Since 2013 there has been a decline in the harvest of Dungeness crab (Metacarcinus magister) in south Puget Sound. The Pacific Northwest Crab Research Group (PCRG) is a network that focuses on crab population monitoring. PCRG runs a large-scale larval trapping network that uses light traps to attract Dungeness crab megalopae via positive phototaxis. The light traps span the Salish Sea, to recognize migration patterns and better understand Dungeness crab population dynamics. In addition to Dungeness crabs, different crab species are caught in the traps, creating an opportunity to study more species. All crab larvae follow the same larval stages, called zoea and megalopa, which appear similar to the naked eye. This creates a problem because population counts are often done by volunteers who don’t have prior knowledge of megalopa morphology. Gathering reliable population data of the marine organisms caught in the traps requires a clear procedure to identify bycatch. In this research project, I will classify the unknown larvae into morphospecies by carefully looking and documenting individual characteristics of each organism. Documents will note features such as: carapace shape, carapace width, lateral edges of carapace, telson shape and additions (e.g. setae), number of spines, location of spines, antennae, length and width of thoracic legs, coloration, and overall shape. Measurements will be taken through Image-J, which will be documented along with photographs clearly differentiating anatomical characteristics to compare to DNA barcoding to be conducted by Seattle University on these samples. When DNA results come back, I will determine if specimens that had identical characteristics are genetically matched. This information will be used to make an accurate guide down to the species level. My results will be shared with PCRG to improve the accuracy of population counts of different crab species which will increase reliability of future PCRG data.

Dungeness crabs (Metacarcinus magister) are culturally and ecologically essential to Washington; they also constitute the most valuable state and tribal commercial fishery. Recently, there have been sharp declines in adult crab catch, resulting in the closure of the south Puget Sound fishery. Previous research by Alan Shanks has shown larval abundance is a clear driver of adult yield in Oregon, but many gaps in research remain regarding population dynamics in Washington, sustainability, and the impact of shifting environmental conditions. To address these gaps, the Pacific Northwest Crab Research Group (PCRG) was formed by the Swinomish Indian Tribal Community. PCRG is a collective of over 110 state and tribal co-managers, federal agencies, academics, commercial crabbers, and non-profit organizations. As part of PCRG, UWT’s Becker Lab deployed standardized light traps in the south Puget Sound from mid-April to September for two consecutive years, with sampling four days per week. In June 2021, the light trap network experienced a large pulse of Dungeness megalopae succeeding an extreme heat event. With the frequency of heat waves doubling over the last century, understanding temperature and other environmental stress responses in Dungeness crab larvae is imperative. Megalopae (n=55) from six PCRG sites were preserved in the field with 100% ethanol, then returned to the laboratory where I imaged them under a microscope and performed morphometric analysis (carapace width, carapace length, total length) in Image-J. I then compared measurements with recorded temperature, pH, dissolved oxygen, and salinity. Analysis is ongoing, but I expect to see an inverse relationship between environmental factors and Dungeness megalopae size. The aim of my work is to quantify larval growth as it relates to varying environmental conditions in order to better plan restoration and predict adult harvest limits. These data will offer valuable insight for restoration and protection of larval Dungeness crab.

Moss is a bioindicator that can be useful in evaluating air quality in metropolitan areas. One study in Portland used a common moss, Orthotrichum lyellii, to locate sources of cadmium pollution, leading to regulations for glass factories in the area. The current study applied a similar methodology to locate sources of metal contamination in and around the South Puget Sound region. O. lyellii was collected from locations with a wide range of vehicular traffic. Additionally, collection sites were divided between industrial, commercial, residential, and forested areas. Moss samples were dried, digested with acid and peroxide, and analyzed for metal content using ICP-MS. Our study shows increased concentration of trace metals such as titanium and vanadium in industrial areas. Some major metals such as calcium may be more closely linked to vehicle traffic. These results may indicate human health hazards in industrial areas in the South Puget Sound area. 

