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Title: UNDERSTANDING THE ROLES OF INTERKINGDOM MICROBIAL INTERACTIONS, MICROBIAL TRAITS, AND HOST FACTORS IN THE ASSEMBLY OF PLANT MICROBIOMES
Creator: Liber, Julian Aaron
Date: 2021
Collection: Electronic Theses & Dissertations
Description: The community of organisms that associate with plants are vital to both the survival of the host plant but also the diseases which may kill it. The processes by which this community, called the microbiome, assemble and function can contribute to the traits of the host, including plants that humans rely on for food, resources, and ecosystems services. This thesis focuses on understanding the assembly of microbiomes at the scale of microbe-microbe interactions and traits of individual microbes,...
Show moreThe community of organisms that associate with plants are vital to both the survival of the host plant but also the diseases which may kill it. The processes by which this community, called the microbiome, assemble and function can contribute to the traits of the host, including plants that humans rely on for food, resources, and ecosystems services. This thesis focuses on understanding the assembly of microbiomes at the scale of microbe-microbe interactions and traits of individual microbes, as well as how characters of the host may change this process. I first address this by examining the in vitro and in planta interactions within small synthetic communities of root-inhabiting bacteria and fungi and with the plant host and viral disease of the host. While intermicrobial interactions in vitro were not predictive of in planta interactions, adding host disease or additional organisms to the system altered the assembly process. I then show the development and applications of the CONSTAX2 classifier, a taxonomic assignment tool for metabarcoding studies, which offers improved accuracy and ease of use for conducting metabarcoding studies exploring the diversity and structure of microbial communities. Last, I present a study testing which factors affected the composition of forest fungal communities to understand the ecology of litter-inhabiting fungi and improve methodologies for sampling leaf-associated fungal communities. The factors affecting the assembly of plant microbiomes are complex and varied but connecting individual interactions to community composition and ultimately function may improve our abilities to predict and manage microbiome processes.
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Title: UNDERSTANDING THE PARASITIC VARIABILITY OF THE NORTHERN ROOT KNOT NEMATODE (MELOIDOGYNE HAPLA) THROUGH MULTIDISCIPLINARY APPROACHES OF SOIL BIOME AND ENVIRONMENT
Creator: Lartey, Isaac
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Managing Meloidogyne hapla remains challenging due to the ban of broad-spectrumnematicides, lack of resistant crops and its broad host range. It also has parasitic variability (PV) where populations (pop) are morphologically and genetically similar but vary in pathogenicity and reproductive potential. Although PV in M. hapla appears to have some relationship to soil types, what soil conditions favor its PV and/or its distribution are unknown. The goal of my research was to understand the soil...
Show moreManaging Meloidogyne hapla remains challenging due to the ban of broad-spectrumnematicides, lack of resistant crops and its broad host range. It also has parasitic variability (PV) where populations (pop) are morphologically and genetically similar but vary in pathogenicity and reproductive potential. Although PV in M. hapla appears to have some relationship to soil types, what soil conditions favor its PV and/or its distribution are unknown. The goal of my research was to understand the soil conditions where M. hapla PV exist by quantifying the biophysicochemical (BPC) conditions from the ecosystem down to microbiome level. I designed observational and experimental approaches and tested four objectives. First, was to evaluate the association between soil conditions and M. hapla distribution at the ecosystem level. My hypothesis was that the presence of M. hapla will be associated with degraded soil conditions. I selected 15 (6 muck and 9 mineral soil) agricultural fields with adjacent natural vegetation in southwest, northwest and eastern regions of the lower peninsula of Michigan as study sites. I collected a total of 75 (5 per field) georeferenced soil samples from agricultural fields and equal number from adjacent natural vegetation soils, quantified the soil food web (SFW) conditions using the Ferris SFW model, and screened for M. hapla presence or absence. The fields were described either as disturbed, degraded (worst-case) or maturing (best-case). Meloidogyne hapla was present in 3 mineral (2, 8 and 13) and 6 muck (4, 5, 6, 10, 14 15) agricultural fields with degraded and/or disturbed soil conditions and absent from maturing soils, partially supporting the hypothesis. Degraded soils had low nitrogen content in both soil groups. The second objective was to isolate and culture the 9 M. hapla populations to test a hypothesis that PV is related to specific SFW conditions. I found three categories of reproductive potential: the highest (Pop 13), medium (Pop 8), both from degraded mineral soils, and lowest from disturbed mineral (Pop 2) and disturbed (Pops 4, 6 and 10) and degraded (Pops 5, 14 and 15) muck soils. Thus, the hypothesis was not supported. The third objective, was to determine relationships between microbial community structure and M. hapla distribution. My working hypotheses were that there is a relationship among microbiome, soil health and M. hapla occurrence. Microbial community structure in the fields was determined from sub-samples of the same samples where the nematodes were isolated. I used 16S (bacteria) and ITS (fungi) rDNA analysis and characterized the microbial composition, core- and indicator-microbes co-existing with M. hapla pop in the field soils and soil conditions relative to the Ferris SFW model description. The results showed that bacterial and fungal community abundance and composition varied by soil group, SFW conditions and/or M. hapla occurrence. I found that a core of 39 bacterial and 44 fungal sub-operational taxonomic units (OTUs) were found variably, 25 bacterial OTUs associated with presence or absence of M. hapla, and 1,065 OTUs were associated SFW conditions. All three hypotheses were supported. The final objective was to determine the relationship between PV and the microbes associated with M. hapla pop. I compared bacteria present in M. hapla pop isolated from the field and greenhouse cultures. The hypothesis was that either presence and/or absence of specific bacteria are associated with M. hapla population. Population 8 shared more bacteria with the lowest reproductive potential pop than Population 13. Presence of several bacteria was unique to Population 8 as was the absence of other bacteria to Pop 13 in either field or greenhouse nematodes. Therefore, the hypothesis was supported. My research findings provide a foundation for: a) testing the relationship between M. hapla PV and the BPC conditions and b) designing soil health-based management strategies.
