Cells' ability to efficiently replicate their genomes is essential for regulating chromosomal division and maintaining chromosome integrity.  Defects in any of these cellular processes may cause genomic instability, potentially leading to cancer.  The Chaos3 allele in the yeast Saccharomyces cerevisiae is a single base pair change causing an amino acid substitution in the Mcm4 protein.  Mcm4, a component of the replicative helicase, is recruited to replication origins to unwind double stranded DNA and initiate replication.  Chaos3 is in a region of MCM4 that is highly conserved across eukaryotes; while mutations in conserved regions are generally non-viable, Chaos3 is a viable allele that causes genomic instability, leading to elevated cancer rates in mice.  In S. cerevisiae, Chaos3 decreases early firing of the autonomously replicating sequences (ARS) where DNA replication begins.  Chaos3 does not affect all early firing ARSs in the genome; rather, a large proportion of origins near centromeres, thereby delaying replication of those centromeres.  Essential for chromosome segregation, the centromere is the location where spindle fibers attach to pull apart sister chromatids during cell division.  I hypothesize that this delay in centromere replication results in chromosomal instability, including the loss of a chromosome.  I am using CRISPR guided cutting directed by a customizable guide RNA to replace centromeric adjacent ARS510, that has decreased firing levels in Chaos3, with unaffected, early firing ARS305, to see if firing levels in the mutants are affected based on ARS chromosome location (i.e., proximity to a centromere) or ARS sequence.  If replacing ARS510 with ARS305 restores early origin firing in this region this will confirm the Chaos3 mutation affects specific ARS sequences rather than ARS location on the chromosome.  Furthermore, if centromere replication delays are the cause of genomic instability in Chaos3, this ARS replacement should rescue chromosome loss.

Bilingualism has been shown to have numerous cognitive benefits, ranging from improved executive function to possible protection against neurodegenerative diseases. Structurally, early childhood bilingualism correlates with expanded subcortical regions, specifically the basal ganglia (BG), an area most famously involved in functions such as motor control. In this project, we explore possible domain-general effects of infant and early childhood bilingualism. Specifically, we investigate the effect of early childhood language environments on motor skills in the form of rhythmically controlled babbling. Audio recordings were made in infants’ natural environments using the LENA system. Infants’ own utterances were captured and preprocessed. From these data, I first calculated the ratios of language use in the environment (English versus Spanish), and from these ratios, I categorized infants into monolingual English, monolingual Spanish, and bilingual groups. To determine the rhythmicity of babbling, I isolated subjects’ utterances from the audio data based on criteria that define canonical babbling (e.g., CV syllable structure where C is supraglottal, 4 or more syllables, and so on). For the purposes of this project, we defined the perceptual center as the peak intensity of each syllable and used it to determine the duration between syllables, or inter-syllable duration. The variation of syllable duration was subsequently calculated. We anticipate more rhythmic (i.e. lower variability across inter-syllable duration) babbling in bilingual subjects than in monolingual English and Spanish subjects. However, in accordance with previous findings on early childhood language development, we do not necessarily expect to see differences in whether or not infants are in the canonical babbling stage based on language group. We expect these findings to contribute to the theory of domain-general benefits of early life bilingualism through the quantification of language development milestones.

Resilience in Alzheimer's Disease (AD) is defined by the difference between a person's expected and actual rate of cognitive decline given the severity of their disease. However, the mechanisms behind resilience are still unclear and I wanted to see if the anatomy of the brain over the course of AD could offer any clues. To accomplish this, cognitive tests and brain scans were obtained from patient data taken at Harborview Medical Center. Brain tissue atrophy in regions of interest were defined and combined into two measures. The first--biological subtypes--is whether the disease primarily affected the limbic regions or the cortical regions, while the second is left-right asymmetry. I found that resilience correlated with biological subtypes but not asymmetry. This suggests a way for us to predict resilience to better personalize treatment and eventually find ways to increase resilience.

Coccidioidomycosis, also known as Valley Fever (VF) is caused by the fungus Coccidioides. Pigtail macaques (PTMs) bred at the Washington National Primate Research Center (WaNPRC) in Mesa, AZ are naturally infected with Coccidioides and are similar to humans in their physiology, symptoms, and immune responses. Populations with a weakened immune system, notably older individuals, are at risk for severe complications from infection. Additionally, there is evidence that males have a higher incidence of VF than females in endemic areas. I characterized the immune responses in a PTM model across age and sex to better understand how VF affects the immune response of these populations. Forty-two PTMs (2.25-19.24 years, 3.66-18.29 kg, 37 female, 5 male) at the WaNPRC were sampled for blood. The frequencies of immune cell subsets in whole blood were characterized by flow cytometry and compared for significant differences based on age and sex. I analyzed sex-based differences with Brown-Forsythe and Welch ANOVA t-tests and found no statistically significant differences. For age-based differences, we used a simple linear regression to analyze differences by age in immune cell subsets. We found that old PTMs (10.07-19.24 years) have higher activation of CD8+ T cells, myeloid dendritic cells, intermediate monocytes, and higher frequency of γΔ T cells and CD4+ γΔ T cells than young PTMs (2.25-9.69 years). Young PTMs have a higher frequency of CD45+ granulocytes, PD-1 High CD8+ T cells, plasmacytoid dendritic cells, and NK cells. By correlating older PTMs with higher immune cell activation, and younger PTMs with higher immune cell frequency, we have a better understanding of how a vaccine or treatment could be developed to support older individuals, who are at greater risk of severe infection.

