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UC San Francisco Electronic Theses and Dissertations

Theses and dissertations published by UCSF Graduate Division students since 1965. Some UCSF theses and dissertations published between 1965 and 2006 are not available in this collection.  If you don't find your thesis or dissertation and would like it to be included on eScholarship, contact the Library.  To search all UCSF dissertation titles from all years, go to the library catalog (select Material Type: Dissertations).

Cover page of Novel Approaches to Delivery of Biomacromolecules

Novel Approaches to Delivery of Biomacromolecules

(2024)

Nature challenges healthy mammals with constant risk of infection by a wide variety of pathogens and with degradation of healthy tissue and control systems. I have been interested in drug delivery and improved delivery of therapeutics primarily to attack pathogens but with incidental value in assessing vital functions of a healthy mammal. My recent work uses protein design to approach such problems. Delivering biomacromolecules remains important both for therapeutics and in discerning and shaping functions of cells.My first thesis project focused on designing a better glomerular filtration rate (GFR) marker to facilitate assessment of renal function and seeking a marker reflecting water distribution in the body, which is relevant to distribution of highly soluble drugs [1]. Tritiated polyethylene glycol (PEG) was known to clear the kidneys effectively and correlated well with a GFR standard assay. A better radioactive label for PEG would allow for easy detection, including imaging. At the time of the project, only one biological conjugation with PEG was reported. Attaching an iodinatable moiety to polyethylene glycol (PEG) polymers of different sizes enabled tracking the compound using radioactive iodine. I made a series of related compounds and studied the pharmacokinetics (PK) and pharmacodynamics (PD) of these in rodents and ultimately in a dog. Using relatively long PEG polymers of molecular weight (MW) 5,000 to 6,000 daltons, the PEG dominated the behavior of the compounds, clearing rapidly through the kidneys. With shorter PEG polymers, the chemistry of the iodinatable group was more significant and the compounds were more likely to clear through the bile, to a degree making them unsuitable for a GFR marker but possibly useful to study liver function. Chapter 1, the published manuscript from my first thesis project, is cited in 20 scientific publications and 51 issued US patents. Variations on the design principles of my project have been used widely in the pharmaceutical industry. During a break in my PhD studies, I improved the formulation of a human Phase-2-ready antifungal drug and designed and organized extensive testing in mice and dogs to show that a sustained-release formulation would overcome PK limitations and made the drug much more potent. This work is discussed briefly in Chapter 2. My second thesis project studied brilacidin activity against 40 fungal isolates from 20 different species, showing useful activity against several important human pathogens [2]. The human and many other innate immune systems includes a variety of peptides known as defensins that weaken or kill a variety of pathogens, including bacteria, fungi, and viruses. Brilacidin is a synthetic defensin-mimic, designed to exhibit the physicochemical properties of defensins as a class. Brilacidin is in human Phase 2 trials. Despite its potential, Brilacidin's efficacy against fungi had not been comprehensively explored until my studies, which showcased its viability as a therapeutic agent against challenging-to-treat fungal infections, thereby offering a beacon of hope for future clinical interventions. Chapter 3, the published manuscript based on this second thesis project, has recently been submitted for review, available online in Preprints.

Worse Morning Energy Profiles Are Associated with Significant Levels of Stress and Decrements in Resilience in Patients Receiving Chemotherapy

(2024)

