a tentative conclusion is that legalization of retail sales to adults removes a barrier for adults who had been interested in trying cannabis, but did not do so, perhaps due to concerns about legal or social consequences faced before legalization.
Show less

Title: The Geography and Recent Activity of Lake Michigan’s Coastal Sand Dunes
Creator: McKeehan, Kevin G.
Date: 2022
Collection: Electronic Theses & Dissertations
Description: This dissertation attempts to fill a gap in knowledge regarding conditions amongst the dunefields of Lake Michigan’s eastern shore. Much is now known about the evolution and geochronology of these unique freshwater dune systems. The region’s coastal dunes began forming during the Nipissing high stand phase (~5.5ka) of ancestral Lake Michigan. Since then, according to the chronology constructed from several studies, the coastal dunes then underwent several periods of stability and instability...
Show moreThis dissertation attempts to fill a gap in knowledge regarding conditions amongst the dunefields of Lake Michigan’s eastern shore. Much is now known about the evolution and geochronology of these unique freshwater dune systems. The region’s coastal dunes began forming during the Nipissing high stand phase (~5.5ka) of ancestral Lake Michigan. Since then, according to the chronology constructed from several studies, the coastal dunes then underwent several periods of stability and instability along the entire shoreline. However, questions remain regarding dune conditions and variability since ~1900. The goal of this dissertation was to determine if changes have occurred to the region’s coastal dune systems in the last ~120 years and what might be driving those changes. Given that dune systems are sensitive to biotic and abiotic variables, examining the last ~120 years of dune behavior could potentially reveal how Lake Michigan coastal dunes are responding to anthropogenic climate change and human development.Three studies, each comprising a dissertation chapter (Chapters 2-4), were conducted to help close this knowledge gap. Each chapter is broadly linked through an ecogeomorphic lens, particularly through the relationship between dunes and vegetation, which are interconnected in important ways. In Chapter 2, changes in dunefield vegetation and morphology were determined at several locations along the eastern Lake Michigan shoreline through the use of ground-level repeat photography. The second dissertation study – Chapter 3 – concerns the spatiotemporal analysis of historical changes of blowouts, which are important indicators of significant disturbance in the dunes. In this chapter, blowouts were mapped from aerial images at three timestamps – 1938, 1986-8, and 2018 – and the changes quantified. Chapter 4, the final dissertation study, explores the relationship between terrain ruggedness and vegetation in a coastal dunefield along Lake Michigan by calculating two terrain indices – Riley’s Terrain Ruggedness Index (TRI) and Sappington’s Vector Ruggedness Measure (VRM) – and the Soil-Adjusted Vegetation Index (SAVI). Through a land systems framework, the results were compared to determine if any correlation exists between the ruggedness of dunes and vegetation.In the first two dissertation studies, the results show a clear expansion of vegetation at the expense of previously bare sand. In the final study, the values from TRI and VRM and the values from the Soil-Adjusted Vegetation Index (SAVI) were not correlated overall, especially where one type of vegetation was dominant. However, within one land system – the dune barrens -- a moderate-to-strong negative correlation existed between terrain ruggedness and vegetation. Moreover, evidence suggests that vegetation has transformed the dune barrens land system area within the modern period. Overall, the results of these three studies demonstrate that vegetation is expanding over previously bare surfaces in coastal dunes along the eastern shore of Lake Michigan and has a considerable influence on regional dune conditions. While the precise driver(s) of this transformation is unclear, the regional-scale nature of these results suggests a uniform control is affecting these changes. As described in this dissertation, it is possible that an increase in precipitation since the 1930s, elevated atmospheric CO2 and N concentrations, a reduction in wind power, some other change in climate drivers, or a combination of many factors is responsible for the expansion in vegetation. It is also possible the trend in vegetation growth in Lake Michigan’s coastal dunes is a lagged response to an earlier climate event.
Show less

Title: The water-energy-food nexus assessments of carbon neutral efforts
Creator: Xie, Yachen
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Efforts toward carbon neutrality are crucial for humans' well-being and the environment. Currently, two main ongoing carbon mitigation efforts are enhancing carbon sequestration and reducing carbon emissions. However, there are debates regarding the tradeoffs of these two efforts' related policies and action plans. This dissertation investigates and assesses the tradeoffs of carbon neutral efforts from a WEF nexus perspective. Three typical efforts were selected as assessment targets to...
Show moreEfforts toward carbon neutrality are crucial for humans' well-being and the environment. Currently, two main ongoing carbon mitigation efforts are enhancing carbon sequestration and reducing carbon emissions. However, there are debates regarding the tradeoffs of these two efforts' related policies and action plans. This dissertation investigates and assesses the tradeoffs of carbon neutral efforts from a WEF nexus perspective. Three typical efforts were selected as assessment targets to answer the overarching question of how carbon neutral efforts would affect the water-energy-food (WEF) nexus. The Chinese conversion of cropland to forestland program (CCFP) is representative of carbon sequestration. The hydropower development in MRB is an example of the energy transition to reduce emissions. The coal power industry is the coupling effort of energy transition and carbon capture, utilization, and storage (CCUS) applications in reducing carbon emissions. This dissertation consists of three main chapters, each corresponding to a journal article to address the three assessment targets. In Chapter 2, I evaluated the accomplishment of CCFP in China and its WEF nexus tradeoffs by applying remote sensing images from 2001 to 2019. The WEF assessment includes the transition matrix generation and the water yield calculation of the converted cropland and irrigation land. Indices related to WEF systems are also considered. In Chapter 3, a diagnostic approach with ten indicators was developed to assess the unilateral change's impacts on the WEF nexus. Using the diagnostic method, I provided statistical evidence of the benefits and tradeoffs of water, energy, food, economic prosperity, and the environment surrounding hydro dams in the Mekong River Basin. In Chapter 4, a scenario-based, life cycle coal power production assessment tool was proposed. By evaluating three portfolios or scenarios, the tradeoffs between reducing coal power production and CCUS application were revealed. This dissertation has successfully assessed the primary tradeoffs of carbon mitigation efforts from the WEF nexus perspective. The three studies can be wrapped up and come to three major conclusions: 1) The cons of major carbon mitigation efforts on WEF nexus and local sustainability exist, but not as speculated, especially for the CCFP and the hydropower dam construction. 2) The carbon neutral policies in China can accomplish their goals if adequately implemented. 3) The adaptive equilibrium between the CCUS application and coal power production reduction in China is crucial and needs to be better planned. The dissertation can enrich the carbon neutrality debate and fill gaps in the current literature on WEF nexus tradeoff studies on carbon mitigation by providing a remote-sensing approach and detailed coal modeling tools. The assessment tools proposed in Chapters 3 and 4 can be widely used by policymakers to understand better the tradeoffs regarding sustainability and WEF nexus in carbon neutral efforts.
Show less

