Image processing using dithering finds important applications for data compression, data encryption, data security and cryptography. Dithering is used for the design of high-quality printers, computers and game consoles. Digitization and compression of images often involve reduction of color palette which gives rise to color bands due to quantization errors. Dithering involves the application of noise to randomize quantization errors which helps preserve key features of images when converted to black and white and other color reduced formats. We applied mathematical matrix-algebra based methods for image digitization, image recognition and image processing. We wrote Python programs to study image quality before and after application of different algorithms for dithering including thresholding, randomization, ordered methods like Bayer’s method, void and cluster methods, error diffusion methods like Floyd-Steinberg techniques, etc. This project offered excellent hands-on opportunities to integrate programming in python with matrix algebra methods for image processing and provides insights into how different dither algorithms enhance visual capabilities along with compressing image size. Dithering introduces some textural contours and color shifts but preserves most features in image data. We also find that in addition to enhancing image quality, dithering modulations offer powerful techniques for digital watermarking and image embedding indicating their key role in data security.

The Mars Rover Sojourner is an autonomous robotic vehicle that was used by NASA for space exploration on Mars. The Mars Sojourner landed in a location called Ares Vallis in 1997 where it explored and took several photos and collected data. Google Maps and network routing programs, often use the popular Dijkstra's algorithm used to find the shortest and most cost-effective routes between various nodes on a graph. Here, we used the free open Cyberbotics Webots code to simulate the Mars Sojourner which was designed to successfully navigate over the rocky terrains of Mars. Robotic simulation software like Webots offers an excellent testing platform to study the stability and routing of autonomous navigation vehicles on different terrains prior to their deployment in outer space. The robotic Mars Sojourner was equipped with a GPS sensor which kept provided measurements of position using geodetic coordinates involving latitude and longitude. We used the Haversine formula to calculate distances between various places it traversed on Mars. We used a python code to map the shortest optimized route to go from point A to point B on Mars using Dijkstra’s iterative algorithm. Such studies are important for future development of robot motion controller software that can be effectively used for cost effective autonomous navigation in outer space.

The Campanian stage of the Late Cretaceous (~84–72 million years [Ma]) was a dynamic interval for North American ecosystems including the evolution of angiosperm plants and the regression and transgression of the Western Interior Seaway (WIS). These dynamics likely impacted terrestrial fauna across the continent. Most studies investigating biodiversity in western North America during the Campanian focus on a single group (e.g., dinosaurs or herpetofauna), whereas few investigate diversity patterns of multiple taxa. This approach is imperative because comparing diversity patterns among taxa can provide rare insight into the synecology of animal communities. Vertebrate microfossil sites are ideal for such a study because they preserve large sample sizes, multiple taxonomic groups that likely coexisted, information about environmental conditions, and they sample multiple stratigraphic intervals. The Judith River Formation (JRF) of north central Montana preserves ~4 Ma of the Campanian (~79–74 Ma) and large regressive and transgressive cycles of the WIS. This formation, which is contemporaneous with the Dinosaur Park and Two Medicine formations, is also rich in vertebrate microfossil sites. To examine vertebrate diversity patterns through this critical interval, we compared taxonomic richness and relative abundances of Dinosauria, Squamata, and Lissamphibia from the JRF from three temporally distinct microfossil sites: Makela-French 1 (~77.5 Ma), Milkshake (~76.5 Ma), and Clamfetti (~75.2 Ma). Over four years, we collected and screenwashed fossiliferous, bulk-sediment samples from these sites. Thus far, we have recovered 998 and aim to recover 1,200 specimens total. We use our data and knowledge from the literature to evaluate the extrinsic factors (e.g., seaway regressions) that drove diversity changes in the JRF fauna.  Our preliminary results suggest a connection between diversity patterns and WIS cycles. We observe shifts in relative abundances and richness near the onset of the WIS transgressive cycle. 