Background: Evidence suggests that lower levels of morning energy are associated with higher levels of stress and lower levels of resilience in patients receiving chemotherapy. Purpose: Study purposes were to identify subgroups of patients with distinct morning energy profiles; evaluate for differences among the profiles in demographic and clinical characteristics, as well as measures of stress, resilience, and coping. Methods: A total of 1,343 outpatients receiving chemotherapy completed a demographic questionnaire and measures of global, cancer-related, and cumulative life stress, and resilience at study enrollment. Morning energy was assessed using the Lee Fatigue Scale at six time points over two cycles of chemotherapy. Results: Latent profile analysis was used to identify subgroups of patients with distinct morning energy profiles. Three morning energy profiles were identified (i.e., High (17.3%), Low (60.3%), Very Low (22.4%)). Compared to High class, the other two morning energy classes were less likely to be employed; had a lower functional status and a higher comorbidity burden; and were more likely to self-report depression and back pain. For all three types of stress, significant differences were found among the three classes with scores that demonstrated a dose response effect (i.e., High < Low < Very Low; as decrements in morning energy increased, stress scores increased). Compared to High class, Very Low class reported higher rates of physical and sexual abuse. The resilience scores exhibited a dose response effect as well (i.e., High > Low > Very Low). Patients with the two worst energy profiles reported a higher use of disengagement coping strategies. Conclusions/Implications for Practice: Findings highlight the complex relationships among decrements in morning energy, various types of stress, resilience, and coping in patients undergoing chemotherapy. Clinicians need to assess for stress and adverse childhood experiences to develop individualized management plans to increase patients’ energy levels.

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Cover page of Improved chemoenzymatic radiosynthesis of fluorine-18 labeled sakebiose for microPET-CT imaging of Staphylococcus aureus

Improved chemoenzymatic radiosynthesis of fluorine-18 labeled sakebiose for microPET-CT imaging of Staphylococcus aureus

(2024)

Staphylococcus aureus (S. aureus) is a gram-positive bacterium that can cause severe infections such as pneumonia, osteomyelitis, and endocarditis when it breaches the skin. This study aimed to enhance the chemoenzymatic radiosynthesis of 2-deoxy-2-[18F]-fluoro-sakebiose ([18F]FSK), a radiotracer potentially useful for imaging S. aureus infections. By optimizing the synthesis of 2-deoxy-2-[19F]-fluoro-sakebiose ([19F]FSK), we identified key factors—such as increased enzyme concentration and decreased precursor levels—that significantly improved the yield. Applying these optimized conditions to the synthesis of [18F]FSK resulted in a 30% increase in the radiochemical yield (RCY%) from the control experiment. In vitro evaluation showed that [18F]FSK was successfully incorporated into two strains of S. aureus, suggesting its potential utility for imaging bacterial infections in vivo. This work lays the groundwork for using [18F]FSK in PET/CT imaging to diagnose and monitor S. aureus infections.

Cover page of Developing Artificial Intelligence Tools for Biologists

Developing Artificial Intelligence Tools for Biologists

(2024)

With the growth of biological and chemical datasets and the development of novel computational techniques, applications of artificial intelligence (AI) and machine learning (ML) methods that leverage these datasets to assist experimentalists become more critical than ever. This dissertation presents an overview of commonly used AL/ML tools for molecular biology and introduces two novel tools, as well as details their specific use cases. In Chapter 1, I provide a review of traditional techniques and their machine learning counterparts for ligand- and structure-based drug discovery and protein structure elucidation and design. In Chapter 2, I introduce Metric Ion Classification (MIC), a method for determining the identity of experimentally identified waters and ions in biomolecular structures. MIC builds upon recent advancements in protein-ligand interface representations and metric learning techniques to introduce a novel classification scheme with extensive validation on a variety of experimental structures. In Chapter 3, we present Autoparty, a tool for AI-assisted human-in-the-loop molecule annotation designed to facilitate the manual assessment of virtual screening results. Autoparty uses the principles of active learning to direct chemists toward useful compounds and limit the amount of labor required when evaluating compounds. These applications do not attempt to replace existing techniques; rather, they act in service of scientists to accelerate both structure determination and drug discovery pipelines. This work broadly highlights the utility of these tools and others like them and encourages their adoption alongside classical approaches.