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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.
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Title: UNDERSTANDING THE FACTORS AFFECTING DIGITAL INCLUSION AND EXCLUSION : A COMPARATIVE STUDY OF THE UNITED STATES AND INDONESIA
Creator: triwibowo, whisnu
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Research on the digital divide and digital inequality is often descriptive. The coexistence of a multitude of theoretical frameworks limits our knowledge to explain and/or predict the phenomenon. This dissertation tries to fill a gap in the literature about digital divides by proposing an integrative framework to explain digital outcomes in addition to access and uses. Informed by Giddens’ structuration theory, the framework conceptualizes the digital divide as social practices that reflect...
Show moreResearch on the digital divide and digital inequality is often descriptive. The coexistence of a multitude of theoretical frameworks limits our knowledge to explain and/or predict the phenomenon. This dissertation tries to fill a gap in the literature about digital divides by proposing an integrative framework to explain digital outcomes in addition to access and uses. Informed by Giddens’ structuration theory, the framework conceptualizes the digital divide as social practices that reflect the interplay of structures and human agency. This dissertation seeks to develop improved measures of digital outcomes and digital skills that can capture current digital practices. Furthermore, it aims to understand three issues that have not been explored in depth. First, it examines the relationships and interactions between social structures, human agency, access, internet use, and digital outcomes. Second, is asks which factors help individuals to improve their utilization of the opportunities offered by the Internet (digital inclusion) and which ones might contribute to falling behind relative to others (digital exclusion). A comparative research design, based on surveys in two countries, enables examining the extent to which models of the digital divide are supported in nations with differing economic, political, and cultural conditions. Three important findings emerge from the dissertation: First, interconnections were revealed between social structures, elements of agency, internet use, and internet outcomes. Second, the research shows that actors are an important factor to predict the second and third level of digital divides. Third, the structuration model of the digital divide can inform studies of digital inclusion and exclusion, and agency remains a key element in understanding digital divides. The effect of agency in influencing internet use and outcomes is moderated by access sustainability in the United States. In Indonesia, the moderation only occurs among users who earn low internet outcomes. However, more research will be necessary to refine the approach and findings developed in the dissertation. In sum, this dissertation provides insights for the future direction of digital divides research and for decision-makers seeking to narrow digital divides.Keywords: access divide, digital capital, digital divides, digital inclusion, digital exclusion, digital outcomes divide, digital skills divide, Giddens, Indonesia, internet use divide, structuration, structural equation modeling, the United States.
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Title: UNDERSTANDING LARGE-SCALE HUMAN-WATER INTERACTIONS FOR SUSTAINABLE HYDROPOWER DEVELOPMENT
Creator: Chaudhari, Suyog
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Hydropower dams have received increased global attention due to their detrimental socioenvironmental ramifications, resulting in increased concerns as to whether their energy benefits can outweigh the detrimental consequences. To fulfill rising energy demands driven by rapid population growth, especially in the developing world, hydropower has often been developed with a primary focus on energy generation. The re-emergence of large dams could very well bring large energy and economic...