The Campanian stage of the Late Cretaceous (84–72 million years [Ma]) was a dynamic interval for North American ecosystems and included the zenith of dinosaur diversity and the regression and transgression of the Western Interior Seaway (WIS). Most studies that investigate vertebrate biodiversity during this interval focus on dinosaurs, whereas few focus on changes in herpetofauna (lizards, frogs, and salamanders). Herpetofauna are important indicator species of ecosystem dynamics, because they are fragile to ecosystem change. Vertebrate microfossil sites are ideal for studying herpetofauna diversity dynamics through time because they can produce large sample sizes, sample aquatic environments, and are plentiful through stratigraphic intervals. The Judith River Formation (JRF) of north central Montana is rich in vertebrate microfossil sites, preserving ~4 Ma of the Campanian (~79–74 Ma). Here we aim to document patterns of herpetofauna diversity change in the JRF by quantifying herptile taxonomic richness and relative abundances using specimens from three temporally separated microfossil sites: Makela-French 1 (~77.5 Ma), Milkshake (76.5 Ma), and Clamfetti (~75.2 Ma). We collected sediment samples from these sites over four years and processed them via underwater screen-washing techniques. Presently we have studied 470 herptile microfossils (600 planned). Our preliminary results show changes in the taxonomic diversity across the sampled sites. Taxonomic richness of herptiles varies through the formation, first increasing and then decreasing. Salamanders have the highest relative abundance, lizards decrease in relative abundance, and frogs fluctuate. We hypothesize that taxonomic patterns are influenced by the impact of WIS cycles on water supply in ecosystems: amphibians thrive in wetter environments, whereas lizards are more terrestrial. These preliminary results reflect a connection between diversity patterns and extrinsic drivers not observable through the analysis of dinosaur fossils. Our continued analysis will provide more fine-scale resolution of herptile diversity during the Campanian.

The El Niño-Southern Oscillation (ENSO) is the most significant year-to-year climate variation, affecting weather and climate systems worldwide. However, current prediction models, both dynamic and statistical, struggle with accuracy due to the complex mechanism of ENSO. This study introduces a regional temperature and salinity prediction method using a Long Short-Term Memory (LSTM) deep learning model, which is well-suited for identifying long-term patterns in sequential data. The model is applied to three specific regions using in-situ data from Argo floats: the central-eastern Pacific, the central tropical Pacific Niño 3.4 region, and the Western Pacific Warm Pool (WPWP). These regions are chosen because they play key roles in ENSO dynamics. Results show that the LSTM model performs best in the WPWP, where the average mean squared error (MSE) is low (0.03), indicating high accuracy and stability. This is likely due to lower noise in the original data. In contrast, the model performs poorly in the central-eastern Pacific, where the average MSE is much higher (7.03), suggesting instability due to high noise in original data. These findings highlight the potential of deep learning for regional climate predictions and suggest that LSTM models could improve local weather forecasting and fisheries management.

Pulmonary Arterial Hypertension (PAH) is a deadly vascular disease, affecting the blood vessels of the lungs, with no existing cure. PAH is characterized by pulmonary arterial smooth muscle cell (PASMC) hypertrophy and hyperplasia, which increases resistance to blood flow within the pulmonary arteries, leading to rapid symptom progression and eventual death from right heart failure. My mentor and I hypothesize that defects in PASMC differentiation and alignment may contribute to PAH. To test whether alignment and phenotypic responses differ in patients with PAH, we designed a micropatterned collagen scaffold atop a glass coverslip. Explanted PASMCs from patients with PAH or failed donors (controls) were cultured on alternating 10-µm wide x 10-µm deep microchannels or unpatterned constructs and alignment, protein expression, and cellular morphology were compared across conditions. I evaluated 3 PAH and 3 control subjects and have collected preliminary data for each condition (control versus PAH), with three technical replicates each. Through these preliminary studies, I have demonstrated success of my model with consistent alignment observed on patterned substrates. Excitingly, PASMCs from patients with PAH expressed significantly decreased levels of the contractile protein, Calponin, when compared with control cells, including after responding to cues that promote alignment and contractility. This suggests that PAH PASMCs remain in an inappropriately synthetic or proliferative state. Moving forward, I plan to evaluate additional micropatterns by varying dimensions of rectangular and sine waves designs using an ablation protocol with a 2-photon microscope laser. Subsequent evaluation will include immunofluorescent staining of contractile and other SMC markers as well as transcriptomic evaluation of cellular responses to micropatterning. This work will enhance understanding of whether SMC abnormalities contribute to disease initiation and progression in PAH and will contribute to the broader effort of developing more complex models of pulmonary vascular disease.

