University of Illinois at Chicago
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Time-of-Flight Secondary Ion Mass Spectrometry Analysis of Microbial Induced Corrosion of Glasses
No full textMicrobially-induced corrosion (MIC) is an emerging topic that has huge environmental impacts, such as long-term evaluation of microbial interactions with radioactive waste glass, environmental cleanup and disposal of radioactive material, and weathering effects of microbes. Improved understanding of relevant bacterial systems and biological secretions help in the development of nuclear waste vitrification materials. A Paenibacillus sp. originating near the Hanford site subsurface was investigated as a model biofilm system. Time-of-flight secondary ion mass spectrometry (ToF–SIMS) – a powerful mass spectral imaging technique with high surface sensitivity, mass resolution, and mass accuracy – is used to study biofilm effects on different substrates. The first study examined the stress response of a biofilm to low carbon source media and suggested that it is a suitable choice to study biomineralization and microbial effects on materials corrosion. Next desalination protocols for thin biofilms adhered to glass surfaces were examined, as desalination is required prior to ToF-SIMS analysis. Comparisons of two desalinating methods, centrifugal spinning (CS) and water submersion (WS), show a decrease of the media peaks up to 99% using CS and 55% using WS, respectively. Next, two types of glass, Granite and Dike, were investigated for MIC of Paenibacillus polymyxa SCE2 biofilms after seven month inoculation. Multimodal imaging and ToF-SIMS were used to verify bacterial coverage, surface and interface compositional and spatial differences, and identify microbial induced corrosion products across the glass surface after long term growth. Finally, a utilization of femtosecond laser ablation in combination with ToF-SIMS is presented for removal of biofilm layers to uncover aerobic and anaerobic differences in a Paenibacillus bacterial biofilm
Conjugation of Zwitterionic and Cationic Peptides to Lipid and Polymer for Gene Delivery
No full textThis dissertation focuses on the new materials that we established by the chemical conjugation between the peptides and the corresponding backbones. In total, we focus on 3 types of conjugates mainly. They are the zwitterionic peptide (EK)x pair lipid DSPE conjugates, THE DSPE-(EK)x, the cationic ionizable peptide RxHy lipid DSPE conjugates, the DSPE-RxHyC, and the cationic ionizable peptide RxHyC polysaccharide sugar mannan conjugates, the RxHyC-mannan. Such three different conjugates focus on different functionalities, with predesigned peptide sequences and the backbone to achieve desired results for siRNA delivery
Patient Perception of Person-Centered Contraceptive Care Quality: A Mixed Methods Study
No full textThe quality of contraceptive care plays a central role in advancing reproductive autonomy, yet inequities persist in how this care is delivered and experienced, particularly for racially and socioeconomically marginalized communities. Person-centered contraceptive care, which prioritizes respect, autonomy, and shared decision-making, is increasingly recognized as a critical component of high-quality care. However, limited research has examined how patients themselves perceive person-centered care, or how these perceptions influence satisfaction and future behavior with regard to contraception care.
This mixed methods study examines patient-perceived contraceptive care quality across four community-based health centers affiliated with Implementing Contraceptive Access Now (ICAN!), a statewide initiative in Illinois committed to person-centered contraceptive counseling. Grounded in person-centered care frameworks and the socioecological model, this study explores how individual, interpersonal, and provider-level factors shape patient experiences.
Aims 1 and 2 use a cross-sectional survey (n=101) to assess patient- and provider-level factors associated with perceived quality of care, measured using the validated Interpersonal Quality of Family Planning (IQFP) scale. Aim 2 explores associations between perceived quality, patient satisfaction, and willingness to return to clinic for future contraceptive care, including potential mediating relationships. Aim 3 draws from in-depth interviews with a purposive subsample of survey participants (n=16) to further explore the meaning behind patient ratings and experiences.
Findings suggest that while most patients report high-quality experiences, notable differences in perceived care emerged based on provider similarity. Patients emphasized the importance of feeling validated in their contraceptive choices, receiving clear and balanced information, and having the space to delay or revisit decisions. Interview data revealed how patient-provider interactions, non-clinical aspects, and provider demeanor shaped perceptions of care.
