Doctor of Philosophy, Case Western Reserve University, 2024, EECS - Electrical Engineering

Quantitative Magnetic Resonance Imaging (qMRI) is a powerful tool for detecting biochemical abnormalities without harmful ionizing radiation and invasive procedure, which can significantly enhance early disease diagnosis and progression monitoring compared to standard morphological MRI. Osteoarthritis is a disease significantly impacting joint function, mobility, and quality of life, often leading to chronic pain and reduced physical activity. Despite the significant impact, the disease lacks sensitive biomarker that can detect and track the disease progression from an early stage which can help improve patient outcomes and develop effective treatment for the disease. qMRI, due to its sensitivity to biochemical properties, provide multiple candidates that may serve as imaging biomarkers for OA. Among them, T2 and T1ρ have advantage of not requiring special coil nor contrast agent. However, challenges need to be addressed to expand the accessibility of the technique and successful translation to be used in large scale clinical trials and in clinical practice. In this study, novel quantitative T2 and T1ρ acquisition techniques were developed to enhance reliability and enable faster acquisition.

Committee: Xiaojuan Li (Advisor); Mark Griswold (Committee Member); Xin Yu (Committee Member); Cenk Cavusoglu (Committee Chair) Subjects: Biomedical Engineering; Electrical Engineering

Doctor of Philosophy, The Ohio State University, 2023, Food Science and Technology

Food and beverage consumption occur in contextual settings where consumers are exposed to various environmental cues important for shaping product expectations. Traditional sensory and consumer testing conducted in isolated, neutral booths lacks ecological validity, which can lead to uninformative results and potential costly product failures. To facilitate evaluations reflective of real-world experiences and reliable data collection, sensory scientists have recently compiled a growing body of research using virtual reality (VR) immersive technologies to restore relevant context during consumer sensory testing. While promising effects of immersive contexts were found on consumer perception and acceptance data, limitations of existing sensory VR systems that prevent widespread adoption of the technologies include a diminished sense of presence, unrealistic visuals, and the lack of interactive capabilities enabling the integration of real-world features that facilitate taste testing and/or data collection. Therefore, we aimed to develop a user-friendly, interactive 360° VR system for sensory and consumer testing. Two system iterations with VR controllers (System 1) and hand tracking (System 2) as interactive techniques were assessed in two separate studies for their ability to deliver realistic consumption contexts and to facilitate a virtual product evaluation experience (Chapter 3). Participants found both systems usable and experienced high levels of presence and engagement during testing. System 1 (VR controllers) performed better at interactions with the virtual tablet interface to answer questionnaires, whereas interactions with the food objects were easier using System 2 (hand tracking). Prior research has applied the same consumption context for all participants without accounting for varying individual consumption habits; evaluating products in a consumption scenario of low personal relevance can also lead to misleading consumer response (open full item for complete abstract)

Committee: Christopher T. Simons (Advisor); Neal Hooker (Committee Member); Yael Vodovotz (Committee Member); Jessica Cooperstone (Committee Member) Subjects: Food Science; Technology

Doctor of Philosophy, Case Western Reserve University, 2023, Biomedical Engineering

Current non-invasive cross-sectional imaging such as MRI and CT provide clinicians with a powerful tool for the diagnosis, monitoring, and treatment planning of patients. The advancements in this field are especially noticeable in chronic diseases like Crohn's, which benefits from early identification but lacks a long term cure and thus requires life time monitoring. However, the current application of imaging is predominantly qualitative, allowing for inter-reader variability and an incomplete view of the diseased regions. Additionally, many patients show significant variation in response to specific therapies with standard radiological and clinical assessment being unable to predict or prognosticate the response for each patient. This variation in response maybe due to underlying phenotypic differences in disease like extent of fibrosis and inflammation, but at present there are no methods to assess this at time of diagnosis with non-invasive imaging. However, the computer-extraction of advanced features from radiographic images (radiomics), has enabled superior disease characterization especially in concert with radiological reading and clinical markers. While, studies have shown the potential for radiomics in the context of treatment response prognostication in cancers there is a lack of similar work in the field of Crohn's. These initial studies have also shown that radiomic features vary as a function of the scanner and the settings. It is therefore important to identify a stable set of radiomic features which are correlated with Crohn's disease treatment outcomes and phenotype. In this dissertation, we provide a comprehensive evaluation of radiomic features in which, we identify pools of radiomic features which are consistent across image variations in both MRI and CT. We leverage these features to construct a prognostic radiomics model for risk stratifying patients with Crohn's based on need for early surgical interventions. Finally, we identify and validate (open full item for complete abstract)