Title: CRANIAL METRIC AND NONMETRIC VARITION IN SOUTHEAST MEXICO AND GUATEMALA : IMPLICATIONS FOR POPULATION AFFINITY ASSESSMENT IN THE UNITED STATES
Creator: Kamnikar, Kelly Rae
Date: 2022
Collection: Electronic Theses & Dissertations
Description: The scientific identification of unknown human skeletal remains in forensic contexts relies heavily on the estimation of demographic parameters (i.e., sex, age, stature, and population affinity). Population affinity, or the likelihood of group relatedness to a defined population of a decedent, can be estimated using measurements and observations from the cranial and postcranial skeleton. These estimations may be less accurate among populations which have been pooled together based on...
Show moreThe scientific identification of unknown human skeletal remains in forensic contexts relies heavily on the estimation of demographic parameters (i.e., sex, age, stature, and population affinity). Population affinity, or the likelihood of group relatedness to a defined population of a decedent, can be estimated using measurements and observations from the cranial and postcranial skeleton. These estimations may be less accurate among populations which have been pooled together based on convention. Latin American individuals—with geographic origins widely distributed throughout Central and South America—are broadly pooled together under the blanket term Hispanic with little regard for the immense cultural and biological diversity represented by these groups. Consequently, forensic anthropologists may be unintentionally disregarding genetic diversity, population structure, and population history and their impact on the formation and morphology of these groups. The purpose of this dissertation is to investigate variation in craniofacial morphology and develop population affinity models for Latin American groups using cranial metric and nonmetric data. The intent is to move beyond a single classification level (i.e., Hispanic) to more refined levels based on geographic origins (e.g., Guatemala, Southeast Mexico). The broad category of Hispanic was adopted by forensic anthropologists in large part because it is still used in medicolegal death investigations in the U.S. to describe individuals with familial origins in Latin America, Spain, and the Caribbean (U.S. Census Bureau 2021). Since the term Hispanic does not narrow down the region of origin for unidentified human remains, it is uninformative for identification and repatriation purposes, particularly regarding forensic investigations along the southern U.S. border. In this context, population affinity estimation benefits from refinement of a broad category to a more focused, population-level group. Craniometric and cranial macromorphoscopic (MMS) data are collected from samples in Guatemala City, Guatemala and Mérida, Mexico—with strong support from the forensic anthropologists in these countries—to capture aspects of skeletal variation associated with these regions. Biological distance and population affinity models are assessed and comparative data from other Latin American and U.S. populations are used to assess how well these model skeletal variation. Biological distance analysis demonstrates that Latin American populations, including the Meridian and Guatemala sample are distinct. Classification models obtain varying accuracy rates; the combined craniometric and cranial MMS model had the highest classification accuracy (70.7%). This study provides further support for the refinement of this broad category and is important for future investigations involved in identification efforts along the U.S.-Mexico border.
Show less

Title: Circuit-Specific Inhibition of Dopaminergic Signaling Associated with Phantom Gustatory Sensations in Disrupted-in-Schizophrenia-1 Mice
Creator: Fry, Benjamin R.
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Schizophrenia is a severe neuropsychiatric disorder characterized by a suite of symptoms occurring across cognitive (delayed processing, paraphasia, attentional deficits), negative (anhedonia, blunted affect, catatonia), and positive (hallucinations, delusions) domains. Antipsychotics are the most commonly prescribed medication to treat positive symptoms, however their use is complicated by substantial side-effects and inadequate efficacy. This reflects a lack of progress in understanding the...
Show moreSchizophrenia is a severe neuropsychiatric disorder characterized by a suite of symptoms occurring across cognitive (delayed processing, paraphasia, attentional deficits), negative (anhedonia, blunted affect, catatonia), and positive (hallucinations, delusions) domains. Antipsychotics are the most commonly prescribed medication to treat positive symptoms, however their use is complicated by substantial side-effects and inadequate efficacy. This reflects a lack of progress in understanding the precise neurobiological mechanisms underlying these symptoms, due in part to a lack of appropriate preclinical animal models. Here, I used an animal model of genetic vulnerability for neuropsychiatric illness known as Disrupted-in-schizophrenia-1 (DISC-1) to examine impaired reality testing, which reflects an aberrant internal representation of an absent event. In mice, this can be observed by an associatively evoked perception of an absent sweet taste. This effect is dopaminergically-dependent and associated with elevated activity in the insular cortex (IC). By combining sophisticated Pavlovian behavioral procedures with chemogenetic inhibition of dopamine neurons projecting from the ventral tegmental area (VTA) to the IC, I show that inactivation of the VTA --> IC dopaminergic circuitry leads to impaired reality testing in wild-type mice, and that DISC-1 mice have significantly less dopamine neurons which send projections to the IC, specifically. These data yield new insights with regard to the neurobiology underlying reality testing and the functional anatomical outcomes following perturbations of the DISC-1 genetic locus. My studies also suggest potential targets for the development of novel pharmacological treatments in humans with schizophrenia.
Show less

