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Instrumentation And Development Of A Mass Spectrometry System For The Study Of Gas-Phase Biomolecular Ion Reactions, Ziqing Lin
Open Access Dissertations
Gas-phase reactions of biomolecular ions are highly relevant to the understanding of structures and functions of the biomolecules. Mass spectrometry is a powerful tool in investigating gas-phase ion chemistry. Various mass spectrometers have been developed to explore ion/molecule reactions, ion/ion reactions, ion/photon reactions, ion/radical reactions etc., both at atmospheric pressure and in vacuum. In-vacuum reactions have an advantage of involving pre-selecting the ions for the reactions using a mass analyzer. Over the decades, a variety of mass analyzers have been employed in the research of ion chemistry. Hybrid configurations, such as quadrupole ion trap with a time-of-flight and or a …
Transcriptional Stress Response In Foodborne Pathogens, Aaron M. Pleitner
Transcriptional Stress Response In Foodborne Pathogens, Aaron M. Pleitner
Open Access Dissertations
Novel molecular method use is leading to better identification and understanding of microbial presence in food and food processing environments. The application of molecular methods targeting foodborne pathogens provides genetic profiling and targeted intervention methods. Whole-genome sequencing (WGS) provides information on the genomic uniqueness of specific pathogens and is being implemented in epidemiological investigations. Transcriptomic profiling allows for tracking the differential expression of genes and elucidating stress responses. Effective methods and treatments require an understanding of intervention (e.g. sanitizers) and treatment (e.g. antibiotics) mechanisms and efficacies. Accurate novel molecular method use requires proper learning of theory and data management. ^ …
Modeling, Optimization, And Sensitivity Analysis Of A Continuous Multi-Segment Crystallizer For Production Of Active Pharmaceutical Ingredients, Bradley James Ridder
Modeling, Optimization, And Sensitivity Analysis Of A Continuous Multi-Segment Crystallizer For Production Of Active Pharmaceutical Ingredients, Bradley James Ridder
Open Access Dissertations
We have investigated the simulation-based, steady-state optimization of a new type of crystallizer for the production of pharmaceuticals. The multi-segment, multi-addition plug-flow crystallizer (MSMA-PFC) offers better control over supersaturation in one dimension compared to a batch or stirred-tank crystallizer. Through use of a population balance framework, we have written the governing model equations of population balance and mass balance on the crystallizer segments. The solution of these equations was accomplished through either the method of moments or the finite volume method. The goal was to optimize the performance of the crystallizer with respect to certain quantities, such as maximizing the …
Mach: A Model For Explaining Molecular And Cellular Mechanisms, Caleb M. Trujillo
Mach: A Model For Explaining Molecular And Cellular Mechanisms, Caleb M. Trujillo
Open Access Dissertations
Biologists use mechanistic explanations to understand behaviors of the immense complexity of molecular and cellular systems. In undergraduate biology courses, students are expected to explain molecular and cellular mechanisms, but teaching this skill presents many challenges due to the highly abstract, intangible nature of the cellular world, the influence of everyday language, and the tendency of students to overestimate how much they can explain. Therefore, across three studies this dissertation addresses these obstacles to teach undergraduate biology students to explain molecular and cellular mechanisms. ^ The first step was to model how biology experts explain molecular and cellular mechanisms, and …
Show Horse Welfare, Melissa A. Voigt
Show Horse Welfare, Melissa A. Voigt
Open Access Dissertations
In recent years there has been an increase in the public's attention to situations where trainers, owners, and handlers have compromised the well-being of show horses for the sake of winning. These situations may be due to training negligence or naivety of individuals working with the horse. Either way, due to these incidents, increasing pressure has been placed on the horse industry to address show horse welfare. The purpose of this research was to expound on the welfare of stock-type show horses through the perspective of those directly involved; considering the understanding of welfare, the value placed on welfare, and …
The Epidemiology Of Coxiella Burnetii In Goats In Indiana, Amy E. Bauer
The Epidemiology Of Coxiella Burnetii In Goats In Indiana, Amy E. Bauer
Open Access Dissertations
