We present optical and infrared photometry of the T Tauri binary KH 15D acquired in the 2017/2018 observing season. The data were obtained from the A Novel Dual Imaging CAMera (ANDICAM) instrument on the 1.3m telescope operated by the Small Moderate Aperture Research Telescope System (SMARTS) at the Cerro-Tololo Inter-American Observatory (CTIO). KH 15D includes two young stars (A and B, with 0.72 and 0.74 solar masses, respectively) orbiting their common center of mass, surrounded by an inclined precessing circumbinary disk. The recent data reveals Star B gradually emerging from the trailing “fuzzy” edge of the disk and is now in a stage that is completely unocculted for the first time since the system’s discovery in 1995. We use time-series photometry, or light curves, to probe the composition of the disk, derive parameters of Star B, and demonstrate the overall mechanics of the system. Recent data also shows reddening during the egress of the last eclipse, proving that the trailing edge of the disk is transparent and consists of dust-sized particles. Additionally, the most recent data displays Star B at a brighter magnitude than ever than before, allowing us to calculate an apparent I magnitude of 14.079, which is 12% brighter than previously computed.

Since 1982, with the introduction of insulin as the first recombinant protein therapeutic, peptide and protein drugs have grown to encompass 10% of the pharmaceutical market and are the fastest expanding class of drugs. Advantages of using peptides over small-molecule drugs include high potency, selectivity, and capability to be engineered for a diverse range of targets, most commonly to disrupt or facilitate key protein-protein interactions (PPIs) in the human body for a therapeutic effect. To search for strong binders for a therapeutic target, combinatorial peptide libraries of up to billions of different sequences are synthesized and screened against promising targets. Due to the enormous library size, screening for high affinity binders often requires multiple rounds of enrichment in order to isolate the most potent molecules, a laborious and potentially bottlenecking step in developing protein drugs. Current approaches that have strategies for enrichment, such as phage display and yeast surface display, are limited to screening a library of binders against one target instead of multiple targets (library-on-library). This proposal describes the development of a peptide binder screen utilizing a simple workflow of repeated mating and sporulation of genetically engineered S. cerevisiae, or baker’s yeast. This technology improves the throughput of established screening methods through a library-on-library format that efficiently isolates high-affinity peptide binding interactions.

The formation of dental biofilm (plaque) is promoted through the consumption of dietary sugars, which serves as a precursor to the metabolic process that bacteria must undergo. Organic acids are byproducts of this metabolism, and encourage the demineralization of the enamel which if left untreated leads to formation of dental caries (tooth decay). Evaluation of the acidity of plaque deposits on patient’s teeth can be used as a preventative measure to allow dentists to detect areas vulnerable to dental decay. A ratiometric fluorescence pH sensing device has been developed using an FDA approved dye, Fluorescein, and blue LED excitation. Fluorescent spectral profiles were collected using a spectrometer and analyzed with a spectral unmixing algorithm for calibration over the pH range of 4.5-7, the ideal range to measure the acidic environment of the mouth. A 420 nm LED housed with an electronic driver served as the fluorescein excitation source. Spectral profiles were collected within the 450-650 nm range. In an in vivo pilot study, we found that the dye solution which consists of fluorescein powder and deionized water causes retention issues on interproximal areas. In order to achieve accurate results from the spectrometer, the fluorescein dye must penetrate and diffuse through the dental plaque. To allow enough time for the fluorescein solution to adhere, glycerol was added to increase viscosity. Tests were performed to evaluate the effect of the glycerol addition on the spectral data. Solutions ranging from 0%-50% glycerol were measured. Glycerol addition increases the peak wavelength of the spectra by no more than 1%. The pH of the solution has no effect on this trend. An in vivo case study was performed for high caries risk patients to validate the device. The pH device has the potential to predict early caries, reducing oral restorative procedures and dental expenses.

The Arab American population is severely understudied despite their recent but also historic presence in the United States. This underrepresentation in research signifies a void that translates to a lack of understanding towards Arab American culture. This qualitative study was conducted to make clearer the correlation between gender norms in the Arab American community and the acculturation of Arab American young adults into mainstream American society. Eight 30-45 minute interviews were conducted in a semi-structured form with Arab American young adults aged 18-24 years. It was hypothesized that Arab American women were more likely to separate, whereas Arab American men were more likely to integrate into American society. The results are discussed through the comparison of the gendered experiences of the participants against the framework of acculturation. This study identifies central questions and issues that are posed for the acculturation of Arab American young adults, and directions for future research.