Title: EXPRESSION AND ROLES OF BLASTOCYST LINEAGE-DETERMING GENES DURING SOMATIC CELL REPROGRAMMING
Creator: Moauro, Alexandra
Date: 2022
Collection: Electronic Theses & Dissertations
Description: In order to properly use stem cells, it is important that we first understand how these cells are establish and maintained. One of the most widely used stem cells are induced pluripotent stem cells (iPSCs) which provide great therapeutic promise and a novel source of ethical stem cells for research models. iPSCs are created by overexpression Oct4, Sox2, Klf4 and c-Myc (OSKM) in a somatic cell. As studies have sought to improve reprogramming efficiency and develop the most embryonically...
Show moreIn order to properly use stem cells, it is important that we first understand how these cells are establish and maintained. One of the most widely used stem cells are induced pluripotent stem cells (iPSCs) which provide great therapeutic promise and a novel source of ethical stem cells for research models. iPSCs are created by overexpression Oct4, Sox2, Klf4 and c-Myc (OSKM) in a somatic cell. As studies have sought to improve reprogramming efficiency and develop the most embryonically identical stem cells, our lab has uncovered that OSKM is not a specific cocktail for pluripotency formation. Instead OSKM induces additional cell fates including the formation of a multipotent stem cell termed induced extraembryonic endoderm stem (iXEN) cells. This raises the question as to how two distinct stem cell types arise in parallel. Interestingly, in embryo development we observe the same pluripotent and multipotent extraembryonic endoderm lineages form in parallel. Using our knowledge of normal embryo development, I set out to identify what blastocyst lineage markers can help us identify early iPSC and iXEN colonies as they start to form and mature. Of these markers, we observed that endogenous OCT4 is expressed in both iXEN and iPSC colonies. Based on the expression pattern of the key embryonic transcription factor, OCT4, we further focused on how this transcription factor may have a dual role in establishing iPSC and iXEN fates. Lastly, we altered the reprogramming cocktail using additional embryonic transcription factors to determine how these factors affect the propensity for pluripotency or extraembryonic endoderm fate.
Show less

Title: Deterministic and Semi-Stochastic CC(P;Q) Approaches : New Developments and Applications to Spectroscopy and Photochemistry
Creator: Yuwono, Stephen Haniel
Date: 2022
Collection: Electronic Theses & Dissertations
Description: The development of electronic structure methods that can accurately describe ground and excited states of molecular systems with manageable computational costs and in a systematically improvable manner continues to be the central theme of quantum chemistry. This dissertation focuses on some of the recent developments in the coupled-cluster (CC) theory and its equation-of-motion (EOM) extension to excited electronic states. One of the key challenges in the development of the CC and EOMCC...
Show moreThe development of electronic structure methods that can accurately describe ground and excited states of molecular systems with manageable computational costs and in a systematically improvable manner continues to be the central theme of quantum chemistry. This dissertation focuses on some of the recent developments in the coupled-cluster (CC) theory and its equation-of-motion (EOM) extension to excited electronic states. One of the key challenges in the development of the CC and EOMCC methodologies is the incorporation of many-electron correlation effects due to higher-rank components of the cluster and EOM excitation operators without incurring significant increase in the computational costs, while avoiding failures of perturbative methods of the CCSD(T) type in multireference situations, such as bond breaking and excited states dominated by two-electron transitions, and in certain weakly bound systems. Among the best ways to address these issues is the CC(P;Q) framework, which provides robust and computationally affordable noniterative energy corrections to lower-order CC/EOMCC calculations. In this dissertation, we discuss the different CC(P;Q) variants relying on both the conventional and unconventional truncations in the cluster and EOM excitation operators. The advantages of the CC(P;Q) hierarchy are illustrated using a few examples ranging from small molecule spectroscopy to photochemistry of large organic species in solution. In particular, we discuss the computational investigations of the novel super photobase FR0-SB, which exhibits a drastic increase in basicity upon photoexcitation, including the energetics and properties of its excited states, the steric effects governing the excited-state proton transfer involving FR0-SB and alcohols, and the enhanced photoreactivity of FR0-SB resulting from two-photon excitations, where the δ-CR-EOMCC(2,3) approach that belongs to the CC(P;Q) hierarchy played a key role. Furthermore, we demonstrate that the relatively inexpensive CC(t;3) and CC(q;4) approaches derived from the CC(P;Q) framework are as accurate in describing the challenging weakly bound magnesium dimer, including its ground-state potential and vibrational levels supported by it, as the much more demanding CCSDT and CCSDTQ parent theories. We also show how the highly accurate ground- and excited-state ab initio potentials obtained in the state-of-the-art CCSDT, CR-EOMCCSD(T), and full configuration interaction (CI) computations allowed us to resolve the existing laser-induced fluorescence and photoabsorption spectra of the magnesium dimer and find the missing high-lying vibrational states of Mg2 that have eluded scientists for half a century. Last, but not least, we discuss our recent extension of the semi-stochastic CC(P;Q) framework, which combines the deterministic CC(P;Q) theory with stochastic CI quantum Monte Carlo (QMC), to excited electronic states, providing rapid convergence to the parent high-level EOMCC methods, such as EOMCCSDT, out of the early stages of QMC propagations. The advantages of the semi-stochastic CC(P;Q) approach targeting EOMCCSDT are illustrated by examining vertical excitations in CH+ and adiabatic excitations in the CH and CNC species.
Show less

