Digital Commons Network^™

Impact Of Renal Cell Carcinoma Molecular Subtypes On Immunotherapy And Targeted Therapy Outcomes, Renée Maria Saliby, Chris Labaki, Tejas R Jammihal, Wanling Xie, Maxine Sun, Valisha Shah, Eddy Saad, M Harry Kane, Soki Kashima, Katherine Sadak, Talal El Zarif, Deepak Poduval, Robert J Motzer, Thomas Powles, Brian I Rini, Laurence Albiges, Sumanta K Pal, Bradley A Mcgregor, Rana R Mckay, Sabina Signoretti, Eliezer M Van Allen, Sachet A Shukla, Toni K Choueiri, David A Braun

Faculty, Staff and Student Publications

Saliby et al. show that a machine learning approach can accurately classify clear cell renal cell carcinoma (RCC) into distinct molecular subtypes using transcriptomic data. When applied to tumors biospecimens from the JAVELIN Renal 101 (JR101) trial, a benefit is observed with immune checkpoint inhibitor (ICI)-based therapy across all molecular subtypes.

Inflammaging In The Alzheimer’S Brain And Beyond: Insights From A Transgenic Mouse Model On The Sex-Specific Pathophysiology Of Alzheimer’S Disease, Alicia Jeanne Barber

Dartmouth College Ph.D Dissertations

Aging and sex are major risk factors for developing late-onset Alzheimer’s disease. Compared to men, women experience worse neuropathological burden and cognitive decline despite living longer with the disease. Similarly, male 3xTg-AD mice, developed to model Alzheimer’s disease, no longer consistently exhibit standard Alzheimer’s neuropathology yet experience higher rates of mortality - providing a unique opportunity to further elucidate this dichotomy. We hypothesized that sex differences in the biological aging process yield distinct pathological and molecular Alzheimer’s disease signatures in males and females, which could be harnessed for therapeutic and biomarker development.

We aged male and female, 3xTg-AD and B6129 …

Building A Data Pipeline And Machine Learning Model For Insurance Data, Connor Weyers

Honors Program: Senior Projects (Public)

Insurance telematics is an emerging and exciting field. It combines the advancements in GPS tracking, computational analytics, data processing, and machine learning into a useful tool to help insurance companies make the best product for their consumers. This is why National Indemnity looked to implement a telematics portion to their business processes of underwriting insurance policies and sponsored a School of Computing Senior Design project. In this report, we will first review existing solutions that been used to solve problems and subproblems similar to that we are given in this project. We then propose designs for the data pipeline and …

Landscape Influences On Thermal Sensitivity And Predicted Spatial Variability Among Brook Trout Streams In The Southeastern Usa, George P. Valentine, Xinyi Lu, C. Andrew Dolloff, Craig N. Roghair, Jacob M. Rash, Mevin B. Hooten, Yoichiro Kanno

Mathematics and Statistics Faculty Publications

Warming water temperatures as a result of climate change pose a major threat to coldwater organisms. However, the rate of warming is not spatially uniform due to surface-ground-water interactions and stream and watershed characteristics. Coldwater habitats that are most resistant to warming serve as thermal refugia and identifying their locations is critical to regional aquatic conservation planning. We quantified the thermal sensitivity of 203 streams providing current and potential habitat for brook trout (Salvelinus fontinalis) across nearly 1000 linear km of their native range in the southern and central Appalachian Mountains region, USA, and characterized their spatial variability …

The Crosstalk Between Macrophages And Cancer Cells Potentiates Pancreatic Cancer Cachexia, Mingyang Liu, Yu Ren, Zhijun Zhou, Jingxuan Yang, Xiuhui Shi, Yang Cai, Alex X Arreola, Wenyi Luo, Kar-Ming Fung, Chao Xu, Ryan D Nipp, Michael S Bronze, Lei Zheng, Yi-Ping Li, Courtney W Houchen, Yuqing Zhang, Min Li

Faculty, Staff and Student Publications

With limited treatment options, cachexia remains a major challenge for patients with cancer. Characterizing the interplay between tumor cells and the immune microenvironment may help identify potential therapeutic targets for cancer cachexia. Herein, we investigate the critical role of macrophages in potentiating pancreatic cancer induced muscle wasting via promoting TWEAK (TNF-like weak inducer of apoptosis) secretion from the tumor. Specifically, depletion of macrophages reverses muscle degradation induced by tumor cells. Macrophages induce non-autonomous secretion of TWEAK through CCL5/TRAF6/NF-κB pathway. TWEAK promotes muscle atrophy by activating MuRF1 initiated muscle remodeling. Notably, tumor cells recruit and reprogram macrophages via the CCL2/CCR2 axis …