Lentivirus is a well-established gene-editing tool commonly used in cellular research. Recently, its widespread adoption has led to the development of numerous protocols for the transduction of primary human T-cells. However, generating high-titer virus for large vectors remains a challenge, and there is a need for optimized protocols – particularly for creating Base Editor lentivirus for a 15 kb vector. By developing a method to estimate transduction efficiency in primary human T-cells using viral titers, significant reduction to the waste of valuable human samples could be achieved. To address these challenges, we tested various variables—including plasmid concentration, media formulations, and transfection reagents—within infection protocols to optimize lentivirus production and improve T-cell transduction efficiency. By refining the protocol for creating Base Editor lentivirus, we aim to base-edit autoimmune-associated variants in human CD4 T-cells and assess their impact on T-cell effector function. This work is crucial for advancing base editing technologies in the Ray Lab and will contribute to the broader field of immunology.

Panãra is a Jê language spoken in the Panará Indigenous Land in the Brazilian Amazon by around 730 people. I am an undergraduate research assistant working as part of the larger Panãra Documentation Team at the University of Washington. I am in the process of transcribing, coding, and archiving field notes taken by team members during the summer of 2024. I have employed my experience with Panãra and Portuguese to resolve ambiguities in the notes and to code materials in a standardized, accessible manner. Many letters, such as ⟨b, d, g, z, l⟩, and sequences, such as ⟨-ät-⟩ or ⟨-me-⟩ are impossible due to Panãra’s phonology and orthography. However, these letters may occur in the notes due to transcriber error or Portuguese loans. When I identified suspect items, I had to use my knowledge of Panãra to determine their status. I typed the notes into text format before transferring items into a spreadsheet. In the spreadsheet, I coded part of speech and added lexical items to the ongoing dictionary. My work is a case study in longer-term, multi-researcher documentary efforts in linguistics. Not only will the body of data I code be valuable in further analysis of the language, but the processes developed will be useful in rethinking how documentary linguistics is carried out. In particular I emphasize the need for a coherent vision of data usage, from collection to coding. As the dictionary work moves forward, my next steps will be to give words that have not yet been checked in the field to the research team for the summer and to code the phonological, orthographic, and lexical information for each word into the FLEx database.

Previous research indicates that males typically outperform females in spatial perspective-taking tasks where an individual is prompted to assess a scene by adopting a perspective other than their own. However, a recent study, with only female participants, found an increase in female perspective-taking performance when the task asked subjects to take the perspective of a social agent. Many have theorized that this performance increase is exclusive to females, who are believed to hold superior social skills. This implies a distinction between purely spatial perspective-taking and social perspective-taking, the latter of which females are theorized to perform better at. More recent studies have countered this notion, suggesting that directional information provided by a social agent could explain the increased performance in females. Assessing the relationship between spatial and social perspective and sex-based differences in performance can provide insight into social perspective-taking in human cognition. To clarify the influence of social agents on perspective-taking performance in both males and females, we administered two spatial perspective-taking tasks, with either a social or non-social agent. We aim to clarify theorized sex-based differences in performance by comparing accuracies and reaction times in social and non-social conditions. We hypothesize that male and female performance in perspective-taking tasks will be equally affected by the presence of a social agent.