The Tacoma-Pierce County Health Department assessed six communities in Tacoma and on the peninsula that are facing limited opportunities for optimal well-being; the objective is to investigate health care quality and efficiency. These communities are called Communities of Focus (CoF). Our work explores state data to evaluate the relationship between hospital length of stay (LOS) and cause-specific hospital readmission rates (CSR) in CoF. The current literature has not reached consensus on understanding the designated relationship. Applying a multivariate logistic regression model, we explored the relationship between length of stay and CSR using data from the Comprehensive Hospital Abstract Reporting System (CHARS). Several covariates including race and gender were included in the regression model. One extra day of hospital stay resulted in a 0.5% higher risk of 30-day CSR [Odds Ratio (OR): 1.005, CI: 1.00–1.01]. The control factor substantially increasing risk of readmission, was age 55-65 years (OR: 3.477, CI: 3.19–3.79). The covariate significantly reducing CSR was being female (OR: 0.816, CI: 0.80–0.83). Individuals of Indian race (OR: 1.120, CI: 1.04–1.20, p <0.05) and Hawaiian race (OR: 1.157, CI: 1.06–1.26, p <0.0001) were more likely to experience CSR compared to White patients. Finally, CoF faced higher risk of CSR (OR: 3.973, CI: 3.77–4.19) relative to other regional patients. CSR is re-admission to the healthcare setting due to a complication or an exacerbation of disease. A single day hospital stay yielding higher risk for CSR suggests that further exploration is needed to understand patient experiences while admitted. Additionally, an investigation into the social, economic, environmental and personal factors placing CoF at risk for CSR is warranted in order to reduce risk. Our research identifies the problem; future work is needed to elucidate the source so that approaches can be identified to lower CSR for CoF.

Illegal, unreported, and unregulated (IUU) fishing poses significant threats, violating the rights of Indigenous Peoples to their traditional fishing grounds, endangering the food security of legitimate fishers and coastal communities, and facilitating human labor trafficking. Of particular concern are bluefin and yellowfin tuna, two highly valuable species greatly impacted by IUU fishing. These tuna are often subjected to tail, fin, and head removal, making visual identification challenging. Current identification methods involve costly and time-consuming processes, hindering swift action by authorities. To address this issue, a novel biological assay and portable heater/reader device are being developed to detect different tuna species. In this proof-of-concept study, we demonstrate the ability to sensitively and specifically detect Yellowfin tuna (Thunnus albacares) within just 30 minutes, from sample collection to results. In the process of conducting bioassays. I used a Python-based algorithm to detect positive samples while the samples were being reactive. This algorithm is based on the cv2 package, which can edit images. After converting the sample image to grayscale, a threshold can be used to eliminate noise in the image. The contours function in the cv2 package can identify all samples in the picture. Finally, the algorithm can determine which target samples are based on the pixel intensity of all samples. The optimized assay specifically detected yellowfin tuna within as little as 5 minutes, crossing a detectable threshold after 13-14 minutes. This proof-of-concept workflow highlights the potential for on-site yellowfin tuna species identification, critical for combating IUU fishing. Future steps involve developing dried reagents for easy on-site setup in low-resource settings and integrating the lighting system with the microcontroller within the portable device. In summary, this combination of assay and device offers a rapid and effective method to combat IUU fishing by identifying yellowfin tuna species on-site.

Infants perceive speech and acquire language amidst noisy and complex auditory environments. Thus, elucidation of the cognitive mechanisms governing speech perception under noisy conditions is crucial. Cortical encoding of the speech envelope has been one approach used to study speech-in-noise perception in adults. For infants, research shows that Infant Directed Speech (IDS) facilitates cortical encoding of the speech envelope in quiet conditions more than adult direct speech. However, it is unclear whether infants are able to track the IDS speech envelope amidst competing speech. To investigate this, we recorded the neural responses from 40 typically-hearing infants (20 seven-month-olds, 20 eleven-month-olds) to continuous IDS using electroencephalography (EEG) in three conditions: Quiet, Co-located Noise, and Separated Noise. The target stimuli consisted of naturally recorded IDS produced by two female English speakers. The noise stimuli consisted of a four-person babble constructed from audiobooks read by 2 male and 2 female English speakers. We presented stimuli at an overall level of 70 dB SPL via speakers placed at 0°, +90°, and -90° azimuth to infants sitting on a caregiver’s lap in a sound-attenuated booth. Our team analyzed EEG signals using the Multivariate Temporal Response Function (mTRF) toolbox in MATLAB. This backward modeling approach assesses whether the stimulus envelope can be reconstructed based on the recorded neural responses. Reconstruction accuracies greater than chance were observed in all three conditions for the majority of infants, suggesting that we were able to decode the speech envelope in both quiet and noise. Participants demonstrated the capacity to process speech, even amidst competing auditory stimuli, emphasizing speech perception competencies from an early developmental stage. These results support using the envelope model and mTRF method as a feasible method for investigating the development of speech-in-noise perception in infants and young children.