Data-Driven Insights Into Spatial Patterns And Disease Etiologies Of White Matter Hyperintensities, Sugandha Roy

McKelvey School of Engineering Graduate Student Theses & Dissertations

In this thesis, we have applied Orthogonal Projective Non-Negative Matrix Factorization (opNMF) to identify spatial patterns of white matter hyperintensities (WMH) within UK Biobank's imaging data. Our selection criteria excluded subjects with a history of neurological, mental, and specific cerebrovascular conditions, allowing us to focus on WMH patterns in a healthy aging population. We have interrogated the association of location-specific WMHs with a variety of demographic, clinical, and genetic factors. Our multivariable regression analysis evaluates the strength and nature of the associations between these factors and WMH distribution. The analysis integrates variables such as age, sex, smoking habits, medication usage …

Assessing Reproducibility Of Brain-Behavior Associations Using Bootstrap Aggregation Methods, Zhetao Chen

Arts & Sciences Graduate Student Theses and Dissertations

在本论文中，随着越来越多地利用静息态功能连接 MRI (rs-fcMRI) 将神经活动与病理状况联系起来，我们面临着对此类数据可靠性的普遍担忧。我们的探索集中于提高人类连接组计划（HCP）数据集框架内大脑行为关联的可重复性。我们采用两种不同的引导聚合方法来研究功能连接可靠性的增强：使用循环块引导（CBB）的单独时间序列装袋和使用线性支持向量回归（LSVR）模型的主题级装袋。我们对 CBB 个体时间序列 bagging 的调查表明，这种方法并不能显着增强大脑行为关联的可重复性。这一发现指出了实现可靠的功能连接措施的复杂性以及某些聚合方法在克服这一挑战方面的局限性。相比之下，我们的学科水平考试 通过 LSVR 模型装袋呈现出更有希望的结果。这种方法显着增强了分析之间模型权重的可靠性，证明了其在提高数据稳健性和可重复性方面的功效。两种方法的这种不同影响强调了适当的分析策略在提高神经影像数据可靠性方面的关键作用。通过描述这两种方法的结果，本论文有助于对神经影像领域的数据可靠性进行更广泛的讨论。它强调了在不同数据集上持续进行方法创新和验证的必要性，以提高 rs-fcMRI 研究的可靠性和可解释性。

Preserving Shawnee Identity Through European Trade: How European Trade In Lower Shawneetown Expressed Indigenous Independence, Kelsey Grace Tuggle

Online Theses and Dissertations

The residents of Lower Shawneetown utilized trade to express independence from colonizing European powers. Unconventionally, the Shawnee articulated their freedom from colonization through direct trade be and diplomacy with European governments in the New and Old Worlds. The dynamics of trade in Lower Shawneetown were volatile, reflecting changes in Shawnee conceptualization of independence. European traders did not understand their actions through Shawnee colonial liberation, instead believing Lower Shawneetown trade furthered colonization efforts. Due to this inherent misinterpretation of Shawnee trade practices, European powers frequently engaged in hostilities against each other to court Lower Shawneetown’s favor.

Development Of An International Standard Set Of Outcomes And Measurement Methods For Routine Practice For Adults With Epilepsy: The International Consortium For Health Outcomes Measurement Consensus Recommendations, Martha Sajatovic

Faculty Scholarship

At present, there is no internationally accepted set of core outcomes or measurement methods for epilepsy clinical practice. Therefore, the International Consortium for Health Outcomes Measurement (ICHOM) convened an international working group of experts in epilepsy, people with epilepsy and their representatives to develop minimum sets of standardized outcomes and outcomes measurement methods for clinical practice that support patient–clinician decision-making and quality improvement. Consensus methods identified 20 core outcomes. Measurement tools were recommended based on their evidence of strong clinical measurement properties, feasibility, and cross-cultural applicability. The essential outcomes included many non-seizure outcomes: anxiety, depression, suicidality, memory and attention, sleep …

Thermal Physiology Of Sceloporus Olivaceus And Sceloporus Variabilis In South Texas, Ian Rockel

Masters Theses (Archived)

This study explores the thermal physiology of two sympatric lizard species, Sceloporus olivaceus (Texas spiny lizard) and Sceloporus variabilis (rose-bellied lizard), in South Texas. I document the metabolic rate and its temperature sensitivity, thermal limits, and performance at different temperatures to better understand the impact of rising temperatures and urbanization on these ectotherms, whose body temperature and, consequently, metabolic rate, activity level, and reproductive success depend on their thermal environment. We hypothesize that S. olivaceus will exhibit greater thermal resilience owing to its broader latitudinal range, variable habitat usage within Texas, and presumed more versatile thermoregulatory strategies. Scelorporus olivaceus's higher …

Agent-Based Modeling And Air Sampling Methods For Studying Aerosol Transmission, Lyndsy Stacy

Masters Theses (Archived)

No abstract provided.

