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Effect Of Bioenergy Crops And Fast Growing Trees On Hydrology And Water Quality In The Little Vermilion River Watershed, Tian Guo

Open Access Dissertations

Energy security and sustainability require a suite of biomass crops, including woody species. Short rotation woody crops (SRWCs) such as Populus have great potential as biofuel feedstocks. Quantifying biomass yields of bioenergy crop and hydrologic and water quality responses to growth is important should it be widely planted in the Midwestern U.S. Subsurface tile drainage systems enable the Midwest area to become highly productive agricultural lands, but also create environmental problems like nitrate-N contamination of the water it drains. The Soil and Water Assessment Tool (SWAT) has been used to model watersheds with tile drainage, but the new tile drainage …

Evaluation Of Negative Energy And Mineral Balance In Periparturient Holstein-Friesian Cattle, Ameer Ahmed Abdelhameed

Open Access Dissertations

Most cows experience a state of negative energy and mineral balance during the periparturient period. This imbalance is a major problem in the dairy industry and it is more frequently seen in multiparous cattle due to their high milk production. A large amount of fat and protein is mobilized in order to address the energy deficit during the periparturient period. The ability to accurately monitor energetics and electrolytes status using accurate, rapid, and low cost point-of-care instruments will assist in optimizing animal health and productivity.

This dissertation contains three studies that evaluated point-of-care instruments for measuring blood and plasma glucose, …

Enhancing Bioethanol Fermentation Through Removal Of Acetic Acid Using Liquid-Liquid Extraction, Mahdieh Aghazadeh

Open Access Dissertations

The concern for the ever growing human population as well as the depletion of fossil fuel resources and their impact on global warming have long been motivations for the researchers to investigate means for sustainable producing carbon-neutral energy. Second-generation biofuel refers to liquid fuels that are produced from non-food resources and reduce the total greenhouse gas emission by at least 60 %. Acetic acid has been shown to be one of the most ubiquitous fermentation inhibitors in a bioethanol production facility which slows down the bioethanol production and reduces its yield through inhibition of the ethanol producing microorganisms. The use …

Improving The Mechanistic Study Of Neuromuscular Diseases Through The Development Of A Fully Wireless And Implantable Recording Device, Rebecca A. Bercich

Open Access Dissertations

Neuromuscular diseases manifest by a handful of known phenotypes affecting the peripheral nerves, skeletal muscle fibers, and neuromuscular junction. Common signs of these diseases include demyelination, myasthenia, atrophy, and aberrant muscle activity—all of which may be tracked over time using one or more electrophysiological markers. Mice, which are the predominant mammalian model for most human diseases, have been used to study congenital neuromuscular diseases for decades. However, our understanding of the mechanisms underlying these pathologies is still incomplete. This is in part due to the lack of instrumentation available to easily collect longitudinal, in vivo electrophysiological activity from mice. There …

Creativity In Organizations: Antecedents And Outcomes Of Individual Creativity, Goran Calic

Open Access Dissertations

In this dissertation I set out to expand our collective understanding of creativity in organizations. I accomplish this through three related studies, each organized into independent chapters of this dissertation.

The first study explores how demands of organizations, particularly strategic contradictions faced by decision makers, affect creative processes and products. In this chapter I develop the theory of paradoxical creativity, which posits that creative discovery is a function of how strategic contradictions are perceived by decision-makers. The key insight of the theory of paradoxical creativity is that strategic contradictions have independent effects on the two stages of creative discovery (generation …

Is Metabolism Goal-Directed? Investigating The Validity Of Modeling Biological Systems With Cybernetic Control Via Omic Data, Frank T. Devilbiss

Open Access Dissertations

Cybernetic models are uniquely juxtaposed to other metabolic modeling frameworks in that they describe the time-dependent regulation of cellular reactions in terms of dynamic "metabolic goals." This approach contrasts starkly with purely mechanistic descriptions of metabolic regulation which seek to explain metabolic processes in high resolution — a clearly daunting undertaking. Over a span of three decades, cybernetic models have been used to predict metabolic phenomena ranging from resource consumption in mixed-substrate environments to intracellular reaction fluxes of intricate metabolic networks. While the cybernetic approach has been validated in its utility for the prediction of metabolic phenomena, its central feature, …

Rearward Visibility Issues Related To Agricultural Machinery: Contributing Factors, Potential Solutions, Shawn Gregory Ehlers