The effects of the fungal pathogen Swiss needle cast (SNC) on its host species, Douglas-fir, and its timber harvest repercussions have been researched. However, more research is needed regarding the effects of SNC on understory species and, consequently, browsing ungulate species. This study analyzes the effects of various thinning methods on SNC and SNC’s influence on understory species richness, diversity, and cover. The goal is to articulate a clear dynamic of SNC in Sitka spruce and Douglas-fir - western hemlock zones to provide insights for guiding forest management. I will analyze the Olympic Natural Resource Center’s pre and post-treatment data from Siuslaw National Forest with statistical analyses to articulate patterns in SNC presence, thinning, and understory change. The early, mid, and late seral/thinned treatments vary in density and by species replanted. I expect that thinning will decrease SNC abundance and increase understory species richness. Additionally, I predict that the stands replanted with red alder and conifers will see a higher abundance of understory due to red alder’s nitrogen-fixing ability. The enhanced understanding of SNC and thinning’s interplay aims to educate current and future forest managers about ecologically responsible management.

This project is the culmination of my capstone, a work of documentary theater called Eldest Daughter Elegy. Half fiction, and half fact, I embarked upon interviewing eldest daughters in an effort to understand my own family, my own sisters, and the relationships I construct. While my interest was originally autobiographical, after over a year of interviewing, writing, and ultimately producing this play, the story turned into something made of a quilt of different stories, none of which are my own. It became a smorgasbord of summer camp, family complexity, and the righteous indignation and profound excitement of childhood. As I looked ahead to the production of this script, I knew that I had an intended and desired effect: to fight back against the loneliness that so many eldest daughters spoke to. Much of theater is made in a relative void, in which collaborators offer opinions, but audiences leave without sharing their opinions with the creators, instead talking amongst themselves, or not at all. With the production of Eldest Daughter Elegy, I employed a phenomenologically based follow-up approach to survey audience members, referencing moments in the script that I thought might be impactful and asking for their undiluted opinions. Through this practice, I hoped to be able to understand how my intentions “landed” on audience members, and further explore the story that was ultimately told onstage, not made up of just my goals but of the actors’ performances, work by designers, and the audience members' own minds and feelings. This presentation will track my impetus for the creation of Eldest Daughter Elegy, the process of writing/producing it, all the way to audience reception. In this way, I hope to offer an example of work created for audience members (eldest daughters) by eldest daughters, gauging what the impact really might be.

This project evaluates the flight mechanics of a class of Autonomous Underwater Vehicles (AUVs) known as gliders using digital simulation via Python code. When used in the real world, these gliders perform vertical profiling of important marine quantities like temperature and salinity. These are then used by oceanographers and others to help them gain a deeper understanding of the ocean environment. The overall goal of the project is to optimize the trajectories of a fleet of vehicles to minimize energy consumption while maximizing uniformity of ocean coverage. Using specific engineering data on real world glider flight as well as public domain ocean environmental models, I have coded a custom Python application with guidance from my mentor at the Applied Physics Lab. We chose a computer simulation of glider flight so that multiple variables could be easily manipulated without the risk of losing a valuable glider if certain parameters are not favorable. This simulation produces data that describes the vehicles’ locations and energy states over time. The software is structured such that important parameters are specified in an easily-modified configuration file. The parameters I alter include geographic area, the number of gliders, the maximum flight depth, the vehicle’s available buoyancy range, and the glide angle. Then, using the data that the simulation produces, I analyze variations in energy consumption, uniformity of coverage, and the time required for each glider to reach their destination. The oceans, which cover about 70% of the planet’s surface, have a huge impact on the climate and health of the Earth as a whole. The result of this analysis is useful to real-world AUV operations by helping determine how to program them to fly more efficiently and maximize their utility as scientific instruments.