This study contributes to the growing literature on person-centered care by centering the voices of patients in diverse clinical settings. Findings offer actionable insights for improving provider training, enhancing patient-provider communication, and developing strategies to support equitable, high-quality contraceptive care
Development of Small Molecules as Broad-spectrum Filoviral Entry Inhibitors
No full textEbola (EBOV) and Marburg (MARV) filoviruses are priority infectious agents due to their high pathogenicity and lethality in infected patients. The current lack of pan-filoviral therapeutics exemplifies the need for effective treatments against diverse filoviruses. The filoviral glycoprotein (GP) has proven to be a drug-targetable site as it is conserved amongst all filoviruses and is used to mediate several steps in filoviral entry. In the effort to develop broad-spectrum antifilovirals, a series of N-substituted pyrrole-based heterocycles and elacestrant derivatives were developed to target GP and effectively inhibit diverse filoviral entry in a pseudovirus assay. Selectivity, potency, and metabolic stability of these viral entry inhibitors were improved by introducing structural modifications. In addition, antiviral activity was validated using replication-competent EBOV and MARV, mutational analysis was used to identify the suggested EBOV GP binding region, and antiviral counter-screens demonstrated reduced off-target activity for these filoviral entry inhibitors. Excellent activity coupled with favorable drug-like properties support these entry inhibitors as promising broad-spectrum antifilovirals
Investigating the Impact of K+ Channel Expression on Mechanosurveillance of Disseminated Cancer Cells
No full textCellular stiffness profoundly impacts cancer metastasis at multiple levels, but mechanisms that regulate cancer cells’ stiffness remain poorly understood. Here, we identified potassium efflux and KCNMB1, an auxiliary subunit of the large conductance potassium efflux (BK) channels, as regulators of cellular stiffness downstream of myocardin related transcription factor A (MRTFA). In primary pericytes, KCNMB1 knockdown increased cellular stiffness, which is consistent with the role of potassium efflux in promoting relaxation during excitation-contraction coupling. In a striking contrast, however, KCNMB1 knockdown decreased cellular stiffness in cancer cells. Softer cancer cells were resistant to NK cell-mediated cytotoxicity and the low KCNMB1 expression was associated with worse survival in breast cancer patients. Importantly, pharmacological activation of BK channels reduced metastatic burden in mice. These results highlight the unique ionic regulation of stiffness in cancer cells and point to BK channel agonism as a plausible therapeutic approach in cancer
The Role of Intermediary Firms in Pakistan’s Integration into Automotive Global Production Networks
No full textThis dissertation examines the organizational form, governance structures, and developmental implications of Global Production Networks (GPNs) in the automotive sector, with a specific focus on the Lahore region of Pakistan. Drawing on the GPN framework, which conceptualizes production as a spatially and institutionally embedded process coordinated across borders, this study introduces and theorizes the concept of OEM-mediated GPNs, a distinct mode of global integration where lead firms delegate regional production to local Original Equipment Manufacturers (OEMs) through licensing or contractual arrangements, rather than direct investment.
Through three interrelated empirical studies, this research explores how OEMs serve as critical intermediaries between global lead firms and local suppliers, shaping network structure, firm behavior, and regional development outcomes. The first study introduces the framework and develops a typology of local firms based on their roles and autonomy within OEM-mediated networks and contrasts these networks with traditional GPN models. The study highlights how OEMs act as gatekeepers of global access, enforcing quality standards and coordinating supply chains while embedding global strategies in localized contexts.
The second study investigates the developmental outcomes of GPN participation for local supplier firms. It finds that while many firms experience growth and improved standards, their roles often remain limited to low-value-added functions. A smaller subset of firms, termed emerging suppliers, manage to leverage their initial positions into more autonomous and innovative roles through strategic repositioning and capability development. These findings underscore that the benefits of GPN participation are unevenly distributed and that structural constraints can inhibit meaningful upgrading.
The third study extends the analysis to the multi-scalar dynamics of strategic coupling, analyzing how regional actors are incorporated into overlapping production networks operating at global, national, and local levels. It reveals a dual structure of industrial organization in Lahore: one anchored by globally integrated OEM-led networks, and another constituted by more flexible, regionally embedded supplier linkages. This study also critiques the limited role of the State in fostering indigenous innovation and calls for more targeted, firm-level policy interventions to support technological upgrading and regional development.
Collectively, the dissertation contributes to GPN theory by identifying OEMs as under-theorized but powerful intermediary actors within global production systems. It demonstrates that OEM-mediated GPNs represent a hybrid network architecture with specific implications for network governance, firm autonomy, and regional development. The findings advocate for a more inclusive and nuanced theoretical understanding of GPNs that address the constraints and potentials of peripheral regions in the Global South seeking meaningful integration into the global economy
Why the Lab? Quantifying General Surgery Resident Motivations to Pursue Dedicated Research Time
No full textBackground: Many general surgery residents choose to pursue time away from their clinical training programs to perform dedicated research time (DRT). Resident motivations to pursue DRT need to be examined in order to provide appropriate programmatic support during this stage of training.
Methods: A 37-item survey was designed utilizing the novel Conceptual Framework for Optimizing DRT. General surgery program directors were asked to distribute this online anonymous survey to their trainees. Chi-squared tests were used to examine the association between various motivations and whether the trainee pursued DRT. Chi-squared tests were then used to determine the satisfaction of DRT participants regarding various aspects of their research time.
Results: 156 trainees completed the survey (pre-DRT: 42, intra-DRT: 41, post-DRT: 37, no-DRT: 36). Trainees pursing DRT were more likely to cite factors such as academic career planning and flexibility of schedule compared to those not pursing DRT who expressed concern about loss of skills and salary. Trainees who participated in DRT were the least satisfied with the support they received transitioning back to clinical duties, however 79% expressed satisfaction with the value of their research experience, and 80.5% were satisfied with their overall experience.