Visual perspective-taking (PT) is a fundamental spatial cognition task, requiring an individual to adopt another’s viewpoint. Previous experiments have shown that response times increase as the angular difference between viewer and reference perspectives grows. Preliminary fMRI results suggest that neural activity in specific brain regions follows a similar pattern, their activity increases as a factor of angular difference, reflecting the cognitive demands of mental perspective transformation. However, little is known about how eye-gaze behavior varies in this task. In this study, we analyze eye-tracking data collected during fMRI scans with an Eyelink 1000 to examine the relationship between gaze patterns and perspective alignment. Specifically, we investigate whether eye-gaze behavior differs between aligned and unaligned trials and whether angular difference influences gaze dynamics. Gaze coordinates (xpos, ypos) will be analyzed trial-by-trial to determine how visual attention is modulated during perspective-taking. Understanding these gaze patterns may provide insights into the strategies used in spatial perspective shifts and their neural underpinnings.

Visuospatial attention is a complex, dynamic process critical to our conscious perception of the world. The N2pc event-related potential (ERP) is a time-locked EEG waveform implicated in the modulation of visuospatial attention and observed in Posner task paradigms. The N2pc ERP functionally represents attention mechanisms, with hypotheses suggesting it could represent target enhancement or distractor suppression. Further, perceptual differences have been found in autism spectrum disorder (ASD) populations, suggesting that these differences could be discriminated in N2pc properties. Visuospatial cueing differences are observed in autistic individuals, yet the neural mechanisms underlying these differences remain unclear. This study investigates possible differences in the N2pc component reflecting distinct patterns of attentional modulation in autism. We conducted 32-electrode EEG recordings of neurotypical and autistic adults engaged in a Posner paradigm visual detection task, detecting grayscale circles embedded in a checkerboard stimulus. Using MatLab and EEGLAB, we expect to localize N2pc ERPs in parietal regions in epochs post-cue and post-stimulus presentation. We hypothesize that we will see different amplitude and latency N2pc ERPs in autistic individuals compared to neurotypical controls, reflecting differences in attention modulation. Results may provide insight into how attentional mechanisms differ in autistic individuals, allowing for a greater understanding of neurotypical and neurodivergent approaches to visuospatial attention.

This study investigates the physical mechanisms driving spatiotemporal variability of

barrier layers in the Western Tropical Pacific (WTP) along 149°E, with a specific focus on the

La Niña phase of the El Niño-Southern Oscillation (ENSO). Barrier layers, which separate the

surface mixed layer from the thermocline, regulate ocean-atmosphere interactions and influence

climate dynamics. This research assesses the relative contributions of freshwater input from

precipitation, and wind stress on barrier layer formation and thickness. Data were collected

during a research cruise in January 2025 aboard the R/V Thomas G. Thompson from an

Underway Conductivity Temperature and Density (UCTD) sensor for temperature profiles, and

public-source meteorological data for atmospheric conditions (ERA5). Seven stations, spaced

two degrees apart in latitude, were sampled along a transect from 4°N to 15°N. Each station

provided data to analyze barrier layer thickness, with spatiotemporal variability determined by

comparing different formation mechanisms across stations. Spearman Correlation analyses were

used to determine dominant factors influencing barrier layer thickness and variability. We found

that barrier layer thickness in the WTP shows a general positive but statistically insignificant

relationship with freshwater (ρ 0.32 and p-value 0.48), and a general negative but statistically

insignificant relationship with wind stress (ρ 0.18 and p-value 0.70). During La Niña conditions,

these effects are expected to drive variability, with thicker layers forming in regions of high

precipitation and weak wind stress. Increased freshwater input enhances stratification, while

strong wind stress likely promotes surface and subsurface mixing, leading to barrier layer

thinning. Understanding these dynamics has implications for improving ocean-atmospheric

interaction climate models in the tropical Pacific.