Coxiella burnetii is an obligate, intracellular bacterium and the etiologic agent of the zoonotic disease Q fever. Through the presence of an environmentally resilient small cell variant, C. burnetii can persist outside of a host in the face of extremes in temperature, humidity, and pressure. C. burnetii is considered to be ubiquitous in the environment and endemic in cattle, sheep and goat populations. These same species are the main reservoirs for human infection with C. burnetii. The overall goal of this project was to develop a baseline understanding of the epidemiology of C. burnetii in goats in Indiana. Specific areas …
Discovery Of Molecules That Modulate Protein-Protein Interactions In The Context Of Human Proliferating Cell Nuclear Antigen-Associated Processes Of Dna Replication And Damage Repair, Matthew David Bartolowits
Discovery Of Molecules That Modulate Protein-Protein Interactions In The Context Of Human Proliferating Cell Nuclear Antigen-Associated Processes Of Dna Replication And Damage Repair, Matthew David Bartolowits
Open Access Dissertations
Integral to cell viability is the homotrimeric protein complex Proliferating Cell Nuclear Antigen (PCNA) that encircles chromatin-bound DNA and functionally acts as a DNA clamp that provides topological sites for recruitment of proteins necessary for DNA replication and damage repair. PCNA has critical roles in the survival and proliferation of cells, as disease-associated dysregulation of associated functions can have dire effects on genome stability, leading to the formation of various malignancies ranging from non-Hodgkin’s lymphoma to skin, laryngeal, ocular, prostate and breast cancers. Here, a strategy was explored with PCNA as a drug target that may have wider implications for …
Design Of An Embedded Fluorescence Imaging System For Implantable Optical Neural Recording, Giovanni Barbera
Design Of An Embedded Fluorescence Imaging System For Implantable Optical Neural Recording, Giovanni Barbera
Open Access Dissertations
The brain is the most complex and least understood biological system known to man. New imaging techniques are providing scientists with an entirely new perspec- tive on the study of the functional brain at a neural circuit level, enabling in-depth understanding of both physiological processes and animal models of neurological and psychiatric diseases which currently lack e↵ective treatments. These new tools come at the cost of meeting the challenges associated with the miniaturization of the hard- ware for in vivo recordings
Control Of Bovine Pyruvate Carboxylase Expression By Saturated And Unsaturated Fatty Acids And Impact On Fatty Acid Metabolism, Katherine Elizabeth Boesche
Control Of Bovine Pyruvate Carboxylase Expression By Saturated And Unsaturated Fatty Acids And Impact On Fatty Acid Metabolism, Katherine Elizabeth Boesche
Open Access Dissertations
Pyruvate carboxylase (PC; EC 6.4.1.1) ostensibly links carbohydrate and lipid metabolism by supplying oxaloacetate (OAA) from the carboxylation of pyruvate. The OAA pool is necessary in maintaining the anaplerotic supply of carbons to the TCA cycle, and to promote the complete oxidation, to CO2, of acetyl-CoA. The actions of PC in supplying OAA are critical during periods of increased cellular lipid load, including the negative energy balance experienced by periparturient dairy cows. The bovine PC gene contains three promoter sequences, with products of the proximal promoter (PCP1) being specific to glucogenic and lipogenic tissues. Previous work links control of bovine …
Non-Fouling Affinity Platforms For Protein Immobilization In Electron Microscopy, Christopher Jerome Benjamin
Non-Fouling Affinity Platforms For Protein Immobilization In Electron Microscopy, Christopher Jerome Benjamin
Open Access Dissertations
Single-particle reconstruction has grown significantly with the improvements in various data collection and computational strategies including CTF fitting, the use of vitrified samples and the utilization of ultra-sensitive direct electron detectors. Although these improvements have contributed significantly to the recent evolution of 3D reconstruction analysis, the way samples are prepared for electron microscopy has remained largely unchanged. We report the development of TEM grids that are modified with non-fouling coatings bearing surface grafted nitrilotriacetic acid substituents that promotes specific capture of protein targets for high resolution TEM analysis. The utilization of these grids for specific adsorption of the targeted protein …
On New Approaches For Variable Selection Under Single Index Model And Dna Methylation Status Calling, Longjie Cheng
On New Approaches For Variable Selection Under Single Index Model And Dna Methylation Status Calling, Longjie Cheng
Open Access Dissertations
This thesis consists of two main components: a regularization based variable selection method for the single index model and a novel classification based method for DNA methylation status calling for bisulphite-sequencing data.
