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Molecular Interactions In Engineering: Peptide-Driven T Cell Activation And Accelerated Drug Discovery Applications, Armin Ahmadi

Dissertations

In pursuit of an interdisciplinary exploration of molecular interactions from an engineering perspective with a focus on protein-protein and protein-small molecule interactions, multiple research projects were undertaken, leveraging both experimental and computational approaches. The focus of the wet-lab experimental project was on the identification and evaluation of a novel peptide ligand that binds specifically to the human CD3ε and study how this interaction influences T-Cell activation, proliferation, and calcium signaling. A novel peptide ligand, WSLGYTG, was discovered through phage display peptide technology. Peptide interaction to the CD3ε receptor was simulated using molecular docking calculations. This peptide ligand was synthesized and …

Extending Machine Learning Of Cyberattack Strategies With Continuous Transition Rates, Edwin Michael Bearss

Dissertations

Cyberattacks are a growing threat to organizations of all sizes and industries. By better understanding these attacks, better ways to defend against them can be developed. Petri Nets with Players, Strategies, and Costs (PNPSC) is an extension of Petri nets specifically designed to model cyberattacks. The PNPSC formalism includes a representation of the strategies used by the competing players, i.e., attacker and defender, to achieve their goals. This formalism has been the basis for a long-running research program consisting of several interconnected research projects. Projects within that program include automatically generating PNPSC nets from the MITRE Common Attack Pattern Enumeration …

Modeling Energetic Particle Acceleration By Dynamic Small-Scale Flux Ropes In The Inner Heliosphere, Keaton Thomas Van Eck

Dissertations

Interplanetary coronal mass ejections (ICMEs) are major drivers of space weather in the inner heliosphere (which can negatively affect our spacecraft, astronauts, etc.). Traditionally, the scientific community has sought to explain energetic particle acceleration near ICME-driven shocks by invoking diffusive shock acceleration (DSA), which has been well studied. However, recent studies suggest that processes related to magnetic reconnection behind ICME-driven shocks can explain observed flux enhancements that contradict predictions by standard steady state DSA theory. In the previous decade, a combination of DSA at and acceleration by dynamic small-scale flux-ropes (SMFRs) downstream of the shock has been introduced to explain …

A Monoadduct Generating Ru(Ii) Complex Induces Ribosome Biogenesis Stress And Is A Molecular Mimic Of Phenanthriplatin, Richard Joseph Mitchell, Sarah M. Kriger, Alexander D. Fenton, Dmytro Havrylyuk, Ankit Pandeya, Yang Sun, Tami Smith, Jason E. Derouchey, David K. Heidary, Edith C. Glazer

Markey Cancer Center Faculty Publications

Ruthenium complexes are often investigated as potential replacements for platinum-based chemotherapeutics in hopes of identifying systems with improved tolerability in vivo and reduced susceptibility to cellular resistance mechanisms. Inspired by phenanthriplatin, a non-traditional platinum agent that contains only one labile ligand, monofunctional ruthenium polypyridyl agents have been developed, but until now, few demonstrated promising anticancer activity. Here we introduce a potent new scaffold, based on [Ru(tpy)(dip)Cl]Cl (tpy = 2,20:60,200-terpyridine and dip = 4,7-diphenyl-1,10-phenanthroline) in pursuit of effective Ru(II )-based monofunctional agents. Notably, the extension of the terpyridine at the 40 position with an aromatic ring resulted in a molecule that …

Computational Investigation Of A Series Of Small Molecules As Potential Compounds For Lysyl Hydroxylase-2 (Lh2) Inhibition, Yazdan Maghsoud, Erik Antonio Vázquez-Montelongo, Xudong Yang, Chengwen Liu, Zhifeng Jing, Juhoon Lee, Matthew Harger, Ally K. Smith, Miguel Espinoza, Hou-Fu Guo, Jonathan M. Kurie, Kevin N. Dalby, Pengyu Ren, G. Andrés Cisneros