Food contamination outbreaks have become increasingly prevalent in the United States. Food processing companies often do not have sufficient resources to accurately monitor pathogenic bacteria and biofilms on their food preparation surfaces. Unfortunately, consumers assume that the food is safe because it is packaged and ‘screened’ but invisible bacterial contamination may be present. This creates an opportunity to improve methods for detecting pathogenic bacteria in food handling and processing environments. BioVizia provides an alternative solution for detecting pathogenic bacteria on food processing surfaces that is efficient yet effective. We have developed a device that uses an LED to excite a fluorescent dye. Fluorescein is an FDA approved dye that exhibits pH dependent spectral properties. When viable pathogenic bacteria metabolize sugar, they produce acidic byproducts. Therefore an optical system using fluorescein as a pH disclosing agent may provide sufficient sensitivity for detecting bacterial contamination. Our optical system records the fluorescein emission spectra which contains two overlapping, pH dependent spectral features. The fractional amount of the two contributing bands are calculated using a spectral unmixing algorithm. A calibration with standardized pH buffers yields a linear relationship between pH and the fractional amount of each band. This noncontact optical pH measurement method has been successfully employed in an in vivo dental study to measure the pH drop produced by dental plaque following a sucrose rinse. We seek to demonstrate that BioVizia can make the detection of pathogenic bacteria and biofilms on food preparation surfaces fast and quantitative.

The University of Washington (UW) has a rich history around diversification and over the past 50 years anti-affirmative educational policies have reconfigured what “achieving diversity” looks like beyond admission statistics. Effective support is critical for the underrepresented minority (URM) student who gets into the UW and faces many disadvantages that make it difficult to succeed. The UW Educational Opportunity Program (EOP) Scholars Academy was created in 1968 to facilitate the metamorphosis (transformation) of low-income, first-generation URM students into independent and successful scholars. However, what is not publicly known is why the EOP Scholars Academy support program is effective and in what ways. This study explores how the EOP’s process of curating the student metamorphosis experience impacts 1) students’ academic outcomes and 2) their sense of belonging. The chosen field of perspective in this study is Organizational Communication (OC), looking at the interaction between parts of an organization (UW’s EOP and students) and the resulting behavior as seen through student actions. Some OC concepts used in exploring students’ responses to EOP affiliation include performance, social support, motivation, sense-making, diversity, and identity. Pre-existing data of two EOP-affiliated student-groups (~165 in EOP-1 and ~165 in EOP-3) include longitudinal grade point average, retention, major acceptance, and campus resource engagement metrics over the 2015-2016 school year. The data was statistically analyzed and compared across the two EOP-affiliated student groups, where EOP-3 consists of conditionally admitted Scholars Academy students and EOP-1 consists of non-conditionally admitted students. It is hoped these findings will assist in informing improved diversification policies, program changes, and future research on URM support programs within similar public selective universities.

My research has worked to develop an automated system that utilizes techniques that will modernize pathology and reduce diagnosis times from days to hours. The current method of diagnosing cancer (histopathology) requires a tissue biopsy that is fixed with formalin for 6-72 hours, dehydrated and embedded with wax, then manually sectioned, mounted on slides, and stained for imaging. This manual process is extremely time and labor-intensive and is the reason diagnoses can take up to ten days. The preferred, and least invasive, way to obtain tissue from a patient is the core needle biopsy (CNB), which is taken by inserting a needle into a region where cancer is suspected to exist, and removing a cylindrical section of tissue. Although CNBs are rapidly becoming the standard-of-care, their small diameters make it difficult to prepare and section the tissue for use in conventional histopathology. My research project over the past year has been to develop CoreView, a device designed to handle CNBs, automatically staining and imaging their entire surface for more complete images used to diagnose cancer. We use deep ultraviolet light to image the outer 2-3 cell layers of fluorescently stained tissue in a lab-built microscope to produce sharp images that can be equivalent to standard histology images from thin sections. I used LabVIEW to develop the rotational and imaging control to image the tissue at different focal points so the biopsy surface stays in focus during rotation. Along with designing necessary components of our system, I have worked on improving processing techniques for staining fixed porcine liver to produce clearer images with high contrast between the nuclei and the cytoplasm/cell boundaries. Our collaborating pathologist has confirmed that these images are at diagnostic quality, proving that CoreView and my improved techniques for processing tissue have the opportunity to revolutionize current histopathology.