Show moreHydropower dams have received increased global attention due to their detrimental socioenvironmental ramifications, resulting in increased concerns as to whether their energy benefits can outweigh the detrimental consequences. To fulfill rising energy demands driven by rapid population growth, especially in the developing world, hydropower has often been developed with a primary focus on energy generation. The re-emergence of large dams could very well bring large energy and economic incentives especially to the developing economies, however, these incentives may come at the expense of altering the natural flow regime of rivers with additional repercussions on the biodiversity and ecological productivity within the basins. With the continued interest in hydropower development, it is imperative to examine and understand the intricate changes to the basin’s hydrology due to dam operations and further rethink hydropower design to avoid potentially catastrophic consequences. To date, several studies have simulated and examined the impacts of reservoir operation on the hydrological characteristics of global rivers. Although, these studies have made great strides in examining the impact of dams on river flow, the observation-based studies alone are not sufficient to disentangle the major drivers of change and there are major deficiencies in simulation-based studies in providing a comprehensive picture of the large-scale and cumulative impacts of dams. Hence, the actual impacts of the existing dams and the potential effects of new dams remain poorly understood. The overarching goal of this dissertation is to address this important research gap by employing a mechanistic approach to develop a holistic understanding of the hydrology of global river basins under the effects of climate change and human interventions, such as LULC change and dam operations. The study is conducted over the Amazon River basin that is increasingly dammed with hundreds of dams planned for the near future. The historical interannual and interdecadal hydrological changes in the Amazon River basin and its sub-basins are first investigated by implementing a high-resolution, physically based, continental-scale hydrological model, LEAF-Hydro-Flood (LHF), to determine the dominant mechanisms that modulate terrestrial water storage (TWS). The historical impacts of existing dams and the potential impacts from collective operation of existing and planned dams on a basin-wide scale in the Amazon are then quantified under the historical climate using a new dam operation scheme in a high-resolution hydrodynamic model, CaMa-Flood-Dam (CMFD). Using this new dam operation scheme, the potential future changes to the hydrology of the Amazon River basin are then quantified under cumulative operation of existing and planned dams and multiple climate change scenarios for the entire twenty first century. Lastly, this dissertation explores viable alternatives for hydropower generation, by assessing the feasibility—with respect to energy potential and cost—of implementing in-stream turbines to harness a large portion of the power that is expected to be generated by building large dams. The results from the aforementioned analysis provide major advances and crucial insights on the understanding of the integrated river-floodplain-reservoir dynamics in a flood and hydropower dominant river system, such as the Amazon, with further implications for sustainable hydropower development. Over the long run, this assessment could prove beneficial in investigating the future of hydropower in the Amazon and other regions worldwide (for example, the Mekong and Congo River basins) where a boom in construction of mega-scale hydropower dams is underway.
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Title: UNBUILT BRIDGES : EXAMINING THE INCLUSION OF THE UNITED STATES IN WORLD HISTORY
Creator: Bronstein, Erin Anne
Date: 2021
Collection: Electronic Theses & Dissertations
Description: This study explored how world history teachers think about the United States and the world in their practice. The purpose of this study was to understand how teachers make decisions about including the United States in their world history instruction and how those choices position the United States in relation to the world. The study sought to consider how teachers describe their roles as world history teachers and the ways they exercise these roles to reinforce or challenge broad cultural...
Show moreThis study explored how world history teachers think about the United States and the world in their practice. The purpose of this study was to understand how teachers make decisions about including the United States in their world history instruction and how those choices position the United States in relation to the world. The study sought to consider how teachers describe their roles as world history teachers and the ways they exercise these roles to reinforce or challenge broad cultural ideas such as American exceptionalism. This qualitative study focused on the reflections and descriptions of four world history teachers in the same Midwestern state. Semi-structured interviews that included prompts and resources were used to collect data over two months in the spring of 2020. Figured worlds and teacher decision making were combined with a macro discourse analysis to examine participant responses and resources. While other studies have examined world history curriculum more broadly or how teachers organize world history content, the findings of this study suggest that while teachers aspire to broaden student views of the world, they are influenced by more than that aspiration. Their instructional decisions are also influenced by broader cultural understandings such as American exceptionalism and Western-influenced theories of democracy. These cultural understandings position the United States as an exemplar, a modern power, an extension of Western actions or as separated from the happenings of the rest of the world at times. This study suggests that teachers, both in and pre-service teachers navigate a variety of considerations and influences in their teaching. It also demonstrates that teachers might benefit from more opportunities to examine the ways that societal views impact their choices as well as access to decolonial knowledge that might also impact their choices.
