The invasion of Indo-Pacific lionfish (Pterois volitans) throughout the western Atlantic, the Gulf of Mexico, and the Caribbean has led to declines in the biodiversity, biomass, and abundance of native coral reef fishes. These ecological consequences have been thoroughly documented in shallow zones of the reef; however, little is currently known about how lionfish interact with deep-reef ecosystems, and which native fish are the most vulnerable to predation. Deep-reefs may serve as refuges for lionfish, as they would avoid being speared by SCUBA divers in the top 30 meters. Thus, deep lionfish populations could potentially serve as a near-infinite source of replenishment for shallow populations. The microchemistry of calcium carbonate fish otoliths has emerged as a powerful tool in examining fish ecology, including their vertical movement. The elemental compositions of these “ear stones” reflect the chemistry of the water in the fish’s environment, ultimately providing insight into natal origin and dispersal events. I am analyzing the oxygen isotopic signatures in a sample of 10 lionfish otoliths collected across the entire depth range of reefs in Curaçao using micromilling and isotope ratio mass spectrometry (IRMS). Specifically, variations in δ18O from the core to the rim of the otolith indicate changes in water temperature, and presumably depth, from settlement to adulthood. This approach provides insight into whether lionfish migrate between deep and shallow reefs throughout their lives or remain in their deep refuge, how frequent and long these migrations are, and ultimately whether they are susceptible to surface removal by spearfishing. Effective management plans will require a holistic understanding of this invasive predator’s vertical migration patterns and where they are on the reef at various life history stages, and a deepened understanding of the connectivity between deep and shallow populations can inform future research to control mesophotic populations.

Plants utilize cell surface protein receptors to recognize insect herbivory through the detection of Herbivore Associated Molecular Patterns (HAMPs) Following the detection of HAMPs, plants initiate specific immune responses, often measured by the increased production of the hormone ethylene gas and by Reactive Oxygen Species (ROS). The Inceptin Receptor (INR), which is specific to legume plants, recognizes the HAMP Inceptin11 (In11). The binding of In11 to INR initiates a signaling cascade, leading to an immune response. However, the signaling mechanism activated by INR is unknown. The Receptor-Like Cytoplasmic Kinase (RLCK) gene Herbivore Induced Kinase 1 (HIK1) is upregulated by In11 treatment in the bean species Phaseolus vulgaris. The goal of this research is to determine if HIK1 and other RLCKs are downstream proteins required for INR signaling. Because of the genetic intractability of P. vulgaris, I transform Arabidopsis thaliana with RLCK genes using Agrobacterium tumefaciens infiltration. Isolated genetic lines are then used to analyze the effect each RLCK has on immune signaling. Transgenic plants are treated with bacterial associated molecular patterns to trigger an immune response, then tissue samples of the leaves are measured for ROS and ethylene gas production. Results are then compared with ROS and ethylene gas production of wildtype plants. If the studied RLCKs are involved in downstream INR signaling, the transgenic plants will have increased ROS and ethylene gas production. I anticipate HIK1 to have the strongest increase in ROS and ethylene gas production due to the upregulation of HIK1 after In11 treatment in P. vulgaris. Understanding the INR signaling pathway is vital for engineering of plants that are resistant to insect herbivory without the use of pesticides.

The last few decades have marked an ongoing struggle between the highland Indigenous groups of Northern Thailand and the Thai government over the settlement and use of lands located inside of protected national parks. According to the Thai government, these native groups, including the Karen people, use practices that are harmful to the local environment and amplify climate change's effects. However, many others, including academics and Karen activists, argue that Indigenous knowledge and practices are in fact more beneficial to the environment than simply leaving nature alone. This paper examines the validity of these assertions by exploring how the Karen group interacts with the environment through their culture and what effect this has on environmental factors such as climate change and biodiversity. Findings from literary research, artifact observation at the Burke Museum, and interviews with various experts with experience involving these land rights issues suggest that Karen people’s culture is in fact what informs their respect for their local environment and the reason why their environmental practices, such as rotational agriculture, usage of natural materials for clothes and tools, and their general treatment of the natural world are mutually beneficial to both Karen people and the environment. My research also suggests that there is immense value in protecting Karen culture both within their communities and from the threats of the Thai government and its dominant culture. By better understanding and appreciating this knowledge that Karen and Indigenous peoples as a whole have based on years of experience on their native land, we will be able to understand the importance of protecting Native peoples’ right to their lands for both the good of the environment and those living within it.