Open Access Dissertations

As the size, complexity, and speed of tractors and other agricultural self-propelled machinery have increased, so have the visibility-related issues, placing significant importance on the visual skills, alertness, and reactive abilities of the operator. Rearward movement of large agricultural equipment has been identified in the literature as causing not only damage to both machine and stationary objects, but also injuries (even fatalities) to bystanders not visible to the operator. Fortunately, monitoring assistance, while not a new concept, has advanced significantly, offering operators today more options for increasing awareness of the area surrounding their machines. In this research, an attempt is …

The Effect Of Voluntary Binge Caffeine And Ethanol Coexposure On Neurobehavioral Sensitivity To Cocaine In Male C57bl/6j Mice, Brandon M. Fritz

Open Access Dissertations

Recently, the co-consumption of highly caffeinated energy drinks and alcohol has become a public health concern. Consumption of these beverages has been linked to a wide variety negative consequences including alcohol poisoning, driving under the influence, physical harm, and sexual violence. The more protracted consequences of caffeinated alcohol consumption have received very little attention, however. Some evidence suggests that individuals that frequently consume energy drinks mixed with alcohol are more likely to develop an alcohol use disorder. Interestingly, both caffeine and alcohol use alone have been linked to polydrug abuse. It is therefore of interest whether combined caffeine and alcohol …

Biophysical Studies Of The Allosteric Regulatory Mechanism Of Syk Tandem Sh2 Domains Interacting With Immunoreceptor Tyrosine-Based Activation Motifs, Chao Feng

Open Access Dissertations

The non-receptor spleen tyrosine kinase (Syk) is an important player in signal transduction from immunoreceptors to various downstream targets. It is widely expressed in both haematopoietic and epithelial cells. Syk disorder is closely related with many inflammatory and autoimmune diseases, as well as cancers.

Syk associates with immunoreceptors through its tandem SH2 domains (tSH2), which contain two SH2 domains connected by interdomain A. The association of Syk with immunoreceptors is regulated by Y130 phosphorylation in interdomain A. The unphosphorylated tSH2 can bind with the doubly phosphorylated immunoreceptor tyrosine-based activation motif (dp-ITAM) of the cytoplasmic domains of immunoreceptors with very high …

Learning The Abc's Of Ribose Transport Using Biophysical Methods, Satchal K. Erramilli

Open Access Dissertations

ATP-binding cassette transporters comprise a large superfamily of proteins that are involved in a variety of biological phenomenon, from bacterial metabolism to cellular homeostasis, antigen-presentation, and drug resistance. These proteins are implicated in a variety of clinically relevant phenomenon, including the human diseases cystic fibrosis, macular degeneration, and cancer. Understanding their structure-function can guide therapeutics and contribute to our overall understanding of these biological phenomena.

This study focuses on understanding the motor protein of the bacterial ribose ABC transporter in the context of transport. This complex is required for the uptake of the nucleotide precursor, ribose. Using biophysical methods, we …

Ultra-Thin Boron Nitride Films By Pulsed Laser Deposition: Plasma Diagnostics, Synthesis, And Device Transport, Nicholas Robert Glavin

Open Access Dissertations

This work describes, for the first time, a pulsed laser deposition (PLD) technique for growth of large area, stoichiometric ultra-thin hexagonal and amorphous boron nitride for next generation 2D material electronics. The growth of boron nitride, in this case, is driven by the high kinetic energies and chemical reactivities of the condensing species formed from physical vapor deposition (PVD) processes, which can facilitate growth over large areas and at reduced substrate temperatures. The use of optical emission spectroscopy during plasma growth provides insight into chemistry, kinetic energies, time of flight data, and spatial distributions within a PVD plasma plume ablated …

Magnesium Regulates Transcription Of The Mgta (Magnesium Transporter) Gene In Salmonella Enterica Serovar Typhimurium Via Prolyl-Bond Formation During Translation Of The Mgtl Leader Orf, Aaron R. Gall

Open Access Dissertations

In Enterobacteriaceae, the mgtA gene encodes a P-type ATPase that mediates Mg2+ uptake and is up-regulated by the PhoQP two-component system during invasion of host epithelial cells and macrophages. The regulation of mgtA has recently gained special interest given that it exists at several stages, including transcription, post-transcription and post-translation, in response to Mg2+availability. The mgtA mRNA has a 264-nucleotide 5’ leader that contains a 17 codon, proline-rich ORF, termed mgtL, whose translation has been proposed to affect the folding of the 5’ leader mRNA, which in turn regulates whether transcription is terminated before the mgtA structural gene at high …