Neural networks are machine learning instruments capable of solving a vast array of problems ranging from image classification to decision making. Developers of neural networks algorithms have many consequential decisions they must make in order to adapt a model to a particular task. Recurrent neural networks (RNNs) are an important instance among these algorithms — they are popular and powerful due to their ability to integrate information over time. A structured understanding of how RNNs are affected by the decisions made during model adaptation will improve RNN performance. Unlike conventional feed-forward neural networks, RNNs are allowed to evolve over time. The study of time-dependent systems is known mathematically as dynamical systems analysis. Hence, we can build upon existing machine learning literature by incorporating a dynamical systems perspective to describe an RNNs regime. Through this lens we investigate how an RNN which operates in different dynamical regimes (chaotic or stable) displays optimal temporal integration abilities. We establish a relationship between a mathematical metric for the dynamical regime and the qualitative solution for the network. Our preliminary results further suggest improved performance when the RNN is encouraged to operate in a chaotic dynamical regime.

We identified an optically varying light source in the night sky labeled PTFS1623al. In our search for interesting stars, this object caught our attention when we found that it was within the X-ray emitting region 1RXS J235728.5+671600. The light that came from the object varied by 2.5 magnitudes over a 96 minute period. An average light source only varies by a tenth of a magnitude over a week, month, or even a year time scale. The large change in magnitude over such a short period sparked our investigation. We confirmed this 2.5 magnitude variability with the Neil Gehrels Swift space based gamma ray observatory using the X-Ray Telescope as well as confirm a correlation between the optically varying source and the X-ray emitting source. Using the Keck telescope on Mauna Kea and the Low Resolution Imaging Spectrometer or LRIS we collected spectroscopic data. Spectroscopic data is a different way of viewing light where the individual molecules in the object radiate light at different wavelength allowing us to identify the specific elements in an object. Geometry of the object can also be identified by the shape of the spectral lines. We identified strong double-peaked Hydrogen and Helium emission lines with phase-dependent morphology. After reading through scientific literature and making comparisons, we concluded that the features present in the spectroscopic data are consistent with a magnetic cataclysmic variable, or a magnetic accreting white dwarf star. Accretion is the process of moving mass from one star to another, so this system is a binary system with an unknown donating star. A white dwarf and cataclysmic variable are two exotic classifications of a star with unique spectral characteristics. We present our observations and discuss their implications for our understanding of the system parameters.

X-ray binaries consist of a star gravitationally bound to a compact object (white dwarf, neutron star, or stellar mass black hole). Matter from the star is pulled onto the compact object and accretes in a disk which emits high-energy X-rays. These objects have variability observable on human time-scales—days and weeks rather than millions of years—and provide insight into high-energy physics. In this project we analyzed the light curves of time-variable objects to identify candidate binary systems. We cross matched data from optical variability surveys such as ASAS-SN, ATLAS and ZTF with the ROSAT all-sky X-ray survey. We were able to confirm known cataclysmic variables (CVs) and active galactic nuclei, and also discovered new CVs. These methods will be useful in identifying these rare objects in LSST’s massive data set in a few years.

2D cell models have traditionally been used in labs to test the effects of new drugs on certain cell types due to the ease and convenience of use. While 2D methods are great, they often simplify the cell-to-cell interactions and may not accurately represent cell systems in humans. 3D methods show the complex cell communication systems and better simulate actual organ systems. Research comparing these two methods can inform scientists on the benefits of 3D models which can help efficiency in creating new drugs. Our lab looked into various 3D models to determine their effectiveness and reliability and looked into the differences in perceived cell mechanics and functionality between 2D and 3D methods. We tried Corning Matrigel and Corning 3D Spheroid microplates for 3D cell modeling using HEK293 cells, which are human embryonic kidney cells that were grown in lab. They are known for being easy to grow and transfect. We used SNAP-Gels, which are protein assays that show the protein levels in the cells, to ensure that the protein levels were similar between the 2D and 3D systems. We then did florescent imaging to determine cell localization and EPIC dynamic mass redistribution (DMR) to determine cell functionality. We found Matrigel to have inconsistent results, so we focused on using the spheroid microplates. Based on our initial results, we saw increased functionality and expression levels for full-length protein cells compared to cells with a truncated N-terminal protein in the 3D method. This increase in functionality and expression levels was not seen in the 2D method. Our results show that 3D modeling methods can be reliable, and do show results that differ from 2D models. This is important for future studies that require cell modeling because 3D models can provide a more accurate and reliable modeling system to create novel therapeutics.