Genomic amplification of specific genes is a common mechanism of adaptation that also underpins many human disorders. We use yeast (Saccharomyces cerevisiae) to investigate the mechanism of one such gene amplification. When yeast are grown in sulfate-limited conditions for many generations, the population becomes dominated by cells possessing an inverted triplication of the SUL1 gene, which produces a sulfate transporter. Because of increased transporter levels, these cells have higher fitness in limited sulfate conditions. The Brewer Lab proposed a model — Origin Dependent Inverted Repeat Amplification (ODIRA) — where this gene amplification is initiated via a DNA replication error. In the ODIRA model, DNA replication fork regression at short inverted repeats leads to template switching of the replication machinery and the extrusion of a replication-competent hairpin molecule, which after replication, recombines at the original locus to produce an inverted triplication. An alternative explanation behind the amplification is that the hairpin molecule is generated by double-stranded DNA breaks (DSB). To distinguish between these possibilities, we used an engineered strain in which the selectable marker gene, URA3, is split into overlapping fragments (“ura” and “ra3”) on two different chromosomes. The complete URA3 gene is only present in yeast that undergo rare direct recombination between chromosomes or by recombination of the replicated hairpin formed by ODIRA or DSB. We used CRISPR-Cas9 to induce DSBs upstream of the ura fragment and identify the type of event that restores URA3 function with contour-clamped homogeneous electric field gels (CHEF gels), Southern blots, and polymerase chain reactions (PCR). If DSBs drive hairpin formation, cutting the chromosome upstream of the ura fragment should increase the frequency of URA3 assembly via hairpin intermediate. We demonstrate that double-stranded DNA breaks do not increase frequency of hairpin intermediates, providing further evidence that ODIRA is responsible for the inverted triplications of SUL1 in yeast.

Deep learning methods for protein sequence and structure generation have shown remarkable success in many design scenarios when combined with structure prediction networks such as AlphaFold2. Despite this advance, many design challenges such as de novo binder design still haven’t been fully solved. Diffusion-based models have demonstrated considerable success in image and language generation yet their application in protein design has not yet been fully explored. Recently, the development of a protein diffusion model called RoseTTAFold Diffusion (RFdiffusion) has shown significant success in protein design and enabled us to explore the challenging problem of designing protein binders. Here I demonstrate utilization of RFdiffusion towards generation of de novo binders to disordered major histocompatibility complex (MHC) peptides. Specifically, we took an MHC peptide from KrasG12D and used RFdiffusion to generate a diverse range of structures that can bind this peptide. To optimize the sequence of these structures we used ProteinMPNN. We used AlphaFold2 to predict the structures of these optimized binders in complex with the peptide and saw promising interaction metrics. Further, structure prediction of the designs in complex with Kras wild type (WT) peptide resulted in lower AlphaFold2 confidence metrics of the interaction occurring. This is a promising preliminary result that RFdiffusion can generate fully de novo MHC-mimics, which can differentiate between neoantigens and WT peptide. Many cancers are caused by a single point mutation such as KrasG12D, thus, designing protein binders with point mutant specificity is exciting as it allows for targeting of disease causing proteins over healthy WT proteins. 

This study examines how undergraduate students majoring in humanities and social sciences navigate the institutional culture of higher education (HE) through a case study at the University of Washington. I identify two different logics within HE that contribute to its institutional culture — the industry logic and the social institution logic. The industry logic refers to the growing trend of business and industry orientations in HE — especially since the emergence of neoliberalism in the 1970s. The social institution logic is the more traditional ideal of HE that aims to cultivate values of citizenship and morals. The goal of this study is to examine how undergraduate students understand and respond to changes in institutional culture. While the commodification of HE is well studied, scholarly attention neglects its evolution and fails to articulate students’ response to this shift. This study is inductive and qualitative — focusing on undergraduate experiences and how students give cultural meaning to their experiences under varying institutional culture. I will conduct 12 semi-structured interviews with undergraduate students majoring in humanities or social sciences to understand their college experiences. Though the anticipated results of the study have yet to be determined due to the inductive nature, I hope to examine how students reconcile their passions and actual experiences under institutional culture of HE. Any disparities observed between universities as institutions and students as agentic individuals might reveal the neglected demands within society. This research will provide insights to which kind of education system our society needs today, which will lead to better policies about the future development of HE.

Although social Virtual Reality (VR) has attracted increasing attention as a new way for people to interact, it faces challenges with harassment, a problem other social platforms face as well, online gaming communities in particular. The embodied environment social VR provides also brings new forms of harassment compared to social media, requiring effective responses from social VR platforms. We examined the safety features of four popular social VR games: VRChat, Horizon World, Altspace, and RecRoom to learn the standard safety practices. To understand how social VR communities share and respond to harassment experiences, we collected 134 posts and comments from online communities for these games on Reddit, Twitter, and Oculus Forum. We used inductive coding to identify themes and trends. We found that the four social VR games have common safety features such as Personal Bubble, Block, and Report, but these features differ in name, effect, and ease of access. This can pose an increased learning curve for players and make them less aware of these functionalities. From the online posts, we found the most common harassment experiences include hate, unwanted sexual attention, and embodied sexual harassment. The most common response to harassment experiences is suggesting strategies or resources. However, these responses include a mix of positive (e.g., empathetic, supportive), neutral, and negative (e.g., gaslighting) tones. We also found a difference between the most commonly adopted safety feature and the most recommended feature, where the former is Personal Bubble and the latter is Block. Based on the findings, we provide design implications to improve safety features and build easier-to-access and informed safety systems for social VR games. This research contributes to developing a more inclusive environment for players from diverse backgrounds and identities by identifying opportunities to provide better safety features and improve safety norms in virtual worlds.

