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  • 1. Nwogu, Onyekachi Use of Antibody Structural Information in Disease Prediction Models Reveals Antigen Specific B Cell Receptor Sequences in Bulk Repertoire Data

    PhD, University of Cincinnati, 2024, Medicine: Biomedical Informatics

    Antibodies are secreted proteins forms of B cell receptors (BCR) that can detect, bind and neutralize antigens. A person's BCR repertoire contains immune information of the antigens they have been exposed to. A substantial amount of modern high-throughput sequencing technologies can be applied to sequencing, monitoring and characterization of antibodies, thereby improving our understanding of how antibodies respond to disease antigens and the antibody compartment responsible for pathogen neutralization. With the vast amount of antibody sequence data created via high-throughput technologies and the advancement in computational methods, there is increasing interest in using machine learning to identify patterns within the BCR repertoire, aiming to leverage these insights for disease classification and predictive diagnostics. However, there exists complexities hindering the success of these goals, including the presence of multiple immune states per individual and the fact that deciphering the relationship between the BCR sequence and its antigen is hard to uncover. Convergent antibodies are highly similar antibodies elicited in multiple individuals in response to the same antigen. Convergent antibodies provide insight into the shared immunological responses and show great promise as diagnostic biomarkers. They have typically been identified using amino acid sequence similarity and used in machine learning models for HIV infection status prediction with high accuracy. However, antibodies with similar sequences can have low structural similarity and with structure linked to specificity, the sequence similarity approach at identifying convergent antibodies has limitations. In this thesis, I extend the definition of convergent antibodies to use isotype and structural information and benchmarked their performance by their ability to predict disease status. Additionally, I obtained a reduced set of highly predictive convergent antibody groups and explored the feature (open full item for complete abstract)
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    Committee: Krishna Roskin PhD (Committee Chair); Corey Watson Ph.D. (Committee Member); Sandra Andorf Ph.D. (Committee Member); Jaroslaw Meller Ph.D. (Committee Member) Subjects: Bioinformatics

  • 2. Abdallah, Salayna The Autism Spectrum Trait Scale: Testing Psychometric Properties

    Master of Arts in Psychology, Cleveland State University, 2024, College of Liberal Arts and Social Sciences

    Autism spectrum condition (ASC) is a neurodevelopmental condition characterized by a spectrum of neuropsychological and behavioral impairments ranging from mild to severe. Formal diagnostic assessments primarily rely on a comprehensive evaluation of behavioral and developmental factors. However, the self-report assessments currently used have limitations which threaten the scales' reliability and validity. The purpose of this study was to develop and assess the psychometric properties of the Autism Spectrum Trait Scale (ASTS), a new self-report scale developed to detect ASC in adults. Exploratory factor analysis (EFA) (n = 764) was conducted to develop the factor structure, and confirmatory factor analysis (CFA) (n = 754) was performed to determine model fit. The results indicated a stable six-factor model with good model fit, metric measurement invariance, and relatively high sensitivity and specificity. These findings provide evidence for the utilization of the ASTS as a component of assessment for ASC in adults.
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    Committee: Amir Poreh (Committee Chair); Kathleen Reardon (Committee Co-Chair); Elizabeth Goncy (Committee Co-Chair) Subjects: Psychology

  • 3. Alsehibani, Razan STATISTICAL MODELING OF THE IMPACT OF MULTIPLICITY POOL TESTING AND THE ESTIMATION OF INFECTION AND RECOVERY RATES OF PARTIALLY KNOWN NETWORKS USING HYBRID SAMPLING

    PHD, Kent State University, 2024, College of Arts and Sciences / Department of Mathematical Sciences