Neutron stars are extremely dense objects that are the remnant of exploded massive stars. The purpose of this project is to try to discover new neutron stars in orbit with normal stars. These new systems will improve our understanding of the processes of stellar evolution. To conduct the research, I cross-matched data from two different instruments, ROSAT and ZTF. ROSAT provides a comprehensive survey of the X-ray sky, while ZTF provides a real time stream of time varying optical sources. The combination of the two can identify neutron star binaries as they change in brightness. I continue to sift through the data on weekly basis to enhance the chance of finding new binary outbursts. By the end of this project, I expect to construct certain data filters that will result in the most outbursts. I expect to find a few objects that could potentially be what we are searching for.

G protein-coupled receptors (GPCRs) contain seven transmembrane domains and are the largest family of cell surface receptors, making up ~1% of the human genome. GPCRs can interact with a variety of ligands, such as odors, pheromones, hormones, and neurotransmitters. At least 30 human GPCRs contain a C-terminal Type-I PDZ ligand that allows for interactions with adapter proteins which can regulate receptor trafficking, stability, and signaling. The Hague Lab has previously found that the α1D-adrenergic receptor, which contains a C-terminal Type-I PDZ ligand, also undergoes an endogenous N-terminal cleavage event, which enhances receptor function and may play a role in which PDZ domain containing proteins interact with this receptor. We propose that this unique observation of the α1D-adrenergic receptor may be prototypical of a new class of GPCRs which contain a Type-I PDZ ligand and undergo an N-terminal cleavage. CysLT2, MAS1, and NPFFR2 are understudied GPCRs and potential members of this family with distinct PDZ ligands, though it remains unknown if their extracellular N-terminal domains regulates receptor function. Thus, I have cloned wildtype and N-terminal truncation mutants of these three GPCRs into the pSNAP vector to create fusion proteins with N-terminal SNAP tags. These constructs were transfected into HEK293 cells and subjected to near infrared PAGE analysis to elucidate the presence of N-terminal processing. Furthermore, dynamic mass redistribution revealed how the N-termini modulate receptor signaling. The combination of biochemical and pharmacological techniques allows me to determine if these receptors belong to this new subfamily of GPCRs. These results increase our understanding of how GPCRs are regulated within the cell, which can lead to the development of more efficient drugs.

G-protein coupled receptors (GPCRs) - characterized by seven transmembrane alpha helical domains - are the largest family of membrane proteins, constituting ~1% of the human genome. The α1D-adrenergic receptor (A1DAR) is a GPCR that regulates function of the cardiovascular, urinary, and central nervous systems. Dysfunction of this receptor can lead to various diseases including schizophrenia, benign prostate hypertrophy, hypertension, and PTSD. Prazosin, a non-specific α1-antagonist is the first line treatment for PTSD, however, chronic use has deleterious side effects including orthostatic hypotension and potentially fatal reflex tachycardia due to interactions with off-target related receptors. Thus, understanding how A1DARs are regulated will allow for the development of targeted therapeutics. To this end, the Hague Lab has previously discovered that A1DAR undergoes an endogenous cleavage of its extracellular N-terminal domain, affecting its membrane localization and response to agonist stimulation. Located within the N-terminal domain of A1DAR are two glycosylation sites at amino acids 65 and 82. Currently, how glycosylation of these sites regulates the cleavage event remains unknown. To characterize this phenomena, I used molecular cloning to mutate the glycosylation sites of A1DAR in the pSNAP vector for expression in Human Embryonic Kidney 293 (HEK293) cells. Near Infrared PAGE analysis revealed that glycosylation of both amino acids is required for cleavage and proper expression of A1DAR. Sucrose density gradient and dynamic mass redistribution further showed that glycosylation controls function and trafficking of A1DAR to the membrane. These results allow for the development of targeted medications specific to the N-terminal glycosylation sites of A1DAR, further reducing the potential side effects experienced by patients.