Visual Perspective-taking (VPT) is the ability to recognize another’s viewpoint, and can play a role in communication and empathy. Previous research supports that VPT in Autism Spectrum Disorder (ASD) populations is altered compared to neurotypicals (NT), but the traits within both populations that contribute to VPT differences remain unknown. This study investigates how VPT differs in ASD compared to NT adults using both animate and inanimate target objects. We also explore how these differences might be associated with ASD traits, measured by the Social Responsiveness Scale-2 (SRS-2). Participants complete computerized tasks that evaluate how stimuli appear from a different perspective. Psychophysical tests determine participants' ability to identify the position of an object from the perspective of an animate object (an avatar in the image) and an inanimate object (a chair), measuring accuracy and reaction time. We expect to replicate past findings of increased reaction time with greater angular disparity between the participants’ viewpoint and the viewpoint of the target object, for both ASD and NT subjects. We hypothesize this interaction between reaction time and angular perspective for both populations may interact with the type of reference object (animate vs. inanimate) and SRS-2 scores. We believe that NT participants will demonstrate greater accuracy and faster reaction times than ASD participants in both animate and inanimate conditions, with the difference being evident in the animate condition for ASD participants, possibly due to challenges in processing social cues reflected by higher scores on the SRS-2. This research can increase the understanding of the psychological disparities in individuals with ASD compared to NT contributing to diagnostic tools and targeted interventions for improving social cognition in ASD populations and potentially other neurodivergent populations with VPT differences.

According to the Centers for Disease Control and Prevention, the U.S. has more than 2.8 million antibiotic-resistant infections each year. The rise of multidrug resistance in bacteria poses an urgent clinical threat contributing to these various infections. UPAB1 is a specific strain of a notoriously drug-resistant bacteria Acinetobacter baumannii associated with catheter-associated urinary tract infections (CAUTI). UPAB1 infects the urinary tract through the introduction of a foreign object, such as a catheter. In response, the immune system coats the catheter with fibrinogen, a glycoprotein complex that assists in wound healing. UPAB1 uses its bacterial adhesin proteins, such as Abp2D, to bind to fibrinogen, deplete essential nutrients, and infect the urinary tract. By designing Abp2D inhibitors as de novo miniproteins, we hypothesize that A. baumannii will be prevented from establishing a bacterial infection and allow us to offer a potential alternative in combating antibiotic resistance in CAUTIs. Targeting UPAB1 Abp2D, we first developed designs of Abp2D inhibitors utilizing computational software like RoseTTAFold Diffusion (RFdiffusion) for miniprotein backbone design, ProteinMPNN for sequence design, and AlphaFold2 (AF2) for structure prediction of the sequences to validate and filter. Afterwards, in the laboratory, we expressed and purified the miniprotein designs. We are currently testing these designs as Abp2D inhibitors via E. coli cultures to determine their success in binding to UPAB1 Abp2D.

The conservation of global marine mammal abundance has been considered largely successful as the widespread ban of the industrial harvest of pinnipeds and large cetaceans has led to their strong recovery in abundance. However, it remains unknown whether the story of their conservation applies to marine mammals that were not heavily harvested such as oceanic dolphins. Here, I plan to fill this knowledge gap by presenting a meta-analysis of global abundance trends of oceanic dolphins by conducting a systematic literature review of government reports, journal articles, and marine biodiversity data sets to gather abundance trend data. I expect to find data for roughly 25% of all 38 oceanic dolphin species, mostly represented by line-transect surveys and mark-recapture evidence in coastal waters. Using a Bayesian multi-population state-space model, I intend to estimate abundance trends for each dolphin population, in addition to the uncertainty in population changes and varying survey methods. I seek to summarize abundance trends of populations by species and regions to identify which of these have declining or highly unknown abundance trends. I expect dolphins with restricted geographic ranges, especially coastal species, to have the strongest declines, and dolphins that occupy high seas to have the least known trends. I aim to highlight which taxa and areas need further conservation and monitoring attention. These findings represent a crucial first step in gaining insight from rising dolphin populations, which can be used to help reverse the decline of other populations.