    Detection and control of epidemic outbreaks require effective testing measures, identification of highly-connected members in social networks, as well as the estimation of important epidemic parameters. Pool testing have been proven to be an efficient testing approach to control epidemic spread by reducing the total number of tests. However, pool testing can also be used to improve the accuracy of the testing process. One objective of this thesis is to improve the accuracy of pool testing using the same number of tests as that of individual testing taking into consideration the probability of testing errors and pool multiplicity classification thresholds. Statistical models are developed to evaluate the impact of pool multiplicity classification thresholds on pool testing accuracy using the receiver operating characteristic (ROC) curve and the area under the curve (AUC). The findings indicate that under certain conditions, pool testing multiplicity yields superior testing accuracy compared to individual testing without additional cost. Modelling the spread of epidemics requires the identification of well-connected nodes in partially known networks where network sampling can be leveraged to detect important nodes in these networks. This thesis extends prior research by developing a hybrid sampling method based on simple random sampling and network sampling to identify well-connected nodes in partially known networks. The performance of the proposed method is evaluated in terms of the Perron eigenvalue of the sampled subnetwork using simulation. The performance evaluation shows that the hybrid sampling method yields significantly superior performance compared to that of simple random sampling. The performance of the different levels of the partial combinations of the hybrid sampling is also evaluated where we find that the different hybrid levels give differing results under varying conditions. The findings reveal that by sampling only a small proportion of the (open full item for complete abstract)
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    Committee: Omar De La Cruz Cabrera (Advisor); Oana Mocioalca (Committee Member); Jun Li (Committee Member); Xiang Lian (Committee Member); Maxim Dzero (Committee Member) Subjects: Computer Science; Epidemiology; Mathematics; Public Health; Statistics

  • 4. Brown, Wyatt MX908®: Sensitivity and Limit of Detection Evaluation of On Swab and Off Table Samples

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

    908 Devices has created a handheld High-Pressure Mass Spectrometer™ (HP-MS), called the MX908®, for field analysis of unknown substances. According to the manufacturer, the MX908® has a theoretical limit of detection in the low to mid parts per billion (ppb) range, but because the device provides qualitative rather than quantitative data, the actual limits of detection are unknown. The purpose of this experiment was to determine a limit of detection and sensitivity of the MX908® for methamphetamine, fentanyl, heroin, and cocaine by comparing known standards for each drug processed on the MX908® and a Shimadzu 8050 triple quadrupole Liquid Chromatograph Mass Spectrometer (LC-MS). Samples were spotted directly on the MX908® swabs and spotted on a table and swabbed off. This was to compare a controlled setting to a simulation of a practical use of the swabs and instrument. Cocaine and methamphetamine were the only two drugs reliably detected by the instrument. More testing is necessary to validate the MX908® for future use
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    Committee: Travis Worst Ph.D (Committee Chair); Jeremy Canfield MS (Committee Member); Jon Sprague Ph.D (Committee Member) Subjects: Chemistry

  • 5. Harrigian, Fiona Elucidating Factors Influencing Chytrid Parasitism on Several Strains of Green Alga Scenedesmus

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

    Parasites can substantially influence the fitness, genomes, and behaviors of their hosts and the ecosystem surrounding the parasite and host. These hosts can be extremely critical organisms such as phytoplankton that produce carbon to fuel the ecosystem and 50% of the total global oxygen produced by photosynthesis. Given phytoplankton's critical ecosystem roles, it is vitally important to understand how and under what conditions parasites have greatest impacts on phytoplankton. My study aimed to understand the host specificity of the fungal parasite Amoeboaphelidium protococcarum KS120 on a range of green algal hosts and how the outcomes of the parasitic interaction changed under different abiotic and biotic conditions. KS120 has a strong preference for the green algal strain Scenedesmus obliquus UTEX 393 but could also parasitize four other Scenedesmus strains and two more distantly related species of green algae. When focusing on a host-parasite model pairing, I found that culture conditions influenced the severity of infection. Starting host density, organic carbon, and bacterial additions all resulted in significant changes in algal density post-infection. Finally, outdoor mesocosm experiments verified that the differential impacts of parasite strains identified in lab assays were indicative of environmental systems. Understanding the factors governing interactions between parasites and their algal hosts provides numerous insights into how parasitism contributes to the regulation of aquatic food webs, primary production, biogeochemical cycling, and industrial algal cultivation.
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    Committee: Christopher Ward PhD (Committee Chair); Timothy James PhD (Committee Member); Shannon Pelini PhD (Committee Member) Subjects: Biology; Microbiology

  • 6. Kurtz, Matthew What Comes After the Blues

    MFA, Kent State University, 2021, College of the Arts / School of Art

    "What Comes After the Blues" is an art installation by Matt Kurtz that uses found objects, video and performance art to reclaim identity in the ruins of industry and faith. The videos and projections exhibit dualities through site-specificity and personal narrative. Spiritual objects are reimagined while abandoned materials are sanctified. Oftentimes the objects in this installation serve as material memory for past experiences and expand on the concepts of the videos they interact with. Viewers are given the opportunity to participate in the installation through sound performance and meditative play. In his artwork, Kurtz enters the sacred voids of his past and considers local mythology, musical familiarity and the evangelical conditions of his background to convey his experience.
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    Committee: Eli Kessler (Advisor) Subjects: American History; Art History; Fine Arts; Folklore; Music; Religion

