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  • 1. Whynott, Rachel The effect of understory vegetation on nestbox utilization by Peromyscus leucopus in differently sized forest fragments

    Bachelor of Science, Miami University, 2010, College of Arts and Sciences - Zoology

    Numerous studies of forest fragmentation have found a negative relationship between the density of Peromyscus leucopus (the white-footed mouse) and forest fragment size. This relationship may be caused, in part, by both more food (primary production) and more cover from predation in smaller fragments, which have more structurally complex understory vegetation than larger fragments. However, the influence of the proximity of understory vegetation on selection of nesting sites in specific locations within the fragment had not been studied. I hypothesized that nestboxes in highly vegetated areas would be utilized more often by P. leucopus than nestboxes in sparsely vegetated areas. I tested this hypothesis by measuring the amount of vegetation near thirty nestboxes in each of nine forest fragments. I also estimated the relative population density of P. leucopus in each fragment. I expected to find both a greater proportion of nestboxes occupied and a greater number of mice in nestboxes with a high amount of nearby vegetation. The structural complexity of understory vegetation was significantly greater in small forest fragments than in large and in edge habitat than interior. However, there was no relationship between any of the variables we measured and the density of mice, other than boxes being occupied more frequently in habitat where more mice were present. Additionally, none of the variables we measured were related to the probability of the nestbox being occupied. My results suggest that the complexity of vegetation immediately surrounding the nestbox may not be as important to mice as vegetation at a larger scale (e.g. throughout the individual's territory).

    Committee: Douglas Meikle PhD (Advisor); Nancy Solomon PhD (Committee Member); Gregg Marcello (Committee Member) Subjects: Agriculture; Animals; Behaviorial Sciences; Biology; Ecology; Environmental Science; Forestry; Zoology
  • 2. Sridharan, Srilakshmi Data Mining-based Fragmentation for Query Optimization

    MS, University of Cincinnati, 2014, Engineering and Applied Science: Computer Science

    A main purpose of a database is to provide requested data efficiently. Query performance can be improved in many ways. One of the efficient ways to handle multiple queries posted simultaneously to the database is to distribute the database across several sites and instead of querying the entire database, only the site that contains the data related to the query is accessed. Distribution of a database involves fragmentation of the data and allocating the fragmented data across various sites. Several research works address the issue of fragmentation of databases based on workload, since the aim of fragmentation is to optimize query response time [MD08]. In particular, clustering the data according to query predicates or attributes is shown to perform well for fragmentation. Mahboubi and Darmont propose the use of a k-means based fragmentation approach [MD08]. The authors do not consider the similarity of query predicates in the workload before performing the k-means clustering in their approach. We cluster similar selection predicates involved in the workload as a pre-processing step for the fragmentation; we expect to further improve the query performance. We investigate clustering techniques and study the resulting performance for a selected case study. We conclude that in general for our workloads and for our experimental parameters, the final clusters obtained using our predicate preprocessing system are tighter and more meaningful. As the number of similar values in the workload decreases, the relative savings of the predicate preprocessing system is reduced. If there are no similar values in the workload, the original fragmentation system is more efficient.

    Committee: Karen Davis Ph.D. (Committee Chair); Raj Bhatnagar Ph.D. (Committee Member); Carla Purdy Ph.D. (Committee Member) Subjects: Computer Science
  • 3. Wilder, Shawn FACTORS AFFECTING THE NEGATIVE DENSITY AREA RELATIONSHIP OF THE WHITE-FOOTED MOUSE (PEROMYSCUS LEUCOPUS)

    Master of Science, Miami University, 2003, Zoology

    Several investigators have documented a negative density-area relationship (i.e. higher population densities in smaller fragments) for Peromyscus leucopus (the white-footed mouse). The purpose of this thesis is to investigate if high densities of P. leucopus are consistent among seasons and if higher densities may be due to greater reproduction, as a result of higher food availability, in small than large fragments. Observations of nest box use suggest that relative density and reproduction in small and large fragments differ among seasons. Higher densities in small than large fragments were only documented during the fall season. Observations of foraging patch use combined with reproductive data suggest that greater food availability in the edge may allow greater reproduction and thus contribute to higher densities in small fragments. Dense edge vegetation may be the primary contributor to greater food availability, although there is some evidence that there may be fewer competitors in small fragments.