A Black Art: Ontology, Data, And The Tower Of Babel Problem, Andrew J. Iliadis

Open Access Dissertations

Computational ontologies are a new type of emerging scientific media (Smith, 2016) that process large quantities of heterogeneous data about portions of reality. Applied computational ontologies are used for semantically integrating (Heiler, 1995; Pileggi & Fernandez-Llatas, 2012) divergent data to represent reality and in so doing applied computational ontologies alter conceptions of materiality and produce new realities based on levels of informational granularity and abstraction (Floridi, 2011), resulting in a new type of informational ontology (Iliadis, 2013) the critical analysis of which requires new methods and frameworks. Currently, there is a lack of literature addressing the theoretical, social, and critical …

Investigating The Role Of The Basic Helix-Loop-Helix Transcription Factor Mist1 In Pancreatic Diseases, Anju Karki

Open Access Dissertations

Acinar cells of the exocrine pancreas are dedicated to synthesize, package and secrete immense quantities of pro-digestive enzymes to maintain proper metabolic homeostasis for the organism. Dysregulation of enzyme secretion in acinar cells can give rise to exocrine diseases including acute pancreatitis (AP), a disease that targets acinar cells, leading to acinar-ductal metaplasia (ADM), inflammation and fibrosis—events that can transition into the earliest stages of pancreatic ductal adenocarcinoma (PDAC). The focus of this thesis is to interrogate transcriptional regulatory networks that are susceptible to AP and the role that these networks play in acinar cell and exocrine pancreas responses. The …

Crop Modeling For Assessing And Mitigating The Impacts Of Extreme Climatic Events On The Us Agriculture System, Zhenong Jin

Open Access Dissertations

The US agriculture system is the world’s largest producer of maize and soybean, and typically supplies more than one-third of their global trading. Nearly 90% of the US maize and soybean production is rainfed, thus is susceptible to climate change stressors such as heat waves and droughts. Process-based crop and cropping system models are important tools for climate change impact assessments and risk management. As data- science is becoming a new frontier for agriculture growth, the incoming decade calls for operational platforms that use hyper-local growth monitoring, high-resolution real-time weather and satellite data assimilation and cropping system modeling to help …

Influence Of The 3d Microenvironment On Glioblastoma Migration And Drug Response, Ruth Marisol Herrera Perez

Open Access Dissertations

Glioblastoma (GBM) is a highly invasive brain cancer characterized by poor prognosis. Despite significant efforts by the basic and clinical research community our understanding of GBM progression and recurrence has been incremental. Improvements in therapeutic response have been dismal, and GBM continues to be the deadliest tumor of the central nervous system, with patient average survival rate of 12 months. Synergistic relationships that the tumor cells establish with the brain microenvironment have been proven fundamental for successful tumor progression and maintenance. Yet, many in vitro GBM studies are performed in formats that fail to recapitulate the most essential component of …

Characterization Of Cu-Rich Aggregates In Neurogenic Niches Of The Rodent Brain By X-Ray Fluorescence Microscopy, Brendan T. Sullivan

Open Access Dissertations

Copper is an essential element in the brain playing several critical roles ranging from neurotransmitter synthesis to ATP production. As Cu is typically present in micromolar concentrations and has a spatially capricious distribution in the brain, determining concentrations has historically been challenging. X-ray fluorescence microscopy (XRF) offers excellent spatial resolution (down to 30~nm) and detection limits (sub parts per million), making it an excellent tool for analyzing metal distributions in the brain. Using XRF, it is demonstrated that Cu-rich aggregates with concentrations in the hundreds of millimolar are present in the subventricular zone of rats and mice. As the subventricular …

Coupled Resonator Based Wireless Power Transfer For Bioelectronics, Henry Mei

Open Access Dissertations

Implantable and wearable bioelectronics provide the ability to monitor and modulate physiological processes. They represent a promising set of technologies that can provide new treatment for patients or new tools for scientific discovery, such as in long-term studies involving small animals. As these technologies advance, two trends are clear, miniaturization and increased sophistication i.e. multiple channels, wireless bi-directional communication, and responsiveness (closed-loop devices). One primary challenge in realizing miniaturized and sophisticated bioelectronics is powering. Integration and development of wireless power transfer (WPT) technology, however, can overcome this challenge.