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Title: UNA ESCUELA PARA TRANSFORMAR : LINKING SCHOOLS TO COMMUNITY SOCIAL AND ENVIRONMENTAL MOVEMENT FOR SOCIAL TRANSFORMATION
Creator: Gonzalez-Flores, Marcos David
Date: 2020
Collection: Electronic Theses & Dissertations
Description: The bourgeoning scholarship on community organizing for educational change suggest positives outcomes when it comes to countering failed school reforms. Early reports on community organizing across the United States have shown an exponential grow since the 1990s and by 2010 there were 500 of 800 community organizing groups were working in the area of school reform. Nevertheless, not all organizing efforts are the same as they are contingent to context, organizational characteristics, phase of...
Show moreThe bourgeoning scholarship on community organizing for educational change suggest positives outcomes when it comes to countering failed school reforms. Early reports on community organizing across the United States have shown an exponential grow since the 1990s and by 2010 there were 500 of 800 community organizing groups were working in the area of school reform. Nevertheless, not all organizing efforts are the same as they are contingent to context, organizational characteristics, phase of organizing, levels of work (i.e. neighborhood, school district, and state). The purpose of this dissertation was to bring front and center the stories of the community leadership from Grupo de las Ocho Comunidades del Caño Martín Peña (G-8, Inc) around their experiences during an educational project that started as a collaborative agreement with the centralized Department of Education of Puerto Rico. Through the interviews and document analysis I present how the G-8’s leadership turned to their apoderamiento comunitario and sentido de pertenencia to implement a curriculum in an elementary school focus on social transformation designed with the participation of residents and community leadership. Following a decolonial stance, I underlined the instances where the community engaged in what I saw as a decolonial act or when there was a manifestation of the logics of coloniality during the emergent collaboration.For G-8’s leadership it was important to organized in order to challenge the historical government neglect towards el Caño that was used as a subterfuge to forced them out of their communities. This historical abandonment towards el Caño was also seen in the pobre educación young people were receiving. Thus, transformar la educación and community-school relationship was also part of their comprehensive plan to transform el Caño. To accomplished this goal, G-8 establish an agreement of collaboration to implement a curriculum in leadership and social transformation build upon the political education of their community organizing work. Thus, the main question in this dissertation is: How has the G8-DEPR collaboration emerged and evolved in the context of the development and implementation of an innovative educational project? The collaborative agreement evolved in a contentious relationship in which the central and the local school leadership joined forces to impeded the full implementation of the curriculum. The educational project for La Escuela de Liderazgo y Transformación Social del Caño Martín Peña geared towards reconfiguring the community’s place inherent in state sanctioned schooling by centering la comunidad and their lucha comunitaria in regards school-community relations. For DEPR leadership the new educational project was both a signal to communities to work together with the centralized system and also a political project that did not align with the ideological and colonial form of state-sanctioned schooling. Thus, the tensions around the curriculum content and its implementation between the colonial DEPR and the G-8’s leadership denotes how forms of community-school collaboration that are institutionalized hinder the transformative work of CBOs. Moreover, the politics of coloniality deemed community knowledge as no important to contribute in bringing educational change will make the collaboration not viable. This was the case of the G8-DEPR’s collaboration. The community leadership took the hard decision to retire from the collaboration and find other ways to have their educational project for La Escuela de Liderazgo y Transformación Social del Caño Martín Peña.
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Title: Types of feedback in peer review and the effect on student motivation and writing quality
Creator: Sloan, Christopher Colgan
Date: 2017
Collection: Electronic Theses & Dissertations
Description: In writing classrooms, peer review has been shown to have numerous practical and cognitive benefits. However, little research has been done that examines how different types of peer feedback motivate adolescent students and the effects that different types of feedback have on writing quality. While the literature has indicated that peers give each other much more positive feedback than their teachers do, the research has yielded conflicting findings on whether comments about strengths or...
Show moreIn writing classrooms, peer review has been shown to have numerous practical and cognitive benefits. However, little research has been done that examines how different types of peer feedback motivate adolescent students and the effects that different types of feedback have on writing quality. While the literature has indicated that peers give each other much more positive feedback than their teachers do, the research has yielded conflicting findings on whether comments about strengths or comments about weaknesses are more helpful. For this study high school seniors in an AP English Language and Composition class were randomly assigned to one of three treatments: a group directed only to provide comments about the strengths in the writing of their peers, a second group directed only to provide comments about weaknesses, and a "business as usual" group who were directed to provide helpful feedback (typically a mix of strength and weaknesses comments). There were no treatment group differences in students' writing quality and motivation (attributions, belongingness, and sociocognitive conflict regulation). However, there were clear indicators that suggest students saw statistically significant differences in how helpful some types of comments were perceived to be. Implications for the theory and practice of peer-based feedback in writing instruction are discussed.