Is On Site Evaporation A Feasible Solution For Produced Water Managment For Oil And Gas Development?, Travis Walla

Masters Theses (Archived)

The last decade witnessed a major transformation of global energy balances. A prime example of is the oil market shift from an era of high oil prices and concerns about short supplies to an era of lower oil prices and supply abundance. This paradigmatic shift in supply dynamics was triggered by the U.S. shale oil revolution; this massive boom in unconventional oil production has turned the U.S. into the world’s largest producer, ahead of both Russia and Saudi Arabia. The result has been an upending the global oil market, aside from geopolitical issues, the shale revolution has had far-reaching implications …

Avoiding Pitfalls In Molecular Simulation Of Vapor Sorption: Example Of Propane And Isobutane In Metal–Organic Frameworks For Adsorption Cooling Applications, Filip Formalik, Haoyuan Chen, Randall Q. Snurr

Physics & Astronomy Faculty Publications

This study introduces recommendations for conducting molecular simulations of vapor adsorption, with an emphasis on enhancing the accuracy, reproducibility, and comparability of results. The first aspect we address is consistency in the implementation of some details of typical molecular models, including tail corrections and cutoff distances, due to their significant influence on generated data. We highlight the importance of explicitly calculating the saturation pressures at relevant temperatures using methods such as Gibbs ensemble Monte Carlo simulations and illustrate some pitfalls in extrapolating saturation pressures using this method. For grand canonical Monte Carlo (GCMC) simulations, the input fugacity is usually calculated …

Parallel Use Of Low-Complexity Automated Nucleic Acid Amplification Tests And Lateral Flow Urine Lipoarabinomannan Assays To Detect Tuberculosis Disease In Adults And Adolescents Living With Hiv, Stephanie Bjerrum, Bada Yang, Johanna Åhsberg, Ruvandhi R Nathavitharana, Laura Olbrich, Devan Jaganath, Alexander W Kay, Andreas Lundh, Maunank Shah

Faculty, Staff and Students Publications

This is a protocol for a Cochrane Review (diagnostic). The objectives are as follows: To compare the diagnostic accuracy of parallel use of lateral flow urine lipoarabinomannan on urine and low-complexity automated nucleic acid amplification tests on respiratory samples versus each test alone for detection of tuberculosis disease in adults and adolescents living with HIV who present with presumptive tuberculosis. Secondary objectives To investigate the following sources of heterogeneity: clinical setting; signs and symptoms of tuberculosis; screening positivity for tuberculosis disease by chest x-ray, C-reactive protein elevation, and molecular World Health Organization-recommended rapid diagnostics; seriously ill; advanced HIV; and CD4 …

Evil We Desire: Akrasia And The Ethics Of Conspiracy Rhetoric, Andrew Ridgeway

Dissertations - ALL

My dissertation reimagines the work of four prominent rhetorical theorists—Aristotle, Plato, Augustine of Hippo, and Kenneth Burke—through the lens of psychoanalysis to develop a theory of rhetorical ethics that accounts for the subject’s relationship to libidinal satisfaction, or jouissance. In each chapter, I will examine a useful example of conspiracist rhetoric, which will double as both a case study and a point of departure for a Lacanian reimaging of a prominent rhetorical theory or concept. In the first chapter, I examine the “Stop the Steal” conspiracy and the January 6th insurrection to argue that Aristotle’s description of akrasia, or moral …

Making Sense Of Learning In Vr, Jason M. Webb

Dissertations - ALL

The goal of this qualitative study was to answer the question: How do educators make sense of learning in virtual reality? This study utilized multimedia learning theory and cognitive load theory to explore how educators understand virtual reality in education. Pre- and postinterviews as well as a VR experience were conducted with 13 educators from higher education institutions. The data was transcribed, coded, and developed into themes that created the data chapters. The findings from this research study revealed that educators identified two themes for extended reality in education. First, the design of virtual reality experiences for students was an …

Chemistry Professor Named 2024 Distinguished Researcher, Clara Turnage

University of Mississippi News

OXFORD, Miss. – The University of Mississippi recognized chemistry professor Nathan Hammer for his exceptional teaching, research, creativity and service during the 2024 spring faculty meeting.