  • 7. Salomone, Joseph Defining Gsx2 Mechanisms that Regulate Neural Gene Expression and Progenitor Maintenance in the Mouse Ventral Telencephalon

    PhD, University of Cincinnati, 2020, Medicine: Molecular and Developmental Biology

    Rapid growth of the embryonic brain requires accurate cell specification and sufficient proliferation to generate a diversity of neuronal subtypes. Neurogenesis in the developing mammalian forebrain is controlled via precise spatial and temporal expression of key transcription factors. The homeodomain transcription factor, Gsx2, is important for three key functions during the development of the mouse forebrain: 1) Dorso-Ventral patterning of neural progenitors by establishing the pallio-subpallial boundary; 2) Balancing the maintenance of proliferative progenitors with neurogenesis in the Lateral Ganglionic Eminence (LGE); and 3) Defining progenitor identity to specify distinct neuronal subtypes. Despite its clear functional importance, little is known about the mechanisms by which Gsx2 performs these functions during forebrain development. Here, I will describe two new molecular functions of the Gsx2 protein. First, we found a novel direct interaction between Gsx2 and the proneural basic helix-loop-helix (bHLH) transcription factor Ascl1, which promotes neurogenesis during forebrain development. We show that physical interactions between Gsx2 and Ascl1 within dividing neuronal progenitors prevents Ascl1 from forming homodimers or heterodimers with other bHLHs, and thereby inhibits Ascl1 binding to DNA. Based on our data, we propose a model in which Gsx2 induces Ascl1 gene expression, but limits Ascl1's ability to promote neuronal differentiation through direct Gsx2-Ascl1 protein-protein interactions that inhibit the activation of neurogenic target genes. Therefore, Gsx2-Ascl1 co-expressing cells are primed for neurogenesis, but will not differentiate until Gsx2 is down-regulated. Second, we have identified two types of Gsx2 DNA binding sites within LGE enhancers: monomer sites (M-sites) that independently bind Gsx2 and dimer sites (D-sites) that cooperatively bind Gsx2. We define the DNA binding site features required for cooperative DNA binding and demonstrate it (open full item for complete abstract)
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    Committee: Brian Gebelein Ph.D. (Committee Chair); Kenneth Campbell Ph.D. (Committee Member); Rhett Kovall Ph.D. (Committee Member); Masato Nakafuku M.D. (Committee Member); James Wells Ph.D. (Committee Member) Subjects: Developmental Biology

  • 8. Keesling, Ashley Reevaluating the species status of the Southern Ghost Pipe, Monotropa brittonii

    Master of Science, The Ohio State University, 2020, Evolution, Ecology and Organismal Biology

    Relationships between members of Ericaceae subfamily Monotropoideae have been notoriously difficult to resolve due to convergent evolution in parasitic plants. Ghost pipes (Monotropa uniflora, L.) are fully mycoheterotrophic, meaning they obtain nutrients by parasitizing ectomycorrhizal fungi rather than through photosynthesis. The southern Ghost pipe (Monotropa brittonii, Small) was a species proposed to be distinct from the closely related and more widespread M. uniflora by John K. Small from his study of Florida flora. It has since largely been treated as a synonym of M. uniflora. Here we use several lines of evidence including genetics, morphology, host specificity, and habitat to investigate whether there is evidence to treat M. brittonii as its own species or if synonymization with M. uniflora is supported. Through morphological and molecular phylogenetic analysis of Monotropa collected throughout their range in the US, we determine there is evidence for two separate lineages in Florida, one of which corresponds morphologically to the description of M. brittonii put forth by Small. We also discovered a high degree of host specificity in M. brittonii, which almost exclusively parasitize fungi in Lactifluus subgenus Lactariopsis section Albati. While M. uniflora have been shown to parasitize many species of Russulaceae, most M. brittonii were found to parasitize a single species; Lactifluus deceptivus. Through principal component analysis we found support for several morphological characters that differ significantly between the two species. Additionally, M. brittonii were almost exclusively collected from Florida scrub habitats, which are dry, shrub-dominated environments that differ greatly from the typical moist woodland habitat where M. uniflora is primarily found. Our results suggest there is genetic, morphological, and ecological support to recognize M. brittonii as a separate species from M. uniflora.
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    Committee: John Freudenstein (Advisor); Alison Bennett (Committee Member); Andrea Wolfe (Committee Member) Subjects: Biology; Botany; Ecology; Evolution and Development; Morphology; Plant Biology