Title: Three Essays on Panel Data Models with Interactive and Unobserved Effects
Creator: Brown, Nicholas Lynn
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Chapter 1: More Efficient Estimation of Multiplicative Panel Data Models in the Presence of Serial Correlation (with Jeffrey Wooldridge)We provide a systematic approach in obtaining an estimator asymptotically more efficient than the popular fixed effects Poisson (FEP) estimator for panel data models with multiplicative heterogeneity in the conditional mean. In particular, we derive the optimal instrumental variables under appealing `working' second moment assumptions that allow...
Show moreChapter 1: More Efficient Estimation of Multiplicative Panel Data Models in the Presence of Serial Correlation (with Jeffrey Wooldridge)We provide a systematic approach in obtaining an estimator asymptotically more efficient than the popular fixed effects Poisson (FEP) estimator for panel data models with multiplicative heterogeneity in the conditional mean. In particular, we derive the optimal instrumental variables under appealing `working' second moment assumptions that allow underdispersion, overdispersion, and general patterns of serial correlation. Because parameters in the optimal instruments must be estimated, we argue for combining our new moment conditions with those that define the FEP estimator to obtain a generalized method of moments (GMM) estimator no less efficient than the FEP estimator and the estimator using the new instruments. A simulation study shows that the GMM estimator behaves well in terms of bias, and it often delivers nontrivial efficiency gains -- even when the working second-moment assumptions fail.Chapter 2: Information equivalence among transformations of semiparametric nonlinear panel data modelsI consider transformations of nonlinear semiparametric mean functions which yield moment conditions for estimation. Such transformations are said to be information equivalent if they yield the same asymptotic efficiency bound. I first derive a unified theory of algebraic equivalence for moment conditions created by a given linear transformation. The main equivalence result states that under standard regularity conditions, transformations which create conditional moment restrictions in a given empirical setting need only to have an equal rank to reach the same efficiency bound. Example applications are considered, including nonlinear models with multiplicative heterogeneity and linear models with arbitrary unobserved factor structures.Chapter 3: Moment-based Estimation of Linear Panel Data Models with Factor-augmented ErrorsI consider linear panel data models with unobserved factor structures when the number of time periods is small relative to the number of cross-sectional units. I examine two popular methods of estimation: the first eliminates the factors with a parameterized quasi-long-differencing (QLD) transformation. The other, referred to as common correlated effects (CCE), uses the cross-sectional averages of the independent and response variables to project out the space spanned by the factors. I show that the classical CCE assumptions imply unused moment conditions which can be exploited by the QLD transformation to derive new linear estimators which weaken identifying assumptions and have desirable theoretical properties. I prove asymptotic normality of the linear QLD estimators under a heterogeneous slope model which allows for a tradeoff between identifying conditions. These estimators do not require the number of cross-sectional variables to be less than T-1, a strong restriction in fixed-$T$ CCE analysis. Finally, I investigate the effects of per-student expenditure on standardized test performance using data from the state of Michigan.
Show less

Title: Subgenome dominance and genome evolution in allopolyploids
Creator: Bird, Kevin Andrew
Date: 2022
Collection: Electronic Theses & Dissertations
Description: The merger of divergent genomes, via hybridization or allopolyploidization, frequently results in a ‘genomic shock’ that induces a series of rapid genetic and epigenetic modifications as a result of conflicts between parental genomes. This conflict among the subgenomes routinely leads one subgenome to become dominant over the other subgenome(s), resulting in subgenome biases in gene content and expression. Recent advances in methods to analyze hybrid and polyploid genomes with comparisons to...
Show moreThe merger of divergent genomes, via hybridization or allopolyploidization, frequently results in a ‘genomic shock’ that induces a series of rapid genetic and epigenetic modifications as a result of conflicts between parental genomes. This conflict among the subgenomes routinely leads one subgenome to become dominant over the other subgenome(s), resulting in subgenome biases in gene content and expression. Recent advances in methods to analyze hybrid and polyploid genomes with comparisons to extant parental progenitors have allowed for major strides in understanding the mechanistic basis for subgenome dominance. In particular, our understanding of the role that homoeologous exchange might play in subgenome dominance and genome evolution is quickly growing. Here I present novel work in several polyploid species investigating the biological and evolution impact of polyploidy and the evolution of these polyploid species. The first chapter introduces concepts like whole-genome duplication and describes advances in genomic sequencing technology that have accelerated the study of polyploid genomes. The second chapter reviews subgenome dominance and recent breakthroughs in understanding its causes and implications for genome evolution. The third chapter explores the repeatability of subgenome dominance in independently resynthesized Brassica napus. The fourth chapter investigates the extent to which genomic rearrangements from chromosomal duplications and deletions and homoeologous exchange can bias the analysis of subgenome expression dominance from RNAseq data. The fifth chapter explores the prevalence and impact of homoeologous exchange on independently resynthesized Brassica napus, providing novel evidence that gene dosage changes from homoeologous exchange are constrained by the need to maintain dosage balance of gene products. The sixth chapter explores the origins and admixture of wild octoploid strawberries Fragaria virgniana and Fragaria chiloensis with newly generated genomic resources applied to global collections.
Show less

