Digital Commons Network^™

Computational Approach: 3d-Qsar, Molecular Docking, Molecular Dynamics Simulation Investigations, Drug- Like-Ness, And Dft Score Evaluation Of A Potential Novel And Retrosynthesis Of Some Tr-H Derivatives As Streptococcus Pneumoniae Drug., Belaidi Mustapha, Tchouar Noureddine, Djelilate Mohammed, Saleh Bufarwa, Dalal K. Thbayh

Karbala International Journal of Modern Science

Streptococcus pneumoniae is the main source of hospital-acquired pneumonia and meningococcal pneumonia in children, adults, and the elderly, especially the immunocompromised. Recently, it has attracted the attention of many research studies around the world as a potential target for remediation. TR-H are considered SP antibacterial agents, as they can inhibit. To describe their mode of action and to identify new antibacterial drugs against Streptococcus pneumoniae exhibiting the TR-H scaffold, the present work included 3D-QSAR, in- silico pharmacokinetic evaluation and molecular simulation modelling of TR-H. Using an atom-based method for quantitative structure-activity relationship (QSAR) study, a comprehensive 3D-QSAR model …

Conformational Change In A Four-Tetrad Dna G-Quadruplex Upon Intercalation Of A Small-Molecule Ligand Pydh2, Kailey N. Martin, Gwendolyn Lam , '24, O. Reznichenko, K. E. Brunner, M. J. Zdilla, Sawyer E. Mccarthy, Liliya A. Yatsunyk

Chemistry & Biochemistry Faculty Works

G-quadruplexes (G4s) are non-canonical DNA structures implicated in a number of biological processes. Small-molecule ligands can alter stability and folding of G4s, which can potentially be exploited for therapeutic purposes. In this work, we investigate the interaction of telomeric DNA fragment from Tetrahymena thermophila (TET25, 5′-G(TTGGGG)₄-3′) with a G4 ligand PyDH2 belonging to the bisquinolinium family. When alone, TET25 adopts a mixture of three conformations, with the most abundant being a four-tetrad hybrid G4. In the presence of PyDH2, surprisingly, TET25 folds into an antiparallel chair G4, with PyDH2 intercalated between G-tetrads 2 and 3, according to our crystal structure. …

Integrative Computational Modeling Of Distinct Binding Mechanisms For Broadly Neutralizing Antibodies Targeting Sars-Cov-2 Spike Omicron Variants: Balance Of Evolutionary And Dynamic Adaptability In Shaping Molecular Determinants Of Immune Escape, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

In this study, we conducted a comprehensive analysis of the interactions between the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and four neutralizing antibodies—S309, S304, CYFN1006, and VIR-7229. Using integrative computational modeling that combined all-atom molecular dynamics (MD) simulations, mutational scanning, and MM-GBSA binding free energy calculations, we elucidated the structural, energetic, and dynamic determinants of antibody binding. Our findings reveal distinct dynamic binding mechanisms and evolutionary adaptation driving the broad neutralization effect of these antibodies. We show that S309 targets conserved residues near the ACE2 interface, leveraging synergistic van der Waals and electrostatic interactions, while S304 focuses on …

Re: Comment Letter For Draft Final Butte Priority Soils Operable Unit (Bpsou) Unreclaimed Sites Ur-05 Remedial Action Work Plan (Rawp) (Dated March 14, 2025), Molly Roby

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Application Of Quechers Extraction Method For Optimization Of Organic Matters In Oil Sand By Ultrahigh Fourier Transform Infrared Orbitrap-Mass Spectrometry, Gbenga Aladekoyi, Emmanuel G. Olumayede, Samuel O. Olusanya, Simeon Schum

Michigan Tech Publications

This work focuses on the performance of composite solvents using the QuEchERs extraction (quick, easy, cheap, effective, rugged, and safe) method in bitumen recovery and determination of organic matters present in the oil sands of the Okitipupa area of southwestern Nigeria. Different correlated parameters, such as extraction time (h), stirring time (r/ min), change in temperature (°C), and type of solvent (heptane—toluene and dichloromethane—toluene), solvent ratios (2: 8, 3: 7, 5: 5, 7: 3, and 8: 2) were used to optimize dissolved organic matters from the oil sands using QuEchERs extraction method. Ratios 1 g/2.5 ml for each solvent mix …

Utilization Of Flow Cytometry, Metabolomic Analyses And A Feline Infectious Peritonitis Case Study To Evaluate The Physiological Impact Of Polyprenyl Immunostimulant, Irene Lee, Amar Desai, Akshay Patil, Yan Xu, Kelley Pozza-Adams, Anthony J. Berdis