Impact Of L-Arginine Transportation On Myeloid-Derived Suppressor Cell Function, Cansu Cimen Bozkus
Impact Of L-Arginine Transportation On Myeloid-Derived Suppressor Cell Function, Cansu Cimen Bozkus
Open Access Dissertations
Inflammatory chronic prostatitis/chronic pelvic pain syndrome has been linked to autoimmune inflammation. Likewise, prostatitis has been linked to prostate cancer development and progression. A better understanding of the mechanisms by which inflammation is regulated may provide the foundation for novel approaches to controlling inflammation. Myeloid-derived suppressor cells (MDSC) are a heterogeneous population of immature cells that expand during benign and cancer-associated inflammation. MDSC are characterized by their ability to potently inhibit T cell responses. Therefore, by dampening inflammation, MDSC benefit autoimmune diseases. Instead, they aggravate cancer by blocking antitumor immune responses. Identification of mechanisms underlying MDSC activities can enable the …
Assessing Inter-Rater Agreement For Compositional Data, Ningning Chen
Assessing Inter-Rater Agreement For Compositional Data, Ningning Chen
Open Access Dissertations
Compositional data are non-negative vectors whose elements sum to one (e.g., [0.1, 0.5, 0.4]). This type of data occurs in many research areas where the relative magnitudes between the vector’s elements are of primary interest. In this dissertation we propose novel methodology for assessing inter-rate agreement based on compositional data. This is needed because existing agreement measures either involve converting the vector to a univariate value, thereby losing information, or they fail to account for the sum-to-one restriction. We propose a novel Bayesian approach, enabled by Markov chain Monte Carlo, to investigate differences in the pattern of compositional vector scores. …
Signal Enhancement And Data Mining For Biological And Chemical Samples Using Mass Spectrometry, Yuezhi Du
Signal Enhancement And Data Mining For Biological And Chemical Samples Using Mass Spectrometry, Yuezhi Du
Open Access Dissertations
Mass spectrometry has been actively involved in the areas of healthcare, pharmaceutics, environmental analysis, food industry and forensics due to its ability to provide molecular information at trace levels. Recently, because of the complexity of chemical and biological samples, computer-assisted mass spectra analysis, including signal enhancement, statistics and machine learning, has been drawn more and more attention especially for researches in biomarker identification, sample classification and omics-related areas where high volume of data is generated.
The Organization Of Mitochondrial Quality Control And Life Cycle In The Nervous System In Vivo In The Absence Of Pink1, Swathi Devireddy
The Organization Of Mitochondrial Quality Control And Life Cycle In The Nervous System In Vivo In The Absence Of Pink1, Swathi Devireddy
Open Access Dissertations
Maintenance of healthy mitochondria is crucial in cells, such as neurons, with high
Detailed Investigations Of Capillary And Van Der Waals Forces In The Adhesion Between Solids, Aaron Harrison
Detailed Investigations Of Capillary And Van Der Waals Forces In The Adhesion Between Solids, Aaron Harrison
Open Access Dissertations
The primary focus of this dissertation is on characterizing two fundamental forces common to adhesion between solids: capillary and van der Waals forces. These two forces have a significant impact on how solids flow, stick to surfaces, agglomerate and break; therefore, understanding their behavior can lead to better processing techniques.
Phage Therapy Applications: Efficacy And Impact On The Animal Intestinal Microbiome, Yingying Hong
Phage Therapy Applications: Efficacy And Impact On The Animal Intestinal Microbiome, Yingying Hong
Open Access Dissertations
Phage therapy is a promising antibacterial intervention that has received renewed interest in recent years. In this study, the antibacterial efficacy of phage treatments was tested in different food matrices, under different conditions, as well as in both phage cocktail and single phage forms. Additionally, this study also examined phage genome sequences, bacterial phage resistance, and the impact of orally administered phages on acute immune response and gut microbiome of the host in effort to more clearly assess the safety and long-lasting efficacy of phage-based treatments.