Remote collaboration today rarely involves a single communication channel. Instead, teams frequently juggle a myriad of communication tools, such as video conferencing, group chat, and email. Each of these platforms provides different mechanisms for relaying information and media to ultimately meet the needs and goals of the team. While discussions occurring on different platforms are often related, existing tools used to support each type of communication are disconnected. To research how to bridge this gap and support seamless collaboration and communication across different platforms, we developed a toolkit that connects conversations between three of the most commonly used remote collaboration platforms: Slack, Google Docs, and Zoom, covering both synchronous and asynchronous modes of communication. We iteratively designed and implemented features such as adding information from Slack chat directly to Google Docs notes to build up meeting agendas and selecting specific snippets of Zoom meetings to be embedded into notes or sent to chat. We also plan to evaluate the effectiveness of our toolkit in helping streamline the transfer of information across different team communication sites and enhancing the remote collaboration experience for teams via subsequent qualitative user studies. Specifically, we will be conducting a week-long field study with existing teams, such as teams from industry, teams working on school projects, research groups, committees, etc. We will use a combination of experience sampling, diary study and post-study interviews to understand their experience. The results we expect to get from these exploratory user studies will help us answer the following questions: Which aspects of the tools work best for the users? Does the current UI and design make sense for how the user interacts with the toolkit? In which scenarios is the toolkit being used most effectively? These results will also guide us in designing additional features for the toolkit in the future.
 

Breast cancer has attracted tremendous research interest in treatment development as one of the major threats to public health. The use of nanoparticle (NP) for therapeutic DNA delivery has shown promise in treating various cancer types, including breast cancer, due to their high DNA loading capacity, high cell transfection efficiency, and design versatility. However, cytotoxicity and large sizes of NPs often raise safety concerns and hinder their applications in the clinic. Here we report the development of a novel nanoparticle formulation (termed NP-Chi- xPEI) that can safely and effectively deliver DNA into breast cancer cells for successful transfection. The nanoparticle is composed of an iron oxide core coated with low molecular weight (800 Da) polyethyleneimine crosslinked with chitosan via biodegradable disulfide bonds. The NP-Chi-xPEI can condense DNA into a small nanoparticle with the overall size of less than 100 nm and offer full DNA protection. Its biodegradable coating of small-molecular weight xPEI and mildly positive surface charge confer extra biocompatibility. NP-Chi-xPEI-mediated DNA delivery was shown to achieve high transfection efficiency across multiple breast cancer cell lines with significantly lower cytotoxicity as compared to the commercial transfection agent Lipofectamine 3000. With demonstrated favorable physicochemical properties and functionality, NP-Chi-xPEI may serve as a reliable vehicle to deliver DNA to breast cancer cells.

Illegal, unreported and unregulated (IUU) fishing violates the rights of Indigenous peoples to traditional fishing grounds; compromises food security of legitimate fishers and coastal populations; and facilitates human labor trafficking. Once caught, tails, fins, and heads are cut off for storage and transportation, which makes identification by phenotype impossible. Polymerase Chain Reaction (PCR) and electrophoresis can detect different tuna species but are time-consuming and require access to a fully equipped laboratory and trained personnel. Thus, I developed a novel biological assay and a 3D printable portable device to detect Ahi tuna, one of the species of interest among three tuna species. The biological assay consists of three steps: DNA extraction by crude lysis method; DNA amplification by Recombinase Polymerase Amplification (RPA); and detection by fluorescence using Clustered Regularly Interspaced Short Palindromic Repeats associated (CRISPR Cas) 12a. qPCR verified Ahi tuna DNA extraction by crude lysis method, generating 10⁶ copies of DNA per reaction comparable to the standard silica-based capture method. Nested qPCR and Tapestation verified RPA’s successful amplification of Ahi tuna DNA extracted by crude lysis method. Quantification of fluorescence by qPCR verified that one-pot RPA and CRISPR Cas12a reactions could generate up to 6000 Relative Fluorescence Units above the negative control within 15 minutes. The isothermal device keeps the samples at a constant temperature (37-42℃) for the RPA and CRISPR Cas12a reactions. I successfully demonstrated a <50 min sample-to-result assay to detect Ahi tuna DNA, and this protocol will be further adapted for testing other types of tuna including Bluefin tuna. By developing such a rapid and affordable isothermal biological assay and a point-of-need 3D printable portable device for tuna identification, I aim to contribute in helping individuals and ecosystems impacted by IUU fishing.