Chemistry Faculty Publications

Measles, hepatitis C, and COVID-19 are significant human diseases caused by RNA viruses. While vaccines exist to prevent infections, there are a small number of currently available therapeutic agents that can effectively treat these diseases after infection occurs. This study explores a new therapeutic strategy using a small molecule designated polyprenyl immunostimulant (PI) to increase innate immune responses and combat viral infections. Using a multi-disciplinary approach, this study quantifies the effects of PI in mice and THP-1 cells using flow cytometry to identify immune phenotypic markers and mass spectroscopy to monitor the metabolomic profiles of immune cells perturbed by PI …

A Complete Transfer Learning-Based Pipeline For Discriminating Between Select Pathogenic Yeasts From Microscopy Photographs, Ryan A. Parker, Danielle S. Hannagan, Jan H. Strydom, Christopher J. Boon, Jessica Fussell, Chelbie A. Mitchell, Katie L. Moerschel, Aura G. Valter-Franco, Christopher Cornelison

Faculty Articles

Pathogenic yeasts are an increasing concern in healthcare, with species like Candida auris often displaying drug resistance and causing high mortality in immunocompromised patients. The need for rapid and accessible diagnostic methods for accurate yeast identification is critical, especially in resource-limited settings. This study presents a convolutional neural network (CNN)-based approach for classifying pathogenic yeast species from microscopy images. Using transfer learning, we trained the model to identify six yeast species from simple micrographs, achieving high classification accuracy (93.91% at the patch level, 99.09% at the whole image level) and low misclassification rates across species, with the best performing model. …

Research On Modeling, Optimization And Application Of Aeroengine Oil System, Shijie Huang, Zhensheng Zhang, Jing Cai, Rui Zhang

Journal of System Simulation

Abstract: In response to the high cost and long cycle of using experimental methods for monitoring, diagnosing, and predicting lubricating oil system, a simulation model for oil system is constructed and optimized, and the application of the model in health management of oil system is proposed. Based on the physical characteristics of the components in the oil system, subsystem models for ventilation, oil supply, thermodynamics, and oil return are constructed using a certain engine oil system as an example, and the whole oil system model is constructed and solved iteratively. The model is optimized by combining particle swarm optimization and …

Leveraging Artificial Intelligence In Education To Drive Cross-Sector Innovation, Brent Terwilliger, John Faraca

Publications

As artificial intelligence (AI) reshapes educational practices, particularly in technical fields such as uncrewed systems, robotics, and aviation/ aerospace, its integration raises promise and complexity. This exploratory study features an investigation of the impact AI tools adoption has on instruction, curriculum support, and workforce preparation, with a focus on online learning environments. Drawing from pilot survey data across aviation and aerospace education stakeholders and hands-on evaluation of AI video production platforms, findings reveal diverse applications, perceived benefits, and critical concerns, including ethical, pedagogical, and institutional challenges. Additionally, the analysis explored how AI-enabled education intersects with broader industry and government innovation …

Histone Methyltransferase Ash1l Primes Metastases And Metabolic Reprogramming Of Macrophages In The Bone Niche, Chenling Meng, Kevin Lin, Wei Shi, Hongqi Teng, Xinhai Wan, Anna Debruine, Yin Wang, Xin Liang, Javier Leo, Feiyu Chen, Qianlin Gu, Jie Zhang, Vivien Van, Kiersten L Maldonado, Boyi Gan, Li Ma, Yue Lu, Di Zhao

Faculty, Staff and Student Publications

Bone metastasis is a major cause of cancer death; however, the epigenetic determinants driving this process remain elusive. Here, we report that histone methyltransferase ASH1L is genetically amplified and is required for bone metastasis in men with prostate cancer. ASH1L rewires histone methylations and cooperates with HIF-1α to induce pro-metastatic transcriptome in invading cancer cells, resulting in monocyte differentiation into lipid-associated macrophage (LA-TAM) and enhancing their pro-tumoral phenotype in the metastatic bone niche. We identified IGF-2 as a direct target of ASH1L/HIF-1α and mediates LA-TAMs' differentiation and phenotypic changes by reprogramming oxidative phosphorylation. Pharmacologic inhibition of the ASH1L-HIF-1α-macrophages axis elicits …

Book Review Of, Participatory Engineering Of Algorithmic Socialtechnologies: An Extended Book Review Of David G. Robinson's Voices Inthe Code, Rajesh Venkatachalapathy