The Role Of Gut Metabolites On Regulation Of Intestinal Immunity, Myunghoo Kim
The Role Of Gut Metabolites On Regulation Of Intestinal Immunity, Myunghoo Kim
Open Access Dissertations
The gastrointestinal tract contains multiple types of immune cells that induce various immune responses to dietary antigens, commensal bacteria, and pathogens. Maintaining homeostasis at this mucosal barrier requires stringent regulation of the immune responses, including mechanisms to convey information about environmental conditions. Dietary nutrients can be converted into gut metabolites through either host or microbial enzymatic activities. Accumulating evidence demonstrates that these gut metabolites have a significant impact on the regulation of intestinal immune responses; however, the underlying mechanisms by which gut metabolites regulate the intestinal immune system are incompletely understood. Thus, we have studied the role of gut metabolites, …
A Comparative Analysis Of Sorghum And Maize As Bioenergy Feedstock For The Us Midwest: Compositional Attributes And System Nitrogen Dynamics, Monique K. Long
A Comparative Analysis Of Sorghum And Maize As Bioenergy Feedstock For The Us Midwest: Compositional Attributes And System Nitrogen Dynamics, Monique K. Long
Open Access Dissertations
The comparative production potential among annual cropping systems grown as bioenergy feedstock in the Eastern Cornbelt of the US Midwest is generally unknown. Two field experiments were conducted to evaluate the compositional attributes, agronomic and economic efficiencies, and environmental impacts of sorghum (Sorghum bicolor M.) and maize (Zea mays L.) as they relate to bioethanol production and nitrogen (N). A 3 site-year fertilizer rate study (0, 67, 135 and 202 kg N ha-1) comparing five distinct sorghum hybrids/lines and a maize hybrid, was conducted to evaluate yields, carbohydrate pools, and associated theoretical ethanol (EtOH) yields. Post-harvest, dried stover was analyzed …
Incorporating A Small-Group Affective Curriculum Model Into A Diverse, Summer Program For Talented Youth: A Design Based Research Study, Enyi Jen
Open Access Dissertations
In this study, I used Design-Based Research (DBR), as a methodological framework, to guide the development and implementation of the GERI Affective Model into a diverse, university-based, summer enrichment residential program for talented youth. The purposes of this study were to build an evidence-based affective intervention, to explore how participation in the affective curriculum influenced high-ability students' social and emotional development and to use the results to refine the GERI Affective Model before dissemination. This research included two phases, an initial design phase in 2012 to 2013 and an outcome study in 2014. In the initial design phase, I designed …
Characterization Of The Function Of The Dead-Box Rna Helicase Dbp2, Wai Kit Ma
Characterization Of The Function Of The Dead-Box Rna Helicase Dbp2, Wai Kit Ma
Open Access Dissertations
In eukaryotes, there are highly coupled mechanisms that require RNA-binding proteins to facilitate gene expression. Proper RNA structure and ribonucleoprotein (RNP) complex formation are critical for gene expression. DEAD-box proteins are the largest class of RNA helicases that play fundamental roles in RNA and RNP structure remodeling. However, the precise biological role of the vast majority of the ~ 40 members in this family has not been completely described. Therefore, my research focused on characterizing the role of the DEAD-box RNA helicase Dbp2 during gene expression in S. cerevisiae.
Second Language Writing Instructor Written Feedback Practices In An Esl Freshman Composition Class: A Complexity Theory Perspective, Masakazu Mishima
Second Language Writing Instructor Written Feedback Practices In An Esl Freshman Composition Class: A Complexity Theory Perspective, Masakazu Mishima
Open Access Dissertations
This case study investigated second language writing instructors’ written feedback practices from a complexity theory perspective. The purpose of the research was to explore and examine contextual factors and their impact on instructor written feedback practices. Data were collected from two ESL writing instructors and two ESL writers through surveys, interviews, and classroom observations. Based on the results, a complexity theory-based model of second language writing instructor written feedback practices was developed to represent the complexity of written feedback practice situated in the specific instructional context. The findings suggest that the instructors were under constant influence of five different contextual …
Manganese Toxicity: Accumulation In Bone, Effect On Brain Neurochemistry, And Impact On Adult Neurogenesis, Stefanie O'Neal
Manganese Toxicity: Accumulation In Bone, Effect On Brain Neurochemistry, And Impact On Adult Neurogenesis, Stefanie O'Neal
Open Access Dissertations
O’Neal, Stefanie L. Ph.D., Purdue University, December 2015. Manganese Toxicity: Accumulation in Bone, Effect on Neurochemistry, Impact on Adult Neurogenesis. Major Professor: Wei Zheng.
Proteogenomic Insights Into The Nature Of Chemoresistance In Chronic Myelogenous Leukemia, Brett Noel
Proteogenomic Insights Into The Nature Of Chemoresistance In Chronic Myelogenous Leukemia, Brett Noel
Open Access Dissertations
Chronic Myelogenous Leukemia (CML) is a hematopoietic cancer caused by the formation of the Philadelphia chromosome, a reciprocal translocation of the ABL1 oncogene on chromosome 9, and the breakpoint cluster region gene (BCR) chromosome 22, resulting in the BCR-ABL oncoprotein. BCR-ABL is a constitutively active tyrosine kinase that regulates cell growth and differentiation, leading to uncontrolled cell proliferation by deregulating downstream signaling pathways.