    Committee: Douglas Meikle (Advisor) Subjects:
  • 4. Bowling, Paige Quantum Mechanical Approaches for Large Protein Systems: Fragmentation, Confining Potentials, and Anisotropic Solvation

    Doctor of Philosophy, The Ohio State University, 2024, Biophysics

    Fragment-based quantum chemistry methods provide a way to circumvent the steep nonlinear scaling of electronic structure calculations, enabling the investigation of large molecular systems using high-level methods. First, we present calculations on enzyme models containing 500-600 atoms using the many-body expansion (MBE) and compare them to benchmarks where the entire enzyme-substrate complex is described at the same level of density functional theory (DFT). When amino acid fragments contain ionic side chains, the MBE exhibits oscillatory behavior under vacuum boundary conditions, but rapid convergence is restored using low-dielectric boundary conditions. This suggests that full-system gas-phase calculations are unsuitable as benchmarks for assessing errors in fragment-based approximations. A three-body protocol maintains sub-kcal/mol accuracy compared to supersystem calculations, as does a two-body approach combined with a low-cost full-system correction. In the next section, we use fragmentation to compute protein–ligand interaction energies in systems with several thousand atoms. Convergence tests using a minimal-basis semi-empirical method (HF-3c) indicate that two-body calculations, with single-residue fragments and simple hydrogen caps, are sufficient to reproduce interaction energies obtained using conventional supramolecular electronic structure calculations, to with 1 kcal/mol at about 1% of the cost. Additionally, we show that semi-empirical methods can be used as an alternative to DFT, to assess convergence of sequences of quantum mechanics (QM) models (of increasing size) generated by different automated protocols. Two-body calculations afford a low-cost way to construct a “QM-informed” enzyme model. This streamlined, user-friendly approach to building ligand binding-site models requires no prior information or manual adjustments, making it accessible and practical for a wide range of applications. For the latter parts of this work, we will be focusi (open full item for complete abstract)

    Committee: John Herbert (Advisor); Sherwin Singer (Committee Member); William Ray (Committee Member) Subjects: Biochemistry; Biology; Biomedical Research; Biophysics; Chemistry; Computer Science; Molecular Biology; Molecular Chemistry; Molecular Physics; Molecules; Physical Chemistry; Physics; Quantum Physics; Technology; Theoretical Physics
  • 5. Zerrudo, Stephanee Joy Development of Isobaric Peptide Probes for Multiplex Disease Detection using Mass Spectrometry-Based Immunoassay

    Master of Science, The Ohio State University, 2024, Chemistry

    Multiplexed biomarker detection has proven to be important in offering a more effective and accurate disease diagnosis compared with single biomarker detection. Mass spectrometry (MS), an analytical technique that provides sensitive and specific analyte detection, has long been employed for signal transduction of immunoassays toward disease detection. Unlike with direct detection of biomarkers, the use of small molecule mass reporters allows the use of simpler and less expensive portable mass spectrometers. Our research group has previously used quaternary ammonium species as mass reporters for MS-based immunoassays performed on inexpensive paper substrates. However, the number of unique masses that could be generated with the quaternary ammonium species was limited by the commercial availability of the starting materials, which in turn limited the multiplexing ability of our MS-based immunoassay platform. The aim of this thesis was to develop isobaric peptide probes that employ small peptides as mass reporters. The isobaric peptide probes were developed by designing and characterizing peptide mass reporters to investigate their fragmentation patterns in tandem MS (MS/MS) and their sensitivity via nano-electrospray ionization (nESI). Results showed that peptides containing two arginines (Arg) that sequester mobile protons and a cleavage site of aspartic acid (Asp) and proline (Pro) provide two dominant b- and y-type ions in MS/MS. The position of the Asp-Pro bond determines the mass of the corresponding b- and y-type ions. By changing the position of the Asp-Pro amino acids with a particular peptide, we can generate different isobaric peptide probes that fragment to give distinct diagnostic ions. The limit of detection (LOD) and quantification (LOQ) of the optimized peptide design (AcIRNPTIDPINR MW 1350.5 Da) in nESI MS/MS were 0.35 ng/mL (0.26 nM) and 1.03 ng/mL (0.77 nM), respectively. In preparation for the use of the isobaric peptides in immunoassay, we synthesi (open full item for complete abstract)