  • 9. Howell, Nathan Substrate specificity of the Trm10 m1R9 tRNA methyltransferase family

    Doctor of Philosophy, The Ohio State University, 2019, Biochemistry Program, Ohio State

    The Trm10 m1R9 methyltransferase family is widely conserved throughout eukarya and archaea, and its deficiency in humans has been linked to disease states. Despite this, little is known about the biological and biochemical function of Trm10 enzymes, especially in organisms like humans where more than one Trm10 gene is present. Using in vitro biochemical approaches, we here report several novel discoveries about the Trm10 enzyme family: we demonstrate 1) human cytoplasmic orthologs hTRMT10A and hTRMT10B have distinct substrate specificities and are not functionally redundant; 2) hTRMT10B is, unexpectedly, a highly specific m1A9 tRNA methyltransferase; 3) Trm10 substrate specificity is not due to overall tRNA affinity, but rather to more nuanced interactions in which Trm10 enzymes probe tRNA core stability; and 4) Trm10 activity is responsive to tRNA stability and tRNA modification in ways that may explain longstanding questions of limited Trm10 activity in vivo. We also report an extreme interaction between an E. coli tRNA methyltransferase and a human tRNA substrate. Together, these results increase our understanding of the important biology of human tRNA modification systems, which can aid in understanding the molecular basis for diseases in which their aberrant function is increasingly implicated.
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    Committee: Jane Jackman (Advisor); Mike Ibba (Committee Member); Kurt Fredrick (Committee Member); Kotaro Nakanishi (Committee Member) Subjects: Biochemistry

  • 10. Zhu, Houxiang Optimal gRNA design of different CRISPR-Cas systems for DNA and RNA editing

    Doctor of Philosophy, Miami University, 2019, Cell, Molecular and Structural Biology (CMSB)

    CRISPR-Cas systems have been successfully applied in DNA and RNA editing, but research, therapeutic, and industrial applications will place high demand on target specificity and efficiency. In this dissertation, we have developed three web services, CT-Finder, CRISPR-DT, and CRISPR-RT, to help scientists design optimal guide RNAs (gRNAs) for different CRISPR-Cas systems with improved target specificity and efficiency. The dissertation is divided into five chapters. Chapter 1 is the introduction section, which mainly introduces CRISPR-Cas systems. In Chapter 2, we describe CT-Finder, a web service to help users design gRNAs for the wild-type Cas9, Cas9 D10A nickases (Cas9n), and RNA-guided FokI nucleases (RFNs) systems with improved target specificity. CT-Finder supports multiple parameter settings, such as the PAM (protospacer adjacent motif) sequence. Optimal target candidates can be chosen based on the off-target effects. On-target and off-target sites can be visualized in the genome and transcript background. CT-Finder covers major model organisms, and can be easily extended to cover other species. Recently, the CRISPR-Cpf1 system has been successfully applied in genome editing with high target specificity. However, target efficiency varies among different gRNA sequences. In Chapter 3, we reanalyzed the published gRNA activity data of the CRISPR-Cpf1 system and found many gRNA sequence and structural features associated with target efficiency. With the aid of Random Forest in feature selection, a support vector machine (SVM) model was built to predict CRISPR-Cpf1 target efficiency for any given gRNAs. In addition, we have developed CRISPR-DT, the first web service to help scientists design optimal gRNAs for the CRISPR-Cpf1 system by considering both target efficiency and specificity. More recently, the CRISPR-C2c2 system has been demonstrated as a powerful tool for RNA editing. In Chapter 4, we describe CRISPR-RT, the first web service to help biologists desig (open full item for complete abstract)
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    Committee: Chun Liang (Advisor); Yoshinori Tomoyasu (Committee Chair); Haifei Shi (Committee Member); Meixia Zhao (Committee Member); Dhananjai Rao (Committee Member) Subjects: Bioinformatics

  • 11. Shrestha, Ujjwal Automatic Liver and Tumor Segmentation from CT Scan Images using Gabor Feature and Machine Learning Algorithms

    Master of Science, University of Toledo, 2018, Engineering (Computer Science)