Markey Cancer Center Faculty Publications

The catalytic function of lysyl hydroxylase-2 (LH2), a member of the Fe(II)/αKG-dependent oxygenase superfamily, is to catalyze the hydroxylation of lysine to hydroxylysine in collagen, resulting in stable hydroxylysine aldehyde-derived collagen cross- links (HLCCs). Reports show that high amounts of LH2 lead to the accumulation of HLCCs, causing fibrosis and specific types of cancer metastasis. Some members of the Fe(II)/αKG-dependent family have also been reported to have intramolecular O2 tunnels, which aid in transporting one of the required cosubstrates into the active site. While LH2 can be a promising target to combat these diseases, efficacious inhibitors are still lacking. We …

Polycomb Deficiency Drives A Foxp2-High Aggressive State Targetable By Epigenetic Inhibitors, Fan Chen, Aria Byrd, Jinpeng Liu, Robert M. Flight, Tanner Ducote, Kassandra J. Naughton, Xiulong Song, Abigail R Edgin, Alexsandr Lukyanchuk, Danielle T. Dixon, Christian M. Gosser, Dave-Preston Esoe, Rani Jayswal, Stuart H. Orkin, Hunter N. B. Moseley, Chi Wang, Christine Fillmore Brainson

Markey Cancer Center Faculty Publications

Inhibitors of the Polycomb Repressive Complex 2 (PRC2) histone methyltransferase EZH2 are approved for certain cancers, but realizing their wider utility relies upon understanding PRC2 biology in each cancer system. Using a genetic model to delete Ezh2 in KRAS-driven lung adenocarcinomas, we observed that Ezh2 haplo-insufficient tumors were less lethal and lower grade than Ezh2 fully-insufficient tumors, which were poorly differentiated and metastatic. Using three-dimensional cultures and in vivo experiments, we determined that EZH2-deficient tumors were vulnerable to H3K27 demethylase or BET inhibitors. PRC2 loss/inhibition led to de-repression of FOXP2, a transcription factor that promotes migration and stemness, and FOXP2 …

Multi-Label Text Classification With Transfer Learning, Likhitha Yelamanchili

Master's Projects

Multi-label text categorization is a crucial task in Natural Language Processing, where each text instance can be simultaneously assigned to numerous labels. This project's goal is to assess how well several deep learning models perform on a real-world dataset for multi-label text classification. We employed data augmentation techniques like Synonym Substitution and Random Word Substitution to address the problem of data imbalance. We conducted experiments on a toxic comment classification dataset to evaluate the effectiveness of several deep learning models including Bi-LSTM, GRU, and Bi-GRU, as well as fine- tuned pre-trained BERT models. Many metrics, including log loss, recall@k, and …

Hate Speech Detection In Hindi, Pranjali Prakash Bansod

Master's Projects

Social media is a great place to share one’s thoughts and to express oneself. Very often the same social media platforms become a means for spewing hatred.The large amount of data being shared on these platforms make it difficult to moderate the content shared by users. In a diverse country like India hate is present on social media in all regional languages, making it even more difficult to detect hate because of a lack of enough data to train deep/ machine learning models to make them understand regional languages.This work is our attempt at tackling hate speech in Hindi. We …

Nitrogen Behavior In A No-Tillage Agroecosystem Located In The Inner Bluegrass Of Kentucky, Alec William Besinger Mr.

Theses and Dissertations--Plant and Soil Sciences

Nitrogen (N) is a crucial element, often limiting productivity in ecosystems. This limitation is relieved N fertilizer additions. No-tillage (NT) agroecosystems are prone to lower N availability translating to lower crop yields. The default explanation for lower N availability in NT is microbial immobilization of added N fertilizer. Historically, N availability is often assessed using chemical extractions such as KCl to evaluate levels of inorganic N in the soil. The possibility of this abiotic clay mineral fixation as mechanism in well-drained NT soils has been overlooked. The objectives of this study are to quantify N availability using KCl, NaCl, and …