Cell division is essential to all living organisms, and microtubules are critical for this process. Microtubules in bundled kinetochore-fibers generate forces to move chromosomes by stochastically switching between assembly and disassembly states. Electron tomographs of mammalian mitotic spindles show that microtubule tips maintain a high level of coordination despite stochastic switching between states. The collective behaviors of microtubule bundles give rise to chromosome oscillation, which promotes the alignment and separation of chromosomes along the spindle equator during metaphase. To understand how stochastically-switching microtubules can produce synchronized motions in vivo, we use a mechanical model that describes the force-dependent dynamics of microtubules. The model reproduces the bistability of microtubule bundles observed in vivo and suggests that this coordination could be explained by sufficiently stiff mechanical coupling. We also propose a new way to characterize microtubule bundle state based on the substates of microtubules within the bundle. We will use this characterization to calculate microtubule bundle switch rates, which are technically difficult to distinguish otherwise, thereby laying the groundwork for future comparisons between bundle switch rates in vivo and in silico. In the future, we plan to explore the assumptions on which this model is based by analyzing the relationship between microtubule velocity and forces. We predict that this result will validate the assumed force-velocity relation of microtubule growth and contribute to a more accurate understanding of kinetochore-fiber behaviors. 

Infection from Mycobacterium tuberculosis is the second leading infectious cause of death worldwide after COVID-19, with rates of tuberculosis infection greatest in low and middle-income countries (LMICs). Tuberculous meningitis (TBM) is one of the most severe forms of M. tuberculosis disease with over 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 am performing in-vitro, site-directed mutagenesis 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.


In every eukaryotic genome, there is a cluster of tandemly repeated ribosomal DNA (rDNA) that is present in high copy numbers. Besides encoding ribosomal RNAs, rDNA is also involved in many non-ribosomal cellular functions. It is still not fully understood how this cluster of rDNA is maintained and how variation in its copy number impacts cellular function. Kobayashi et al found that Fob1, a protein that binds to replication fork blocking (RFB) sequences, is involved in the expansion and contraction of the rDNA region, however, the underlying mechanism of this copy number control is unknown. To explore the interactions between FOB1 and rDNA I would like to utilize CRISPR/Cas9-mediated editing to edit specific sequences in each rDNA repeat in wild-type and fob1Δ strains of Saccharomyces cerevisiae. Previous studies in our lab utilizing CRISPR/Cas9-mediated editing of the rDNA found that the rDNA copy number was initially significantly reduced, resulting in very slow cellular growth, and after many cell generations, rDNA copy number would expand through a proposed mechanism of reintegration of excised repeats and unequal sister recombination. These observations raise an important question: if FOB1 is needed for rDNA expansion, would it even be possible to perform rDNA editing and recover rDNA copy number in a fob1Δ strain? To address this, I am performing CRISPR/Cas9 editing of rDNA in fob1Δ cells alongside a wild-type control. I am characterizing viable transformants by studying their growth rate, ploidy, and rDNA copy number expansion. I am expecting to see no rDNA expansion occur in strains that do not have the presence of FOB1. By understanding the phenotypic impact of rDNA copy variation in a fob1Δ strain of Saccharomyces cerevisiae, we can come closer to understanding the interactions between RFB, FOB1, and rDNA copy number along with its effects on cellular processes.

The brain is one of the most complex and vital organs in our body. While thousands of people get treated for concussions, our knowledge of the impacts of brain injury is fairly limited. Brain injury caused by concussions occurs in about 1.9 million youth. Coupled with anxiety, this type of injury can become further complicated, which is why a holistic approach is necessary when treating patients, and even more critical when considering pediatric cases. There is research evaluating concussions and anxiety independently, but there is little research analyzing the joint relationship between the two. The Care4Kids study at the Seattle Children's Research Institute is one site in a multi-site study that examines post-concussive symptoms in children between the ages of 11-18; in conjunction with this work, I present the findings of a literature review evaluating the intersectionality between anxiety and concussions, asking the question, “What are the effects of pediatric sports-related concussions on anxiety?” The methodology for this review primarily focuses on synthesizing previously conducted research studies and reviews to present a comprehensive picture on the current discussion in research involving anxiety and concussion, and also its impact in the scientific community. In this review, I analyze the various aspects of pediatric sports concussion symptoms, focusing specifically on the manifestation of anxiety in post-concussive children, the degree of this anxiety faced across all ages, and a comparison of the short and long-term effects. With the findings from this literature review, we can gain a more comprehensive understanding of the relationship between anxiety and concussions in children to better predict and detect concussive symptoms in the future in order to ultimately provide children with efficient and conclusive post-concussive care.