Title: DISRUPTIONS IN HEPATIC ONE CARBON METABOLISM AND THE GUT MICROBIOME DURING THE PROGRESSION OF NON-ALCOHOLIC FATTY LIVER DISEASE
Creator: Fling, Russell Ryan
Date: 2022
Collection: Electronic Theses & Dissertations
Description: The etiology of non-alcoholic fatty liver disease is complex, with multiple contributing factors including dietary, environmental, gut microbiome and genetic mechanisms. Accumulating evidence suggests exposure to polychlorinated dibenzo-p-dioxins and similar compounds may increases risk for NAFLD development. These environmentally persistent dioxin-like compounds bind and activate the aryl hydrocarbon receptor, a transcription factor that regulates intestinal homeostasis, xenobiotic and...
Show moreThe etiology of non-alcoholic fatty liver disease is complex, with multiple contributing factors including dietary, environmental, gut microbiome and genetic mechanisms. Accumulating evidence suggests exposure to polychlorinated dibenzo-p-dioxins and similar compounds may increases risk for NAFLD development. These environmentally persistent dioxin-like compounds bind and activate the aryl hydrocarbon receptor, a transcription factor that regulates intestinal homeostasis, xenobiotic and central metabolism. In a AhR-dependent manner, mice orally gavaged with 2,3,7,8-tetracholordibenzo-p-dioxin (TCDD) exhibit steatosis progressing to steatohepatitis with fibrosis akin to NAFLD progression. NAFLD and hepatocellular carcinoma (HCC) is also closely correlated with dysregulation of central metabolism e.g., hepatic one carbon metabolism (OCM), and gut dysbiosis contributing to NAFLD progression and worsening prognosis. This report investigates mechanisms involved in the dysregulation of the gut microbiome and OCM associated pathways relevant to NAFLD progression through comparisons of molecular analyses of TCDD-treated mice to human NAFLD and HCC. OCM describes the biosynthesis, homeostasis, and utilization of the cell’s main methyl donor, S-adenosylmethionine (SAM) including high flux anabolic biosynthesis of polyamines, phosphatidylcholine and creatine. In later stages of NAFLD, OCM is dysregulated with altered OCM gene expression as well as SAM and s-adenosylhomocysteine (SAH) levels. To assess TCDD-elicited effects on OCM, mice were orally gavaged with TCDD every 4 days for 28 days. Serum and livers collected at early (8 days) and late (28 days) time points were subjected to metabolomic analyses with integration of chromatin immunoprecipitation sequencing, transcriptomics and protein levels. Results from these studies suggest AhR-mediated repression of OCM required prolonged repeated TCDD-treatment and indirect effects elicited by AhR activation e.g., oxidative stress. Gut dysbiosis with disrupted enterohepatic bile acid metabolism is commonly associated with NAFLD and recapitulated in TCDD-treated mice. Similar to NAFLD, TCDD also increases systematic levels of secondary bile acids. These microbial transformed secondary bile acids are involved in modulation of host bile acid signaling pathways relevant to NAFLD. To investigate the effects of TCDD on the gut microbiota, the cecum contents of TCDD-treated mice were subjected to shotgun metagenomic sequencing. Taxonomic analysis identified dose-dependent increases in Lactobacillus species, notably Lactobacillus reuteri. Top enriched species were also associated with increased abundances of bile salt hydrolase sequences, responsible for the initial deconjugation reaction in secondary bile acid metabolism. L. reuteri levels were also attributed to enrichment of mevalonate-dependent isopentenyl diphosphate (IPP) biosynthesis genes, a pathway that was also elevated in cirrhosis patients. These results extend the role of Lactobacilli in the AhR/intestinal axis and NAFLD progression as well as highlight the similarities between TCDD-elicited phenotypes in mice to human NAFLD. Collectively, these studies evaluated TCDD-elicited mechanisms involved in disruptions in host and microbial metabolism, highlighting the AhR’s role in NAFLD progression.
Show less

Title: ASSURING THE ROBUSTNESS AND RESILIENCY OF LEARNING-ENABLED AUTONOMOUS SYSTEMS
Creator: Langford, Michael Austin
Date: 2022
Collection: Electronic Theses & Dissertations
Description: As Learning-Enabled Systems (LESs) have become more prevalent in safety-critical applications, addressing the assurance of LESs has become increasingly important. Because machine learning models in LESs are not explicitly programmed like traditional software, developers typically have less direct control over the inferences learned by LESs, relying instead on semantically valid and complete patterns to be extracted from the system’s exposure to the environment. As such, the behavior of an LES...
Show moreAs Learning-Enabled Systems (LESs) have become more prevalent in safety-critical applications, addressing the assurance of LESs has become increasingly important. Because machine learning models in LESs are not explicitly programmed like traditional software, developers typically have less direct control over the inferences learned by LESs, relying instead on semantically valid and complete patterns to be extracted from the system’s exposure to the environment. As such, the behavior of an LES is strongly dependent on the quality of its training experience. However, run-time environments are often noisy or not well-defined. Uncertainty in the behavior of an LES can arise when there is inadequate coverage of relevant training/test cases (e.g., corner cases). It is challenging to assure safety-critical LESs will perform as expected when exposed to run-time conditions that have never been experienced during training or validation. This doctoral research contributes automated methods to improve the robustness and resilience of an LES. For this work, a robust LES is less sensitive to noise in the environment, and a resilient LES is able to self-adapt to adverse run-time contexts in order to mitigate system failure. The proposed methods harness diversity-driven evolution-based methods, machine learning, and software assurance cases to train robust LESs, uncover robust system configurations, and foster resiliency through self-adaptation and predictive behavior modeling. This doctoral work demonstrates these capabilities by applying the proposed framework to deep learning and autonomous cyber-physical systems.
Show less