In this dissertation, I propose the use of coupled resonator WPT for …

The Things They Carried: The Biological Residue Of Childhood Misfortune, Patricia M. Morton

Open Access Dissertations

There is a well-established relationship between childhood misfortune and adult health, but how these early-life experiences “get under the skin” to later manifest as poor health is less clear. To elucidate this process, this dissertation investigates (1) how childhood conditions influence immune functioning and (2) whether these physiological consequences of early misfortune lead to poor health, indicated by ischemic heart disease (IHD) onset. Guided by cumulative inequality theory and biological embedding, this dissertation also examines adult health lifestyles and socioeconomic status (SES) as possible mechanisms linking childhood misfortune to inflammation and IHD in later life. Data come from six waves …

Mechanistic Characterization Of Acetic Acid Resistance Enzymes Of Acetobacer Aceti, Jesse R. Murphy

Open Access Dissertations

Acetobacter aceti (A. aceti) is a Gram-negative, acidophilic bacterium that is used for the industrial production of acetic acid from ethanol. Oxidation of ethanol by membrane-bound oxidoreductases provides energy for A. aceti and the production of high concentrations of acetic acid is an effective defense mechanism. Acetic acid diffuses through cell membranes at low pH and effectively kills many bacteria, including E. coli, at low millimolar concentrations. The ability of A. aceti to thrive in molar concentrations of acetic acid is partially due to the twin subjects of this thesis, the acetic acid resistance factors AarA (citrate synthase, …

Functional And Structural Analysis Of Fst1 In Fusarium Verticillioides, Chenxing Niu

Open Access Dissertations

Fusarium verticillioides causes an important seed disease on maize and produces fumonisin B1 (FB1), a mycotoxin that is detrimental to human and animal health. Previous studies discovered that expression of FST1 is required for FB1 production and wild-type level of virulence on maize seeds. FST1 encodes a putative protein with 12 transmembrane domains with sequence similarity to hexose transporters. However, those studies have failed to prove its ability to transport glucose, fructose or mannose. I identified another three phenotypes associated with the lack of a functional FST1, which includes reduced hydrophobicity of hyphae, reduced macroconidia production, and increased sensitivity to …

Direct Drug Screening And Lipid Profiling Using Ambient Mass Spectrometry, Yuan Su

Open Access Dissertations

Mass spectrometry (MS) stands in an outstanding position in analysis of biological specimens owing to its abundant structural information, high accuracy, incomparable sensitivity, high speed, and the large variety of its applications. The ion source, an instrumental part for converting the analyte into ions, has played an important role in analyzing biological specimens by MS. However, the performance of conventional spray-based ionization methods always suffers from chemical interferences derived from complex biological matrices. A series of sample extraction, purification, and separation steps is required before the ionization, so as to ensure excellent performance of MS analysis. In order to simplify …

Advancing Multiple Model-Based Control Of Complex Biological Systems: Applications In T Cell Biology, Jeffrey P. Perley

Open Access Dissertations

Activated CD4+ T cells are important regulators of the adaptive immune response against invading pathogens and cancerous host cells. The process of activation is mediated by the T cell receptor and a vast network of intracellular signal transduction pathways, which recognize and interpret antigenic signals to determine the cell's response. The critical role of these early signaling events in normal cell function and the pathogenesis of disease ultimately make them attractive therapeutic targets for numerous autoimmune diseases and cancers.

Scientists increasingly rely on predictive mathematical models and control-theoretic tools to design effective strategies to manipulate cellular processes for the advancement …

Braf Inhibitor (Vemurafenib) Resistance Confers Sensitivity To Arginine Deprivation In Melanoma, Ying-Ying Li

Open Access Dissertations

Melanomas harboring BRAF mutation (V600E) have been reported to recur frequently following treatment with BRAF inhibitors (BRAFi) despite a high initial response rate. Combination of MEK inhibitor (MEKi) and BRAFi significantly improves the progression free survival but patients eventually relapse. Hence, there is an urgent need for second line treatment for BRAF (V600E) mutant melanoma patients. In this study, we propose arginine deprivation to treat BRAFi-resistant (BR) melanoma cells. Around 70% of melanomas do not express argininosuccinate synthase (ASS) to generate arginine through urea cycle, and hence require exogenous arginine to compensate for this defect. Arginine deprivation is achieved by …