    Committee: Abraham Badu-Tawiah (Advisor); Heather Allen (Committee Member); Vicki Wysokci (Committee Member) Subjects: Analytical Chemistry; Chemistry
  • 6. Rair, Sara Assessing permeability through a mixed disturbance landscape for vertebrates

    Doctor of Philosophy (Ph.D.), Bowling Green State University, 2024, Biological Sciences

    Conflict with wildlife continues to escalate as human population increases and development expands. Understanding how vertebrates interact with the environment is a critical component to conservation ecology. Movement patterns reflect spatial and temporal changes associated with resource availability, life history stages, and habitat use. This study explored how vertebrate mortality could be used to understand the critical factors impacting the consequences of permeability, i.e., ability to move between patches on the landscape, in a mixed disturbance landscape. We assessed how spatial and temporal heterogeneity influenced terrestrial vertebrate mortality. In the biodiversity hotspot of the Oak Openings Region (OOR) of northwest Ohio, we surveyed repeatedly, across three years, approximately 50 kilometers of road segments. Vertebrate mortality locations (N=654) were related to road (e.g., traffic, road width), structural (e.g., canopy cover, soil average water capacity), compositional (e.g., landcover) and productivity (e.g., NDVI) measurements. We found vertebrate mortality locations were positively related to traffic, road width, canopy cover, and normalized difference vegetation index (NDVI) but negatively related to landcover as it becomes more altered (i.e., natural to agricultural). Our consistent findings across years suggest that the spatial components were influencing mortality differences more than temporal differences, and intra-year differences do not impact mortality in a way that would steer long term mitigation of permeability issues. We developed spatially explicit models for predicting current vertebrate mortality probabilities across the entire OOR. Proportion of residential/mixed landcover area was the most influential variables of mortality occurrence probability. We found mortality was well predicted and the results of the same key variables were robust across taxa and years. The models developed can serve as an assessment tool for evaluating co (open full item for complete abstract)

    Committee: Karen Root Ph.D. (Committee Chair); Timothy Schetter Ph.D. (Committee Member); Raymond Larsen Ph.D. (Committee Member); Jeffrey Miner Ph.D. (Committee Member); Erin Labbie Ph.D. (Other) Subjects: Biology; Conservation; Ecology; Wildlife Conservation; Wildlife Management
  • 7. Thenuwara, Sharmila Structural Identification of Biodegraded Microcystins and Other Cyanopeptides in Cyanobacterial Blooms using Liquid Chromatography and High-Resolution Mass Spectrometry

    Doctor of Philosophy, University of Toledo, 2023, Chemistry

    The formation of cyanobacterial harmful algal blooms (cyanoHABs) in waterbodies, including Lake Erie, has become a global issue. CyanoHABs can generate toxic metabolites, such as cyanotoxins, or beneficial natural products. Microcystins (MCs) are cyclic cyanopeptides that have attracted enormous attention, primarily due to the known human hepatotoxicity and their wide distribution. Anabaenopeptins (APs) and cyanopeptolins (CPs) are two understudied classes of cyclic cyanopeptides that co-occur with MCs in similar abundance and frequency, and their toxicity profiles are yet to be understood. Since they can reach the drinking water systems, more studies are needed to determine whether they should be included in drinking water monitoring and management protocols. Also, their ability to inhibit proteases makes them suitable drug candidates. MC biodegradation is considered an environmentally friendly approach to detoxifying MC-containing drinking water. Detecting and identifying the degradation products of MCs enable their toxicity studies and ensure the safety of human health. Ultra-high performance liquid chromatography (UHPLC) coupled to high-resolution mass spectrometry (HRMS) is a gold standard in state-of-the-art compound identification. This dissertation accelerates the studies on cyanopeptides besides MCs and advances cyanopeptide research by incorporating LC-HRMS. It is divided into five main chapters with respect to five research projects I conducted during the last five years. The first project focuses on identifying linear MCs with C-terminal Arg in Lake Erie water samples using UHPLC-HRMS/MS and in-source fragmentation. The novel in-source fragments of linear MCs containing a modified Adda moiety and C-terminal Arg were discovered, and their structures were putatively assigned using HRMS and MS/MS data. The fragment ion at m/z 175.11 was used as the major diagnostic ion to identify whether a MC is linear with arginine at the C-terminus. The distinguishi (open full item for complete abstract)

    Committee: Dragan Isailovic (Committee Chair) Subjects: Analytical Chemistry
  • 8. Schappert, Mikayla Examining the effects of landscape heterogeneity on lepidoptera richness, abundance, and community composition across an agricultural to exurban gradient