Title: Interactions Between Plasma and Material Surfaces for Sterilization and Impurity Adsorption
Creator: Mackinder, Madeline Ann
Date: 2022
Collection: Electronic Theses & Dissertations
Description: As the worldwide population increases, maintaining a standard of public health becomes more critical. Two major concerns in this area are nosocomial infections (NI) and water contamination. Current processes in sterilization and water treatment have limitations that could be overcome using plasma techniques. The unique characteristics of plasma make it a promising alternative for energy-intensive processes. This work investigated the characteristics of plasma that have the greatest impact on...
Show moreAs the worldwide population increases, maintaining a standard of public health becomes more critical. Two major concerns in this area are nosocomial infections (NI) and water contamination. Current processes in sterilization and water treatment have limitations that could be overcome using plasma techniques. The unique characteristics of plasma make it a promising alternative for energy-intensive processes. This work investigated the characteristics of plasma that have the greatest impact on sterilization and the reactivation of activated carbon. Previous studies have researched the physical and chemical surface properties of biochar but have not been able to establish an efficient process to activate biochar with desired characteristics. Plasma treatment would offer a way to etch the surface of biochar and specifically functionalize the surface. Successfully activating biochar would increase its adsorption ability and enable its use for water treatment. This project aims to harness these plasma properties and use plasmas to address three important topics related to public health: sterilization of surfaces, modulating commercial activated carbon (AC), and activations of biochar.Cold plasma sterilization offers an efficient way to sterilize medical components and instruments without the risk of deformation to heat-sensitive materials. This paper reports the use of magnetized plasma to realize low-temperature sterilization. A radio frequency dielectric barrier discharge was created in a quartz tube using a mixture of argon and oxygen gas. Glass slides inoculated with a uniform amount of Escherichia coli were exposed to the plasma afterglow at different pressures with and without a magnetic field. A global model was developed to evaluate the magnetically enhanced dielectric barrier discharges and predict species densities. Optical emission spectroscopy identified the plasma species present and validated the model. The magnetic field significantly promoted the intensity of the plasma and the sterilization efficiency. A process gas pressure of 100 mTorr presented the most effective treatment with a sterilization time less than one minute and sample temperature below 32 °C. The effects of O2 plasma on the adsorption capacity of activated carbon (AC) was investigated by varying treatment times. Transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR), and Zeta potential were used to characterize the surface properties of the AC. The carbon was then applied to remove methylene blue (MB) from an aqueous solution. The adsorption kinetics and isotherm were also studied. Results showed that pseudo-second-order kinetics was the most suitable model for describing the adsorption of MB onto AC. Equilibrium data were well fitted to the Freundlich and Langmuir isotherm models. The highest adsorption capacity resulted from 4 minutes of O2 plasma treatment. This work shows that activation of AC by plasma can open the micropore and increase the effectiveness of chemical removal.Biochar was activated using a combination of O2 plasma and KOH. The adsorption capacity was investigated for different O2 plasma treatment times, KOH concentrations, and treatment temperatures. The adsorption capacity of methylene blue (MB) by the plasma activated biochar was evaluated. The adsorption kinetics and isotherm were also investigated. Results showed that pseudo-second-order kinetics was the most suitable model for describing the adsorption of MB onto biochar. Both the Freundlich and Langmuir isotherm models fit the equilibrium data. The highest adsorption capacity resulted from 10\% KOH + 300 °C for 5 minutes. This work shows that activation of biochar by plasma can improve adsorption capacity. The plasma treated AC and the plasma activated biochar were applied to the removal of PFOA. It was demonstrated that plasma treatment can improve PFOA adsorption. The negative surface charge was shown to negatively impact PFOA adsorption which aligns with the hypothesis that PFOA would preferentially adsorb onto more positive surfaces due to its anionic state in water.
Show less

Title: Food Access, Insecurity, and Health : The Experience of International Students
Creator: Khandelwal, Shruti
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Food insecurity is rising among college students and minority groups in the United States. This is closely associated with poor health outcomes, including chronic health risks and poor mental health outcomes. Two key parameters, namely physical access and affordability have been commonly employed for assessing food insecurity by various institutions and researchers. While the food security is assessed for US populations and hinged upon measuring access to healthy and nutritious foods, food...
Show moreFood insecurity is rising among college students and minority groups in the United States. This is closely associated with poor health outcomes, including chronic health risks and poor mental health outcomes. Two key parameters, namely physical access and affordability have been commonly employed for assessing food insecurity by various institutions and researchers. While the food security is assessed for US populations and hinged upon measuring access to healthy and nutritious foods, food security among international students is difficult to comprehend. Moreover, perceptions and experiences of food access for international students does not encompass access to healthy and culturally appropriate foods. Therefore, if international students cannot access healthy and culturally appropriate foods, they are more likely to be food insecure and therefore, suffer from poor health and behavioral outcomes. The aim of this study is to explore perceived access to healthy and culturally appropriate foods for South Asian students that mitigate their food related health risk. The main research question examines if international students experience poor health and behavioral outcomes due to food inaccessibility than domestic students. Three hypotheses were tested to investigate the main research question. The first hypothesis is that international students perceive greater food inaccessibility than domestic students. The second hypothesis is that international students perceive greater food insecurity due to food inaccessibility than domestic students. The third hypothesis is that international students perceive poor health and behavior outcomes due to food insecurity than domestic students. Using mixed-methods research approach, quantitative assessment (n=427) was supplemented with qualitative – thematic coding to understand the perceptions of accessing healthy and culturally appropriate foods for Indian students (n=88) which formed the majority of the sample population (77%). Additionally, to comprehend the local-level access to foods, built area analysis (n=53) was conducted for one university in the Midwest (with the maximum responses) to explore the experiences of accessing healthy and culturally appropriate foods and the parameters of the modes of transit (mode of transportation, frequency of trips, travel time).The quantitative assessment utilized chi-square test for hypothesis one and two and logistic regression for the third hypothesis. The affirmation of all three hypotheses showed that access is a critical aspect in assessing food security/insecurity and in turn, good health and behavior outcomes for international students studying in the US universities. The qualitative assessment was based on interviews (n=88) and food journal responses (n=87). This method illustrates two important factors. First, the key definition for culturally appropriate foods emerged from interviews and second, acceptability to healthy and culturally appropriate foods was most preferred among interviewees. However, it was ranked lower in all other dimensions of access, i.e., accessibility, accommodation, availability, and affordability. The built area analysis (n=53) helped in understanding the local level assessment of the food environment of one university. The study concludes with recommendations on improving access to healthy and culturally appropriate foods through interventions at local planning level in three area- zoning, mobility, and governance.
Show less