Angiogenesis, or the formation of new blood vessels, is crucial for normal bodily function but is especially important in diseases that cause blood vessel breakdown such as diabetic vasculopathy. Angiogenesis is regulated by activation of the Tie2 receptors in endothelial cells, which have two main ligands: angiopoietin-1 (Ang1) and angiopoietin-2 (Ang2). Ang1 binding has been shown to stabilize blood vessels and inhibit vascular leakage, while Ang2 antagonizes these effects. We have previously shown that a computationally designed Tie2 super-agonist which presents eight copies of the Ang1 F-domain strongly activates Ang1-like signaling in human umbilical vascular endothelial cells (HUVECs). In this project, we hope to assess the Tie2 super-agonist’s ability to rescue diabetes induced blood vessel defects in a diabetic blood vessel organoid (BVO) model. To model diabetic conditions, a three-dimensional blood vessel organoid model has been cultured in a high glucose media along with inflammatory cytokines associated with the diabetic phenotype. Western blotting and immunofluorescence staining will be used to assess the relative quantities and localization of proteins involved in vascular stability and inflammations upon treatment with the Tie2 super-agonist. Vascular degeneration is a very harmful condition associated with many prevalent diseases including diabetes, so the Tie2 super-agonist could potentially be a new therapeutic drug candidate for treating blood vessel dysfunction in patients with these conditions in the future.

Vaccines have successfully reduced global infectious disease burden, but there is room to improve vaccination technologies. Because many pathogens infect at mucosal sites, a goal of new vaccines is to promote strong mucosal and systemic antibody and T-cell responses. Integrated fiber microneedle devices (iFMN) are a novel oral vaccination method that may achieve this goal. These devices are patches with a polymer backfill matrix and multiple >1 mm pyramidal needles that penetrate immune cell-rich mucosal tissue in the mouth, inducing immune responses at draining lymph nodes. To test the hypothesis that priming with iFMN delivery of a DNA vaccine increases mucosal and systemic antibody responses after systemic booster immunization with the same vaccine, male rhesus macaques (n=6) were primed with an iFMN delivery of a DNA vaccine encoding Influenza A Virus (IAV) Nucleoprotein (NP) at weeks (0) and (6). The macaques then received a single boost of the same NP DNA vaccine at week (12) using the proven delivery modality of Gene Gun epidermal delivery (GG). Mucosal secretions (including bronchoalveolar lavage, saliva, and nasal/tracheal swabs) and serum were collected 2-4 weeks before and after each immunization. I conducted enzyme-linked immunosorbent assays (ELISAs) to quantify antigen-specific IgG and IgA binding antibody at each timepoint. To characterize the priming effect of iFMN oral delivery on systemic and mucosal antibody responses, I compared these animals’ responses to macaques (n=8) previously immunized with a single GG dose of the same NP DNA vaccine. The iFMN-primed animals had robust post-GG boost NP-specific IgG responses in serum but these responses were not significantly higher than for macaques boosted solely with GG DNA. These results demonstrate that iFMN delivery did not effectively prime for robust systemic and mucosal antibody responses. Additional experiments will be done to confirm these findings.

Brain-computer interfaces (BCI) are systems that allow direct control of machines or computers by decoding neural signals from the motor cortex, particularly the signals associated with movement intention. Existing BCI designs tend to combine signals from the premotor and primary motor cortices, treating them as a unified source for processing despite their functional and anatomical differences. Preliminary data indicates that different depths within these motor cortical areas perform different computations. Based on this data, my hypothesis is that shared computations are performed in the output layers of the premotor cortex and the input layers of the primary motor cortex. Addressing this hypothesis is difficult due to technological limitations. Many sensors used to measure neural activity in the motor cortex do not provide layer-specific information. To counteract this, my project leverages Neuropixel probes, which are high-density microelectrode arrays that record the activity of individual neurons (spiking activity) and groups of neurons (local field potentials). I developed a fixture capable of holding multiple Neuropixel sensors to simultaneously capture neural signals at known depths from the primary and premotor cortices. After determining the depth of each neuron by analyzing the local field potentials, we will compare spiking activity patterns across depths as a non-human primate learns a motor task. I expect to see similar patterns of spiking between the output layers of the premotor cortex as the input layers of the primary motor cortex. The analysis of this data will reveal how movement-related information is transmitted through motor cortical areas, which will inform the design of future BCIs.

The content of sexual education within public schools in the United States varies significantly by location due to differences in state laws and funding. The study identifies the spatial variation of adolescent health outcomes as a result of variations within the content of sexual education in public schools in the states of California and Texas. As the scale of the study includes two states containing large population sizes, the methodology employs secondary data collection and analysis from enacted state legislation as well as a variety of sources such as the Centers for Disease Control, the World Health Organization, the American Community Survey, and the U.S. Census among others. Data has been collected for the individual years of 2010 and 2020 in order to examine changes that have emerged over the past decade. Historically, California and Texas have had contrasting policies in regard to sexual education, and the preliminary results have indicated this as well. The study analyzes the possible correlation between abstinence-only sexual education and health outcomes for adolescents including increased rates of teen pregnancy, rates of sexually transmitted infections, and risky sexual behaviors, and whether there are disparities geographically as a result of these variations in state laws. Understanding how spatial variation impacts sexual education, which in turn, may relate to adverse health outcomes, is crucial in terms of targeted intervention and improving access to resources and knowledge for at-risk youth across the nation.