    Automatic segmentation of liver is a difficult task and moreover, segmenting tumor from liver adds extra dimensionality of difficulty. It is very unfavorable to segment the liver and tumor from abdominal Computed Tomography (CT) images solely based on gray levels or shape alone because of the overlap in intensity and variability in position and shape of soft tissues. To deal with these issues, this thesis proposes a more efficient method of liver and tumor segmentation from CT images using Gabor Features (GF) and three different machine learning algorithms: Random forest (RF), support vector machine (SVM), and Deep Neural Network (DNN). The texture information provided by GF is expected to be uniform and consistent across multiple slices of the same organ. In this thesis, first, an array of Gabor filters is used to extract pixel level features. Secondly, liver segmentation is performed to extract liver from abdominal CT image using three different classifiers: RF, SVM, and DNN trained on GF. Finally, tumor segmentation is done on the segmented liver image using GF and same set of classifiers. The Gabor filter is similar to perception in the human visual system (HVS), and all the mentioned algorithm for classification are robust and accurate ML techniques that have been applied for pixel-wise segmentation. Thirty-one CT image slices were used to validate our proposed method. The 3D-IRCADb (3D Image Reconstruction for Comparison of Algorithm Database) was the source for CT image slices. The classification accuracy for liver segmentation was 99.55%, 97.88%, and 98.13% for RF, SVM, and DNN respectively, while the classifier accuracy for tumor segmentation on the extracted liver segment was 99.52%, 98.07% and 98.45% for RF, SVM, and DNN, respectively. The Dice Similarity Coefficient (DSC) for liver segmentation was 99.03%, 96.79%, and 97.11% for RF, SVM, and DNN, respectively, while the DSC for tumor segmentation on the extracted liver segment was 99.43%, 96.18%, and (open full item for complete abstract)
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    Committee: Ezzatollah Salari (Committee Chair); Junghwan Kim (Committee Member); Jackson Carvalho (Committee Member) Subjects: Computer Science

  • 12. Bennett, Robert Enhancing Our Understanding of Human Poverty: An Examination of the Relationship Between Income Poverty and Material Hardship

    Doctor of Philosophy, The Ohio State University, 2017, Social Work

    The purpose of this study was to investigate the Official Poverty Measure's (OPM) classifications and predictions of ten material hardships: unmet essential need, rent or mortgage nonpayment, eviction, skip or cut meal, a day without food, utility nonpayment or disconnection, phone disconnection, unmet medical need, and unmet dental need. The basis for the OPM was developed in 1965, and it has been used by the United States' federal government to estimate the prevalence of poverty since 1969. Many criticized the OPM for its single price index, its definition of income and family, and its lack of geographic variation in prices. These limitations were expected to affect the OPM's accuracy to identify and predict hardship. Respectively, classification and predictive probabilities are statistical metrics of a binary test's efficacy to indicate the presence or absence of a condition (e.g., material hardship) and the trustability of that indication. The OPM's correct positive classifications (i.e., sensitivity) exceeded the evaluative guideline for interpretation, nevertheless, they were low. The probabilities of true-positive results (i.e., OPM and hardship positive) were lower than those for false-negatives (i.e., OPM negative but hardship positive). It was more likely the OPM would erroneously classify families as nonpoor. The correct negative classifications (i.e., specificity) for all but one hardship indicator failed the evaluative criterion and were uninterpretable. The probabilities of false-positive results (i.e., OPM poor but without hardship) were too near the probabilities of OPM positives. The OPM's capability to predict a true-positive or true-negative was also low or uninterpretable. Therefore, a positive or negative OPM prediction had little association with the presence or absence of hardship. The OPM's sensitivity to material hardship (i.e., the odds of a true-positive result) varied across the sociodemographic and labor-power variables assoc (open full item for complete abstract)
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    Committee: Lisa Raiz PhD (Committee Chair); Audrey Begun PhD (Committee Member); Joseph Guada PhD (Committee Member); Erinn Hade PhD (Committee Member) Subjects: Social Work

  • 13. Liu, Shuohui HIV-1 Gag Binding Specificity for Psi: Implications for Virus Assembly

    Master of Science, The Ohio State University, 2017, Chemistry

    Human immunodeficiency virus type 1 (HIV-1) Gag is a polyprotein consisting of matrix (MA), capsid (CA), nucleocapsid (NC) and p6 domains, as well as two short spacer peptides, SP1 and SP2. During virus assembly, two copies of viral genomic RNA (gRNA) are selectively packaged into viral particles via specific interactions between Gag and gRNA packaging signal, despite the vast abundance of cellular RNAs and spliced viral RNAs. However, the mechanism by which Gag specifically recognizes gRNA is not completely understood. In this study, several elements that are important for Gag's binding specificity for gRNA packaging signal were investigated using salt-titration binding assays.
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    Committee: Karin Musier-Forsyth (Advisor); Thomas Magliery (Committee Member) Subjects: Chemistry