    Master of Arts, Miami University, 2023, Geography

    In the Midwestern USA (Southwest Ohio), landscape heterogeneity is changing drastically due to exurbanization. Recent studies suggest that an increase in landscape heterogeneity can have a positive effect on species diversity, abundance, and community composition, making this an exemplary location to research the effects of landscape modifications on species richness and composition. Lepidoptera (butterflies) in particular have been documented to be effective indicators of compositional and configurational landscape heterogeneity shifts which naturally make them a great model organism to study this novel system. Applying the concept of fragmentation per se, I found compositional heterogeneity to be a significant indicator of species richness and diversity. In contrast, configurational heterogeneity did not have an effect on lepidoptera. This suggests that fragmentation per se and increased compositional heterogeneity may have a positive effect on butterfly richness regardless of the configurational heterogeneity. Thus, conservation efforts should focus on diversification of the landscape cover types as well as supporting the conservation of small and large habitat patches.

    Committee: Amelie Davis (Advisor); Mary Henry (Committee Member); Michelle Boone (Committee Member) Subjects: Biology; Conservation; Ecology; Environmental Science; Geography; Physical Geography; Remote Sensing
  • 9. Esquivel, Angelica Planned Obsolescence

    Master of Fine Arts (MFA), Bowling Green State University, 2023, Creative Writing/Fiction

    "Planned Obsolescence" is a novel about a Midwestern Xicana artist that explores themes of visual art, chronic illness, addiction, grief, mental illness, colonialism, violence, and intergenerational trauma. This novel, which takes place over a year, focuses on the cycle of seasons. This timeline, and the fragmented, hybrid nature of the novel, are inspired by forms like the koan, zuihitsu, and prose poem. The manuscript title, "Planned Obsolescence," is derived from the idea that under capitalism, goods are purposefully built to fall apart fast, creating an accelerated cycle of creation and destruction. The concept of “planned obsolescence” is then extrapolated and applied to colonialism, white supremacy, mental illness, the apocalypse, and capitalism itself as it relates to the destruction of the environment and society.

    Committee: Reema Rajbanshi Ph.D. (Committee Member); Lawrence Coates Ph.D. (Committee Chair) Subjects: Art History; Ethnic Studies; Fine Arts; Hispanic American Studies; Hispanic Americans; Latin American History; Latin American Literature; Latin American Studies; Literature; Spirituality; Womens Studies
  • 10. Britton, Sean Wetland Habitat Use by Semiaquatic Fauna in a Hydromodified and Fragmented Landscape

    Master of Science (MS), Bowling Green State University, 2022, Biological Sciences

    Northwest Ohio has been heavily impacted by ditching and draining of the landscape as well as impoundment and pond construction. These features can reduce baseflows, alter wetland hydroperiods, or otherwise impair ecosystem services. However, they may also create aquatic habitat, serve as refuges from wetland habitat loss and promote connectivity of wildlife populations. It is critical to identify the effects of hydromodification on semiaquatic fauna such as the common muskrat (Ondatra zibethicus), the American mink (Neovison vison) and cambarid crayfishes (Cambaridae), which may be sensitive to associated changes in fine- and coarse-scale wetland habitat and landscape characteristics. To evaluate potential wetland habitat use patterns, sign and nocturnal spotlight surveys were conducted in the Oak Openings Region from May 15th to October 18th 2021. Habitat, environmental and spatial data were also collected. As predicted, focal organisms used modified wetlands to a lesser degree, although the effect depended on organism and wetland type. As expected further, muskrats and crayfishes were more likely to use higher order or deep streams/ditches; crayfishes were more likely to use seasonal and restored wetlands. Results were consistent with isolation-area based predictions of habitat use insofar as mink and muskrats were more likely to use large nonlinear wetlands, and muskrats used less isolated wetlands. Crayfish and, unexpectedly, mink used more isolated wetlands. Open canopy and anthropogenic landcover classes in the landscape neighborhood of wetlands featured in many habitat use models. Fine-scale habitat variables tended to predict habitat use as well as or better than coarser-scale variables. Treating presence or relative activity of each organism as a predictor variable in habitat use models of the other organisms produced competitive models, although results for mink occurrence were inconsistent with predictions based on predator-prey relationships. Results su (open full item for complete abstract)