Committee: David Wilson (Committee Chair); Satish Viswanath (Advisor); Anant Madabhushi (Committee Member); Shuo Li (Committee Member); Erick Remer (Committee Member) Subjects: Biomedical Engineering; Biomedical Research

Master of Science in Biomedical Engineering, Cleveland State University, 2021, Washkewicz College of Engineering

The usage of radiomics for extracting high-dimensional features from radiographic imaging to quantify subtle changes in tissue structure and heterogeneity has shown great potential for disease diagnosis and prognosis. However, radiomic features are known to be impacted by acquisition-related changes (e.g., dose and reconstruction variations in CT scans) as well as technical variations between cohorts (i.e., batch effects due to varying dosage and tube currents). Using features which are not resilient to such imaging variations can result in poor performance of the downstream radiomics classifier models. In this study, we present a framework to systematically identify radiomic features that are resilient to both batch effects and acquisition differences, as well as evaluate the impact of such variations on radiomic model performance. We demonstrate the utility of our approach in the context of distinguishing active Crohn's disease (CD) from healthy controls using a uniquely accrued cohort of 164 CTE scans accrued from a single institution, which included (a) batch effects due to variations in effective dosage and tube current, as well as (b) scans simultaneously acquired at multiple doses and reconstructions (3 variations per patient). Our framework involves systematically evaluating the impact of acquisition variations (based on feature robustness to explicit dose/acquisition changes) and batch effects (based on feature stability to implicit dosage/current variations). Resilient radiomic features identified after accounting for both types of variations yielded the best random forest classifier performance across both discovery (AUC=0.819 ± 0.043) and validation (AUC=0.787) cohorts when using full-dose images; also found to be significantly more generalizable than features that were not optimized for such variations (AUC=0.419 in validation). This subset of radiomic features that were both robust and stable (resilient) also maintained their performance when evaluate (open full item for complete abstract)

Committee: Satish E. Viswanath (Committee Chair); Hongkai Yu (Committee Member); Moo-Yeal Lee (Advisor) Subjects: Biology; Biomedical Engineering; Biomedical Research; Medical Imaging; Radiology

Master of Science, The Ohio State University, 2019, Comparative and Veterinary Medicine

Exponential growth in technological advancements have given rise to the emergence of next generation sequencing (NGS). NGS has given us the ability to look into the nucleotide sequences, DNA and/or RNA, of the trillions of microbes that are present inside every living and non-living thing. Since the advent of NGS, studies investigating the genetics of microbes, known as the microbiome, have increased exponentially. In fact, the impact of the microbiome in human health has been deemed so important that the microbiome was compared to the necessity of an organ. Currently, most of the studies revolving the microbiome focus on the gut; this is especially true when it comes to poultry. Numerous studies have revealed that the poultry gut microbiota is a critical component of animal health, performance, and production. However, unlike the gut, the respiratory microbiota is understudied. The extent of which the poultry respiratory microbiota contributes to animal health is currently unknown. To properly identify the respiratory microbiota, sampling techniques need to be established and evaluated so that we may strive towards method standardization. In addition, current methods of respiratory tract sampling rely on invasive techniques, which require bird euthanasia. In order to sample individual birds longitudinally, non-invasive sampling methods need to be assessed and compared with the currently used invasive sampling methods. The main goal of this research is to evaluate sampling methodologies for the collection and study of respiratory bacterial microbiota. In order to address these issues we collected respiratory samples from two experiments. In experiment 1, we first established invasive sampling techniques that were able to sample the upper and lower respiratory tract. In experiment 2, we compared both invasive (require euthanasia) and non-invasive (normally done on live birds) upper respiratory sampling techniques to determine if non-invasive swabbing could be an al (open full item for complete abstract)