Cover page of Stem cell models of axial patterning and their implications for V2a neurons and engineered neural systems

Stem cell models of axial patterning and their implications for V2a neurons and engineered neural systems

(2024)

Human pluripotent stem cells have opened up unprecedented opportunities to model human development and disease. Critical to these models is differentiation of stem cells toward relevant cell identities. Axial elongation of the neural tube is crucial during mammalian embryogenesis for anterior-posterior body axis formation and spinal cord development, but these processes cannot be interrogated directly in humans as they occur early post-implantation. However, this developmental period of regionalization significantly influences downstream cell fate. Here, I explore how models of axial patterning influence neural development and how these developmental models can influence engineered neural systems. First, I report an organoid model of neural tube extension derived from human pluripotent stem cell aggregates which recapitulate aspects of the morphological and temporal gene expression patterns of neural tube development. Next, I investigate the effect of early progenitor regionalization on mature V2a interneurons which reside in the hindbrain and spinal cord. Using a multiomic approach, I identify lasting epigenetic and transcriptional differences as a result of early developmental regionalization. The epigenetic differences suggest that uniquely open regions of chromatin are accessed by different transcription factor families, while the differences in transcription point to differences in axonal extension and synapse formation. I also observe differences in spontaneous activity produced from regionally distinct neuron populations. Computational modeling and knockdown validation studies identify CREB5 and TCF7L2 as mediators of some of the region-specific differences in gene expression. Finally, I show that attempting to ‘skip’ developmental patterning by induced transcription factor expression yields a population unlike either developmentally relevant V2a population, highlighting the importance of following developmental steps in establishing cell identities in vitro. This observation leads me to explore ways to achieve cell type specificity by contrasting directed and induced differentiation strategies and proposing ways they can complement one another to better recapitulate target cell type identity.

Cover page of Encoding of social behavior by psychiatrically relevant cell types of the medial prefrontal cortex

Encoding of social behavior by psychiatrically relevant cell types of the medial prefrontal cortex

(2024)

Our behaviors during social interactions are wide-ranging and highly contextual. The norms that dictate how we should act vary based on who we are interacting with, societal context, and past experiences. Social cognition refers to the ability of animals to utilize both experience and the knowledge of learned social norms to select appropriate behaviors for specific contexts. The medial prefrontal cortex (mPFC) has a long-established role in executive function and cognition, and has also been found to be critical for the production of normal social behavior. However, the precise role of the mPFC in social behavior and the neural dynamics that occur in this region during social interaction have not been explored in great detail. Elucidating the precise role of the mPFC during social interaction is critical to understanding how abnormal social phenotypes arise in the array of psychiatric illnesses that impinge upon the PFC. One way to approach this problem is to utilize rodent models in combination with the wide array of molecular and genetic tools available in this system. These tools allow for studying the role of particular brain regions, neuron subtypes, and genes in behavior. Particularly, one tool that has expanded our understanding of the neural foundations of complex behavior is in vivo calcium imaging of neuronal activity with miniaturized, head-mounted microscopes. In combination with tools that allow for expression of the genetically encoded calcium indicator GCaMP in genetically-defined neuron subpopulations, this approach makes it possible to record activity specifically from cell types that have relevance to psychiatric disorders while animals can move and behave freely. Here, we describe two distinct studies that utilize this approach to record activity in the mPFC of mice from neuron populations that have been implicated in psychiatric disorders. In the first study, we record activity in layer 5 projection neurons of the mPFC in both wild-type mice and mice that have the Tbr1 gene deleted specifically in cortical layer 5 neurons. Tbr1 is a high-confidence autism risk-gene, and mPFC layer 5 projection neurons have been identified as a hub of autism risk-gene expression. We find that these Tbr1 layer 5 conditional knockout animals (Tbr1-cKO) display abnormal social and anxiety-related avoidance behaviors. During social interactions, encoding of behavior by correlated activity of mPFC neurons is diminished in cKO animals, while correlated activity remains intact during anxiety-related behavior. We also identify signals in mPFC neural ensembles that are predictive of approach-avoidance decisions, but are lost in the Tbr1 cKO mouse model. In the second study, we record specifically from mPFC neurons that express the dopamine receptor D2R, which has been implicated in disorders including schizophrenia and depression. We also record from mPFC D2R+ neurons after knocking out the D2R, to assess the role of the receptor itself in socially recruited activity. These animals performed the 3-chamber social assay, and we find significant center chamber associated activity in D2R+ neurons that is lost when the D2R is deleted. Inhibition of mPFC D2R+ neurons specifically in the center chamber of this task leads to an overall increase in the number of social interactions.