Bridging The Gap: Neglect And Misunderstanding In Mother-Daughter Relationships, Yuhui Zheng

Theses - ALL

This thesis examines the conflicts between mothers and daughters within the Chinese cultural background. First, it states the domestic and social factors that impact the dynamic of maternal relationships with daughters in China. Then, by analyzing artworks like Everything Everywhere All at Once and Turning Red, it sheds light on how mother-daughter conflicts are represented in the plot and how filmmakers conceive such films to showcase mother-daughter relationships artistically. Finally, the thesis concludes by combining the above research with my own experiences, culminating in a visual thesis about a mother-daughter pair’s journey from conflict to reconciliation. The dissertation provides an …

Analysis Of Dilemmas And Self-Expression In The Highly Sensitive Person, Zixiao Song

Theses - ALL

This thesis primarily analyzes the definition of the highly sensitive person (HSP), the psychological issues this personality trait may cause, and coping mechanisms. It explores the experiences and challenges of HSPs, as described by psychologists and authors with extensive research in this field, such as Dr. Aron, to explore the inner world and coping mechanisms of highly sensitive individuals. Subsequently, through analyzing classic films and picture books such as The Perks of Being a Wallflower and All Too Much for Oliver, I observed how certain characters display the behavioral traits and psychological activities of HSPs from an artistic perspective. Finally, …

Burning Calories, Burning Ocean: Metabolic Rate In Bivalves As A Predictor Of Extinction Selectivity Through Time And During Rapid Global Warming, Siddharth Gavirneni

Theses - ALL

Organismal metabolic rate is linked to environmental temperature and oxygen consumption, and as such, may be a useful predictor of extinction risk during major climate- driven crises. However, metabolic attributes can be quantified in many ways, highlighting differing aspects of organisms’ ecology. Here, we estimate resting whole-body and mass-specific metabolic rates in post-Carboniferous bivalve taxa using body size and seawater paleotemperature to assess how metabolic rate determines survival both during and outside of intervals of rapid climate warming, or ‘hyperthermals’. Accounting for the effects of geographic range size, we find a pattern of preferential extinction of bivalves with lower total …

Non-Compressible Grade 4 Hemorrhagic Liver Injury Model For Assessment Of Shape Memory Polymers As A Hemostatic Agent, Shi S. Dong

Theses - ALL

Uncontrolled hemorrhage is a leading cause of trauma-related deaths, particularly in combat situations. The most administered treatment is gauze and tourniquets, which are shown to be ineffective for up to 80% of wounds, including non-compressible hemorrhage sites, such as those in the torso region. Shape memory polymer (SMP) foams have been shown to be an effective hemostatic dressing for traumatic wounds due to the tunability of their rapid clotting, mechanical properties, biocompatibility, biodegradability, and drug-loading abilities. The SMP foam design can be characterized with animal models, and a porcine liver injury is the current ‘gold standard’ animal model. To address …

The Girls: Queering The Family Archive, Kathleen Warren

Theses - ALL

My research and artistic practice explore how queerness can offer a liberatory framework for confronting intergenerational cycles of grief that reinforce the dual closets of emotional and sexual repression. Rooted in my own family’s history of traumatic loss, I explore the dialectics of memory and identity in my project The Girls. I explore how closeting operates in families and archives through several theoretical frameworks, with perspectives from Marianne Hirsch, bell hooks, and Michael Foucault’s History of Sexuality. By investigating the gendered roles imposed by the traditional family gaze, religion, and shame, the text examines how photography, archives, and performance can …

Dead Woman Walking: Articulating Historical Violence Toward The Femme Through Visual Art And Cultural Experience, Angelica Elizabeth Starcovic

Theses - ALL

Individual identity formation is a crucial tool in my artistic practice. I rely on articulating my experiences as femme to reclaim and denounce the signifiers of femininity invented and perverted by patriarchy. Using historical survey of instances and explorations of fear and violence through art and visual culture, my works reckon with how archaic gender beliefs still entrench themselves in our contemporary worldviews and their psychological results. The deconstructions of these facades uncover the violence and fear ingrained in feminine identity inflicted through bodily control in culture. Here I argue for her humanity against the abject violence culture and media …

Knockout Of Highly Conserved Seminal Fluid Protein Ablates Male Fertility In Drosophila Melanogaster, Dominic Hockenbury

