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Acetylation, Phosphorylation’s Maligned Little Brother: Acetylation of Non-Muscle Myosin II in Drosophila Cells
No full texthttps://rdc.reed.edu/v1/resources/d35ee22a-ea7c-4f38-b79b-498816603350/thumb/128.jpgThe cytoskeleton is the web of proteins that form the outside shape of a cell, one protein heavily featured is non-muscle myosin II (NMII). NMII is one type of myosin, of which there are many. All myosins fall into the category of motor proteins, referred to as such because they are capable of generating mechanical force from chemical energy. Myosins are involved in a breadth of cellular functions and features, NMII specifically is critical for chromosome organization and splitting, the final splitting of daughter cells in cytokinesis, cell migration, cell adhesion, cell polarity, as well as involvement macro level disease processes including arthrogryposis, vascular disease, ALS, Alzheimer’s, cancer, and cancer metastasis. Given this wide a range of involvements, understanding how NMII works is critical to understanding how it can stop working and cause problems. Proteins can be modified in many ways, this thesis focuses on post translational modifications (PTMs), specifically acetylation. Acetylation of a protein involves adding an acetyl group to ε-amino group of the side chain of lysine. When S2R+ cells are treated with deacetylation mimicking gene transfections, I find that myosin networks become disorganized and dysfunctional, and acetylation mimics prompt more organized myosin. In assessing the relationship between phosphorylation and acetylation I find that deacetylation mimics yield higher phosphorylation, leading me to believe that the two PTMs may be mutually exclusive. Treatment with TSA yielding a hyper acetylated state created unusually large filopodia and halted actin retrograde flow, hinting at other significant roles of acetylation in the cell
An Efficient Privacy-Preserving Satellites Collision Detection Method: Applying Private Set Intersection Using Garbled Circuit
No full texthttps://rdc.reed.edu/v1/resources/2661017d-3d9e-482b-8346-3dbfd9bcdfe0/thumb/128.jpgSatellite operators have high incentives to protect their satellites from collision due to the high cost of designing, building, launching and maintaining the satellites. Unfortunately, the fact that satellite owners often view the satellite trajectories as private posts a serious barrier to coordination between different operators for more accurate collision detection and prevention. This privacy concern becomes more apparent for satellites used for military purposes given that satellites location could reveal countries’ military operations, intelligence-gathering methods, interests in specific regions of the Earth, or technology capabilities. A 2014 report from the RAND Corporation proposed a method that enables satellite operators to calculate collision probabilities (conjunction analysis) without sharing private information about the trajectories of their satellites using cryptographic tools for the first time. Two years later, a paper optimized the implementation proposed in the RAND paper. However, even with the optimization, this method is still too slow to feasibly run it on all of the objects to detect possible collisions and thus is impractical if the operator owns multiple satellites. In my thesis, we propose and implement a new method that is able to detect the satellites at risk of collision without revealing the location information using “fuzzy” private set intersection (PSI) and PSI with significantly reduced running time. The running time of our method is dramatically quicker and making our method much more scalable. Thus, it is able to run on every pair of first 751 satellites extracted from the most recent satellites tle data provided by Space-Track with 5.5 × 107 AND gates, where the sate of art of conjuction analysis would take 5.7 × 1010 MULT gates. And each MULT gate requires different number of AND gates depending on the number of bits and implementations. However, the speed comes with the expense of accuracy. With difference choice of parameters, there are different levels of false positives and false negatives rates. When the collision distance is 500km, there can be around 20% false negatives rates
Nebulous Truths: Climate, Science, and Empire in Late Nineteenth Century England
No full texthttps://rdc.reed.edu/v1/resources/57b36ced-4fbd-4c2c-a818-1b4092a8e911/thumb/128.jpgThis thesis investigates the relationship between climate, climate science, and the British empire during the period 1875-1900 using archival publications from the journals of the British Royal Geographical Society. Taking the framework that knowledge and power are reflexively enmeshed, and, following this, that the objects and infrastructures of knowledge can be co-constitutive, I argue that climate naturalized and patterned British colonial authority, while, correspondingly, the networks of empire produced and entrenched the naturalizing power of climate
One Letter at a Time: Emily Dickinson and the Technologies of Voice
No full texthttps://rdc.reed.edu/v1/resources/5a85f530-b676-477d-a8dc-0e7c85a674e6/thumb/128.jpgThe poet Emily Dickinson was witness to the transformative trajectory of industrialization in later-nineteenth-century America, access to print periodicals and consistent correspondence with close friends and family bringing the news of the world to her, at home. This thesis thus reveals Dickinson as an individual actively engaged with contemporary technological advances whose writing offers a canny reflection on the shifting social dynamics around labor and gender within a rapidly industrializing country. The first chapter examines in detail a small selection of her poems, tracing the history of technology and industry as it appears in her work. Chapter two looks at the impressive scope of her correspondences, with a focus on the epistolary relationships with Susan Dickinson, Frances and Lavinia Norcross, and Thomas Wentworth Higginson. The third chapter analyzes how themes of gender, manuscript, and music are deployed in the 2019 television show Dickison to represent a version of the poet that is familiar to modern viewers and yet true to the rebellious and untamed spirit of Emily Dickinson