Medical image segmentation modeling is a high-stakes task where direct communication and interpretation of uncertainty is crucial for addressing visual ambiguity. Prior work has developed segmentation models utilizing probabilistic or generative mechanisms to infer uncertainty from labels where annotators draw a singular boundary. However, as these annotations cannot directly represent an individual annotator's uncertainty, even specialized models trained on these standard representations produce uncertainty maps that are difficult to interpret. We propose a novel segmentation representation, Confidence Contours, which uses high- and low-confidence ``contours’’ to capture uncertainty directly, and develop a novel annotation system for collecting contours. We collect both standard and Confidence Contours annotations on the Lung Image Dataset Consortium (LIDC) and a synthetic dataset simulating the structural ambiguity of many medical segmentation problems, FoggyBlob. Our analysis show that Confidence Contours provide high representative capacity without requiring significantly higher annotator effort. Moreover, general segmentation models trained on Confidence Contours can produce significantly more interpretable uncertainty maps than models with specialized mechanisms for uncertainty, and they can learn Confidence Contours at the same performance level as singular annotations. We conclude with a discussion on how we can infer regions of high and low confidence from existing segmentation datasets. Our data-centric approach crucially brings attention to the importance of human factors in responsible and robust AI, which have often been overlooked in model-centric medical segmentation work. By troubling and rethinking the very way that the ground truth is represented, our work opens up new paths of inquiry towards more human-friendly models -- paths which begin from the data.

Human-machine interfaces, which map signals measured from a user into inputs for a device, hold promise to allow efficient and individualized device usage, whether for rehabilitation or recreation. Surface electromyography (sEMG) can non-invasively measure muscle activity through the skin to provide many potential user inputs to control a computer. Despite sEMG’s promise for user-controlled programs, clinical and commercial success has been low, in part due to poor user training regimens. sEMG-based interfaces are often unintuitive to learn, and not all motions will contribute equally to control, due to inherent limitations in electrode placement and sensitivity. Training users by presenting them with visual feedback of which actions can contribute to the task may enhance learning by discouraging strategies using undetectable motions. Thus, I propose training users to learn an adaptive decoder using an sEMG radar plot which displays real-time visualizations of the user’s sEMG signals, with each channel arranged in a circle such that motions appear as unique conformations of the radar. I hypothesize that showing users the radar plot before completing a sEMG-controlled computer task will confer greater task success. To test this, I conducted a set of experiments with adult subjects using the radar plot as brief, pre-task training for a two-dimensional, cursor-control game, comparing user performance between those trained and untrained. I anticipate that users who received radar plot training will demonstrate faster task learning and lower tracking error. Such a result would shed new light on how to streamline sEMG-based interface training, and may encourage further modifications or improvements of the radar plot. Optimizing the human-machine interface training process will be integral to their path to clinical and commercial success.

In this research project, our multidisciplinary team is developing environmental forensic technology to identify illegally caught seafood, with a focus on high-value species such as bluefin tuna. To tackle the difficult task of immediately detecting illegal, unregulated, and unreported (IUU) fishing, we are developing a rapid, affordable, and portable detection device that uses isothermal amplification and blue LEDs to detect resultant green fluorescent products indicating the presence of tuna DNA. As the lead Electrical Engineer, I designed an electrical circuit to precisely and stably control the temperature of a resistive heater using a microcontroller, thermistor, and PID algorithm along with an LED circuit. The requirement for the process involves the utilization of isothermal amplification technique at a fixed temperature of 37°C (33-42°C range) and green fluorescence detection (at 550 nm) in DNA using blue LEDs (at 470 nm) and an orange acrylic filter to filter the blue wavelength. The result is a circuit that meets the requirements for the biochemical process and enables real-time feedback without the need for shipping samples to a laboratory. With the development of the device finished, the next step is to streamline the user experience. I am leading the software development effort to create a phone application that facilitates the assay setup process and automates image capturing and analysis. With a capable research team, including colleagues shaping the user interface, a junior researcher connecting the device to the phone application, and a Ph.D. candidate in Computer Science and Engineering developing a proprietary camera software, our team's effort culminates in a user-friendly phone app that streamlines the assay workflow and provides real-time sample analysis. With the completion of this project, we will be able to make a difference by helping communities and marine ecosystems.