The Boomplaas cave is located in the Cango Valley in South Africa and has been the site of many recent archaeological inquiries. The cave contains archaeological deposits spanning the Middle to Late Stone Age. Cave environments, like Boomplaas Cave, are ideal for the preservation of sediment deposits and can tell us about past environments and changes in human occupation patterns over time. Archaeologists can use the magnetic susceptibility of sediments as an indicator of human occupation intensity and climatic changes. Activities such as burning increase the magnetic susceptibility of soil, and warmer climates will result in higher magnetic susceptibility of soil compared to colder climates. We used an Bartington MS2 meter to measure the magnetic susceptibility of 44 sediment samples collected from the cave to infer climatic changes and occupational patterns over time. Our results show clear periods of more intensive human occupation. With this information, we can provide a more comprehensive understanding of variation in the intensity of hominin occupation within this region of South Africa.

The measurement problem is the challenge of reconciling the probabilistic and deterministic aspects of Quantum Mechanics. In this study, our primary aim is to unravel the measurement problem by investigating the possibility that quantum collapse occurs according to the probabilities presented by Born's Rule due to a perturbation on the system, appearing during the measurement process. Our group employs a multifaceted approach, where we examine the interplay between time dynamics and classical limits, alongside the influence of time-(in)dependent perturbations. Computational simulations serve as our primary tool in this exploration. One part of our group worked with a 3-well system with a time-independent perturbation, another part looked at a 2-well system with a time-dependent perturbation, and the last part saw what a time-independent perturbation does to a 2D-well system. We anticipate that our investigations will uncover critical parameters that are expected to yield probabilities consistent with Born's Rule, a foundational principle of Quantum Mechancis. This research points towards a potential reconsideration of quantum collapse as a dynamical, affected by the perturbation introduced by measurement. While preliminary, these findings contribute to the ongoing discourse in Quantum Mechanics and may offer insights for future theoretical developments and applications.

Going into an academic career is a path frequently chosen by archaeology graduate students after their graduation. Job listing websites often serve as the first place for these students when seeking academic positions. It's crucial to understand the expectations of institutions, given the limited number of available positions and the abundance of candidates. This study examines tenure-track job advertisements over the past decade to gain insights into the academic job market for archaeologists. Using data from the community-edited Academic Jobs Wiki for Archaeology, we examine the evolution of the academic job market over time. We studied the text of 449 job ads posted from 2013-2023. Our analysis focuses on shifts in archaeological topics and methods requested in job ads. We investigate whether the burden on applicants has changed over time: do institutions request more information and documents from applicants at the initial stages of application, compared to a decade ago? We also examine whether there is an increasing trend in job advertisements highlighting diversity and inclusivity, thereby encouraging a broader range of applicants. Additionally, we assess the influence of socio-political factors on the changing focus of research topics in the field.
Our data analysis indicates an uptrend in the complexity of application requirements and a more pronounced emphasis on diversity and inclusivity in job advertisements. This research aims to assist current and future archaeology students and graduates in better understanding the job market and the requirements of employers, thereby aiding them in effectively preparing for their applications for positions in archaeology.
 

The effective treatment of individuals with HIV relies on maintaining therapeutic drug concentrations, necessitating accurate measurement of antiretroviral (ARV) drug levels. Current methods, such as liquid chromatography tandem mass spectrometry (LC-MS/MS), are limited by cost and accessibility. Our research addresses this gap by developing the INTEGRase activITY (INTEGRITY) assay for measuring integrase strand transfer inhibitors (INSTIs), a leading class of ARV drugs. This 2-step assay quantifies INSTIs using a DNA strand transfer reaction and quantitative polymerase chain reaction (qPCR). The presence of INSTI drugs disrupts the strand transfer reaction, inhibiting full-length target DNA formation, which is then measured through real-time qPCR. My work focused on optimizing the limit of detection of INTEGRITY by altering the strand transfer reaction conditions and protocol. Specifically, I conducted experiments altering INSTI drug concentrations and optimizing pre-incubation times of integrase with the drug to enhance the LOD. I observed that preliminary incubation of integrase and INSTI drugs for 5 minutes at 37 degrees Celsius improved the LOD of INTEGRITY by an order of magnitude. The simplicity of the INTEGRITY assay, utilizing standard laboratory equipment, holds immense promise for broadening access to routine clinic-based ARV drug level monitoring. This advancement has the potential to significantly enhance HIV care on a global scale by offering a cost-effective and accessible solution for monitoring therapeutic drug concentrations.