Cover page of The Association of Demographics, Opioid Use History, Mental Health History, and/or Surgery Type with Administration of Low-dose Intravenous Ketamine in the Post-Anesthesia Care Unit

The Association of Demographics, Opioid Use History, Mental Health History, and/or Surgery Type with Administration of Low-dose Intravenous Ketamine in the Post-Anesthesia Care Unit

(2024)

Introduction: Patients on chronic opioid therapy (COT) who are admitted for a planned surgical procedure may experience inadequately controlled pain in the post-anesthesia care unit (PACU) due to drug tolerance. This is disruptive for not only patients but PACU nurses and can lead to increased utilization of hospital resources and extend PACU and hospital length of stay. Pain management may be optimized in this group using low-dose intravenous (IV) ketamine. However, in a pilot study, we found that administration of this medication occurred 114 minutes (range 14 minutes to 394 minutes) after admission to the PACU, with resultant sub-optimal pain management and delays in PACU throughput. We hypothesize that identifying patients in the preoperative phase who may benefit from this therapy could reduce administration delays and improve pain management. However, specific patient-level variables that may be useful to screen for are largely unknown. Purpose: Examine demographics, opioid use history, mental health diagnosis, and/or surgical service type associated with the administration of low-dose IV ketamine in the PACU. Methods: Retrospective study in 6,419 consecutive adult patients (≥18 years) presenting for a scheduled surgical procedure between Jan 1, 2020, and Dec 31, 2021. The outcome variable was the administration of a low-dose IV ketamine infusion in the PACU. Hypothesized patient predictors were obtained from the electronic health record. A stepwise regression model was used to identify statistically significant variables. Results: In 6,419 consecutive patients, 90 (1.4%) received low-dose IV ketamine in the PACU. Significant variables in the final stepwise model included: age of 55-71 years (p=0.029); history of opioid or substance use disorder (p<0.001); outpatient opioid prescription (p=0.025); outpatient methadone prescription (p=0.049); and morphine milligram equivalency (MME) ≥90/day (p<0.001). Conclusion: Two variables had the highest odds ratio associated with low-dose IV ketamine in the PACU. Patients with an MME ≥90/day were 13.26 times more likely to have received low-dose IV ketamine in the PACU and those with SUD/OUD were 4.02 times more likely to have received low-dose IV ketamine in the PACU. Implications for Practice and Future Research: Nurses should consider evaluating patients in the preoperative phase of care for MME ≥90/day and those with SUD/OUD, as these appear to be important predictors of low-dose IV ketamine in the PACU. However, a larger patient cohort of patients who received low-dose IV ketamine in the PACU is needed to further develop and test a preoperative screening tool.

Rapid motor learning and epidural stimulation in primate cortex

(2024)

Understanding how the nervous system explores and then finds optimal solutions during the process of motor learning is fundamental for rational electrotherapy design. Plasticity in the motor cortex has been implicated in motor learning across a variety of tasks and model organisms. Translational approaches to modulating motor cortical activity have also demonstrated great potential for restoring or relearning motor tasks following brain injury. In this thesis, I begin in Chapter 1 by summarizing the modern understanding of the motor learning network, outlining how the primary motor cortex is uniquely positioned to regulate rapid adaptations to task demands. Then, I provide a historical perspective on brain stimulation methods used in humans for clinical and research applications, including the strengths and limitations and current approaches. In Chapter 2, I present a novel, translatable electrical brain stimulation technique – the ringtrode – which allows for the flexible and precise modulation of the primate cortex. In Chapter 3, I characterize the neural dynamics in motor cortex that underly rapid motor learning during brief breaks. Then, I apply the ringtrode to manipulate these dynamics and assess whether they are causal for motor learning. Finally, I present a model for how stimulation delivered via the ringtrode interacts with motor learning processes in the brain to explore why stimulation-induced effects on motor learning may depend on stimulation frequency.