The trapping of individual ions has allowed physicists to control and observe otherwise inaccessible phenomena. Ion traps have enabled the most precise measurements of fundamental physical constants, mass spectrometry for chemical characterization, atomic clocks that would only lose a fraction of a second over the entire age of the universe, and the direct observation of many core concepts in quantum mechanics. Many crucial developments in ion traps occurred here at the University of Washington in the group of Hans Dehmelt, who shared the 1989 Nobel Prize in physics for that work. Today, techniques in ion trapping continue to be developed because trapped ions are one platform for creating qubits in quantum computers. With the growth of quantum information science in academia and industry, there is a need for inexpensive, scalable educational labs to introduce students to concepts in quantum computing. To fill this need, we developed a reproducible lab, which demonstrates key concepts in ion trapping. Our process utilized, first, a comparative approach with reference to literature and, second, iterative improvement on built components. The lab consists of two, independent quadrupole traps: a four-rod trap and a planar five-rail trap. To reduce cost and complexity, we trap charged particles with 25 µm and 50 µm diameter, rather than atomic ions. The particles are trapped in air, at atmospheric pressure. Due to the damping forces provided by this background gas, the trapped particles are easy to control. The result of our project is a lab capable of several experiments, including controlling the number of particles trapped through voltage modulation at a constant frequency, studying the phase transition between one- and two-dimensional Coulomb crystals, exploring micromotion compensation, observing two- and three-particle secular modes, and demonstrating particle shuttling along the trapping axis of the planar trap.

Trapped ions are one of the promising candidates for an operating quantum computer. Ions trapped in an electromagnetic trapp serve as a physical qubit, where the qubit states are manipulated by applying lasers to the system. As quantum computers use quantum gates with a given precise angle of rotation of the qubit state within the Bloch sphere, applying a laser with very narrow bandwidth is essential for minimizing errors, and thus stabilization of laser frequency is a required process for trapped ion qubit control. In our project, we stabilize the 1762 nm InfraRed fiber laser by using an optical cavity lock, where we obtain the resonant frequency of the cavity by measuring the intensity of the laser across the Fabry-Perot cavity, while varying the laser frequency. However, this model cannot distinguish between the laser intensity noise and the laser frequency noise. To address this, we eliminate the intensity noise by analyzing the signal reflected back from the cavity, where we observed a frequency dependent signal which reaches zero at resonance, allowing us to stabilize the laser to the desired frequency. A deeper understanding of the laser stabilization techniques may help us to minimize the trapped ion qubit control errors.

Atrial fibrillation (AFib) is the most common sustained cardiac arrhythmia, contributing to significant morbidity and mortality worldwide. Patient-specific computational models of the left atrium are currently studied to predict characteristics of reentrant activity that promotes fibrillation. However, current models’ patient-specificity is limited to anatomical structure and the distribution of disease-related remodeling (fibrosis), whereas electrical properties of cells and tissue are based on literature values. In cases where patients are clinically known to present with either AFib or atrial flutter (AFl), this lack of personalization can lead to inaccuracies in simulation outcomes (e.g., AFib-like behavior in simulations for a patient who actually had AFl, or vice-versa). My goal was to derive parameter sets that favor the initiation of one type of arrhythmia or the other (AFib or AFl). Ten fibrotic left atria were reconstructed from late-gadolinium enhanced (LGE)-MRI scans and the bioelectric parameter space (comprising ion channel expression levels and impulse propagation rates) was explored using a Taguchi L27 Design of Experiments (DoE) approach. Arrhythmias were induced by initializing four atrial regions to different phases of the action potential under each parameter permutation. I ran 300 simulations and manually classified each arrhythmia episode as either AFib- or AFl-like based on prior definitions. I pinpointed a pro-AFl parameter set – bioelectrical conditions under which 89% of all induced arrhythmias were AFl and only 11% were AFib. The pro-AFib parameter set in these preliminary simulations was comparatively less robust (61% vs. 39% for AFib vs. AFl inductions, respectively). My future work on this project will establish stronger relationships between model configurations and simulation outcomes by probing a wider array of possible parameters in a larger population of patient-specific models. Data from the present study will guide future simulations to accurately tailor models to represent the arrhythmic state in patients predisposed to AFl.

Phonemic proficiency refers to the ability to manipulate the phonemes, or unit of sounds, in a word. Speech perception deficits has been linked to lower phonemic proficiency, as children have difficulty isolating, manipulating, and blending sounds that they cannot perceive. Autistic children commonly report difficulty perceiving speech in noisy real-world environments where many people are talking at the same time, such as a classroom or playground. Thus, in this study, we investigate the relationship between phonemic proficiency and multitalker speech perception in autistic children. We hypothesized that we would observe a stronger correlation between speech perception and phonemic proficiency in autistic children compared to the neurotypical comparison group. Moreover, we expected that autistic children will have worse multitalker speech perception thresholds overall, suggesting difficulty perceiving speech under complex conditions. We tested 19 7-to-10-year-old autistic children and a comparison group of 19 age- and biological sex-matched neurotypical children. The Phonemic Proficiency subtest of the Weschler Individual Achievement Test – Fourth Edition was administered to assess phonemic awareness. Multitalker speech perception thresholds were obtained under 2 conditions: Co-located Noise and Segregated Noise. In the Co-located Noise condition, the target speaker spoke sentences from 0° azimuth with two additional distracting talkers, referred to as maskers, co-located from the same location. In the Segregated Noise condition, the distracting talkers were spatially segregated to ±90° azimuth, while the target talker remained at 0°. Preliminary analyses suggest that a relationship between phonemic proficiency and multitalker speech perception is observed. These results will advance our understanding of the difficulty autistic children have perceiving speech and have the potential to lay the groundwork for novel assessment and intervention strategies to improve how children with and without autism listen and learn in a noisy classroom. All authors participated in data acquisition, analysis, and preparation of this presentation.