  • 14. Niland, Coutrney SPECIFICITY LANDSCAPE OF RIBONUCLEASE P PROCESSING OF PRE-TRNA SUBSTRATES BY HIGH-THROUGHPUT ENZYMOLOGY

    Doctor of Philosophy, Case Western Reserve University, 2017, Biochemistry

    To fully understand the roles of RNA processing enzymes in cellular processes and human health, it is essential to dissect their substrate specificity. Using Ribonuclease P (RNase P) as a model system, this body of work seeks to better understand multiple substrate recognition by RNA processing enzymes. The ubiquitous endonuclease RNase P removes the 5' leader from all pre-tRNAs in the cell. To understand how variation in the 5' leader is accommodated by the active site of RNase P, we comprehensively determined the processing rates of pre-tRNA substrates with all possible sequence combinations in the 5' leader. This quantification involved Illumina(R) sequencing of the residual substrate population at different reaction times to monitor substrate depletion and calculate relative rate constants, a technique termed HTS-Kin. Additionally, the 5' leader of pre-tRNA is recognized by both the catalytic RNA subunit (P RNA) and smaller protein subunit of RNase P, C5. We therefore hypothesized that variation in substrate sequence contacting one enzyme subunit may alter the recognition or energetic contribution of contacts to the other enzyme subunit. Upon comprehensive determination of RNase P specificity for 5' leader sequences, we have determined that this enzyme is tuned for specificity at association as the catalytic rate constant is unaffected by substrate variation. We have also performed mechanistic analysis to identify the key sources of error in the HTS-Kin technique: experimental error and Illumina sequencing error. Finally, we ascertained that the sequence identity of 5' leader nucleotides contacting P RNA does not alter C5 protein specificity but rather modulates its energetic contribution to the processing rate.
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    Committee: Michael Harris Ph.D. (Advisor); Hung-Ying Kao Ph.D. (Committee Chair); Eckhard Jankowsky Ph.D. (Committee Member); Blanton Tolbert Ph.D. (Committee Member); Michael Weiss M.D., Ph.D. (Committee Member) Subjects: Biochemistry

  • 15. Zetzer, Emily Examining Whether Instrument Changes Affect Song Recognition the Way Talker Changes Affect Word Recognition

    Master of Arts in Psychology, Cleveland State University, 2016, College of Liberal Arts and Social Sciences

    In this study, I examined whether or not the representations underlying music processing and spoken word recognition are similar. Previously, talker effects -an advantage for recognizing a repeated word spoken by the same talker relative to two different talkers - have been found when processing is relatively slow (McLennan & Luce, 2005). Research has previously shown that there are similarities between language and music (Patel, 2003; Lim & Goh, 2012; McMullen & Saffran 2004). Therefore, I extended previous work on talker effects to music perception by examining whether or not I would obtain instrument effects - an advantage for recognizing a repeated song played by the same instrument relative to a different instrument. That is, I compared listeners' responses to songs were repeated across two blocks of trials when the instrument remained the same (e.g., harp to harp) and when the instruments changed (e.g., harp to trumpet). The results demonstrated that the instrument match condition was significantly faster than the instrument mismatch condition, demonstrating instrument effects. Results support the notion that the representations underlying language processing are analogous to the representations underlying music processing.
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    Committee: Conor T. McLennan PhD (Committee Chair); Kenneth E. Vail PhD (Committee Member); Eric S. Allard PhD (Committee Member); Albert F. Smith PhD (Committee Member) Subjects: Cognitive Psychology; Experimental Psychology; Language; Music

  • 16. Greenberg, Talia The Complicated Relationship Between Music and Foreign Language Learning: Nuanced Conditions Required for Cognitive Benefits Due to Music