    Committee: Karen Root Ph.D. (Committee Chair); Enrique Gomezdelcampo Ph.D. (Committee Member); Jeffrey Miner Ph.D. (Committee Member) Subjects: Biology; Ecology; Wildlife Conservation; Wildlife Management
  • 11. Mohammad, Somayya Potential of βII-spectrin as a biomarker of cardiac health

    Doctor of Philosophy, The Ohio State University, 2022, Biomedical Sciences

    Management of atrial fibrillation (AF) progression is challenging and places a significant financial burden on the US health care system. Approximately 57% of persistent patients progress to heart failure. Cardioversion to restore sinus rhythm is the primary treatment for AF; however, it is ineffective in 9-20% of the patients. Approximately 30% of the patients re-experience AF within a year post treatment. Notably, 60% of patients are asymptomatic when they revert to AF, thus increasing the risk for disease progression. Research from our lab has demonstrated the important role of cardiac cytoskeleton proteins, namely βII spectrin, in maintaining the structural integrity of cardiomyocytes. Tissue level expression of βII spectrin is known to decrease with AF and heart failure. Thus, we hypothesize that cardiac βII spectrin breakdown products/fragments could serve as early diagnostic biomarkers of cardiac health, making them clinically significant. To this end, we show that βII-spectrin fragments are secreted in human serum and packaged in exosomes. At tissue level, βII spectrin is responsive to acute stress resulting in fragmentation and can be protected with atorvastatin pre-treatment. Our cardiac specific βII spectrin antibodies have identified c-terminal and n-terminal fragments in human serum which decrease in circulation based on both age and AF status. Moreover, we are the first to show that βII spectrin fragments are present in exosomes and the protein concentration differs based on age, disease state, and statin use. Hence our translational project has important clinical applications and can lead to a new biomarker for the assessment of AF progression.

    Committee: Sakima Smith (Advisor) Subjects: Biology; Medicine; Molecular Biology; Oncology; Pharmacy Sciences; Physiology; Toxicology
  • 12. Altany, Kate A Gallery: Memory, Trauma, and Time

    Bachelor of Arts (BA), Ohio University, 2022, English

    I argue that writing in the style of a “pillow book”--a collection of fragmented poetry and nonlinear narratives--allows for a different conception of self that avoids the pitfalls of humanist ideas that represent trauma as being able to heal through narrative. My collection, A Gallery, demonstrates the power and potential of this form's fragmentation by relaying trauma as it manifests in the individual's subjective memory.

    Committee: Thomas Scanlan (Advisor); Mary Kate Hurley (Advisor) Subjects: Literature
  • 13. Russo-Petrick, Kelly Evaluating the effects of anthropogenic land use and habitat fragmentation on bat diversity and activity in the Oak Openings Region

    Doctor of Philosophy (Ph.D.), Bowling Green State University, 2022, Biological Sciences

    Bats are critically important for their control of insects but are experiencing population declines. The biggest reason for these declines is anthropogenic land use. Despite negative impacts, anthropogenic land use has variable impact on bats, with tolerance for more developed areas being species dependent and varying depending on the spatial or temporal scale. Previous studies on land use and bats lack spatial variability and are often single year. My goal was to determine how habitat factors related to human land use impact bat activity and species richness at multiple spatial scales over a period of several years. This research was conducted in the Oak Openings Region, which is a highly developed mixed-use region with high biodiversity that serves as important bat habitat. Specific objectives included determining (1) changes in bat activity and species richness over time, (2) differences in bat activity and species richness between protected and non-protected areas, (3) how factors related to human land use impact bat activity and species richness, and (4) to map current bat habitat suitability and see how it may change in the future. Calls increased each subsequent year during the 2019-2021 period, showing a trend of consistently increasing bat activity. However, during 2011-2019 bat activity significantly decreased. Protected areas had higher species richness and activity than unprotected areas. Higher activity and species richness were found in areas with greater percent upland prairie, sand barrens, and savanna and less floodplain and conifer forest and wet prairie. Activity was higher with less structural clutter at 3-6.5 m, lower understory height, taller canopy height, more canopy cover, and more structural clutter 0-3 m. Number of habitats was positively associated with bat species richness and activity along transects, but negatively associated with activity at stationary points. An opposite trend was observed for cropland. Activity and species richnes (open full item for complete abstract)