The stratigraphic integrity of stone artefacts found in Australia’s earliest archaeological site, Madjedbebe in northern Australia, has been questioned due to the potential impact of termites burrowing through the deposits. Studies have claimed that the 65,000-year date of early human settlement in Madjebebe is invalid due to biodisturbance - in particular, termite disruption, which causes vertical and horizontal displacement of artefacts. Here we analyse the chemical composition of the archaeological sediments and termite mound sediments to investigate the claim that bioturbation processes have impacted the dating of the Madjebebe site. We used a micro-X-Ray Flouresence instrument to analyse the elemental composition of micromorphology samples from the Madjedbebe. Our prediction is that there are distinctive, non-overlapping chemical fingerprints for termite sediments and the archaeological sediments, suggesting minimal termite activity in the archaeologial deposits. The results will provide new information on the validity of the stratigraphic integrity of deposits in Madjebebe, clarifying its significance for debates about the movement of modern humans out of Africa.

Cannabidiol (CBD), a non-psychoactive cannabinoid compound found in cannabis, has been reported to attenuate morphine tolerance and can potentially be used as an alternative to opioids in treating chronic pain. Previous work has established connections between morphine tolerance and Reactive Oxygen Species (ROS) production through JNK-mediated Peroxiredoxin 6 (PRDX6) activation. Excess ROS production promotes desensitization of opioid receptors, which in turn leads to opioid tolerance. CBD administration is associated with decreasing pain-related Reactive Oxygen Species (ROS) production, and it was hypothesized that CBD directly interacts with JNK, blocking JNK’s activities. This project aims to investigate the connections between CBD administration and ROS production to determine CBD’s effects on JNK-mediated ROS production. To quantify ROS production through fluorescence imaging, I will transfect wild-type HEK 293 cells with oROS, a genetically encoded sensor, which fluoresces proportionally to ROS production. Coverslips of HEK 293 cells expressing oROS are treated with buffer (control) and CBD before administration of Tumor Necrosis Factor alpha (TNFα), a known activator for JNK released during pain states. After imaging with oROS, I will quantify ROS production and compare this between groups with and without CBD pretreatment to determine CBD’s activity on inhibiting JNK-mediated pro-inflammatory pathways. I predict that relative to the control, cells treated with CBD will have significantly less ROS production. If the results are consistent with this prediction, CBD could be a potentially promising co-treatment with opioids in managing chronic pain as it can potentially attenuate opioids' side effects like tolerance. 

Repeat thrombotic events have been associated with increased levels of Von Willebrand Factor (VWF) in patients prescribed dual antiplatelet therapies (DAPT), medications designed to prevent thrombosis. VWF is a protein that regulates platelet adhesion during hemostasis, allowing platelets to aggregate at sites of vascular injury. A microfluidic device containing a rigid block that simulates vascular injury and a flexible post to measure platelet contractile force through its displacement will be used to form shear-induced thrombi. I will determine how VWF affects platelet activation by testing whole blood samples and samples doped with DAPT (0.3 mM ASA and 10 μΜ 2-MeSAMP), 50 μg/ML VWF, or both VWF and DAPT. Platelet activation is measured through the area of platelet-plug, intracellular calcium levels, and platelet-plug contractile force. Preliminary experiments have shown that high VWF levels produced the largest platelet plugs whereas adding DAPT led to opposite effects. My results present that adding both VWF and DAPT to whole blood leads to similar platelet activation and larger platelet plug size as whole blood doped solely with VWF. The data obtained from this research can provide new insights into the improvement of therapeutic agents that aim to target VWF’s interaction with platelets and ultimately prevent repeat thrombotic events.

The Tanginak Spring site on Sitkalidak Island, Alaska contains lithic technologies dating back to 7,500-6,000 cal BP. This is one of the earliest records of human activity in the Kodiak archipelago and contains key artifacts reflecting how the settlement developed and how people adjusted to the island environment. The prevalence of stone tool technology on Sitkalidak Island begins an operation examining how scrapers are used in the process of modifying wood and skins. I investigate how the prevalence and types of lithic scraper technology changed through time. Shifts in stone technologies related to bifacial projectile points and blades allude to shifts in technology and activities performed at the site. I use typological and technological analysis through visual inspection to examine the scrapers and their use wear, which reflects how long these artifacts were utilized and for what purpose. Additionally, I apply a stratigraphic analysis to investigate how scraper types change through the layers of the site. Analyzing the stratigraphical location of tools within this assemblage allows me to evaluate ideas about relatedness in the technological sequence through scraper morphology. This examination contributes to an ongoing investigation of changing scraping activities through time at the site. Continuing to explore the progression of scraping technology in the Kodiak archipelago can provide context to how people began to sustain their livelihoods on the island during a period of significant climatic cooling.