Infection from Mycobacterium tuberculosis is the leading cause of death due to infectious disease worldwide, with rates of tuberculosis infection greatest in low and middle-income countries (LMICs). Tuberculous meningitis (TBM) is the most severe form of M. tuberculosis disease with nearly half of all cases resulting in death or neurological consequences. Recent studies in our lab have found that single-nucleotide polymorphisms (SNPs) in MUC5AC, a secretory lung mucin, are associated with increased TBM susceptibility, morbidity, and mortality. The purpose of my study is to identify the functional MUC5AC SNP. Four candidate SNPs were selected within the MUC5AC promoter region based on high linkage-disequilibrium scores across multiple global populations with a SNP in the MUC5AC promoter, rs28737416. I utilized molecular cloning techniques to combine a luciferase-expressing plasmid with isolated regions of the human MUC5AC promoter containing the SNPs of interest and subsequently transformed this recombinant plasmid into competent cells. Next, I performed site-directed mutagenesis at the SNPs of interest and am currently transfecting mutants into HEK293T cells to investigate how genotypic variation in each candidate SNP influences promoter function by measuring luciferase expression. I anticipate variants in at least one SNP of interest will reduce gene expression (measured by luciferase expression), indicating functionality. Characterization of this genetic mutation will provide insight into TBM susceptibility across populations and could inform studies of novel therapeutics to treat TBM.


A critical feature of autonomous cars is the ability to follow a road or predefined path. Classical methods often rely on extensive prior mapping with precise GPS positioning. These methods are labor intensive and struggle with changing, unstructured environments. Instead, machine learning (ML) models are trained to recognize paths and follow directions. In this work, we combine simulated and real-world data to train a neural network policy that controls an autonomous ground vehicle down a hallway, avoiding collisions. Training a ML road-following model consists of three steps: data collection and preprocessing, model training, and model evaluation. While all three steps pose challenges, collecting high-quality, real-world data can be expensive and dangerous in road environments. Because of this, simulator data is useful as it allows for data to be collected safely and inexpensively. Thus, we study how much the required amount of real-world data can be reduced to successfully train a road-following robot with the use of simulator data. So, we collected simulator data using AirSim to train a convolutional neural network that follows a path in simulation through live environment images. We then fine-tuned the model using real-world data collected from MuSHR cars through hallways of a building. Next, we test the fine-tuned model on the simulator to ensure limited degradation to the model solely trained from AirSim data. Finally, we deploy the model on a robotic car in a real-world environment and evaluate the model’s performance compared to the baseline model trained on real-world data. We demonstrate that we can successfully train a model in simulation (MSE <= 0.01radians), and we expect to show a comparable performance in reducing the number of collisions and minimizing trajectory differences between expert and learned controller from a model trained on simulator + less real-world data and a model trained solely on real-world data.

Chronic nonbacterial osteomyelitis (CNO) is an autoinflammatory bone disease that causes bone pain and destruction in children. Anti-inflammatory treatments for CNO can be effective, but there are not any FDA-approved medications specifically for CNO use, so there is interest in determining the effectiveness of different treatments for CNO. While CNO etiology is unknown, previous pathology studies indicate osteoclastogenesis plays a critical role in CNO pathogenesis. Cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) was shown to inhibit osteoclastogenesis derived from peripheral blood mononuclear cells (PBMCs) in adults with active rheumatoid arthritis. Our objectives are to determine whether osteoclastogenesis is altered in children with CNO and the effect of abatacept, a CTLA-4 analog, on osteoclastogenesis. We collected samples of PBMC and serum from healthy subjects and children with active or inactive CNO. We incubated patient serum samples with CD14+ cells isolated from a commercial PBMC pooled sample with MCSF and RANKL, which are necessary for osteoclast proliferation and differentiation, for 7 days before staining for osteoclasts. To determine abatacept’s effect, we incubated PBMCs from patients with MCSF and RANKL with or without abatacept (CTLA-4 analog), performed DAPI and TRAP staining, and counted osteoclasts using the computer software, Image J. Osteoclasts were defined as TRAP-positive cells with 3 or more nuclei. We intend to use multivariable linear and mixed-effects regression models to estimate the average group effect on osteoclast counts from the serum study and PBMC study and the impact of abatacept on osteoclast counts. Expected statistical results of the Serum and PBMC study include an increase in osteoclastogenesis from PBMCs of children with active CNO compared to other groups, and a decrease in osteoclastogenesis with abatacept treatment. This is an ongoing study, and the results will shed light on the effect of abatacept on osteoclastogenesis and its potential therapeutic use in children with CNO.