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Title: Two years' results on production of early spring lambs
Creator: Willson, Charles Albert
Date: 1922
Collection: Electronic Theses & Dissertations

Title: Two sides on "normal" : a comparison of eight views on U.S. rapprochement with Vietnam, 1989-1995
Creator: Clason, Nathan Robert
Date: 2017
Collection: Electronic Theses & Dissertations
Description: ABSTRACTTWO SIDES ON "NORMAL:" A COMPARISON OF EIGHT VIEWS ON U.S. RAPPROCHEMENT WITH VIETNAM, 1989-1995ByNathan Robert Clason This thesis is a comparative study of the views of eight entities regarding the prospect of normalization of diplomatic relations between the United States and the Socialist Republic of Vietnam from 1989-1995. It first describes the views and actions of five entities in favor of normalization. These include the four US presidential administrations from Carter to...
Show moreABSTRACTTWO SIDES ON "NORMAL:" A COMPARISON OF EIGHT VIEWS ON U.S. RAPPROCHEMENT WITH VIETNAM, 1989-1995ByNathan Robert Clason This thesis is a comparative study of the views of eight entities regarding the prospect of normalization of diplomatic relations between the United States and the Socialist Republic of Vietnam from 1989-1995. It first describes the views and actions of five entities in favor of normalization. These include the four US presidential administrations from Carter to Clinton, the Vietnamese Communist Party, the Senate Select Committee on POW/MIA Affairs (1991-1993), US Senators John McCain and John Kerry, and US businesses. It then examines the views and actions of three entities opposed to normalization. These include Ann Mills Griffiths, the Executive Director of the National League of POW/MIA Families; Texas billionaire Ross Perot; and politicians such as Robert Dornan and Vietnamese Americans from Orange County, California. By using a comparative approach, this thesis identifies several strange political alliances and enmities that would not have been clear in a more linear history. It includes a review of Vietnamese Communist Party documents that challenges some of the conclusions of the earliest diplomatic histories about normalization. It uses primary sources from key Senate Hearings to challenge elements of cultural histories about the myth of live US prisoners of war abandoned in Southeast Asia, and it personalizes the views of Ann Mills Griffiths and some Vietnamese Americans to give better context to their ardent opposition to normalization.
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Title: Two beginning teachers' intervention in small groups in figured worlds of mathematics classrooms
Creator: Pak, Byungeun
Date: 2020
Collection: Electronic Theses & Dissertations
Description: The purpose of this dissertation study is to understand beginning teachers' intervention in small groups. In this qualitative study, drawing on the notion of figured worlds (Holland, Lachicotte, Skinner, & Cain, 1998), I examined how beginning elementary teachers intervene in small groups and for what purposes in mathematics classrooms through the lenses of teacher noticing, teacher identity, and perceptions of students in mathematics classrooms. Working with two beginning teachers, I...
Show moreThe purpose of this dissertation study is to understand beginning teachers' intervention in small groups. In this qualitative study, drawing on the notion of figured worlds (Holland, Lachicotte, Skinner, & Cain, 1998), I examined how beginning elementary teachers intervene in small groups and for what purposes in mathematics classrooms through the lenses of teacher noticing, teacher identity, and perceptions of students in mathematics classrooms. Working with two beginning teachers, I collected data including survey responses, video-recordings, and interview transcripts.Building on thematic analysis of these data, I present three findings in relation to in terms of teacher noticing, teacher identity, and perceptions of students. First, I offer a noticing-mediated intervention framework that contributes to understanding how beginning teachers may make decisions related to intervention in small groups. This framework provides several ways to (re-)construct individual teachers' decision-making process related to intervention. Second, I demonstrate how current and designated teacher identities shape their intervention in small groups. I detail multifaceted aspects of current and designated teacher identity that each beginning teacher invoked to explain, make sense of, and reason about their intervention in small groups. Third, I illustrate how teachers' recognition of students in terms of categories shapes their intervention in small groups, sometimes through mediation by their recognition of power and authority dynamics at the micro-interaction level.Building on these findings, I present four points to discuss. First, this dissertation study can serve as a call for research on extending the understanding of novice teachers' intervention in diverse contexts. Second, this study suggests one possible example related to how to draw upon professional noticing to examine intervention in small groups in a detailed way. Third, this study details potential resources (e.g., knowledge, expectations, and experiences; teacher identity; and categories of students) beginning teachers may use when they make decisions to intervene in small groups. Fourth, this study supports the field to understand figured worlds of mathematics classrooms from beginning teachers' perspectives of intervention in small groups.This dissertation study has implications for research as well as for teacher education. For research, this study contributes to understanding how teacher noticing can be used to explore teachers' intervention in small groups. It also holds promise for ways to understand mathematics classrooms as figured worlds. For teacher education, teacher educators can use this study to design instructional activities that help novice teachers explore their intervention in small groups in relation to the noticing-mediated intervention framework, the multiple aspects of their current/designated identities, and their recognition of students in terms of different categories in mathematics classrooms. This study broadens and deepens the understanding of how beginning teachers intervene in small groups and for what purpose by relating it to teacher noticing, to teacher identity, and to figured worlds of mathematics classrooms.