A Phase Change Memory And Dram Based Framework For Energy-Efficient And High-Speed In-Memory Stochastic Computing, Supreeth Mysore

Theses and Dissertations--Electrical and Computer Engineering

Convolutional Neural Networks (CNNs) have proven to be highly effective in various fields related to Artificial Intelligence (AI) and Machine Learning (ML). However, the significant computational and memory requirements of CNNs make their processing highly compute and memory-intensive. In particular, the multiply-accumulate (MAC) operation, which is a fundamental building block of CNNs, requires enormous arithmetic operations. As the input dataset size increases, the traditional processor-centric von-Neumann computing architecture becomes ill-suited for CNN-based applications. This results in exponentially higher latency and energy costs, making the processing of CNNs highly challenging.

To overcome these challenges, researchers have explored the Processing-In Memory (PIM) …

Application Of Conventional Feedforward And Deep Neural Networks To Power Distribution System State Estimation And State Forecasting, James Paul Carmichael

Theses and Dissertations--Electrical and Computer Engineering

Classical neural networks such as feedforward multilayer perceptron models (MLPs) are well established as universal approximators and as such, show promise in applications such as static state estimation in power transmission systems. This research investigates the application of conventional neural networks (MLPs) and deep learning based models such as convolutional neural networks (CNNs) and long short-term memory networks (LSTMs) to mitigate challenges in power distribution system state estimation and forecasting based upon conventional analytic methods. The ability of MLPs to perform regression to perform power system state estimation will be investigated. MLPs are considered based upon their promise to learn …

Modeling The Early Visual System, Nicholas Lanning

Theses and Dissertations--Electrical and Computer Engineering

There are two encoding schema present in simple cells in the early visual system of vertebrates: the retinal simple cells activate highly when the receptive field contains a center surround stimulus, while the primary visual cortex’s (V1) simple cells activate highly when the receptive field contains visual edges. Work has been done in the past to enforce constraints on visual machine learning such that the retinal or V1 encoding is learned, but this work is often done to emulate retinal and V1 encoding in a vacuum. Recent work using convolutional neural networks focuses on anatomical constraints along with a supervised …

Phys 275: Intro To Scientific Computing, David Goldberg

Open Educational Resources

No abstract provided.

Astr 1: General Astronomy, David Goldberg

Open Educational Resources

No abstract provided.

Examining The Role Of Place Attachment In Climate Justice Engagement And Jewish Relationships To The Environment, Madeline Medina

Environmental Studies Honors Projects

It is critical that environmental justice and marginalized identities are the focus of climate-related discussions and research. Solutions must support the long-term wellbeing of people, especially and importantly those who are most vulnerable to the consequences of climate change. Psychological research suggests that place attachment–the meaningful bonds that occur between people and their environment (Scannell & Gifford, 2010)–is a key factor in motivating environmental behavior, but little research has examined its connection to environmental justice oriented behavior. This two-part exploration first evaluated the role of place attachment on engagement with both a typical climate change centered message and a climate …

Putting The “U” In Shore U: Expanding Postsecondary Education On Virginia’S Eastern Shore, Katelyn D. Jones, Karen Belanger, Katharine Wise, Takeya Mclaurin

Doctor of Education Capstones

The University of the Eastern Shore of Virginia Foundation (Shore U) submitted a Request for Assistance to examine opportunities to expand postsecondary education on Virginia’s Eastern Shore. In response to this request, a doctoral research team conducted a mixed-methods study that explored potential pathways for a four-year degree option on the Eastern Shore. Eastern Shore Community College (ESCC) students, ESCC employees, and Eastern Shore community members were surveyed during the quantitative phase of the study. Secondary data was used to understand the postsecondary positionality of Eastern Shore high school students. The President of ESCC, Eastern Shore community members, and Virginia …

Assessing Graduate Student Needs And Structures Of Support At Virginia Commonwealth University, Trisha Saunders, Kiama Anthony Bishop, Herbert Hill Iii, Tameka Fitzgerald Burroughs