    Committee: Karen Root (Advisor); Juan Bes (Other); Moira van Staaden (Committee Member); Kevin McCluney (Committee Member); Shannon Pellini (Committee Member) Subjects: Acoustics; Animals; Biology; Climate Change; Conservation; Environmental Science; Geographic Information Science; Macroecology; Wildlife Conservation; Wildlife Management
  • 14. Skinner, Aaron Using GPS-Tracking to Fill Knowledge Gaps in the Full Annual Cycle of an Elusive Aerial Insectivore in Steep Decline

    Master of Science, The Ohio State University, 2021, Environment and Natural Resources

    Migratory bird populations can be limited by events in disparate parts of the world. Despite that roughly two-thirds of a migrant's annual cycle is spent migrating and on the winter grounds, these periods are poorly studied, limiting our ability to design effective conservation strategies. An understanding of basic migratory and winter ecology is critical for a full annual cycle approach to the conservation of rapidly declining species. The Eastern whip-poor-will (hereafter, whip-poor-will) is a rapidly declining (-70% from 1966-2016) nightjar, yet data remains elusive for the species outside of the breeding season where they are highly vocal. We extracted data from 52 archival GPS tags from individuals across the Midwestern U.S. to understand large-scale migratory movements and space use on the wintering grounds. We also used satellite imagery and stable-Carbon (measuring habitat moisture) and -Nitrogen (relative trophic level) isotope ratios from winter-grown claws to analyze how land use and habitat moisture impact home range size and relative trophic level. Whip-poor-wills circumvented the Gulf of Mexico, and populations across a large latitudinal gradient came together in eastern Texas in early October, resulting in increasing spatial overlap throughout migration. Migratory connectivity was low (MC = 0.22), with extensive overlap of core wintering areas in southern Mexico and Guatemala. The overlap of wintering areas by individuals across a large latitudinal span suggests that whip-poor-wills are telescopic migrants, although a single line of weak evidence pointed towards a leapfrog migration pattern. We examined predictors of home range size at three spatial scales (broader geographic region, site, and home range), and found that forest fragmentation in the site and the presence of agriculture in the home range were positively related to home range size. These results suggest that both landscape configuration and composition variables within the site and t (open full item for complete abstract)

    Committee: Chris Tonra (Advisor); Stephen Matthews (Committee Member); Mazeika Sullivan (Committee Member) Subjects: Environmental Science
  • 15. Smith, Zachary Loading and Material Constraints on the Strain Rate Dependence of Brittle Damage Fabrics

    Master of Science, The Ohio State University, 2021, Earth Sciences

    Brittle fragmentation is a common rock failure process near Earth's surface and occurs at strain rates ranging from tectonic to shock. At the scale of fault damage zones, brittle damage by tensile fragmentation during earthquake rupture introduces intense fracturing and secondary porosity, altering both the mechanical constitutive behavior and permeability of the damage zone rocks. Modeling and experiments suggest that there exists a relationship between fragment size and strain rate above a given strain rate threshold, yet the factors that control this threshold are not fully understood. Factors that are thought to influence the relationship between strain rate and fragmentation include (i) differences in applied stress state (e.g., tension vs. compression), and (ii) material properties (e.g., crystalline vs. granular rocks, variations in mineralogy, or preexisting damage). In this study a modified sample configuration for a Split Hopkinson Pressure Bar is used to investigate tensile fragmentation in comparison to deformation formed by traditional uniaxial compression experiments. This study begins with an analysis of the influence of lithology on brittle fragmentation under dynamic tensile loading. Four rock types are compared, including diabase, granite (Westerly Granite), welded tuff, and sandstone (Berea Sandstone). Over the range of strain rates tested, diabase and granite have the greatest rate of increase in tensile strength with strain rate. The strain rate and tensile strength measurements performed in this study are combined with results in the literature to develop an empirical equation for rock strength as a function of strain rate that follows a sigmoidal trend. This empirical relationship is then used to predict fault damage zone widths by comparing the dynamic tensile strength to the tensile stress decay predicted by the analytical model for dynamic mode-II rupture. The second section of this study focuses on the influence of preexisting macroscopi (open full item for complete abstract)

    Committee: William Griffith (Advisor); Joachim Moortgat (Committee Member); Derek Sawyer (Committee Member) Subjects: Earth; Geology; Geophysics
  • 16. Panczyk, Erin Characterization of Peptides, Proteins, and Protein Complexes using Infrared Multiphoton Dissociation Spectroscopy, Ion Mobility Spectrometry, and Surface-induced Dissociation Mass Spectrometry