Committee: Chang Won Lee (Advisor) Subjects: Microbiology

Doctor of Philosophy, Case Western Reserve University, 2019, Clinical Research

Brain metastases (BM) are the most frequent type of brain tumor, and cause significant morbidity and mortality. As imaging modalities improve, treatments improve and diagnoses increase in frequency, epidemiological studies of BM and its clinical outcomes become increasingly relevant and potentially beneficial to cancer patients. Here, we use large population-level data from the Surveillance, Epidemiology, and End-Results (SEER) program combined with Medicare claims to identify measures of BM incidence, claims algorithm concordance with SEER data, treatment patterns, and treatment efficacy for patients with BM arising from primary lung, breast, or skin cancers. We make use of both traditional epidemiological approaches to minimize confounding, such as age adjustment to a standard population, and more advanced methods, such as propensity score matching. By examining the Medicare claims of patients diagnosed with BM, the following chapters shed light on which patients develop BM, how BM patients benefit from an antineoplastic drug that may simultaneously relieve intracranial hypertension, and which patient populations are underserved with respect to BM treatment.

Committee: Jill Barnholtz-Sloan PhD (Advisor); Fredrick Schumacher PhD (Committee Chair); Jeremy Bordeaux MD (Committee Member); Andrew Sloan MD (Committee Member) Subjects: Biostatistics; Epidemiology; Health Sciences; Medicine; Neurology; Oncology

Master of Sciences (Engineering), Case Western Reserve University, 2018, Biomedical Engineering

Radiomics has enabled the development of a number of prognostic and predictive imaging based tools, but there is limited work on benchmarking radiomic features across multiple sites and scanners; especially in the context of MRI. We benchmarked 5 radiomic feature families in terms of discriminability and reproducibility in a multi-site setting; specically attempting to characterize prostate tumors. 147 patient T2w MRI datasets from 4 different sites were pre-processed to correct for acquisition-related artifacts and differences. 406 3D radiomic features were extracted and evaluated across sites via quantitative measures of cross-site reproducibility and discriminability. We demonstrated that the majority of Haralick features were both highly reproducible and discriminable across sites. By contrast, Laws features were extremely variable in terms of both benchmarks. Our results indicate that only a subset of radiomic features and parameters may be generalizable enough for use in machine learning.

Committee: Satish Viswanath (Committee Chair); Anant Madabhushi (Committee Member); David Wilson (Committee Member); Andrei Purysko (Committee Member) Subjects: Biomedical Engineering

PhD, University of Cincinnati, 2010, Engineering and Applied Science: Biomedical Engineering

Magnetic resonance spectroscopy (MRS) is a non-invasive and non-destructive in vivo technique available on magnetic resonance imaging (MRI) scanners that is used to measure biochemical profiles from localized regions, or volumes-of-interest (VOIs), inside the body. A confounding factor for interpretation and analysis of MRS is spatial inconsistency in selection of VOIs for data collection, which may obscure biochemical alterations and reduce the statistical power of a study. Because VOI selection is performed manually by the MRI operator, consistency both between sessions and among subjects requires careful protocol design and experienced staff. Inter-subject anatomic variation, imprecise experimental protocols, and inter-operator variation contribute to VOI positioning error. In this work, automatic targeting of VOIs using a standard anatomic atlas was hypothesized to improve spatial consistency for VOIs, both among subjects and between sessions. Subject anatomy is aligned to a template during acquisition of routine high-resolution 3D anatomic imaging. Alignment is computed parallel to acquisition and completes prior to the end of the scan allowing immediate use of the template coordinate system for the next scan. Once aligned, preselected VOIs are transferred from the template for acquisition. Two real-time alignment techniques are compared. The first performs affine alignment of the subject to the ICBM452 template, and the second rigidly aligns subject anatomy between baseline and followup sessions. The technique was developed using simulations based on archived data from 79 subjects randomly segregated into training (40 subjects for development) and testing groups (39 subjects for evaluation). The accuracy of real-time spatial normalization was evaluated as disagreement with SPM5-derived nonlinear normalization. Median disagreement within the brain was 1.9 mm (largest: 9.1 mm). For comparison, optimal affine alignment was computed directly from nonlinear SPM5 re (open full item for complete abstract)