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition associated with deficits in social interaction and the presence of restricted patterns of behavior. ASD is clinically and phenotypically heterogeneous. The most recent update to the diagnostic definitions for mental disorders (DSM-5) provides additional flexibility for capturing the diverse array of phenotypes shown by diagnosed individuals. Despite categorized behavioral symptoms across core and comorbid dimensions of ASD, the neural mechanisms are unknown. Studies have shown atypical neuroanatomy and functional connectivity of the brains of individuals with ASD, suggesting a neural etiology. Here, we focus our attention on the superior temporal sulcus (STS), a region of the brain demonstrated to play a role in processing communication, social information, and theory of mind. Our research question evaluates whether neural activity in STS is affected by behavioral phenotype in children with ASD. We speculate that neural activity between individuals with ASD varies significantly more than typically developing (TD) children, who show more clustered, similar outcomes. Functional near infrared spectroscopy (fNIRS) distinguishes concentrations of oxygenated (HbO) and deoxygenated (HbR) hemoglobin in regions of cortical vasculature, signifying neurovascular coupling. This study uses HbO and HbR measured as subjects watch the events of a social scene on a monitor and analyzes ASD individuals’ deviance from average TD activity. Eye-tracking, clinical assessments, and parent questionnaires are considered to extrapolate possible correlations between ASD individuals’ variation in neural outcome and the behavioral phenotype expressed. We expect that individuals showing higher degree of neural variance from TD activity will show more severe autism behavioral phenotype. It is possible that in the search for neural mechanisms of ASD, considering behavioral factors signifying atypical variance could reveal significant differences. This exploratory analysis aims to examine the wide range of possible influential factors on neural heterogeneity within the social brain of individuals with ASD.

Cancer is increasingly a global health issue. Access to radiation therapy, the primary method of cancer treatment, is limited in low- and middle-income countries due to difficulty translating technologies in resource-limited settings. We are developing a new generation of cost effective IMRT (intensity modulated radiotherapy) devices for low- and middle-income countries. The current IMRT is performed using linear accelerators with multi-leaf collimators (MLC) which is very expensive and challenging to maintain in low- and middle-income countries. As a team, we are replacing the current technology with an alternative one using physical compensators which have lower commitments in terms of cost, overhead, and complexity. During my time working in the Imaging Lab, I have implemented all of the custom scripting protocols in a Python script (IronPython Interpreter) which is connected to the treatment planning system (RayStation - RaySearch Laboratories). Treatment planning systems are at the heart of radiation therapy systems and the key to improved patient outcomes. My script has enabled the creation of a compensator map and contour from the fluence data of the beamset. To test validity and correctness of the equations derived - I created a treatment plan based on the CT image for a head and neck cancer patient. The preliminary results of my script on this treatment plan indicate that compensators with ray lines divergent with the radiation source can be constructed for use in the treatment planning system. My contribution satisfies a key requirement of the project. A prototype of the compensator will be developed in commercial and partner sites in India, validating the script with a large number of patients.

The Wrangel Island State Nature Reserve (WISNR) serves as a vital refuge for the Alaska-Chukotka (AC) population of polar bears (Ursus maritimus) during the ice-free season. In September 2017, a total of 181 polar bears were observed near a bowhead whale (Balaena mysticetus) carcass on the island. This gathering is the largest aggregation of polar bears ever recorded for the AC population. This study sorted, labeled, and processed photographs of the polar bear aggregation taken by a professional photographer from a boat a day before initial ground-based observations were made. Our objective was to use the photographs to evaluate characteristics of the polar bear aggregation including animal sex, age, reproductive composition (e.g., adult females that have first-year or second-year cubs), and body condition (i.e., fatness). To do this, we selected representative subsets of photos, categorized them by time and location, and labeled individual bears across multiple photographs. The resulting set of processed photographs was evaluated by multiple polar bear experts, and the results were statistically analyzed. Based on knowledge of polar bear social systems and an initial review of the photographs, we hypothesized that both feeding activity and the locations of bears in the vicinity of the carcass will be structured by sex, age, reproductive status, and time of day. This study provides a unique opportunity to collect information on a large number of polar bears and document behavioral interactions. The resulting information will help address key conservation challenges for the AC polar bear population, including the effects of sea-ice loss due to climate warming, increased industrial activity, and identifying a sustainable rate for subsistence harvest.