    Doctor of Philosophy, The Ohio State University, 2021, Chemistry

    Mass spectrometry-based techniques have emerged as powerful analytical tools to investigate the structure of proteins from the primary to quaternary levels. The advancement of mass spectrometry instrumentation and methods has allowed researchers to go beyond just measuring an analyte's mass-to-charge ratio, but to also probe gas-phase dissociation behaviors and conformations of peptides, proteins, and protein complexes. The primary structure of a protein refers to the linear sequence of amino acids linked together via peptide bonds. The presence, and the order, of specific amino acids in a peptide can strongly influence how a peptide fragments in the gas-phase. Particular amino acids can direct where along the peptide backbone fragmentation is favored and the structure of the fragment ions formed. One method for probing the structure of peptide fragment ions is infrared multiphoton dissociation (IRMPD) mass spectrometry coupled with theoretical quantum chemical calculations. This approach is used to investigate the role of peptide bond conformation on the structure of b2+ fragment ions formed from proline and dimethylproline-containing peptides (Chapter 3). Additionally, IRMPD is used to study the fragmentation patterns of proline containing pentapeptides into b3+ ions (Chapter 4). Native mass spectrometry (nMS) analyzes the intact structures of proteins and protein complexes and offers complementary information to traditional biophysical methods, such as NMR or cryo-EM. Tandem mass spectrometry, specifically surface-induced dissociation (SID), provides information on protein complex connectivity, stoichiometry, and gas-phase structural rearrangement. SID is utilized to monitor deviation from native structure for protein complexes generated from submicrometer nanoelectrospray capillaries (Chapter 5), as well as to provide insight into connectivity of protein complexes selected by trapped ion mobility spectrometry (Chapter 6). In addition to SID, ion mobility (open full item for complete abstract)

    Committee: Vicki Wysocki (Advisor) Subjects: Chemistry
  • 17. Guan, Shanshan Mass Spectrometry-based Fragmentation Chemistry of Small Biological Compounds

    Doctor of Philosophy (PhD), Ohio University, 2021, Chemistry and Biochemistry (Arts and Sciences)

    In this dissertation, the gas-phase fragmentation chemistries of different biological compounds were characterized. We employed the tandem mass spectra of the analytes and detailed density functional theory (DFT) reaction pathway calculations to rationalize the gas-phase fragmentation mechanisms. We investigated the fragmentation characteristics of doubly protonated small peptides of different lengths and compositions (Chapter 2). We studied the fragmentation mechanism of deprotonated peptide that can offer complementary information for the most utilized protonated peptide analysis (Chapter 3). The fragmentation chemistries of different peptidoglycans which were characterized in Chapter 4. In addition, we have developed a method for facile differentiation of acidic, isomeric metabolites by attaching high proton affinity, piperidine-based chemical tags to carboxylic acid groups followed by LC-MS/MS analysis (Chapter 5).

    Committee: Benjamin Bythell (Advisor) Subjects: Chemistry
  • 18. Redding, Jeremy Deformation, Fragmentation and Vaporization of Volatile Liquid Droplets in Shock-Laden Environments

    MS, University of Cincinnati, 2020, Engineering and Applied Science: Aerospace Engineering

    This study quantitatively investigates the fundamental physics underlying the deformation, atomization, and vaporization of volatile liquid fuel droplets impacted by a normal shock wave using a high-fidelity, VOF-DIM (volume of fluid – diffuse interface method)-based methodology. The “Stiffened Gas” equation of state is used to model the liquid and a modified Kapila method is used to account for surface tension and viscosity. A thermal-mechanical-chemical equilibrium relaxation procedure is implemented to simulate vaporization. Because of the unavailability of experimental data on a fragmenting and vaporizing droplet as it interacts with shock waves, the framework is first validated against measurements of droplet-shock interactions of a non-vaporizing water droplet, showing excellent agreement. Next, the vaporization model is benchmarked against the d2-law. Once both vaporization and shock wave dynamics have been validated against available experimental data, we investigate the atomization and vaporization of a dodecane droplet as it interacts with a shock wave traveling at a Mach number of 6.5. When the vaporization model is not enabled, heat transfer and mass transfer are not considered, and shockwave dynamics are similar to that of water, where their breakup morphology is dependent on Weber number. When vaporization is enabled, aerothermal heating from shockwave impact and high temperatures in the post shock region provide sufficient heating for volatile liquid droplets to undergo vaporization. When the droplet is vaporizing, it can be shown that some of the vapor plume is forced in the direction opposing the shockwave, an effect which is lessened as the Mach wave strength increases. Furthermore, regions of entrainment of the liquid, as well as spacing between the retransmitted wave and the end of the vapor plume are discussed with respect to Mach number. Due to the significant effect the Mach number has on the dynamics of the vapor flow field, it is used for (open full item for complete abstract)

