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Processing Compressed Genetic Data Using Hybrid Parallelism and High Performance Computing
No full textvii, 22 p.FASTQ files are a common file structure used to store DNA sequence information and the quality scores for the associated DNA reads. These files are stored in a plain text format, so it is advantageous to compress these files to minimize the storage used. Dr. Sandino Vargas- Pérez performed previous research to develop a hybrid parallel algorithm called phyNGSC. This algorithm allows for fast compression and decompression of FASTQ files using distributed and shared memory programming models utilizing the MPI and OpenMP libraries. This research expands on this algorithm by introducing in compresso, an approach using hybrid parallelism with MPI and OpenMP that allows for the processing of genetic data without the need for total data decompression. This technique greatly reduces the storage needed to work with these genetic datasets and offers significant performance increases relative to comparable algorithms. This SIP showcases in compresso data processing for DNA sequence pattern finding and FASTQ to FASTA format conversion. The code for this implementation is available at [1]
Appreciating p-adics, the Fake Numbers
No full text66 p.What does the phrase “Fake Numbers” mean? For me, the origins are in the semantics of food. If you will bear with me for a moment, please consider the term real food and its implied opposite, fake food. Taken literally fake food would refer to a plastic apple. However, that is not the comparison that is being made when real food is brought up. It references healthy food, natural food, or perhaps the food that people have been eating for most of history. Therefore, we know that the implied fake food is the modern, in this case processed and industrialized food. However, we can note that the latter is still edible. It still has calories, and by most definitions would qualify as food. Let this then inform our understanding of “fake numbers”. Much of the early if not full mathematical journey of many of my peers has been to learn about the real numbers (R). I content the p-adic numbers are the implied, albeit often omitted, fake number counterpart to R. A more modern construction, one with quite the overlap and enticing features that fake food has, yet not necessarily a full substitute for the original and all of its properties. With some semantics and analogies over with, we can discuss the layout what this paper and what we wish to accomplish over its duration. On a personal level it has been the culmination of my undergraduate experience with mathematics. A chance for me to appreciate much of what I have learned, apply past concepts to new landscapes, finally get my head around some key ideas, left me with a clearer picture of how little I know, and has been a continued exploration my newly kindled love of seeing math1. Therefore, I have a goal for us to accomplish. We will enjoy looking into the interesting, weirdly shaped, sometimes counterintuitive, yet also very accessible world of the p-adics. Along the way we will make several comparisons with R. We should also not believe in the above analogy so much as to begin viewing the p-adics as unhealthy or as a full replacement for R. To accomplish this goal, we will start at the beginning, what are the p-adics
The Consequences of Nuclear Testing on a Nation: Lasting Impacts on Human Health and Identity in Semipalatinsk, Kazakhstan
No full text13 p.Entitled “The Consequences of Nuclear Testing on a Nation: Lasting Impacts on Human Health and Identity in Semipalatinsk, Kazakhstan,” this piece will examine the impacts of the Soviet Union’s nuclear program on Kazakhstanis living in or around Kazakhstan’s Semipalatinsk Test Site, now called Semey, wherein hundreds of nuclear explosions occurred in the name of scientific development from 1949 to 1989. This is the Science essay winner of the 2025 Voynovich Essay Competition
Synthesis and Characterization of Manganese (II) Complexes with (N)-Heterocyclic Carbene
No full textvi, 52 p.Transition metal chromophores with long-lived charge-separated excited states that can be accessed via visible light are popular within the field of inorganic chemistry and photophysics given their applications in settings where light is converted to chemical energy. Traditionally, these complexes are comprised of 2nd and 3rd row transition metals though their scarcity has necessitated that more abundant options be evaluated. Manganese is an exciting alternative given that it is the third-most earth abundant transition metal, is relatively nontoxic, and exhibits rich redox properties. Herein, we discuss the synthesis of two Mn(II) complexes with the (N)-heterocyclic carbene ligands 2,6-bis(3-isopropylimidazol-1-yl)pyridine and 2,6-bis(3- phenylimidazol)pyridine. Magnetic studies revealed that the phenyl-substituted complex is an uncommon example of an air-stable S = ½ Mn(II) complex. Spectroscopic characterization of this complex revealed panchromatic absorption with two bands in the visible region with extinction coefficients that are consistent with a charge-transfer transition. This is further supported by computational chemistry results. We also observed both bands to be emissive with one having a 1 ns lifetime in solution. These results are described herein, as well as their implications for the development of new photoactive manganese complexes
Empire of Filed Teeth
No full textDuration: 36 minutes; MP4 videoEleven original music compositions on MP4 video.