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Title: Two Studies in Nonlinear Biological System Modeling and Identification
Creator: Yan, Jinyao
Date: 2018
Collection: Electronic Theses & Dissertations
Description: Biological systems are often complex, nonlinear and time-varying. The modeling of biological systems, therefore, presents significant challenges that are not overcome by the classical linear methods. In recent decades, intensive research has begun to produce methods for analyzing and modeling isolated classes of nonlinear systems. However, this vast class of models still presents many challenges, especially in complex biological systems. In this research, two novel methods are introduced for...
Show moreBiological systems are often complex, nonlinear and time-varying. The modeling of biological systems, therefore, presents significant challenges that are not overcome by the classical linear methods. In recent decades, intensive research has begun to produce methods for analyzing and modeling isolated classes of nonlinear systems. However, this vast class of models still presents many challenges, especially in complex biological systems. In this research, two novel methods are introduced for analyzing time series resulting from nonlinear systems. In the first approach, we study a class of dynamical systems that are nonlinear, discrete and with a latent state-space. We solve the probabilistic inference problem in these latent models using a variational autoencoder (VAE). Compared to continuous latent random variables, the inference of discrete latent variables is more difficult to solve. However, stochastic variational inference provides us with a general framework that tackles the inference problem for this class of model. We focused on an important neuroscience application – inferring pre- and post-synaptic activities from dendritic calcium imaging data. For it, we developed families of generative models, a deep convolutional neural network recognition model, and methods of inference using stochastic gradient ascent VAE. We benchmarked our model with both synthetic data, which resembles real data, and real experimental data. The framework can flexibly support rapid model prototyping. Both the generative model and recognition model can be changed without perturbing the inference. This is especially beneficial for testing different biological hypotheses. As a second approach, we treat a subclass of nonlinear autoregressive models: linear-time-invariant-in-parameters models. This class of models is useful and easy to work with. We propose an identification algorithm that simultaneously selects the model and does parameter estimation. The algorithm integrates two strategies: set-based parameter identification, and evolutionary algorithms that optimize fitness measures derived from these solutions. The algorithm can identify nonlinear models in novel noise scenarios. We show the performance of the algorithm in various simulated systems and practical datasets. We demonstrate its application to identify causal connectivity in a graph. This problem is often posed in recovering functional connectivity in the brain. The main contribution of this thesis is that we provide two framework for identifying nonlinear, biological systems from time series data. These two classes of nonlinear models and their applications are significant as each class is broad enough for modeling many complicated biological systems. We develop general, fast algorithms for learning these systems from data for these two model classes.
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Title: Triangulation of the Michigan agricultural campus
Creator: Anderson, Egnar S.
Date: 1920
Collection: Electronic Theses & Dissertations

Title: Tree studies
Creator: Baker, Hugh P. (Hugh Potter), 1878-1950
Date: 1901
Collection: Electronic Theses & Dissertations

Title: Transplanting as a factor in growing plants
Creator: Boyle, Jesse G.
Date: 1914
Collection: Electronic Theses & Dissertations

Title: Transparent multijunction organic photovoltaics
Creator: Young, Margaret (Process engineer)
Date: 2017
Collection: Electronic Theses & Dissertations
Description: "The widespread adoption of conventional solar cells based on inorganic semiconductors has been gaining traction in recent years but is still often hindered by high cost and lack of aesthetic appeal. Transparent organic semiconductor-based solar cells that selectively absorb in the UV and the NIR enable integration into building windows, automobiles, and consumer electronics in ways that traditional solar cells cannot. Moreover, integration onto existing infrastructure reduces the racking and...
Show more"The widespread adoption of conventional solar cells based on inorganic semiconductors has been gaining traction in recent years but is still often hindered by high cost and lack of aesthetic appeal. Transparent organic semiconductor-based solar cells that selectively absorb in the UV and the NIR enable integration into building windows, automobiles, and consumer electronics in ways that traditional solar cells cannot. Moreover, integration onto existing infrastructure reduces the racking and installation cost. In this work, we investigate routes to improve the efficiency of transparent solar cells by utilizing multijunction architectures. A transfer-matrix optical interference model is developed as a framework to optimize the full device stack considering the angle-dependent PV performance that is critical for matching subcell photocurrents in series tandem solar cells. In addition, a new method of fine tuning energy levels of low-bandgap small molecules with infrared selective absorption was demonstrated using a series of organic heptamethine salts. By exchanging the counterion from a small, hard anion to a fluorinated weakly coordinating anion, the frontier energy of the salt is shown to shift without affecting the bandgap, thus enabling simultaneous optimization of photocurrent generation of photovoltage. We further utilize this tunability to develop heptamethine molecules with absorption as deep as 1600 nm, the deepest infrared photo-response demonstrated to date with organic small molecules ideal for multijunction integration. Ultimately, transparent solar cells are an exciting new paradigm for solar deployment enabled by organic and excitonic semiconductors that offer a pathway to integrate solar onto virtually any surface without impacting the view."--Page ii.