    Committee: Prashant Khare Ph.D. (Committee Chair); Shaaban Abdallah Ph.D. (Committee Member); Jongguen Lee Ph.D. (Committee Member) Subjects: Aerospace Materials
  • 19. Hunsinger, Tiffany The Silos of American Catholicism and Their Connections to Cultural and National Identities: An Examination of Contemporary Catholicism with Fr. James Martin, SJ and R.R. Reno

    Master of Arts (M.A.), University of Dayton, 2020, Theological Studies

    The objective of this thesis is to outline the path of the American Church's current polarization. Those represented by Father James Martin are not as engaged in the Traditional aspects of the Church, which loses credibility among those on the other side. On the other hand, those represented by R.R. Reno have embraced Tradition, but have the risk of falling into extremism that ignores Catholic Social Teaching as it is most widely interpreted. At the same time these sides are disputing, young adults are leaving the Church altogether at a drastic rate, which might make all this scholarship for naught. Through examining these sides from the viewpoint of migration into the United States, a common thread emerges that will bring the two sides together rather than further cleave them apart. However, as the American political stage shows in our current times, there appears to be no simple solution.

    Committee: William Portier (Advisor); Timothy Gabrielli (Other); Angela Ann Zukowski (Other) Subjects: American History; American Studies; Ethics; History; Political Science; Religion; Religious Congregations; Religious History; Social Structure; Theology
  • 20. Santhanakrishnan, Rajalakshmi Mitochondria-Dependent Cellular Toxicity of α-synuclein Modeled in Yeast

    Doctor of Philosophy (PhD), Wright State University, 2019, Biomedical Sciences PhD

    Parkinson's disease is the second most common neurodegenerative disease. This disease is caused by the degeneration of dopaminergic neurons, leading to debilitating motor symptoms and early mortality. The protein α-synuclein (α-syn), encoded by SNCA, misfolds and forms inclusions in Parkinson's disease brains. When α-syn is overexpressed in yeast, it causes cellular toxicity and an increased number of aggregates, recapitulating the toxic phenotypes observed in humans and animal models. Yeast models are a powerful tool to perform high-throughput overexpression screening to identify modifiers of α-syn toxicity. α-syn causes mitochondrial dysfunction by inhibiting complex I and inducing mitochondrial fragmentation. Prior screening of α-syn were limited to only the galactose condition, where mitochondrial function is dispensable. Previous screening was performed exclusively with the GAL1 promoter, restricting the genes to only those induced by galactose. We have validated an overexpression system using GAL3 alleles that can induce genes under mitochondrial-dependent glycerol-ethanol condition and other non-galactose conditions (calorie restriction, nitrogen starvation and raffinose). α-syn showed discrepancy in the correlation of toxicity and aggregation in non-galactose conditions. Compared to galactose, under glycerol-ethanol condition, α-syn exhibited higher toxicity, formed more aggregates, and decreased viability and respiratory competency despite having similar expression under the two conditions. We screened 14,827 human gene clones and identified 87 that can suppress α-syn toxicity in glycerol-ethanol. Genes involved in RNA polymerase II function, anterior-posterior axis and nucleoplasm were overrepresented. Among the suppressor hits, we identified four 14-3-3 protein isotypes (β, γ, θ, and ζ). None of the four suppressors suppressed the toxicity under galactose. However, the 14-3-3 suppressors did not reduce aggregates under glycerol-ethanol. No increase in res (open full item for complete abstract)

    Committee: Quan Zhong Ph.D. (Advisor); David R. Cool Ph.D. (Committee Member); Paula Ann Bubulya Ph.D. (Committee Member); David R. Ladle Ph.D. (Committee Member); Weiwen Long Ph.D. (Committee Member) Subjects: Biology; Cellular Biology; Molecular Biology