Cover page of Implant Risk Assessment Validation Study with One Year Follow-up

Implant Risk Assessment Validation Study with One Year Follow-up

(2024)

Objective: This short-term prospective pilot study aimed to assess the validation of the patient-centered implant risk assessment tool in patients recruited at the University of California, San Francisco (UCSF) School of Dentistry.Materials and Methods: Patients seen in the university periodontal clinics were enrolled in the study based on their eligibility for dental implant treatment. For each implant placed, dental surgeons completed a survey tool, called the Implant Risk Assessment Questionnaire (RAQ). After at least one year of loading with the implant final prosthesis, patients were seen for a recall visit at which point, the implant was diagnosed as healthy or having peri-implant disease. The peri-implant disease was subcategorized as peri-implant mucositis and peri-implantitis. The survey output classifies the implant as low, medium, or high aggregate risk, which was correlated to diagnoses of healthy, peri-implant mucositis, or peri-implantitis respectively. The RAQ scores and diagnoses were used to compute sensitivity, specificity, and positive and negative predictive values to determine the tool's validity. Results: In total, seventy-three patients with 187 implants were initially recruited for the study. However, only thirty-three patients, representing eighty-seven implants, participated in the one-year follow-up and were consequently included in the study results. Among these implants, fifty-four were diagnosed as healthy, ten as peri-implant mucositis, and six as peri-implantitis. Additionally, four implants experienced early failures before the delivery of the prosthesis. Initially, the sensitivity, specificity, and positive and negative predictive values of the RAQ tool were low, indicating a limited predictive value within this timeframe. However, these parameters were notably improved by omitting questions that were found to diminish the predictive ability of the test. Specifically, questions related to treated periodontitis, smoking, tissue phenotype, maxillary posterior placement, clinician experience, and restoration emergence angle were removed to improve the validity parameters for this short-term study. Following the omission of these questions, there was a significant increase in sensitivity from 22.22% to 74.07%, while specificity decreased from 100.0% to 62.5%. The positive predictive value also experienced a shift from 100.0% to 86.96%, whereas the negative predictive value showed improvement from 27.59% to 41.67%. When comparing the results before and after the exclusion of these questions predictive value also increased from 0% to 62.5%. Conclusion: In a short-term context, the RAQ survey tool might have limited utility in its original form to identify cases of health and disease, but if modified to omit certain risk categories, its predictive capacity could be increased. A long-term follow-up study is necessary to evaluate the validity of the original RAQ survey tool across different risk categories.

Cover page of Generative Neural Activity Patterns in the Hippocampus

Generative Neural Activity Patterns in the Hippocampus

(2024)

Animals can leverage prior experience to guide adaptive decision making. To decide where to forage, for instance, an animal may recall previous locations and internally simulate paths to take next. These functions are thought to rely on the hippocampus, a brain structure long implicated in learning, memory, and navigation. Accordingly, hippocampal neural activity can represent an animal’s current position, as well as generate representations of alternative possible locations. These representations of alternative “non-local” possibilities are hypothesized to enable internal simulation of previous experiences, alternative pasts, and potential futures to support cognition and, in turn, experience-guided decision making. However, it remains unclear whether or how internally generated hippocampal non-local representations are regulated during active behavior depending on changing cognitive needs for learning about and deciding among alternatives. In this work, I first synthesize evidence describing hippocampal non-local representations that suggests that they are well-suited to serve a wider range of cognitive abilities than previously thought. This work advances the idea that hippocampal function is well characterized not only by its representation of actual experience, but also by its regular representation of alternatives to actual experience. I then present experimental findings that show that the hippocampus generates representations of a wide range of spatial possibilities during active navigation, and that representations of these distinct possibilities are distinctly modulated with learning and decision making in a complex and dynamic foraging environment. These findings indicate that the brain regulates the generation of alternatives in the hippocampus to meet momentary cognitive demands for adaptive behavior.