Doctor of Education Capstones

The purpose of this multi-case study was to explore how the institutional landscape is designed to support graduate student success at Virginia Commonwealth University (VCU), a large, public, urban, R1 research university. The study included review of existing literature on the various factors that contribute to or limit graduate student success at institutions across the country. A major aim of this study was to collect qualitative data from participants with a key stake in this issue, including enrolled graduate students, and faculty/staff supporting graduate (master’s and doctoral) programs at VCU. Participants included 39 graduate students and 23 institutional stakeholders. All …

A Brighter Future For Sms: Cultivating School Coherence Through A Shared Vision, Nicole K. Herndon, Heather Holcomb, Audra Krupp

Doctor of Education Capstones

Staunton City Public Schools submitted an RFA (Request for Assistance) to Virginia Commonwealth University (VCU) to address concerns at Shelburne Middle School related to teacher satisfaction, student discipline, and student achievement. Document and data analysis, a site visit, and partner interviews surfaced issues of organizational fragmentation; the capstone team identified the need for a collaboratively constructed and implemented vision to better cohere the school. Through document analysis and stakeholder surveys, our mixed methods study aimed to understand stakeholder views on three aspects to support the work of the leadership team at SMS. First, the capstone team identified the needs in …

A Case Study Exploring William & Mary Military Alums' Experiences With Career Transition, Dirron Allen, Amanda Baldwin-Estep, Matthew Grinsell, Kimberly Lintag-Nguyen

Doctor of Education Capstones

Background: The purpose of this qualitative study was to understand William & Mary (W&M) Master of Business Administration (MBA) military alums’ experiences with their career transitions post-graduation and the influence of the program on their experiences.

Methods: This study utilized a case study design, including focus groups and interviews with 21 alums from the last 10 years and formal, semi-structured interviews with six current faculty and staff. We used Schlossberg’s (1981) individuals’ situation, self, support, and strategies to analyze data using thematic analysis, and then iteratively reducing codes into themes.

Results: Demographic findings showed a lack of diversity, such as …

Hydrogeologic Field Trip Of Northeast Nebraska, Sue Olafsen Lackey, Kathleen Cameron, Matt Marxsen

Conservation and Survey Division: Faculty and Staff Publications

No abstract provided.

2023 Nebraska Water Leaders Academy, Mark E. Burbach, Robert Matthew Joeckel

Conservation and Survey Division: Faculty and Staff Publications

Eighteen participants completed the 2023 Water Leaders Academy bringing the total number of graduates to 186 since the inception of the program in 2011. Assessments of participants’ transformational leadership skills, champion of innovation skills, water knowledge, engagement with water issues, civic capacity, entrepreneurial leadership behaviors, boundary spanning skills, and curiosity increased significantly over the course of the year, according to both the participants and their raters. Feedback from the participants was highly positive and constructive. Academy planners are addressing participant concerns. Results of the program assessment indicate that the curriculum is meeting the Academy’s objectives. Therefore, only minor changes are …

Telescopic Megafans On The High Plains, Usa Were Signal Buffers In A Major Source-To-Sink System, Jesse T. Korus Dr., Robert Matthew Joeckel

Conservation and Survey Division: Faculty and Staff Publications

No abstract provided.

3d Hydrostratigraphic And Hydraulic Conductivity Modeling Using Supervised Machine Learning, T. A. Tilahun, Jesse T. Korus Dr.

Conservation and Survey Division: Faculty and Staff Publications

No abstract provided.

Nebraska's Water, Nawaraj Shrestha, Ann Briggs, Aaron R. Young, Robert Matthew Joeckel

Conservation and Survey Division: Faculty and Staff Publications

No abstract provided.

Conservation And Survey Division 2023 Annual Report, R. M. Joeckel, M. M. Waszgis

Conservation and Survey Division: Faculty and Staff Publications

No abstract provided.