Conclusions: Resident motivations for pursing DRT include career planning purposes, professional development needs, and personal rejuvenation reasons. These considerations are tempered by concerns for loss of future salary and clinical skills due to time away from residency. Programmatic support for residents in DRT should be designed to address these motivations and concerns
Novel Phase I/II Designs for Cytotoxic and Cytostatic Agents, and Combination Treatments
No full textThis dissertation develops innovative Bayesian adaptive dose-finding designs for early-phase oncology trials, aiming to improve the identification of optimal biological doses (OBDs) by jointly modeling safety and efficacy. Unlike conventional Phase I designs that rely solely on binary toxicity outcomes to estimate the maximum tolerated dose (MTD), this work focuses on Phase I/II trials using dual continuous endpoints—Normalized Equivalent Toxicity Score (NETS) and continuous efficacy measures—to optimize the risk-benefit profile of investigational therapies.
Three novel designs are introduced. First, the EWOUC-NETS design extends the Escalation with Overdose and Underdose Control (EWOUC) framework by incorporating NETS and continuous efficacy outcomes. This model-based approach enhances accuracy in OBD identification for single-agent cytotoxic therapies, using posterior utility functions to guide dose escalation while safeguarding patient safety.
Second, for cytostatic agents with non-monotonic dose-efficacy relationships, a model-assisted design—STEIN-NETS—is proposed. By integrating NETS and continuous efficacy, it improves robustness and efficiency in trials where efficacy does not increase linearly with dose.
Third, the EWOUC-NETS-COM design generalizes the EWOUC-NETS framework to two-agent combination therapies, addressing the complexity of multidrug regimens. It enables estimation of OBD contours in a multidimensional dose space while maintaining overdose and underdose control.
Extensive simulations across varying toxicity-efficacy scenarios demonstrate that the proposed designs consistently outperform existing methods in dose estimation accuracy, patient safety, and therapeutic benefit. Real trial applications and sensitivity analyses further validate their practical utility and robustness.
By leveraging all available toxicity and efficacy data, these designs offer a significant advancement in adaptive trial methodology, aligning with regulatory initiatives such as FDA’s Project Optimus. This work provides flexible, efficient, and clinically interpretable tools to improve early-phase oncology drug development
Majorana-based Topological Quantum Algorithms in Magnet-Superconductor Hybrid Structures
No full textMajorana zero modes harbored by topological superconductors may be the key ingredient for the realization of fault-tolerant quantum computing and topologically protected quantum devices. Magnet-superconductor hybrid (MSH) systems have proven to be an experimentally versatile platform for quantum engineering the emergence of topological superconductivity and the associated Majorana modes. In this dissertation, I will show how the exotic phase of topological nodal-point superconductivity can be realized in two-dimensional MSH systems using a checkerboard and spiral magnetic structures. This intriguing topological phase shows unique and edge-dependent low-energy modes, which can be used to identify the underlying topology.
Moreover, I will show how the ability to manipulate the magnetic structure of a 1D MSH network can be employed to simulate topological quantum gates and algorithms with Majorana zero modes. In particular, I will demonstrate the simulation of the Clifford gates as well as the Bernstein-Vazirani algorithm, which lets one extract a hidden number from the topological system. Finally, I will extend this to low-energy Majorana edge modes in 2D MSH systems and show how they, in combination with magnetic vortices, can be employed as a quantum memory for topological quantum computing.</p
Novel Methods for Extending Causal Inference to a Target Population
No full textThis dissertation presents two methods to address positivity violations in extending causal inference from study samples to broader target populations, enhancing the robustness and applicability of study findings to real-world settings. Positivity violations occur when selection bias, due to restrictive inclusion criteria or practical constraints, limits the representativeness of the study sample. This mismatch weakens external validity, making it difficult to generalize findings beyond the study population. In real-world applications, such violations can lead to unreliable or unidentifiable estimates. As evidence-based decisions increasingly rely on data, developing robust methods to account for these challenges is crucial.
The first part of the dissertation addresses positivity violations for binary treatments by proposing a unified framework that categorizes the target population into unrepresented, underrepresented, and well-represented groups based on the overlap with the study sample. This framework identifies unrepresented subpopulations, where the average treatment effect (ATE) is unidentifiable, and underrepresented subpopulations, where estimation is inefficient. Inference for the well-represented group is conducted using a weighting estimator, while a sensitivity analysis assesses the impact of unrepresented and underrepresented groups on the overall population-level ATE.
The second part develops a semiparametric framework for generalizing causal effects under multiple treatment arms, addressing limitations of existing methods that rely on parametric assumptions for binary treatments. This work introduces the transportability score, combining the propensity and sampling scores, to improve estimation under covariate shift. To address positivity violations, a smooth inclusion weight is introduced to restrict inference to the well-represented subpopulation. The framework incorporates flexible machine learning tools to enable valid and efficient inference, even under model misspecification, improving generalizability in complex real-world settings.
Together, these methodologies form a comprehensive toolkit for enhancing causal inference under positivity violations. They improve the validity and applicability of study findings, with significant implications for evidence-based interventions that bridge the gap between research and practical impact
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