Title: MEMBRANE-LOCALIZED TRANSCRIPTION REGULATORS : UNDERSTANDING POST-TRANSLATIONAL REGULATION AND SINGLE-MOLECULE DYNAMICS OF TCPP IN VIBRIO CHOLERAE
Creator: Demey, Lucas Maurice
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Vibrio cholerae is a Gram-negative gastrointestinal pathogen that has evolved an elegant regulatory system to precisely time production of essential virulence factors. A key step in this regulatory system is the transcription of a soluble AraC-like transcription factor, ToxT. ToxR and TcpP, two membrane-localized transcription regulators (MLTRs), positively regulate toxT. Much work has contributed to our understanding of TcpP and ToxR regulation, yet major gaps remain in our knowledge of...
Show moreVibrio cholerae is a Gram-negative gastrointestinal pathogen that has evolved an elegant regulatory system to precisely time production of essential virulence factors. A key step in this regulatory system is the transcription of a soluble AraC-like transcription factor, ToxT. ToxR and TcpP, two membrane-localized transcription regulators (MLTRs), positively regulate toxT. Much work has contributed to our understanding of TcpP and ToxR regulation, yet major gaps remain in our knowledge of these MLTRs. MLTRs are unique one-component signal transduction systems because they respond to extracellular stimuli by influencing gene transcription from their location in the cytoplasmic membrane. In Chapter 2, I explore the prevalence and diversity of MLTRs within prokaryotes to enhance our understanding of TcpP and ToxR. I show that MLTRs are far more common among prokaryotes than previously anticipated and that MLTRs are an understudied class of transcription regulators. In Chapter 3, I describe the use of super-resolution single-molecule tracking to investigate how TcpP, a model MLTR, identifies the toxT promoter. I provide evidence that TcpP binds to the toxT promoter independent of ToxR, and TcpP transitions to a specific diffusion state. The data support the first biophysical model for how TcpP-like MLTRs locate their target promoters. TcpP is subject to a form of post-translational regulation known as regulated intramembrane proteolysis (RIP). RIP of TcpP results in its complete inactivation, resulting in loss of virulence factor production. TcpH inhibits RIP of TcpP under certain pH and temperature conditions. In Chapter 4, I describe the mechanism TcpH employs to inhibit TcpP RIP while V. cholerae is present in the mouse gastrointestinal tract. I demonstrate that the dietary fatty acid α-linolenic acid enhances inhibition. I also show that α-linolenic acid promotes TcpH-mediated inhibition of TcpP RIP by increasing association of both proteins with detergent-resistant membrane (DRM) domains. My work provides the first evidence that DRMs influence virulence factor transcription in V. cholerae and that a dietary fatty acid promotes V. cholerae pathogenesis.
Show less

Title: THE RELATIONSHIP BETWEEN REASONS FOR PARTICIPATION AND ACHIEVEMENT
Creator: Arnold, Brian J.
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Asynchronous Online Discussions (AODs) are often used to encourage online learner participation as they are believed to approximate the verbal interactions of face-to-face (F2F) learning environments while facilitating learners' metacognitive and critical thinking skills (Deng and Tavares, 2013). Despite mixed and somewhat context dependent research on the relationship between AOD participation and achievement, there appears to be a tendency among teachers and instructional designers to...
Show moreAsynchronous Online Discussions (AODs) are often used to encourage online learner participation as they are believed to approximate the verbal interactions of face-to-face (F2F) learning environments while facilitating learners' metacognitive and critical thinking skills (Deng and Tavares, 2013). Despite mixed and somewhat context dependent research on the relationship between AOD participation and achievement, there appears to be a tendency among teachers and instructional designers to encourage greater participation as it is believed that greater participation promotes greater achievement. Additionally, the act of online participation itself is often measured using visible artifacts like discussion and assignment posts submitted by students and evaluated by instructors and/or peers. This can lead educators to infer that the learners who participate more will earn higher grades than those who participate less.To explore this tendency, this quantitative descriptive study examined students enrolled in an introductory college English course (n = 76) using Learning Management System (LMS) activity reports and survey results. This was done to better understand the relationship between (what may appear to be limited) participation and course achievement. Similarly, the study sought to better understand the relationship between the learners' reasons for participation and their actual achievement. The primary results contribute to a wide range of studies that examine the relationship between participation and achievement. The results share a finding with two other studies in particular; Graff, (2005) and Wikle and West (2019), namely that this study showed no statistically significant correlation between participation and achievement for students who finished the course. Meaning that students who completed the course saw no statistically significant change in achievement for over or under participating. An unexpected finding of this study was that reasons for not participating contributed more to student behavior than reasons for posting.This study also showed that learners’ primary self-identified reasons for participating favored performance, information seeking, UX and interest; however, empirical performance data suggests that the relationship between learners' reasons for participation and their actual level of achievement is strongest when those reasons revolve around topic complexity, UX, time management and social risk. The gap between learners’ metacognitive perception of participation reasons and their data-driven demonstrable reasons is explored in this paper.
Show less

Title: CONSTRAIN NEUTRON STAR PROPERTIES WITH SpiRIT EXPERIMENT
Creator: Tsang, Chun Yuen
Date: 2022
Collection: Electronic Theses & Dissertations
Description: The study of nuclear matter is an interdisciplinary endeavor that is relevant to both astrophysics and nuclear physics. Astrophysicists need to understand the properties of nuclear matter as some astrophysical objects are made of nuclear material. Nuclear physicists also need to understand the properties of nuclear matter as they are fundamental to the understanding of the existence of nuclei, their composition and the dynamics of nuclear collisions.Recent measurements of gravitational waves...
Show moreThe study of nuclear matter is an interdisciplinary endeavor that is relevant to both astrophysics and nuclear physics. Astrophysicists need to understand the properties of nuclear matter as some astrophysical objects are made of nuclear material. Nuclear physicists also need to understand the properties of nuclear matter as they are fundamental to the understanding of the existence of nuclei, their composition and the dynamics of nuclear collisions.Recent measurements of gravitational waves from binary neutron star mergers and precise neutron star radii from X-ray data of pulsars open a new channel for physicists to study nuclear matter. Such astronomical observations of neutron stars are sensitive to nuclear matter at high density that is usually inaccessible on earth. One of the ways physicists are able to reach such high density in laboratory is through heavy-ion collision. Transport model calculations that simulate nuclear collisions show that head-on collisions of heavy nuclei at high beam energy compress the overlapping region momentarily to densities comparable to that of the interior of neutron stars. To study neutron star where number of neutrons far exceeds that of protons, the dependence of nuclear properties on neutron-to-proton ratio (N/Z) needs to be understood. This dependence is quantified by the symmetry energy, which describes the difference in binding energy between pure neutron matter and matter with equal amount of protons and neutrons. The latter is also known as symmetric nuclear matter (SNM) which has been fairly well constrained. The amount of internal neutron star pressure that supports itself from gravitational collapse depends on the value of symmetry energy. Most of the existing heavy-ion collision data comes from collisions of stable isotopes. This limits the range of available N/Z in nuclear experiments. Extending results to a wider range of N/Z is one of the goals of SpiRIT experiment using projectiles provided by the cutting-edge Radioactive Isotope Beam Factory in RIKEN, Japan. SpiRIT time projection chamber (TPC) is constructed to measure charged pions spectra from the collision of neutron-rich system (132Sn + 124Sn), neutron-poor system (108Sn + 112Sn) and intermediate system (112Sn + 124Sn) at 270 MeV/u. By comparing fragmentation patterns for reactions with different number of neutrons, symmetry energy effects can be isolated. Some results from the analysis of pion spectra have been published and will be briefly reviewed in this work before we focus on light fragment observables that are also available from the TPC data. The data analysis software, with highlights on correction of some major detector aberrations, is discussed in details. Monte Carlo simulation of the SpiRIT TPC is then performed to understand the behavior of SpiRIT data and validate our data analysis procedure. Finally, Bayesian analysis is performed to compare transport model simulations with selected light fragment measurements using Markov-Chain Monte Carlo and Gaussian emulators. The observables are chosen to minimize systematic uncertainties from both the experiment and model. The posterior provides a comprehensive constraint on the symmetry energy parameters. Although previous analyses of pion spectra have already constrained the slope of symmetry energy at saturation density (L), its uncertainty can be reduced by 39% if pion results are combined with our new Bayesian posterior. The implications of symmetry energy constraint for neutron star will be discussed to demonstrate the importance of data from rare isotope heavy-ion collisions.
Show less