 Children are tasked with listening and learning in noisy environments where many people are talking at the same time every day. Conceptual models of listening under complex conditions posit that working memory plays a role in the ability to extract the target speech from the distracting noise. Hard-of-hearing (HoH) children, in particular, do worse listening in noisy environments. Thus, in this study we investigate the relationship between working memory and multitalker speech perception in HoH children. We hypothesized that we would observe a correlation between working memory and speech perception in both HoH and the typical hearing comparison group. Moreover, we expected that HoH children will have worse multitalker speech perception thresholds overall, suggesting difficulty perceiving speech under complex acoustic conditions. We tested 7-to-18-year-old HoH children and an age- and biological sex-matched typical hearing (TH) comparison group. Working memory was assessed in both visual and auditory domains; participants were asked to recall either a sequence of visually presented letters or auditorily presented numbers. Multitalker speech perception thresholds were obtained under 2 conditions: Collocated noise and Segregated noise. In the Collocated Noise condition, the target speaker spoke sentences from 0° azimuth with two additional distracting talkers, referred to as maskers, collocated from the same location. In the Segregated Noise condition, the distracting talkers were spatially segregated to ±90° azimuth, while the target talker remained at 0°. Preliminary analyses suggest that a relationship between working memory and multitalker speech perception is observed. These results will advance our understanding of why HoH children experience difficulty perceiving speech under noisy conditions and have the potential to lay the groundwork for novel assessment and intervention strategies to improve how TH and HoH children listen and learn in a noisy classroom. All authors participated in data acquisition, analysis, and preparation of this presentation.

Electrochemical water splitting, a promising green energy solution, produces O2 and energetically rich H2 gas molecules as products on the anode and cathode, respectively. Attachment of O2 and H2 bubbles on the surface can decrease the overall efficiency of electrochemical water splitting.Therefore, continued investigation of nanobubble characteristics is of utmost importance to improve the technologically relevant electrochemical generation of H2 gas. Nanobubbles can interfere with the efficiency and productivity of industrial processes by blocking electrode surfaces, however, they could also potentially be utilized to catalyze reactions themselves. To better understand these processes, it is important we create consistent samples of nanobubbles that can be formed individually and reproducibly, and gain a deeper understanding of their properties. We have been working to create a procedure that efficiently and reliably produces carbon nanoelectrodes for single nanobubble analysis. To accomplish this, we pull quartz capillaries to a nano-sized tip to create a nanopore, and heat the nanopores while applying a flow of methane in an oxygen-free environment to deposit carbon inside the capillaries, producing nanoelectrodes. We test the electrochemical properties of the nanoelectrodes by measuring the observed current when applying a potential and evaluating whether the cyclic voltammetry graph generated suggests that the nanoelectrode is capable of generating a nanobubble. Certain elements of our current procedure may need to be adjusted to improve the reliability of the nanoelectrodes, but so far our experimentation in nanoelectrode fabrication has allowed for a more reliable process in generating ideal hydrogen nanobubbles. This procedure has helped us gain a better understanding of the impact of nanobubbles on an electrochemical system and provide a better physicochemical description of the bubble. In the future, we plan to apply the knowledge gained through these experiments on theta nanoelectrode fabrication, which is an electrode with a partition in the middle.