Deep Learning for Spiral Galaxy NGC 1365 Embedded Star Clusters Detection Based on PHANGS–HST
No full texthttps://rdc.reed.edu/v1/resources/786a9b14-da91-43f4-9761-c7c06cfc36fe/thumb/128.jpgThis research is an investigation of the deep learning methods used to detect embedded star clusters in Galaxy NGC 1365 with only Hubble Space Telescope (HST) data. This research was motivated by the recent James Webb Space Telescop (JWST) infrared observations showing that 15 out of 30 massive young embedded super star clusters in New General Catalogue (NGC) 1365 remain undetectable or missing in the optical HST bands, highlighting the limitations of optical detection methods. We developed and compared two distinct deep learning approaches: a photometry- based method using aperture sums and an image-based method utilizing 11×11 pixel matrices. From experimentation with various neural network architectures, we discovered that image-based methods largely outperformed the photometry-based method, achieving up to 84.26% accuracy in detecting embedded clusters while maintaining 99.92% accuracy for non-embedded sources
"When Philoi clash with Philoi in Strife": Familicide in Greek Tragedy and Fragility of the Family in Athens
No full texthttps://rdc.reed.edu/v1/resources/5c9567ff-15e8-4c48-91a4-f9ca665148b5/thumb/128.jpgThis thesis will seek to show the use of familicide in Greek Tragedy as an expression of civic discussion of the role of women in political and personal spaces as the playwrights consider the intrinsic nature of men and women and the issues of traditional and emergent philia relationships. It will do so by analyzing spoken lines, stagecraft, and symbolic object use on stage, considering tragedy as a medium for storytelling, showcasing Athenian culture, and engaging in contemporary civic discourse. The introduction provides background and insights on civic Athenian culture, tragic stagecraft, and the perceived nature of women and their role within the Athenian polis. Chapter 1 discusses Aiskhylos' Agamemnon, working through the play's characterization of Klytaimnestra and the effects of her nature and actions upon her family. It analyzes multiple scenes of stagecraft, focusing on the symbolism and visual impact of the tapestry scene, which shows the perversion of hierarchical family and the corruption of marriage. Chapter 2 covers Euripides' Medeia and its emphasis on the detriment of women's interaction with the male political sphere and the takeaway that their involvement in male affairs and in marriage lead to the downfall of the state and their family. Chapter 3 focuses on Sophokles' Trakhiniai and the characterization of Deianeira in opposition to that of Medeia and Klytaimnestra and Sophokles' emphasis on the importance of children's alignment with their father over their mother and his apparent assertion that despite the intention or good nature of a woman, she will bring about the downfall of her family and state
A Computational Approach to Renal Cell Carcinoma: Single-Cell Analysis of Organoids in Drug Treatment Response
No full texthttps://rdc.reed.edu/v1/resources/ad35082c-d236-416f-90c6-cf014b9a80a2/thumb/128.jpgRenal cell carcinoma (RCC), a highly heterogeneous and treatment-resistant malignancy, poses significant challenges to current therapeutic strategies. In this study, we integrate single-cell RNA sequencing (scRNA-seq) with patient-derived organoid models to investigate the molecular responses of RCC to two therapeutic agents: RSL3, a ferroptosis inducer, and Cabozantinib (Cabo), a dual inhibitor of MET and VEGFR2. Our objective was to systematically characterize the cellular heterogeneity and drug-specific molecular alterations while addressing technical batch effects and intrinsic biological variability across five organoid replicates. The methodology involved scRNA-seq data preprocessing using Seurat to filter low-quality cells, normalize gene expression, and apply dimensionality reduction via principal component analysis (PCA). Batch effects were corrected using Harmony, followed by Leiden clustering to identify cellular populations across treatments. To validate clustering consistency and resolve potential biases, we employed alternative clustering approaches, including Clustermap and Jointly clustering, each capturing distinct aspects of the data. Differential gene expression (DGE) analysis and pathway enrichment were performed on drug-specific clusters to elucidate molecular mechanisms. The results reveal significant inter-organoid variability, highlighting the unique cellular compositions of each organoid. Harmony-corrected clusters demonstrated consistency across batches; however, their lack of alignment with RCC marker gene expression suggested limitations in capturing biologically meaningful cell types. Jointly clustering identified treatment-specific clusters, with RSL-responsive clusters exhibiting both favorable and unfavorable RCC-associated gene expression changes. Pathway enrichment analysis of these clusters revealed key roles for ferroptosis regulation, mitochondrial function, and redox homeostasis. Notably, RSL treatment induced paradoxical upregulation of both anti- and pro-ferroptotic pathways, reflecting the complex interplay of ferroptotic mechanisms in RCC. The discussion underscores