Chronic nonbacterial osteomyelitis (CNO) is an autoinflammatory bone disease that mainly affects children and adolescents. Disease monitoring is challenging as reported pain is not reliable and imaging is not always obtained at all clinic visits. To date, patient-reported outcomes used in CNO research have not yet been validated in this population. The Patient-Reported Outcomes Measurement Information System (PROMIS) questionnaires, validated in other pediatric rheumatic diseases, are administered to patients enrolled in the prospective multisite Chronic Nonbacterial Osteomyelitis International Registry (CHOIR) since 2018. Our objective was to assess the convergent and responsive validity of the PROMIS instruments in patients with CNO. Patients with CNO consented and enrolled in CHOIR. Self-reported PROMIS questionnaires of fatigue, pain interference (PI), pain behavior (PB), mobility, upper extremity (UE), physical activity (PA), and strength impact (SI) were administered to patients. External validation surveys were administered to assess patients’ perception of the difficulty of use of limb/back/jaw, fatigue, sadness, and worry on a 0-10 scale, disease status, and status change. More than 1,000 clinical visits from 184 patients were associated with self-reported PROMIS questionnaire entries. PROMIS scores correlated significantly (p<0.01) with patient-reported variables and physician global assessment (PHGA). The correlation with function and PHGA was good for Mobility, PB, and PI. All PROMIS scores, except physical activity, correlated significantly (p<0.05) with patient-reported disease status. After effective treatment when the clinical disease activity score improved by at least 2.5 points, the change of PROMIS scores from Mobility, PB, PI, and UE was significant. PROMIS questionnaires provide valuable information about the disease status of children with CNO and correlate well with self-reported functional and other psychosocial domains. Mobility, PI, and PB show sensitivity to change after effective treatment or with disease status change. These instruments are useful for CNO clinical disease monitoring and research.

Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart defect, requiring patients to undergo multiple invasive cardiac procedures, including pulmonary valve replacement (PVR). However, with recent clinical advances, new tools are needed to optimize PVR timing. We believe noninvasively collected cardiopulmonary exercise testing (CPET) data can provide insight into a patient’s need for PVR. Specifically, we hypothesize that patients with a more severe stage of pulmonary valve dysfunction have a limited ability to increase their stroke volume during exercise, an abnormal response that can be assessed by analyzing the behavior of the oxygen pulse (O2-pulse) curve during CPET. A ‘flattening’ of this curve suggests impaired augmentation of stroke volume and potentially a more urgent need for PVR. This research aims to identify metrics that can characterize patterns in O2-pulse. Data were collected from 44 participants with TOF undergoing CPET PVR evaluation and 10 healthy individuals. To find a maximum O2-pulse, we fit a penalized bilinear regression model to this curve. We extracted 8 parameters to mathematically describe the O2-pulse curve, as well as 20 traditional CPET performance metrics. One important parameter that was calculated is the ‘lost area under the curve’ (LAUC), defined as the area under the two calculated regression lines over time subtracted from the area under the curve as determined if the first regression line were to continue on the same slope as is typically expected during a maximal CPET. This value captures both the change in slope and when participants transitioned from a steep increase in O2-pulse to a relatively flattened O2-pulse. The LAUC, among our other identified metrics, can potentially provide insight into the optimal timing of PVR in patients with TOF. Unsupervised machine learning may be a useful tool to characterize patterns in these metrics and search for clinically relevant patient phenotypes.

Budding yeast cultures grown in limited sulfate conditions are overtaken by cells with an inverted triplication of the gene SUL1, which encodes for a sulfate transporter. The extra copies of the sulfate transporter provide a selective advantage because these cells outcompete other yeast cells for the limiting resource. To explain the mechanism behind this type of amplification the Brewer and Dunham Labs proposed a model (Origin Dependent Inverted Repeat Amplification or ODIRA), which requires both a DNA replication origin and inverted repeats flanking SUL1. ODIRA starts with a DNA replication error involving replication fork regression that leads to an extrachromosomal DNA intermediate. This intermediate then replicates and recombines into the genome, producing the observed amplification. Because similar triplications are observed in the human genome, including in human disorders, the mechanism of ODIRA offers insights into human genome evolution and disease. While the yeast research is consistent with ODIRA, we still do not know which proteins are responsible for the process. I am testing whether the genes RAD5 and RAD54 — involved in fork regression and strand switching, respectively — are involved in ODIRA. To do so, I am measuring the ODIRA frequency in strains with each gene deleted compared to a wild-type control. If either gene deletion leads to a statistically significant change in ODIRA frequency compared to the wild-type strain, I can conclude this gene is involved in ODIRA. To measure ODIRA frequency, I grow the deletion strains under selection for DNA recombination events and use whole chromosome gel electrophoresis and Southern blotting to detect ODIRA events. Preliminary data analysis suggests that there is a reduction in ODIRA events when either RAD5 or RAD54 is deleted, indicating that these genes are likely needed for ODIRA. These results may provide insight into how inverted triplications may arise.