Inherited retinal diseases (IRDs) are a diverse family of disorders which cause vision loss and retinal degeneration. With only 1-2% of the genome being protein-encoding, genetic variation within the expansive noncoding genome is critical to the development of disease phenotypes in the retina. Macular Telangiectasia Type II (MacTel) is an IRD resulting in disruption of central vision and greatly impacting vision-related quality of life. MacTel has an estimated prevalence of 1 in 1000 individuals, affecting approximately two million people globally. Though MacTel etiology largely remains unknown, accumulation of improperly degraded lipids within the retina is a leading hypothesis in its pathogenesis. Additionally, genome-wide association studies have implicated numerous loci in the development of MacTel, including the novel gene locus ceramide synthase 4 (CERS4). As CERS4 plays a critical role in the synthesis of lipid precursors and is highly expressed in the retina, it stands as a promising candidate for influencing MacTel development. We hypothesize that cis-regulatory element (CRE) mutations are central to the genetic frameworks underlying MacTel. We aim to characterize the sufficiency of putative enhancer regions to drive gene expression. We have identified potential CERS4 enhancer regions through a machine learning approach using adult human retina ATAC sequencing datasets. Sufficiency of candidate enhancer regions will be evaluated by insertion to a barcoded reporter library and electroporation into mouse retinas. Following proof of sufficiency, we will perform saturation mutagenesis on identified enhancers to investigate the impact of all possible single nucleotide variants (SNVs) within these regions. The results of our investigation will aid in identifying SNVs of interest within the CERS4 locus, potentially implicating specific mutations towards the development of MacTel. Greater understanding of CRE mutations will improve early clinical diagnosis and inform future therapies for patients with MacTel.

Diffusion-weighted imaging (DWI) shows great potential for improving breast cancer detection and diagnosis. Primary findings from the ECOG-ACRIN A6702 multi-site, multi-vendor clinical trial indicate that DWI apparent diffusion coefficient (ADC) values may help reduce false positives and unnecessary biopsies. Gradient nonlinearity (GNL) correction was previously found to improve the accuracy of ADC mapping within and across MRI vendor systems. In this study, we evaluated the impact of GNL correction on breast lesion ADC measures in the A6702 dataset. The dataset comprised 81 suspicious breast lesions (28/81 malignant) in 67 women. Standardized DWI scans were acquired across 9 different MRI scanners. ADC maps were created from DWI scans, and ADC values were measured for each lesion. Direction-averaged GNL correction maps were constructed based on scanner-specific gradient specifications. ADC map correction was then performed through pixel-wise scaling by the GNL correction maps using custom software developed in MATLAB. Lesion ADCs before and after GNL correction were compared using a two-tailed z-test. ADC diagnostic performance (benign vs. malignant) was evaluated using area under the receiver-operating-characteristic-curve (AUC), and optimal ADC cutoffs were chosen to maximize specificity while maintaining 100% sensitivity. GNL-corrected lesion ADCs were significantly lower than uncorrected ADCs (1.12±0.29 vs 1.17±0.30x10-3mm2/s, p<0.001). GNL error in lesion ADCs varied across gradient systems (mean ∆ADCvendorA=0.14±0.08, ∆ADCvendorB=0.03±0.02, ∆ADCvendorC =0.004±0.01, p<0.001). GNL correction produced a slightly lower optimal ADC cutoff (1.33 vs. 1.35x10-3mm2/sec). However, no overall difference in diagnostic performance was detected: AUCuncorrected=0.78 (95% CI 0.68-0.88), AUCcorrected=0.79 (95% CI:0.69-0.89), p=0.22, and 18% potential biopsy reduction for both. This study showed GNL substantially affects lesion ADC measures, with significant variability across different vendor platforms. These findings suggest that GNL correction should be implemented to ensure uniformity and consistency in diagnostic breast lesion ADC measures across MRI platforms, especially for multi-center clinical studies.

The National Archives in Seattle provides access to permanent records created by Federal agencies and courts for Alaska, Idaho, Oregon and Washington in its 56,000 cubic foot warehouse. Researchers, historians, government officials, and the general public consult the facility for many reasons including genealogy, tribal records research, land use, geographic study, and citizen engagement in federal activities. Not only do the archival records hold information from the past, the ways and spaces in which documents have been held form a hidden history that reflects our culture. In 2020, NARA’s Seattle location was announced to be sold. Although community members gathered to successfully prevent the closure, the vulnerability of archival spaces was exposed in this process.Site/Archive/Cite uses mixed reality to intervene into the hidden history of the NARA building, establishing an augmented ghost archive that questions how materiality and meaning shifts when translating materials from a physical to digital space. The art installation examines the relationship between the public, the archival record, and its physical presence in our region. Revitalizing archival materials using new technology allows viewers to explore how we view and store records of the past. This mixed reality experience furthers public conversation regarding the role of digitization in archival access. My role includes researching fabrication techniques to create digital and physical components of the exhibit. I have been building software to allow images of archival materials to appear in the gallery space and be responsive to the viewer's presence within an AR experience. I support finding methods for installing the exhibit and planning components for the larger work including plexiglass with motion sensing lighting. A teaser of our larger exhibit was shown at the Seattle Art Book Fair in May, 2023, and acted as a test “trial” for the larger exhibit being developed.