Committee: Jing-Huei Lee PhD (Committee Chair); Wen-Jang Chu PhD (Committee Member); James Eliassen PhD (Committee Member); William Ball MD (Committee Member) Subjects: Biomedical Research

Master of Arts (MA), Bowling Green State University, 2011, German

The invention of the printing press and movable type has been established by sociological, art historical, and media studies scholarship as a pivotal turning point in media consumption and production across Europe, but especially in Germany in the decades following 1517. The press opened up new possibilities for dissemination of texts such as books, pamphlets, and single-leaf broadsheets. Images, either woodcut or engraved, often accompanied these texts. Recent scholarship has undertaken the task of proving the effectiveness of such texts in spreading the Reformation message, but most analyses have bypassed highlighting the wider shift in media consumption with regard to images. This study attempts to chart this broader shift in how the common folk, the target audience of the evangelical Reformation message, interacted with images. The ease of production, affordability and consequent wide dissemination of broadsheets shifted the location of viewing of sacred images. Images thus far seen only by the aristocracy or within liturgical settings were now brought into the street, the tavern, or private homes. This led to a separation from the original ritual, whereby the previous understanding of images as containing the holy made present began to be questioned, most notably visible in moments of iconoclasm. Reproducibility thereby effectuated a breakdown in understanding images as unifying signifier (image) and signified (original, unique thing the image represents). In addition, broadsheet images of this time evoked an analogous effect to Mikhail Bakhtin's conception of the carnivalesque, where mockery, laughter, and desacralization open up room for the observer to interact and take part in the discourse of the image. Finally, relying upon the fundamental argument of Robert W. Scribner's work "For the Sake of Simple Folk" that broadsheet images were recycled from orthodox and popular origins, it will be seen how recycled images of the peasant remade him as empowered, the (open full item for complete abstract)

Committee: Edgar Landgraf Ph.D (Advisor); Geoffrey Howes Ph.D (Committee Member) Subjects: Germanic Literature; Mass Communications; Mass Media

Master of Arts (MA), Bowling Green State University, 2011, German

This study examines Steve Reich's reflections on his early works in the context of Walter Benjamin's thesis in “The Work of Art in the Age of its Technical Reproducibility.” While Reich's thoughts as expressed in interviews and selected writings show a similar attitude to Benjamin's toward changes in human perception, Benjamin's notion of auratic demise in the age of technical reproducibility is challenged by Reich's understanding of the role of technology in music and the effects of gradual musical processes. Reich's assertions regarding the aesthetic autonomy of his compositional process are reminiscent of Romantic ideals of art, particularly those embodied by the “poeticized” as defined by Benjamin in “Two Poems by Friedrich Holderlin.” However, the means by which Reich claims to have reintroduced artistic autonomy are those that Benjamin attributes to aura's deterioration, such as impersonality and gradual presentation of the artistic subject. This study determines that, while Reich uses mechanical process to accommodate the change in human perception as Benjamin anticipates, aura is not eliminated as proposed in “The Work of Art in the Age of its Technical Reproducibility.” Although the “here and now” of the original is destroyed, aura survives through the authority and transcendent nature of musical process, and singularity is achieved by the unique reception of individual audience members with each hearing. Reich's work may not politicize aesthetics as Benjamin predicts, but through the authority of autonomous musical process and the decentralization of interpretation, the fascist aestheticization of politics may still be averted in the age of technical reproducibility.

Committee: Edgar Landgraf Dr. (Advisor); Geoffrey Howes Dr. (Committee Member) Subjects: Germanic Literature