Theses - ALL

ABSTRACT In Drosophila, seminal fluid proteins (SFPs) are key components of the male ejaculate and are essential determiners of reproductive fitness. SFPs are required for inducing a range of post-mating physiological responses in females. To date nearly 300 SFPs have been identified, however the vast majority of these remain uncharacterized and their role in reproduction and/or postcopulatory sexual selection is not clear. SFPs are functionally diverse and contain proteins from a variety of biochemical processes, most notably proteases and protease inhibitors that are thought to be critically important in biochemical interactions with female proteins. Another class of proteins that is …

Exploring The Impact Of Lake Browning On The Production Of Singlet Oxygen In Adirondack Surface Waters, Birdem Oz

Theses - ALL

Many inland lakes in temperate and boreal regions, including those in the Adirondack region of New York, are experiencing browning due to increased terrestrial inputs of colored dissolved organic matter (DOM). This phenomenon results from watershed recovery following declines in atmospheric acid deposition and shifts in precipitation patterns. Close coupling of changes in dissolved organic carbon levels and DOM quality in Adirondack lakes has important implications for ecosystem services, ranging from aquatic food web functioning to drinking water production. However, comparatively little is known about the potential effects of lake browning on carbon cycling and contaminant attenuation driven by the …

Intraguild Competition Is More Severe In Obligate Mutualisms Than In Facultative Mutualisms, Thomas Johnson

Theses - ALL

Mutualism, or the beneficial interaction of species, is an important and widespread interaction type in nature. Mutualist species exchange goods or services that benefit the species involved. These benefits can include protection from predators, parasites, and disease, dispersal of individuals, offspring, or gametes, and provisioning of various nutrients. Well-known mutualisms include the pollination of flowering plants by insects, birds, and other animals and the interaction between clownfish and sea anemones. Many mutualistic associations are less visible than these examples, as organisms often form beneficial relationships with microorganisms, like the many beneficial bacteria that live in the human gut, or the …

Examination Of The Relationship Between Adhd-Related Symptoms And Pre-Attentive Auditory Processing In A Sample Of Autistic Children And Adolescents, Connor K. Mackenzie

Theses - ALL

Autism Spectrum Disorders (ASD) and Attention-Deficit/Hyperactivity Disorder (ADHD) are two of the most prevalent neurodevelopmental conditions that also exhibit a high rate of co-occurrence. This co-occurrence leads to decreased efficacy of interventions and increased levels of impairments. This suggests that it might be relevant to examine the impact of ADHD symptoms on ASD research findings. Given that both these disorders have neurodevelopmental origins that share differences in sensory processing, the study of sensory neurophysiology might be a relevant avenue to explore. Neurophysiology has focused on pre-attentive auditory processing in both conditions compared to the neurotypical population by focusing on a …

Stochastic Algorithms For Simulating Protein Assembly In Biological Cells, Advait Shukla

Theses - ALL

Understanding membrane protein assembly using computational methods is critical in developing drug delivery strategies for tight junction diseases such as Alzheimer’s and Crohn’s diseases. While experimental methods, such as freeze-fracture micrographs, provide microscopic details of the protein strand networks, they cannot offer molecular-level information, which is necessary for drug design. This work attempts to close the gap by computationally predicting strand networks of the claudin family of proteins that form tight junctions across neighboring cells in epithelial and endothelial tissues. Using claudin dimer data collected by the Protein AssociatioN Energy Landscape (PANEL) method coupled with some Markovian approximations, we built …

Wearing Endangered Species, Kylie Perry

Honors Theses

The biodiversity of our ecosystems is under constant threat every day; this makes public awareness of environmental issues incredibly important. Since this is such a time sensitive issue it is necessary to increase public awareness immediately. The constant threat was caused by humanity so we should be the ones to help save the endangered species before they are gone. My thesis focuses on how art can bring awareness to environmental issues and more specifically endangered species. This project involves linocuts printed on recycled paper on the topic of five species of endangered animals. Through the medium of printmaking, this project …

Development And Application Of Small-Molecule Probes Targeting Ghrelin O-Acyltransferase, Jacob Moose

Dissertations - ALL

Ghrelin is a 28-amino acid peptide hormone that has wide-ranging physiological effects, including on metabolism, adipogenesis, insulin regulation, and addiction. Ghrelin offers an intriguing option for treatment of pathophysiologies related to these effects, as it requires a unique post-translational octanoyl modification to bind and activate its cognate receptor, growth hormone secretagogue 1a (GHSR). The enzyme responsible for this modification, ghrelin O-acyltransferase (GOAT) therefore offers the ability to modulate ghrelin signaling through inhibition of the maturation pathway. Due to a lack of structural or mechanistic information about GOAT, pharmaceutical development of molecules capable of GOAT inhibition has been desired, but few …