VirScan, a revolutionary technology based on Phage Immunoprecipitation Sequencing (PhIP-Seq), allows the interrogation of antibody responses to all known human viruses using a small blood volume, providing information on an individual's previous viral exposures. This study aims to provide a comprehensive data quality assessment system for VirScan, which will improve its reliability and interpretability by routinely assessing VirScan data quality at both the sample, assay (N=96 samples in replicate), and sequencing batch levels (N=192 samples in replicate). The study focuses on creating standards and thresholds for data quality at all three levels, considering aspects such as aligned reads, read depth, percent of epitopes discovered, and correlation of sequence counts between replicates. The assay/batch-level analysis provides metrics like the mean, median, standard deviation, and range of mapped reads and correlations for count and peptide detection, evaluating consistency, accuracy, and comparability across assays and batches. Further, these criteria can effectively categorize sample quality into Good, Questionable, and Failed, identifying samples that may need to be repeated or excluded from analysis. These quality calls were all encoded within an R Shiny App, enabling a user-friendly and flexible interpretation of VirScan data. Implementing this systematic quality control strategy will considerably improve the usability of VirScan in research and clinical contexts, allowing for more trustworthy interpretations of an individual's viral exposure history while also contributing to a better knowledge of immune response dynamics.

Respiratory viruses are a major cause of mortality and morbidity in vulnerable populations. Together, Respiratory syncytial virus (RSV) and Human metapneumovirus (HMPV), are responsible for over â…“ of serious viral respiratory infections in hematopoietic stem cell transplant (HCT) recipients. Currently, no treatments are available for RSV or HMPV in immunocompromised adults. While monoclonal antibodies (mAbs) show promise as a treatment, challenges arise, including limited efficacy when administered post-infection. Our goal was to enhance the therapeutic efficacy of a newly discovered cross-neutralizing human mAb to RSV and HMPV. We aimed to investigate whether modifying the Fc domain of the antibody could increase its binding to Fcγ receptors (FcγRs) found on different types of immune cells. Activation of FcγRs initiates important cell processes such as clearance of virus-infected cells, also known as Antibody-dependent cellular cytotoxicity (ADCC). This modification potentially makes the antibody a more effective treatment option for RSV and HMPV infections. To do this we looked at the binding kinetics and affinity of modified antibodies to human FcγRIIIa, FcγRIIa and FcγRIIb receptors using Bio-Layer Inferometry (BLI). Our data indicate that certain amino acid modifications or afucosylation of the Fc region can increase the antibody’s binding affinity to different human FcγRs. Since hamsters are an important preclinical model used to determine RSV and HMPV drug efficacy, it was important to examine the binding affinity of our human antibody to hamster FcγR’s. Our data indicate that the wild-type Fc region does bind to the homologous hamster receptors. Moreover, certain modifications in the Fc region led to increased binding to hamster FcγR’s. Together, these data indicate that modifications in the Fc region of human antibodies can increase their binding affinity to both human and hamster FcγRs. This increase in binding affinity could translate to enhanced potency in the preclinical hamster model and in humans.

Music box, invented in the 18th century, has been reimagined by the design industry as an interactive and assembly-friendly toy product. This innovation serves as a seamless integration of a nostalgic object with the demands of contemporary life experience. However, such "packaged in box" products face significant customization limitations from the user's perspective, including fixed music options and predetermined model parts. Given the burgeoning resources in digital modeling and rapid prototyping, the product design process is poised to advance into the computational fabrication era. Our interdisciplinary student team has been re-envisioning the structure and functionality of our music box through programming, Computer-Aided Design, and 3D printing. Specifically, our team developed the three parts to construct the music box: a digitally constructed spinner, where its 3D model was transformed from MIDI file, allowing for a wide range of musical expression; an adaptable mechanical connection structure for spinners of various sizes; and an innovative mechanism that triggers keyboard notes without direct spinner contact, maintaining sound quality and reducing wear out plastic parts. These designs enable customizable features, easy part replacement, and solve sound and durability issues associated with plastic components. With the goal of creating a customizable product in mind, each member of our team contributed to and took responsibility for the components in which they specialized. The purpose that our music box serves does not stagnate as a mere music playback machine; rather, its functionality expands across various aspects. Our innovation is not only ideal for those who wish to integrate artistic perspectives with functional machine prototyping and customize their songs , but also boosts creativity for individuals and institutions, enabling further projects that could benefit early education and future engineering workshops.

The backsplash galaxies of the Milky Way are galaxies that have once entered the virial radius of the Milky Way but reside outside of which today. As a backsplash galaxy enters the Milky Way, its gravitational interaction with the Milky Way causes its star forming material to be stripped away and causes it to appear to be more diffused and older. The evolution and properties of a backsplash galaxy depend significantly on the properties of its dark matter halo as it makes up the majority of its mass. In my research, I use cosmological simulations of Cold Dark Matter (CDM) and Self-Interacting Dark Matter (SIDM) of Near-Milky Way halos done by my mentors and their colleagues to identify and analyze the properties of backsplash halos during their evolution and compare the results across the two dark matter models. Significant differences between the results from the CDM and the SIDM models are anticipated, with the major difference caused by the interactions between the SIDM particles allowing the exchange of energy and momentum between particles, causing the energy to transfer between regions of the halo, resulting in altered density profiles which influences the tidal evolution history. After the analysis of both models are completed, the results can be compared and matched to observational data of the candidates of backsplash galaxies of the Milky Way, and conclude in each model’s ability to make accurate predictions. This research contributes to the ongoing investigation of the properties of dark matter particles and the analysis of the evolution of backsplash galaxies.