Track 1 ------- Lonely ------- 0:00:10
Track 2 ------- Matt Daddy ------- 0:03:56
Track 3 ------- I Love to Pretend ------- 0:06:54
Track 4 ------- Slowpoke ------- 0:10:46
Track 5 ------- Throw a Fit ------- 0:14:18
Track 6 ------- Wake Up ------- 0:18:10
Track 7 ------- The First Week in the Box ------- 0:20:47
Track 8 ------- Matt Daddy (Reprise) ------- 0:24:56
Track 9 ------- A Slide into Hell ------- 0:26:07
Track 10-------Take the Job ------- 0:29:58
Track 11 -------One Score Old ------- 0:33:0
Recollecting Doorways
No full textix, 45 p.All in all, I’ve found that this collection became about caretaking, about what it means to live in this world with the vulnerability of open eyes and arms, about what it means to find care in each other and in ourselves. It’s funny, I worried I wouldn’t find cohesion, and then discovered I was writing variations on the same themes even when I thought I had written about entirely different subjects. I think one truth reveals itself to me and I cling to it until I see it everywhere. But the interesting thing is in approaching it through differing forms, differing tones, the truth means different things, it takes on new facets of reality each time. Sometimes care is the glorious detail of the everyday which sings out and persists in the face of hardship, sometimes care is the millstone around my ankles, pulling my head underwater. I have often worried that I contradict myself, that I have built myself as an unreliable narrator simply by not knowing myself well enough, by changing my mind too frequently. On the other hand, I sometimes worry that I don’t change my mind often enough, that I am still harping on the same themes I have clung to since I was tapping out painfully sincere essays on my parents’ desktop computer. But I’m starting to realize that if I wrote without contradiction, I wouldn’t be writing the truth. I am constantly living in contradiction, so shouldn’t my writing reflect that? If I really am constantly finding the same epiphanies, isn’t it right to think about what that means? In fact, this collection is an experiment in contradiction and repetition, in the very things I have so often tried to avoid, an interrogation of that phenomenon. What does it mean if the truth shifts through time, through form? What does it mean if it remains the same? How do I live in a way that holds all of it at once
Connecting RNA Methylation and TDP43 Pathology in ALS/FTD
No full textvi, 39 p.Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are neurodegenerative diseases characterized by mislocalization and aggregation of transactive response DNA-binding protein 43 (TDP43), a pathology that disrupts RNA metabolism and neuronal health (Arai et al., 2006; Neumann et al., 2006). TDP43 autoregulates its own transcript (TARDBP) and relies on m6A RNA methylation to modulate RNA binding, splicing, and stability (McMillan et al., 2023; Dermentzaki et al., 2024). This study investigates the relationship between m6A modifications and TDP43 pathology, focusing on its role in ALS and FTD. We found that inhibiting the m6A writer enzyme METTL3 disrupted TDP43 autoregulation, resulting in elevated full-length and short TARDBP isoforms. Reduced m6A levels also altered TDP43 subcellular localization by reducing its cytoplasmic pool, in agreement with studies linking m6A to nuclear export and RNA dynamics (Wang et al., 2014). Conversely, inhibition of the m6A eraser ALKBH5 increased global m6A levels, leading to a shift in TDP43 localization toward the cytoplasm, a phenomenon previously associated with hypermethylation in ALS patient tissue (McMillan et al., 2023). These results reveal m6A as a dual regulator of TDP43 homeostasis, balancing nuclear regulatory functions while preventing pathological cytoplasmic accumulation. Dysregulation of m6A, whether through hypo- or hypermethylation, disrupts TDP43 function, contributing to ALS and FTD pathology. This work underscores the therapeutic potential of targeting m6A pathways to restore RNA stability and mitigate TDP43 dysfunction
A Reflection on Gynecological and Obstetric Primary Care Experience
No full textii, 21 p.This senior integrated project (SIP) is a reflection and analysis of the study of gynecology and obstetrics (OB/GYNs) through healthcare experience and focuses on the necessity of primary care in this field. Delving into several sections of this specific area of health, a better understanding of the impact of preventative care is found. Diseases, cancers, menstruation, birth control, infertility, pregnancy, and menopause are all addressed, as they all greatly affect the female reproductive system. Looking into potential areas of growth is also written, as well as including my own experiences to further acknowledge real-life situations. My experience in primary care has allowed me to learn and grow in passion for this specialty, as well as see the importance of primary care within it. Spreading awareness of the importance of gynecological care is an immeasurable action that must occur to educate and help women of all ages
Pigskin vs Bamboo Blade
No full text3 p.In my SIP called 「ピッグスキン対竹刀」or in English “Pigskin vs Bamboo Blade” I wanted to convey power, movement, American and Japanese culture, anime, and sports. Being a digital artist and football athlete, with a minor in Japanese, I wanted to create a dynamic piece that captures movement and a relationship between cultures in sports
Experiential Internship : Edison Neighborhood Association
No full text9 p.This summer, I had the privilege of interning at the Edison Neighborhood Association (ENA), a community-driven nonprofit organization located in the heart of Kalamazoo. As a student in Kalamazoo College's Business program, I was excited to gain hands-on experience and apply the concepts I had learned in the classroom to real-world situations. This internship was a significant step in my journey toward understanding how businesses, nonprofit organizations, and communities intersect. Over the course of the summer, I had the opportunity to engage with a wide range of community projects, including marketing efforts, event planning, environmental sustainability initiatives, and youth engagement programs. Reflecting on my time at the ENA, I recognize how profoundly this experience has shaped my understanding of the challenges and opportunities in community development, marketing, and nonprofit management