Ethical Design Of Computers: From Semiconductors To Iot And Artificial Intelligence, Sudeep Pasricha, Marilyn Wolf

School of Computing: Faculty Publications

Computing systems are tightly integrated today into our professional, social, and private lives. An important consequence of this growing ubiquity of computing is that it can have significant ethical implications of which computing professionals should take account. In most real-world scenarios, it is not immediately obvious how particular technical choices during the design and use of computing systems could be viewed from an ethical perspective. This article provides a perspective on the ethical challenges within semiconductor chip design, IoT applications, and the increasing use of artificial intelligence in the design processes, tools, and hardware-software stacks of these systems.

Holocene Variations In Lake Titicaca Water Level And Their Implications For Sociopolitical Developments In The Central Andes, Stéphane Guédron, Christophe Delaere, Sherilyn C. Fritz, Julie Tolu, Pierre Sabatier, Anne-Lise Devel, Carlos Heredia, Claire Vérin, Eduardo Q. Alves, Paul A. Baker

Department of Earth and Atmospheric Sciences: Faculty Publications

Holocene climate in the high tropical Andes was characterized by both gradual and abrupt changes, which disrupted the hydrological cycle and impacted landscapes and societies. High-resolution paleoenvironmental records are essential to contextualize archaeological data and to evaluate the sociopolitical response of ancient societies to environmental variability. Middle-to-Late Holocene water levels in Lake Titicaca were reevaluated through a transfer function model based on measurements of organic carbon stable isotopes, combined with high-resolution profiles of other geochemical variables and paleoshoreline indicators. Our reconstruction indicates that following a prolonged low stand during the Middle Holocene (4000 to 2400 BCE), lake level rose rapidly …

Teaching Forensic Entomology With Common Grocery Items: Decomposition And Insect Succession Studies, Erin Bauer, Charles Murrieta, Larry Barksdale

Department of Entomology: Faculty Publications

Forensic science and entomology programs may benefit from using deceased pigs as teaching resources due to anatomical similarities to humans. The use of such animals provides opportunities for students to learn the effects of geographical location and climate on insects; understand insect succession; practice insect collection and identification; and learn post-mortem interval procedures, taphonomic principles of decomposition, and crime scene investigation and management techniques. Forensic entomology and taphonomic studies fit well with educational interests in experiential learning. Pigs may be readily available through animal science departments or local producers, and many institutions may have property where this research can be …

Intercontinental Comparisons Of Subterranean Host-Parasite Communities Using Bipartite Network Analyses, Altangerel Tsogtsaikhan Dursahinhan, Sebastian Botero-Cañola, Scott L. Gardner

Scott L. Gardner Publications

Rodents living in a subterranean ecotope face a unique combination of evolutionary and ecological pressures and while host species evolution may be driven by the selective pressure from the parasites they harbour, the parasites may be responding to the selective pressures of the host. Here we obtained all available subterranean rodent host-parasite records from the literature and integrated these data by utilizing a bipartite network analysis to determine multiple critical parameters to quantify and measure the structure and interactions of the organisms present in host-parasite communities. A total of 163 species of subterranean rodent hosts, 174 parasite species, and 282 …

Micro-Shear Bond Strength Of Bioactive Restorative Materials To Dentin And Analysis Of Interfaces: A Laboratory Study, Doha M. Zahran, Ali A. Elkaffas, Hamdi H. Hamama, Salah H. Mahmoud

Mansoura Journal of Dentistry

Objectives

The study aimed to assess and compare micro-shear bond strength (µSBS) to dentin, micromorphological and chemical changes of newly introduced bioactive restorative materials/dentin interfaces.

Materials and methods

Total of 56 molars were used in this study, for μSBS, 28 molars (n=28) were randomly assigned into 4 groups (n=7) according to the type of restorative material used: group A; Activa, Pulpdent, group B; Beautifil II LS, Shofu, group C; Cention N, Ivoclar Vivadent and group D; Surefil one, Dentsply Sirona. The other 28 molars (n=28) were tested for elemental analysis of restoration/tooth interface using EDX and micromorphological analysis under SEM, …