In the context of computer-aided design, researchers have studied how to reconstruct an input geometry in CAD by decomposing it into CAD primitives. Such reconstruction is useful for creating CAD designs for manufacturing applications. What we want to study is also object decomposition but towards a different goal: understanding object affordances and interactability. For example, a handle of a basket can be grasped or hung from a sticky hook, and we recognize this affordance or functionality because it has a certain shape (e.g. hook or rod). Prior research has identified eight types of shape primitives that are common in everyday objects, but the existing tagging process requires a high degree of modeling expertise. We aim to create a more automatic and easy-to-use tagging tool. Our proposed research is to develop user-in-the-loop methods for tagging shape primitives given an object geometry. This takes advantage of human intuition for how objects function and interact. We start with building an interface, where users sketch over the input mesh to indicate the region for fitting and select the type of primitive to be fit. On top of this, we plan to crop the selected mesh data to generate a reduced mesh that encompasses only the area selected by the user. Finally, we utilize differentiable rendering techniques to automatically optimize the shape parameters of user-selected primitives to fit our reduced mesh data. With this tagging tool, we can enable more people without modeling expertise to tag objects. Data generated with this tool can support future research that studies object affordances with learning, as well as improve applications in robotics, product design, and assembly design like FabHacks.

Community-based Archaeology can allow researchers to interact and cooperate with descendant populations to establish a more ethical and accessible discipline. This past summer, I traveled to Kodiak, Alaska to conduct archaeological fieldwork as part of the Old Harbor Archaeological History Project. This year, the project set out with an added goal; the facilitation of a cultural camp for local Indigenous youth. Serving as a counselor, I aimed to expose Indigenous youth to archaeology by showcasing an ancestral site of their heritage while working with adult community members to create an enriching, and fun, cultural learning environment. Community members of varying ages from Old Harbor, Alaska, joined me at the camp on Sitkalidak Island for this experience. This poster will share my experience in facilitating the cultural camp and discuss the importance of archaeologists' connections with community members. It will also spotlight the knowledge that the archaeological team and Indigenous youth took away from Alutiiq community presenters, including subsistence methodologies as well as Indigenous language, dance, and arts. Ultimately, this poster will demonstrate how community-based work can have wide-reaching, positive impacts on both descendant populations and the quality of archaeological research.

Mobile genes are commonly found in bacteria, and they are capable of being transferred between unrelated bacterial cells via a process termed horizontal gene transfer (HGT). Mobile genes that undergo HGT can evolve in various “host” bacteria and thereby evolve in several different genomic backgrounds. In a recent publication, my lab constructed a mathematical model to assess the effects of HGT (i.e “host-switching”) on mobile gene evolution. I have built upon this work by probing additional factors that may influence mobile gene evolution. In phase one of my project, I compared the original evolutionary model used in the publication to a newly expanded, more ecologically realistic model in which growth rates of the bacteria depend on resource availability. To compare the models, I ran simulations with both models on a set of bacterial-host pairs and compared the resulting evolutionary outcomes from both models. I found that the categorical effect of HGT occurring (i.e. HGT confers a higher, lower, or neutral change in host fitness) was the same across both models, indicating that ecological factors are less predictive of mobile gene evolutionary outcomes. For the second phase of my experiment, I assessed the effect of variable HGT rate on mobile gene evolutionary outcomes. I ran simulations using a set of bacterial host-pairs while varying the HGT rate along a biologically relevant range, and found a positive correlation between HGT rate and the magnitude of positive fitness effects conferred by a mobile gene that has undergone HGT. This indicates that HGT rates play an important role in governing the evolutionary outcomes of mobile genes. Using evolutionary simulations has allowed us to gain insight into the predictive factors governing mobile gene evolution and thereby mobile gene-containing bacterial evolution. This is especially important, as many genes conferring antibiotic resistance are mobile.

The human genome is associated with numerous variations, some of which can be pathogenic. Any variations larger than 50 base pairs (bp) are considered structural variants (SVs), and SVs impacting copy number of the genome are termed copy number variants (CNVs). By studying CNVs, we can understand the underlying mechanisms of damage and repair within DNA, which can help work towards prevention and cure in other fields, such as cancer genomics. My project investigates a CNV on chromosome 2 of a pediatric patient, who presents with tetralogy of Fallot, global development delay, and multiple other congenital anomalies. Using array comparative genomics hybridization (aCGH), we identified a 3.2 megabase (Mb) complex genomic rearrangement (CGR) spanning the 2q31 region of the proband’s chromosome 2. Detailed analysis of the short-read whole genome sequencing (WGS) allowed us to locate the exact coordinates of each junction, or the beginning and end points of each extra copy. PacBio long-read genome sequencing and optical genome mapping detected the same junctions and facilitated confirmation of the overall structure. The CGR can be characterized as a duplication-triplication-duplication-triplication-duplication (DUP-TRP-DUP-TRP-DUP), meaning this segment of the genome contains a segment of alternating 1 and 2 extra copies of this region. The CGR is de novo, or not inherited from the proband’s parents. Due to the nature of this variant, it is likely to be impacting the phenotype of our patient. To establish a genotype-phenotype correlation, I did a literature review of patients with overlapping CGRs, comparing their phenotypes to our proband, as well as reviewing any known disease-associated genes in the region using the online catalog of human genes and genetic disorders (OMIM). Patient and disease comparison revealed the extreme rarity of our patient’s CGR, leading us to believe the phenotype of the proband results from impact of multiple genes in the affected region.