As computing continues to evolve, there are few fields with more extensive and revolutionary prospects than quantum computing. Advanced quantum technologies have the potential to see into a world that classical computing cannot, enabling more advanced encryption methods, precision atomic interaction modeling, and molecular simulations for pharmaceutical drug research. Students should be exposed to modern quantum technologies, but providing students with hands-on experience is challenging at the undergraduate level. Our project aims to remove that barrier. Ion traps are the fundamental mechanisms for information storage in trapped ion quantum computers, so we designed and built a scaled-up version of one of these traps for use in a classroom setting. Our trap, a linear quadrupole trap, is based around 4 conductive electrodes that utilize alternating current (AC) to confine charged particles to a linear trapping axis, bounded on either end by 2 direct current (DC) rods. The trap features a 3-D printed polylactic acid (PLA) base and lid with a locking mechanism to prevent undesired air movement within the trapping region. We implemented a high-voltage lower DC plate in combination with a grounded upper plate to emulate an infinite parallel plate capacitor when the distance between the two is minimized and the plate area is maximized, allowing for additional vertical manipulation of the particles. To guarantee student safety, all high-voltage components remain covered while trapping, and each conductive element has undergone distance and breakdown voltage calculations to ensure that no electrical arcing can occur. As a result, undergraduate students in the lab are able to manipulate different aspects of the electric field geometry to observe micromotion, Coulomb Crystals, secular frequencies, and determine the charge-to-mass ratios of different charged particles such as lycopodium moss spores (25µm) or polyethylene microspheres (50µm).

Mitosis is the fundamental biological process that ensures equal separation of genetic material during cell division. Microtubules and their associated structures in the mitotic spindle execute this partitioning by carefully aligning and separating duplicated chromosomes. Despite intrinsically variable growth rates across microtubules and stochastic assembly and disassembly phases, chromosome-bound microtubules exhibit highly coordinated behavior that drive mitosis. The basis for this high degree of synchronization is currently unknown. Previously, we used a novel dual laser trap assay to show that microtubule pairs growing in vitro are coordinated by mechanical coupling (Leeds et al. 2023). A simple model incorporating both force-dependent pausing and growth speed heterogeneity explains the measured coordination of microtubule pairs. Our findings illustrate how microtubule growth may be synchronized during mitosis and provide a basis for modeling multiple microtubules in a bundle. In this project, we expand on the techniques we used with the dual optical laser setup and combine them with a cutting laser to induce disassembly in our microtubules. Studying the coordination of shortening microtubules encompasses a broader spectrum of microtubule dynamics and sheds light on other aspects of microtubule regulatory mechanisms. We can then extend our model to include the degree by which mechanical coupling can coordinate microtubules in disassembly in addition to growth. Bundles of multiple microtubules are in mixed states of shortening and growth while executing the coordinated motion necessary to drive mitosis, so understanding how mechanical coupling affects disassembling microtubules gives insight into the complete picture of the mechanisms behind their synchronous motion essential for life.

Trapped ion quantum computing (TIQC), with its large decoherence times and small operation times relative to other physical quantum computing architectures, has garnered significant attention in the public and private sectors. Planar Paul traps, which simultaneously utilize radio frequency and static voltages in a two-dimensional electrode array to spatially confine ions, are the primary candidates for trapping ions for TIQC due to their manufacturability and ability to shuttle ions between multiple trapping zones for quantum logic gates and memory storage. The growing relevance of this technology necessitates educating students about the advanced electrodynamics of ion trapping and ion shuttling. Therefore, I developed a macroscopic planar Paul trap which utilizes 50µm diameter proxy-ions along with high voltage (HV) alternating currents (AC) at 60 Hz and HV direct currents (DC). These are applied to a 5-rail electrode geometry to demonstrate ion shuttling and ion-group splitting along a linear trapping axis. The goal is to educate students on the electrodynamics of ion traps by allowing them to experiment with the tunable trapping parameters, such as AC voltage amplitudes, DC voltage magnitudes, and applied shuttling waveforms and observe the changes in the dynamics of the proxy-ions relative to theoretical predictions. I designed the trap by implementing the recommended relative electrode dimensions into COMSOL Multiphysics and optimizing the geometry by maximizing the pseudopotential confinement while simultaneously minimizing electrode surface area. Afterwards, I utilized an analytic model of a 5-rail planar Paul trap, along with the method of Lagrange multipliers, to optimize the voltage magnitude and waveform of the segmented electrodes for smooth, effective shuttling and ion-group splitting. I then integrated an HV relay circuit and the 5-rail electrode geometry onto printed circuit boards to allow for student-controlled ion shuttling via an Arduino microcontroller.