Investigation Of Noise Sources And Propagation In External Gear Pumps, Timothy John Opperwall
Investigation Of Noise Sources And Propagation In External Gear Pumps, Timothy John Opperwall
Open Access Dissertations
Oil hydraulics is widely accepted as the best technology for transmitting power in many engineering applications due to its advantages in power density, control, layout flexibility, and efficiency. Due to these advantages, hydraulic systems are present in many different applications including construction, agriculture, aerospace, automotive, forestry, medical, and manufacturing, just to identify a few. Many of these applications involve the systems in close proximity to human operators and passengers where noise is one of the main constraints to the acceptance and spread of this technology.
Associations Between The Built Environment And Physical Activity From Analyses Of Spatial Clusters, Trail Use, And Locations Where Physical Activity Occurs, Kosuke Tamura
Open Access Dissertations
Over the past two decades, an increasing number of scientific studies have examined associations between the built environment and physical activity and obesity. These studies have documented positive associations between environmental variables, such as population density, street connectivity, and composite measures of neighborhood walkability and physical activity. Studies have also shown inverse relationships between the presence of neighborhood grocery stores and recreational facilities and obesity. Despite this evidence, there continues to be limitations in built environment studies conducted to date. The three dissertation studies described here were designed to address several different aspects of built environment research that warrant greater …
Mental Health And Human Minds: Some Theoretical Criteria For Clinical Psychiatry, Natalia Washington
Mental Health And Human Minds: Some Theoretical Criteria For Clinical Psychiatry, Natalia Washington
Open Access Dissertations
When it comes to the topic of mental illness, there are three broad areas of concern that are of interest to all of us as human beings—and to the theorists, researchers, and clinicians who wish to offer help—besides knowing what our symptoms are. First, we might be interested in finding out some normative facts about ourselves as individuals, such as whether or not we are mentally healthy, perhaps to what extent, and how this should affect our motivations. A second area of concern involves descriptive facts our minds. In what ways do we deviate from typical human psychological nature, and …
The World Become Image: Nonrepresentational Discussions Of Film And The Natural World, Gary Matthew Varner
The World Become Image: Nonrepresentational Discussions Of Film And The Natural World, Gary Matthew Varner
Open Access Dissertations
This dissertation investigates the relationships between film and the natural world. Building upon extant work in the burgeoning field of Ecocinema, this project attempts to move beyond the scholarly work on Ecocinema that satisfies itself with questions of representation. The issues and arguments taken up here tend to be more programmatic. This work is interested in ecological exchanges, encounters, and relationships, not representations. The first chapter introduces the project, its origins, and the philosophical motivations for working outside the mode of representation. The second chapter excavates a concern for animals and the environment within the margins and subtext of classical …
A General Purpose Programmable Microfluidic Platform For Screening And Optimization Of Biological Assays, Raviraj Thakur
A General Purpose Programmable Microfluidic Platform For Screening And Optimization Of Biological Assays, Raviraj Thakur
Open Access Dissertations
Screening is a fundamental process in today’s medicine and clinical diagnostics, comprising of several processes ranging from finding new target molecules having the desired therapeutic potential to identifying biomarkers for accurate diagnosis of a spectrum of diseases. Current high throughput screening (HTS) platforms leverage sophisticated robotics to perform a large number of experiments very quickly, an otherwise unmanageable task with manual labor. However, these systems are capital intensive which limit their use to large pharmaceutical companies or larger research labs. Additionally, reagent consumption is of the order of 10-100 µL per assay, which leads to substantial consumables cost. Recently proposed …
Framework For Incorporating Network Connectivity In Transportation Systems Evaluation, Wubeshet Woldemariam
Framework For Incorporating Network Connectivity In Transportation Systems Evaluation, Wubeshet Woldemariam
Open Access Dissertations
In transportation investment evaluation, agencies often do not consider the impact of proposed projects in terms of the increased connectivity of the parent network. Thus, agencies may be inadvertently omitting a key and critical goal of transportation investment evaluation and decision making, particularly in regions and countries with sparse networks. This dissertation develops a framework for measuring network connectivity performance for use as an input for the evaluation process and is applicable to existing or proposed networks in any mode of transportation. The steps for the framework include selection of network performance measures (PMs), scaling the PMs, determining the level …