    BA, Oberlin College, 2015, Psychology

    Many people enjoy listening to music while they study, but others find music distracting. Research about the effect of music on performance during a cognitive task mirrors the equivocal nature of this subjective debate. Across 3 experiments, music, either in the background or as an active encoding device, was found to have no effect on foreign language learning. In Experiment 1, participants studied foreign language vocabulary in silence, while listening to instrumental music, or while listening to music with lyrics. There was no effect of music on recall at immediate (p = .52) or delayed testing (p = .80). Participants in Experiments 2 and 3 listened to and then repeated foreign language phrases by speaking or singing them aloud. No significant differences were found in recall for phrases learned by singing and for phrases learned by speaking (p = .827). Experiment 3 assessed whether using a self-composed melody as a musical mnemonic device was more effective than singing a given melody in learning foreign language phrases. Recall for foreign language phrases sung to given melodies was not significantly different than recall for phrases sung to self-composed melodies at any retention interval (all p-values > .50). Despite finding only null results, this research sheds light on the question of when music may be successfully employed to enhance learning and suggests that familiarity of the music and difficulty of the learning task may be important factors.
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    Committee: Patricia deWinstanley (Advisor); Nancy Darling (Advisor); Paul Thibodeau (Committee Member) Subjects: Cognitive Psychology; Educational Psychology; Experimental Psychology; Foreign Language; Language; Music; Music Education; Pedagogy; Psychology; Teaching

  • 17. Luechapanichkul, Rinrada Determination of the Sequence Specificity and Protein Substrates of Protein Phosphatases

    Doctor of Philosophy, The Ohio State University, 2014, Chemistry

    Protein phosphorylation is a post-translational modification controlled by two counteracting enzyme families, protein kinases and phosphatases. Protein phosphatases have been demonstrated to regulate many physiological pathways and exhibit distinct specificity in vivo. However, the factors determining their specificity are not well understood. In this study, the intrinsic specificity of various families of phosphatases has been explored utilizing combinatorial peptide library screening. The sequence specificity of eight classical-protein tyrosine phosphatases (PTPs) (PTPRA, PTPRB, PTPRD, PTPRO, PTP-PEST, PTP1B, SHP-1, and SHP-2) was determined. While PTPRA showed no selectivity, the other PTPs exhibited similar preferences for peptides containing acidic residues but disfavored basic ones. However, the enzymes differed in their level of selectivity and catalytic activity. Most of the classical-PTPs screened in this study also contains substrate recruiting/regulatory domains; it is likely that the in vivo PTP specificity is enhanced by the recruiting/regulatory domains. The sequence specificity of atypical dual-specificity phosphatases (DUSPs), which only contain a single catalytic domain, was examined to determine whether they exhibit more stringent specificity than the classical-PTPs. The screening of Vaccinia VH1-related (VHR) DUSP against pY-peptide libraries revealed two distinct classes of substrates. While class I peptide substrates are similar to the pY motifs derived from reported VHR protein substrates, the novel class II peptide substrates of the consensus (V/A)P(I/L/M/V/F)X1-6pY exhibit an alternative-binding mode to VHR, as suggested by site-directed mutagenesis and molecular modeling. ROBO1 and LASP1, which contain the class II consensus motif, were demonstrated to be VHR substrates in vitro. The haloacid dehydrogenase superfamily (HADSF) phosphatases have been shown to dephosphorylate a wide range of substrates including sequence with pY, phosphoseri (open full item for complete abstract)
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    Committee: Dehua Pei Professor (Advisor); Ross Dalbey Professor (Committee Member); James Cowans Professor (Committee Member) Subjects: Chemistry

  • 18. Selner, Nicholas PROFILING THE INTRINSIC SEQUENCE SPECIFICITY OF PROTEIN TYROSINE PHOSPHATASES

    Doctor of Philosophy, The Ohio State University, 2013, Chemistry

    Many signaling pathways are mediated by protein tyrosine phosphorylation. Regulation of protein tyrosine phosphorylation is balanced between protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs). Numerous studies have shown PTPs to exhibit site-specific dephosphosphorylation in vivo, although much is still unknown regarding the factors that determine the substrate specificity of PTPs. Our lab has developed a method to profile the sequence specificity of PTPs by using combinatorial peptide libraries with an enzyme-coupled assay to detect PTP activity. In this study, the PTP screening method was applied to nine PTPs (PTP1B, SHP1, VHR, TCPTP, SHP2, LMW-A, LMW-B, PTPH1, and PTPRC) which resolved several different aspects of PTP sequence specificity that was previously unknown. Many potential PTP substrates contain multiple pY motifs in close proximity. Previous studies have suggested that PTP1B specifically recognizes a tandem pY motif. As a result, the sequence specificity of PTP1B, SHP1, and VHR PTPs for multiple pY motifs were profiled and validated with solution-phase kinetics. Our results suggest that PTPs do not preferentially recognize specific multiple pY motifs, but prefer additional pY residues due to their role as an acidic residue. Low molecular weight protein-tyrosine phosphatases (LMW-PTPs) have been classified as the fourth class of PTPs due to their unique primary sequence. Although LMW-A and LMW-B are isoforms, studies have implicated them with having different substrate specificities. Therefore, the sequence specificity of LMW-A and LMW-B were determined and exhibited differences in both activity and protein recruitment. The sequence specificity of many PTPs have been studied in our lab (HePTP, PTP-PEST, SHP1, SHP2, PTP1B, TCPTP, PTPH1, PTPD2, PTPRB, PTPRC, PTPRD, PTPRO), which also demonstrated a similar preference for pY peptides rich in acidic residues (e.g., Asp and Glu) and disfavor positively charged sequences librari (open full item for complete abstract)
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    Committee: Dehua Pei (Advisor) Subjects: Biochemistry; Chemistry