Mediating Prostate Cancer Metastasis Through The Microrna Cluster Mir-23b/-27b, Meghan A. Rice

Open Access Dissertations

Deregulation of microRNAs contributes to progression and metastasis of prostate and other cancers. MiR-23b and miR-27b, encoded in the same miR cluster (miR-23b/-27b), are down-regulated in human metastatic prostate cancer compared to primary tumors and benign tissue. Expression of miR-23b/-27b decreases cell migration, invasion and results in anoikis resistance. Conversely, antagomiR-mediated miR-23b and -27b silencing produces the opposite result in a more indolent prostate cancer cell line. However, neither miR-23b/-27b expression nor inhibition impacts prostate cancer cell proliferation or viability suggesting that miR-23b/-27b selectively suppresses metastasis. To examine the effects of miR-23b/-27b on prostate cancer metastasis in vivo, orthotopic prostate …

Sparse Model Learning For Identifying Nucleotide Motifs And Inferring Genotype And Phenotype Associations, Indika P. Kuruppu Appuhamilage

Open Access Dissertations

Variation in gene expression is an important mechanism underlying phenotypic variation in morphological, physiological and behavioral traits as well as disease susceptibility. A connection between DNA variants and gene expression levels not only provides more understanding of the biological network, but also enhances the mapping of these quantitative traits. Thus, an understanding of the mechanism of gene expression and the genotype/phenotype relationship is of paramount importance to both scientific research and social economics. The primary functionality of the gene expression process is to convert information stored in genes into gene products such as RNAs or proteins. The fundamental of this …

Reduced Surrogate Light Chain In Old B Cell Precursors Compromises B Lymphopoiesis And Increases B Cell Reactivity To Common Self Antigens, Kelly M. Khomtchouk

Open Access Dissertations

In murine bone marrow, old age (>2 yrs.) is characterized by low production of pre-B and immature B cells, alterations in the “read-out” of the B cell repertoire and increased autoreactivity within mature B cell populations. In addition, there are changes in the composition of B cell subsets: in the bone marrow early CD23 expression on immature B cells is linked to an activated phenotype, while in the periphery there is increased representation of “antigen experienced” B cells, exemplified by Age-associated B cells. I propose that: 1) Old age-associated reductions in expression of the surrogate light chain not only …

Analysis Of Region-Specific Transcriptomic Changes In The Autistic Brain, Dmitry Velmeshev

Open Access Dissertations

Autism is a highly prevalent neurodevelopmental disorder that affects 1 in every 68 children in the US. Autism comprises a spectrum of highly heterogeneous disorders defined by characteristic deficits of communication and by presence of repetitive and stereotyped behavior. At the same time the disease is highly heritable and genetically heterogeneous, with hundreds of genetic variants that have been associated with it. Previous systems biology studies have provided first insights into convergence of various disease-associated genetic variants onto specific pathways, developmental windows and cell types in the brain. Additionally, transcriptomic and epigenetic studies have identified genes and pathways affected by …

A Novel Stacking Method For Multi-Label Classification, Abdulaziz Alali

Open Access Dissertations

Classical machine learning algorithms were tailored to automatically classify examples that belong to mutually exclusive classes; each example may belong to one class out of a finite set of classes. In realistic applications, however, examples often belong to more than one class at the same time. For example, a text document that belongs to Geography may also be labeled as Geology. Perhaps due to the popularity of its applications, targeting this category of problems has garnered great research interest over the past decade. A widely popular approach, called Binary Relevance (BR), is to induce a separate classifier for each class; …

The Spatial Structure Of Unified Consciousness, Bartlomiej Chomanski

Open Access Dissertations

In this dissertation, I defend two theses: first, that experiences with spatial phenomenology represent space as single and unitary, and, second, that every experience has a spatial phenomenology. The two theses entail the conclusion that the unity of conscious spatial representation is necessary for the unity of consciousness. This means that unified consciousness has a (partially) spatial structure. In what follows, I adopt the mereological conception of unified consciousness according to which experiences are unified just in case they are parts of a subject’s total phenomenal state. I also assume that the unity relation is a relation among experiences. Most …