Title: An Experimental Study of the Steadily Plunging Airfoil in Uniform-Shear Flow
Creator: Albrecht, Mitchell Baxter
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Freestream shear may be found in many unsteady aerodynamic situations, such as the fighter jet landing through the air wake of an aircraft carrier and the micro air vehicle (MAV) navigating wind currents around buildings in urban environments. Despite the prevalence of shear in aeronautics, literature concerning its effects on unsteady airfoils is scarce. To address the need to understand the fundamental, complex aerodynamics of moving airfoils coupled with freestream shear, a novel...
Show moreFreestream shear may be found in many unsteady aerodynamic situations, such as the fighter jet landing through the air wake of an aircraft carrier and the micro air vehicle (MAV) navigating wind currents around buildings in urban environments. Despite the prevalence of shear in aeronautics, literature concerning its effects on unsteady airfoils is scarce. To address the need to understand the fundamental, complex aerodynamics of moving airfoils coupled with freestream shear, a novel experimental setup was implemented to investigate the case of the airfoil steadily plunging across a canonical uniform-shear approach flow in a water tunnel. The effect of unsteadiness on the NACA 0012 airfoil in shear is examined by using a servo motion system to plunge the airfoil from the high- to low-speed extremes of the shear zone and varying the steady plunge speed. The aerodynamic load (lift and drag coefficients), streamwise velocity component of the flow, separation and reattachment locations, and boundary layer thickness are characterized such that the flow measurements are correlated to the observed behavior of the load measurements. First, uniform flow measurements are performed that confirm the unique experimental setup reproduces the expected Galilean transformation between the stationary and steadily plunging airfoils. It is confirmed that minimal blockage, confinement, or other artifacts result from the airfoil traversing over a large fraction of the test section's width. Molecular tagging velocimetry is uniquely implemented such that tag lines are created over the entire airfoil surface, image pairs are formed with the entire airfoil in view, and flow measurements are enabled for the moving airfoil. The airfoil aerodynamics are characterized in uniform flow at the same Reynolds numbers of the shear flow at three primary cross-stream locations of interest to provide baselines for the measurements in shear. For Reynolds numbers 13,500 and 16,500, a multi-region behavior is observed in the slope of the lift coefficient curve where the observed rapid rise in lift is related to the flow switching from an open separation to a closed separation bubble. By contrast, a steady rise in lift is observed at Reynolds number 9,800 which correlates to only open separation being observed.Next, the basic effect of shear on the stationary airfoil is studied by placing the airfoil at the three primary cross-stream locations in the shear flow, which also provides baseline measurements for the plunging airfoil in shear. It is observed that the current study reproduces the negative lift at zero angle of attack that is opposite of inviscid theory but consistent with recent computational and experimental literature from our group. A common observation in the lift and drag coefficient curves for the stationary airfoil in shear is asymmetry, as exemplified by the different stall behavior between positive and negative angles of attack. A multi-region behavior is observed among the lift curves which is connected to the airfoil switching from open separation to a closed separation bubble, like for uniform flow. Except for the Reynolds number 13,500 case, there is no observed difference in the angle of attack at which the flow switches from open separation to a closed separation bubble in shear compared to uniform flow. For the highest shear, lowest Reynolds number case, only open separation is observed at positive angles of attack, like the corresponding results in uniform flow.Finally, the effect of the steadily plunging airfoil motion in shear is studied in comparison with its stationary airfoil counterpart. For the range of dimensionless shear rates (0.40-0.69) and chord Reynolds numbers (9,800-16,500) in this study, it is observed that the slope of the lift coefficient curve for the plunging airfoil begins to rapidly increase at lower effective angle of attack than for the stationary airfoil, which is found to be a result of the flow reattaching at a lower effective angle of attack for the former than for the latter. Near stall, the magnitude of the lift coefficient on the plunging airfoil is typically greater than that on the stationary airfoil, which is found to be related to the reattachment point occurring farther upstream for the former than for the latter. It is found that the airfoil must plunge as slowly as 1% of the freestream speed for the load on the plunging airfoil to be well-approximated by that on the stationary airfoil for the same effective angle of attack and freestream conditions.
Show less

MSU Libraries

Digital Repository

Enabled Filters

Pages

Pages

MSU Libraries

Digital Repository

You are here

Search results

Pages

Pages