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Title: Transmission timing modulation for information coding in energy-constrained wireless networks
Creator: Feng, Dezhi
Date: 2020
Collection: Electronic Theses & Dissertations
Description: The objective of this thesis is to develop a framework of transmission timing-based modulation framework for improving energy efficiency, security, and information transfer capacity in embedded wireless networks with very thin energy budgets. The key idea is to modulate both intra-PDU (Protocol Data Unit) and inter-PDU timing for addressing energy, security, and information transfer capacity in wireless embedded networks. As for energy efficiency, we developed a novel pulse position-coded PDU...
Show moreThe objective of this thesis is to develop a framework of transmission timing-based modulation framework for improving energy efficiency, security, and information transfer capacity in embedded wireless networks with very thin energy budgets. The key idea is to modulate both intra-PDU (Protocol Data Unit) and inter-PDU timing for addressing energy, security, and information transfer capacity in wireless embedded networks. As for energy efficiency, we developed a novel pulse position-coded PDU (PPCP) paradigm. The core idea is to encode a protocol data unit (PDU) in terms of the silence duration between two sets of delimiter pulses, whose positions are modulated based on the value of the PDU. This PPCP architecture achieves significant energy savings by using a lesser amount of bit/pulse transmissions, and by eliminating long multi-bit preambles and headers, which are normally used in traditional packets. The proposed multi-access pulse-based PDU scheme enables medium sharing among many sensor nodes without requiring per-PDU frame synchronization. As for security, we developed the concept of a novel chaotic pulse position coded protocol data unit (CPPCP) for secure embedded networking. The core idea of CPPCP is to encode a protocol data unit (PDU) with a wideband pulse train with chaotically-varied inter-pulse intervals. The architecture ensures communication security by introducing randomness between data symbols, noise-like frequency spectrum, and significant energy savings by using a smaller number of pulse transmissions compared to existing secure coding schemes such as Bluetooth Low Energy (BLE). Compared with the traditional key-based cryptographic techniques, CPPCP suppresses decipherable information by eliminating symbol periodicity. The mechanism can also be piggy-backed on traditional cryptography solutions to achieve higher levels of security. Finally, for enhancing the information transfer capacity, we developed a data packet position modulation (DPPM) paradigm. Packet transmissions in low duty cycle networks are often scheduled as TDMA slots, whose periodicity is determined based on application sampling requirements and the energy in-flow, often in the form of energy harvesting. The key idea of DPPM is to modulate the inter-packet spacing for coding additional information without incurring additional transmission energy expenditures. We first developed a have a DPPM based networking solution for single-hop transmit-only networks in which a number of low-energy nodes transmit data to an aggregator. The architecture is developed for a two-node point-to-point link, followed by a multipoint-to-point multi-access network. Detailed analytical and simulation models are developed to demonstrate the performance of a symmetric and an asymmetric version of DPPM.
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Title: Transmissibility and localization of tetrodotoxin in the rough-skinned newt, Taricha granulosa
Creator: Wegener, Sarah (Graduate of Michigan State University)
Date: 2017
Collection: Electronic Theses & Dissertations
Description: "Tetrodotoxin (TTX) is a powerful neurotoxin that prevents the propagation of action potentials, leading to paralysis and sometimes death in nearly all animals. However, a diverse group of marine and freshwater animals possess TTX, which they use for offense, defense, and communication. One of most studied TTX-mediated interactions is the predator-prey arms race between the rough-skinned newt (Taricha granulosa) and common garter snake (Thamnophis sirtalis). Variation in toxicity among...