Complex Systems Faculty Publications and Presentations

David G. Robinson’s Voices in the Code, reviewed here, approaches the issue of governance and regulation of algorithmic social technologies with a case study orientation that offers a grounding in the details, illuminating the fundamentally sociological and processual nature of modern governance issues that are mostly missed or left implicit in academic, regulatory, and legislative discussions. This important book urges us to design adaptive, malleable, and evolvable participatory organizational structures instead. Accepting the author’s invitation to carry the torch forward, this review builds on and extends the book’s arguments by presenting broad and transferable insights on regulation and governance …

Sustainability In The Cruising Industry: Innovations In Air Quality, Energy Efficiency, And Waste Management, Fikret Durmus, Mi Ran Kim

ICHRIE Research Reports

The cruise industry, a cornerstone of the global hospitality and tourism sector, faces increasing scrutiny over its environmental impact. As passenger numbers grow, so does the industry's responsibility to adopt sustainable practices. This report examines key innovations in air quality management, energy efficiency, and waste management, highlighting the industry's transition from historically high emissions and waste production to advanced sustainability initiatives. Key focus areas include evolving maritime regulations, adopting cleaner propulsion technologies, integrating energy-efficient solutions, and improving waste treatment practices. Findings indicate that industry leaders are investing in liquefied natural gas engines, exhaust gas cleaning systems, and onshore power supply …

Human Endogenous Retroviruses (Hervs) Associated With Glioblastoma Risk And Prognosis, Harun Mazumder, Hui Yi Lin, Melody Baddoo, Wojciech Gałan, Diana Polania-Villanueva, Chindo Hicks, David Otohinoyi, Francesca Peruzzi, Zbigniew Madeja, Victoria P. Belancio, Erik K. Flemington, Krzysztof Reiss, Monika Rak

School of Medicine Faculty Publications

Emerging evidence suggests expression from human endogenous retrovirus (HERV) loci likely contributes to, or is a biomarker of, glioblastoma multiforme (GBM) disease progression. However, the relationship between HERV expression and GBM malignant phenotype is unclear. Applying several in silico analyses based on data from The Cancer Genome Atlas (TCGA), we derived a locus-specific HERV transcriptome for glioma that revealed 211 HERVs significantly dysregulated in the comparisons of GBM vs. normal brain (NB), GBM vs. low-grade glioma (LGG), and LGG vs. NB. Our analysis supported development of a unique HERV scoring algorithm that segregated GBM, LGG, and NB. Interestingly, lower HERV …

Setting Up Students For Success: Analysis Of Effectiveness Of Mathematics Placement, Jeff Carvell, Jason Ho, David Klanderman, Sarah Klanderman

University Faculty Publications and Creative Works

How do we e!ectively and equitably place students into math classes in a way that provides them the best chance of success? As many higher education institutions veer away from placement based on standardized testing, many departments are seeking placement alternatives that will properly support students. Additionally, math placement determines not only a student’s mathematics courses but also influences their progress in related fields, including physics, chemistry, engineering, and more. This paper will describe three di!erent existing placement systems at each of our liberal arts institutions as well as the a!ordances and constraints of each approach. Further, we analyze data …

Re: Comment Letter For The Butte Priority Soils Operable Unit (Bpsou) Insufficiently Reclaimed Sites Bres No. 158 – Waste Rock Dump Remedial Action Work Plan (Rawp) (Dated March 28, 2025), Molly Roby

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Decarbonized Shipping: Is It The Best Sustainable Shipping Solution?, Olivia Akers

Sustainable Supply Chain Management

In the era of globalization and the fourth industrial revolution, the maritime shipping industry has grown exponentially in the twenty-first century. In fact, 90% of today’s goods travel across the ocean before reaching the end consumer, meaning that ocean transportation of goods contributes significantly to overall environmental impacts on the ocean. Awareness of this impact has increased as humans strive to eliminate unsustainable practices in an effort to protect the long term health of our planet. Decarbonized shipping has been proposed as a possible solution for unsustainable shipping practices, and the goal of this chapter is to evaluate this solution …

Re: Approval Letter For The Butte Priority Soils Operable Unit (Bpsou) Revised Draft Final Insufficiently Reclaimed Sites Bres No. 158 Site Evaluation Summary Report (Dated February 24, 2025), Molly Roby

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Investigating The Microbial Communities In Freshwaters Of Northern Sweden, Maizy Wilcox