  • 19. Jenkins, Megan Viewpoints: Visual Narratives in the Promenade Architecturale

    MARCH, University of Cincinnati, 2013, Design, Architecture, Art and Planning: Architecture

    As society shifts towards an understanding of the environment through the visual mediation of images, it has become increasingly important to define the architectural relationship between movement and view. The promenade architecturale strings interrelated spaces along a series of progressive views. Because this type of observation requires movement, there follows a relationship between the performance piece that can be formed through architecture, and the site-specific theatricality of the promenade architecturale, each bringing the action of architecture into site, space, and time. This thesis will examine the role of spatial manipulation through the progressive view in the promenade architectural, and theatricality's ability to reorient the occupant to their surroundings. Analysis of key works, in particular Le Corbusier's Villa Savoye and Villa La Roche, among other works, demonstrate movement's role in sequential progression, and re-introduce the idea of multiple viewpoints in performative architecture. The Barcelona Pavilion in particular suggests that the constantly shifting view is at the foundation of an experience of movement. Through these investigations, a proposed architectural design will use site-specificity in combination with progressive movement to bring the action of the site into space, time, and motion. A design for a public promenade correlated to the Santa Fe Train Depot, the trolley station, and the MCASD in downtown San Diego will make an inquiry into the possibilities of spatial sequence and the primacy of the interrelated visual experience in architecture. This paper weighs architecture as a type of site-specific theatricality because of its potential to combine the elements of context and view with movement and sequence.
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    Committee: Michael McInturf M.Arch. (Committee Chair); Aarati Kanekar Ph.D. (Committee Member) Subjects: Architecture

  • 20. Austin, Christina Functional Requirement and Redundancy of Egfr Ligands in Drosophila Development

    Doctor of Philosophy, The Ohio State University, 2013, Molecular Genetics

    In both vertebrates and the fruit fly Drosophila melanogaster, the Epidermal growth factor receptor (Egfr) pathway is required for development and homeostasis. Dysfunction of the pathway is implicated in many human pathologies including heart disease, schizophrenia and multiple types of cancer. The Egfr receptor is a member of the ErbB family. In vertebrates there are four genes that encode ErbB receptors. The receptors function as homodimers or heterodimers leading to many different active configurations. There are also multiple EGF ligands, which bind and activate the receptors. In vertebrates there are eleven ligand genes, some of which encode multiple isoforms. To understand the pathway and its specific biological roles it is necessary to examine the function of individual components. The many ligands and many possible receptor combinations make this type of analysis prohibitively complex in vertebrates. In contrast, the Drosophila pathway is much simpler—there are four Drosophila EGF ligands and a sole Egfr receptor. This makes Drosophila a very attractive system for asking questions of ligand requirement and specificity in vivo. Drosophila has four ligands representing two major classes of vertebrate ligands: three TGFa-like ligands spitz (spi), gurken (grk), and Keren (Krn) and one neuregulin-like ligand, vein (vn). To investigate the requirement for ligands in Drosophila Egfr signaling, as well as the functional redundancy of the Drosophila Egfr ligands, I employed two strategies. In the first, I removed ligands to reveal possible redundant roles in development. In the second, I tested ligand specificity by determining if the TGFa ligands were able to replace the unique role of the neuregulin ligand vn in development. For ligand removal, I generated fly stocks bearing all possible combinations of single and multiple ligand mutants, examined phenotypes in the embryonic cuticle and compared these to the cuticles of Egfr receptor mutants. If (open full item for complete abstract)
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    Committee: Amanda Simcox (Advisor); Cole Susan (Committee Member); Vaessin Harald (Committee Member); Guttridge Denis (Committee Member) Subjects: Genetics
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