Show more"Tetrodotoxin (TTX) is a powerful neurotoxin that prevents the propagation of action potentials, leading to paralysis and sometimes death in nearly all animals. However, a diverse group of marine and freshwater animals possess TTX, which they use for offense, defense, and communication. One of most studied TTX-mediated interactions is the predator-prey arms race between the rough-skinned newt (Taricha granulosa) and common garter snake (Thamnophis sirtalis). Variation in toxicity among populations of newts matched by TTX-resistance in predatory snakes has captured the focus of much research centered on the hypothesis that the arms race is the sole driver of variation. Nevertheless, recent studies suggest a more complex dynamic. Explanations of the dramatic variation in TTX among different populations of newts can only be constructed once fundamental questions about the origin, function, and transmission of TTX in newts have been more thoroughly explored. In this study, I took two approaches to address the origin, function, and transmission of TTX: 1) a cohabitation experiment in which I paired toxic and non-toxic newts to test whether toxicity can be acquired through contact, and 2) an experiment to determine the distribution and concentration of TTX in different tissues. The cohabitation experiment revealed no detectable change in the toxicity of non-toxic male newts, suggesting that a physical or physiological impediment prevents non-toxic newts from becoming toxic. The tissue toxicity experiment demonstrated that TTX is present throughout the body in structurally and functionally diverse tissues, which has many implications for the involvement of TTX in communication and reproduction in addition to defense."--Page ii.
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Title: Towards machine learning based source identification of encrypted video traffic
Creator: Shi, Yan (Of Michigan State University)
Date: 2019
Collection: Electronic Theses & Dissertations
Description: The rapid growth of the Internet has helped to popularize video streaming services, which has now become the most dominant content on the Internet. The management of video streaming traffic is complicated by its enormous volume, diverse communication protocols and data formats, and the widespread adoption of encryption. In this thesis, the aim is to develop a novel firewall framework, named Soft-margined Firewall, for managing encrypted video streaming traffic while avoiding violation of user...
Show moreThe rapid growth of the Internet has helped to popularize video streaming services, which has now become the most dominant content on the Internet. The management of video streaming traffic is complicated by its enormous volume, diverse communication protocols and data formats, and the widespread adoption of encryption. In this thesis, the aim is to develop a novel firewall framework, named Soft-margined Firewall, for managing encrypted video streaming traffic while avoiding violation of user privacy. The system distinguishes itself from conventional firewall systems by incorporating machine learning and Traffic Analysis (TA) as a traffic detection and blocking mechanism. The goal is to detect unknown network traffic, including traffic that is encrypted, tunneled through Virtual Private Network, or obfuscated, in realistic application scenarios. Existing TA methods have limitations in that they can deal only with simple traffic patterns-usually, only a single source of traffic is allowed in a tunnel, and a trained classifier is not portable between network locations, requiring redundant training. This work aims to address these limitations with new techniques in machine learning. The three main contributions of this work are: 1) developing new statistical features around traffic surge periods that can better identify websites with dynamic contents; 2) a two-stage classifier architecture to solve the mixed-traffic problem with state-of-the-art TA features; and 3) leveraging a novel natural-language inspired feature to solve the mixed-traffic problem using Deep-Learning methods. A fully working Soft-margin Firewall with the above distinctive features have been designed, implemented, and verified for both conventional classifiers and the proposed deep-learning based classifiers. The efficacy of the proposed system is confirmed via experiments conducted on actual network setups with a custom-built prototype firewall and OpenVPN servers. The proposed feature-classifier combinations show superior performance compared to previous state-of-the-art results. The solution that combines natural-language inspired traffic feature and Deep-Learning is demonstrated to be able to solve the mixed-traffic problem, and capable of predicting multiple labels associated with one sample. Additionally, the classifier can classify traffic recorded from locations that are different from where the trained traffic was collected. These results are the first of their kind and are expected to lead the way of creating next-generation TA-based firewall systems.
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Title: Towards interpretable face recognition
Creator: Yin, Bangjie
Date: 2019
Collection: Electronic Theses & Dissertations
Description: Deep CNNs have been pushing the frontier of visual recognition over past years. Besides recognition accuracy, strong demands in understanding deep CNNs in the research community motivate developments of tools to dissect pre-trained models to visualize how they make predictions. Recent works further push the interpretability in the network learning stage to learn more meaningful representations. In this work, focusing on a specific area of visual recognition, we report our efforts towards...
Show moreDeep CNNs have been pushing the frontier of visual recognition over past years. Besides recognition accuracy, strong demands in understanding deep CNNs in the research community motivate developments of tools to dissect pre-trained models to visualize how they make predictions. Recent works further push the interpretability in the network learning stage to learn more meaningful representations. In this work, focusing on a specific area of visual recognition, we report our efforts towards interpretable face recognition. We propose a spatial activation diversity loss to learn more structured face representations. By leveraging the structure, we further design a feature activation diversity loss to push the interpretable representations to be discriminative and robust to occlusions. We demonstrate on three face recognition benchmarks that our proposed method is able to achieve the state-of-art face recognition accuracy with easily interpretable face representations.
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