On June 29, 2023, the United States Supreme Court ruled that using affirmative action in college admissions is unconstitutional in the case, Students for Fair Admissions, Inc. v. President and Fellows of Harvard College. This research analyzes arguments presented by both parties to reveal the effects of this policy removal on the future of underrepresented minority students applying to college. I analyze Harvard’s admission statistics through regression models cultivated by each party’s expert witness to identify the lack of true diversity in Harvard’s admission process. The statistical findings the experts present highlight the use of the Asian American experience to justify the removal of affirmative action measures in higher education. Additionally, I conduct a complex legal analysis of prior Supreme Court cases through the lens of reparation jurisprudence to expose the lucrative, and performative, system of affirmative action in higher education. The Court’s decision to remove affirmative action requires universities to develop a new form of admission criteria that aids underrepresented minority students in the college admission process. Statistical evidence provided by the Department of Education and economist, Richard D. Kahlenberg, points to a new form of affirmative action that considers varying intersectional factors to develop a complex method of class-based affirmative action. Such studies identify the benefits of looking at various demographic factors contributing to an applicant’s experience to cultivate a diverse class of students that goes deeper than race.

Local Group galaxies are the closest ones we can study in detail to decipher the processes that shape the universe around us. An interesting property of these galaxies is their star formation history (SFH), which provides a fossil record of when stars were formed in a galaxy. The process by which this occurs is a complex interplay between the gas, the interstellar medium (ISM), and the energy from newly formed stars. By pairing SFH measurements with data on the galaxy’s gas content, we can investigate the timescales on which young massive stars affect the structure of the surrounding gas in the (ISM) as well as its ability to form more stars. Furthermore, since star formation is closely linked to the properties of the gas in a galaxy, such as metallicity and extinction, the SFH also probes these properties. By utilizing resolved stellar photometry from the Hubble Space Telescope (HST), I measured the SFH for four Local Group galaxies (IC10, IC1613, WLM, and NGC 6822) that already have detailed imaging of their gas content from radio observations. First I measured the colors and brightnesses of resolved stars in each galaxy from the HST imaging. Next, I generated and processed a set of artificial stars using the same photometry pipeline as the real observations to provide statistical measures of our data quality. With the processed artificial stars and the original photometry, I then fitted a series of model Hess diagrams for a range of ages and metallicities to obtain each galaxy’s SFH. These measurements allow us to pair this SFH with other observational data. For example, we can map star formation and compare it with observations such as supernovae locations, and we can explore links between the star formation and the ISM as measured through emission from neutral and ionized hydrogen.

The expected launch of the Nancy Grace Roman Space Telescope (Roman), a next-generation space-based infrared observatory, will soon allow us to observe fields in minutes that would previously have taken months to cover. As such, it will advance our knowledge of galactic structure and evolution at a rapid rate. To better leverage the influx of science that will come out of the launch and commissioning of Roman, we are developing a pipeline that simulates observational images taken by Roman and then performs photometry on the images. As a first step, we are testing methods for recovering dwarf galaxies from photometry catalogs that contain both a dwarf and a surrounding stellar halo. In order to produce mock Roman observations, we use the Space Telescope Science Institute's Space Telescope Image Product Simulator (STScI-STIPS) software tools, which are able to add background galaxies, realistic background levels, and noise along with source catalogs to produce simulated images. Our early testing uses input catalogs designed to simulate typical dwarf galaxy characteristics added to stellar catalogs generated from numerical simulations that mimic the nearby spiral galaxy M81. The ultimate goal of this pipeline software is to determine the observational strategy to resolve structures in extended stellar halos of nearby galaxies. Such measurements would allow us to distinguish between formation and evolution scenarios for these halos. This work is part of the Roman Infrared Nearby Galaxies Survey (RINGS), a large Roman Wide-Field Science (WFS) program funded by NASA under grant 80NSSC24K0084.