the challenges of integrating computational tools to resolve biological heterogeneity while minimizing technical artifacts. Harmony effectively corrected batch effects but may obscure biologically significant variability, whereas Jointly clustering preserved unique drug responses but introduced complexity in cross-condition comparisons. The identification of RSL-specific clusters enriched in ferroptosis-related pathways underscores the therapeutic potential of ferroptosis induction in RCC. However, the heterogeneity of gene expression responses highlights the adaptability of RCC cells and the need for further experimental validation to disentangle these molecular dynamics. This thesis exemplifies a robust computational framework for leveraging scRNA-seq and patient-derived organoids in translational oncology. The integration of multi-dimensional clustering methods, differential expression analysis, and pathway enrichment provides insights into RCC drug responses and establishes a foundation for future investigations into therapeutic resistance mechanisms. Our findings advance the understanding of ferroptosis as a promising strategy in RCC treatment and highlight the critical role of interdisciplinary approaches in cancer research
Hands-On Experience: A Pedagogical RISC-V Simulator
No full texthttps://rdc.reed.edu/v1/resources/853ff130-fdf8-49f3-ad26-f8438e7134d9/thumb/128.jpgComputer Systems is a critical field of computer science, but it can also have a rather harsh introduction for undergraduate students. Many of them go into introductory Computer Systems courses with little to no experience in lower-level programming languages, nevermind any assembly; and while one can learn well enough how a computer microprocessor functions over the first few weeks, it may take quite some time for them to grow familiar with the topic. This is especially true for trying to learn how information flows through a chip to make the execution of computer programs possible. In order to help such students gain a more intuitive understanding of CPUs as they are taught in introductory Computer Systems courses, I have developed a CPU simulator made explicitly for educational purposes. The simulator focuses on simplicity, ease-of-use, and transparency. Simple CPU simulators, such as SPIM MIPS, are already in use throughout college classrooms for this sort of purpose, but they are focused solely on displaying the results of a program, and keep the simulated CPU's state opaque. Therefore, the primary goal of my simulator is not to obtain the results of running assembly programs, but rather to cleanly display its own internal state while doing so and be easy to interact with. It gives potential users the opportunity to not only write and run their own low-level assembly code programs, but to then also watch them in action; or, if a user is interested in a particular feature of CPUs, they can see how that feature is used in a variety of different scenarios. The simulator is not meant to teach how a CPU works on its own, but rather to function as an interactive tool that can supplement existing instruction
Verifying Arithmetic Incompleteness
No full texthttps://rdc.reed.edu/v1/resources/9d3e7456-a33a-4251-9a0a-40baba817ed0/thumb/128.jpgThis paper extracts an equivalent to representability, consistency, and completeness for recursive functions from O'Conner's verification of Arithmetic incompleteness through Coq. We find that consistent arithmetic systems require that provability is total recursive; the provability function in Robinson Arithmetic is recursively enumerable; the self-representable systems are a language of theorems decided by primitive recursive functions. A secondary goal is to give the philosophical, rather than mechanical, background for proof verification from the foundations of type theory to this landmark proof. We will introduce formal systems, give the proof of both of G\"odel's incompleteness theorems, then discuss Martin L\"of's dependent type theory and prove L\"ob's theorem using MLTT with the rules of provability logic. Finally we will create an arithmetic system type in Coq and prove its incompleteness
Kratom's Kinetic Conundrum: An Exploration of Kratom Alkaloidal Competition in Human Liver Metabolism
No full texthttps://rdc.reed.edu/v1/resources/ca80a29e-f711-4a3e-ae84-459be3ca9637/thumb/128.jpgKratom is made from leaves of Mitragyna Speciosa, a Southeast Asian tree whose leaves have been used for centuries as pain-relievers and relaxants. In recent years, kratom has risen in popularity in the United States for its use in self-treatment of pain as well as in self-medication for opioid withdrawal symptoms. Small molecules, or alkaloids, in kratom have been shown to be agonists to μ-opioid receptors in the brain, binding to the same receptors as many addictive opioids with supposedly less of a risk of addiction and overdose death. The mechanisms of these miraculous characteristics are poorly understood. Research has thus far focused on the conversion of the most prevalent alkaloid, mitragynine, to the more biologically potent 7-hydroxymitragynine. While the kinetics of pure mitragynine to 7-hydroxymitragynine conversion has been characterized, the kinetics of mitragynine to 7-hydroxymitragynine conversion in the presence of the over forty-five different alkaloids present in kratom has not. This thesis finds that, while the kinetics of pure mitragynine to 7-hydroxymitragynine follow a Michaelis-Menten pattern of enzyme kinetics, the kinetics of mitragynine conversion in the presence of other alkaloids follows an atypical, heterotropic model of enzyme kinetics. These findings have the potential to influence pharmacokinetic estimations of kratom’s clearance from the body as well as kratom’s possible interactions with other drugs