Undergraduate University Honors Capstones

Climate change is shifting the stability of sensitive ecosystems in the Arctic region due to global warming, with widespread impacts on permafrost regions, including the Stordalen Mire region of Sweden. Due to climate change, the Stordalen Mire is composed of thawing permafrost shifting into a wetland (V onk et al., 2015). As permafrost thaws, the landscape transforms due to changing water environmental conditions, causing lower pH changes and higher temperatures in the water, impacting the underlying soil chemistry and biology, vegetation, and microbial communities (Webb et al., 2022). The increased temperature can enhance methanogenic microbial growth by expanding the groundwater …

Enhancing Water Supply Resilience & Sustainability: Potential Solutions To Address Water Scarcity In Bogotá, Colombia, Sophia Alvarez Wong

Master's Projects and Capstones

Municipal water utilities are in urgent need of adapting to the intensifying impacts of climate change and population growth—key drivers of urban water scarcity worldwide. In rapidly expanding cities like Bogota, Colombia, these pressures have contributed to a severe water crisis driven by prolonged droughts, ecosystem degradation, increasing water demands, and overdependence on limited water sources. This study explores potential adaptation and management strategies that utilities can implement to sustainably strengthen supply system resilience and enhance water security, in the context of low- to middle-income regions. A series of comparative and case study analyses were conducted to assess the feasibility …

An Investigation Into The Inclusivity, Methodology, And Education Of Severe Weather In K-12 Schools, Stephen Holden Wooten

Theses and Dissertations

Schools are a focal point in the lives of everyone in the community, especially teachers, parents, and students. Investigating the connection between these individuals and tornadoes by identifying shortcomings in education, training, and emergency procedures can induce more effective and informed decision-making for future encounters. This study evaluated the inclusivity of tornado protocols for students with disabilities, uncovered where parents prefer their child to shelter in early dismissal situations and clarified how extensively natural hazard education and tornado drills are covered in schools. Two surveys and semi-structured interviews were used to obtain responses from earth science teachers, K-12 guardians, and …

06.16.2025 Ored Connect, Liz Williamson

ORED Newsletter

Email address Matters with SPAN and ARC Forms

Participant Support Costs training for PIs available in Blackboard

First Annual Advances In Business Education Conference 2025 Proceedings, Kelsey Metz, Joshua Ray

Advances in Business Education (ABE) Conference Proceedings

Conference Overview: The First Annual Advances in Business Education (ABE) Conference was held on May 16, 2025, at Lincoln Memorial University in Harrogate, Tennessee. Hosted by the LMU School of Business, the ABE Conference was established to promote teaching excellence through innovation and collaboration in business education. With a focus on fostering meaningful dialogue among educators, researchers, and students, the conference welcomed participants from across disciplines and institutions. The event was structured around three key tracks:

Pedagogy & Teaching Excellence: Showcasing innovative teaching methods and strategies for enhancing student learning and engagement.

Business Research: Presenting research focused on advancing knowledge …

California Kelp Forests: An Analysis Of Macrocystis Pyrifera And Nereocystis Luetkeana Restoration After Decades Of Decline, Gabrielle K. Farrer

Master's Projects and Capstones

California’s kelp forests are some of the most biodiverse and productive ecosystems on the planet. Centuries of anthropogenic degradation via habitat destruction and climate change have culminated in decreased kelp forest habitat at an accelerated rate since at least the 1850s (Scarborough et al. 2022; Rogers-Bennett & Catton, 2019; Kumagai et al. 2024; Smith et al. 2023). This study synthesizes major threats, past and present, to California’s kelp forests, including the overharvesting of multiple species, pollution from coastal development, and climate change impacts. I also examine current management practices regarding kelp forests such as the use of marine protected areas …

A Roadmap For Greywater Reuse At The University Of San Francisco Hilltop Campus: A Financial, Regulatory, And Technical Feasibility Study, Apama'bo Anand Oszkar

Master's Projects and Capstones

Abstract

Water scarcity is increasing in California, so we need strategies to reduce potable water demand. Decentralized greywater systems offer promising solutions to this problem. This study provides a roadmap for successfully implementing greywater reuse at the University of San Francisco (USF) by addressing financial, technical, and regulatory considerations. By deploying a mixed-methods approach that combines qualitative expert interviews and quantitative water usage analysis, policy review, cost analysis, and case studies, this study established USF’s annual recycled water demand as 8 million gallons, with two primary uses: irrigation, which accounts for 67% of the demand, and toilet-urinal flushing, which represents …

Development Of Non-Precious Iron-Cobalt Alloy Catalyst For Electrocatalytic Reaction, Harsh Panchal

Electronic Theses & Dissertations

The development of a FeCo alloy catalyst with tunable Fe/Co ratios is examined to improve electrocatalytic performance in reactions like the oxygen evolution reaction (OER), hydrogen evolution reaction (HER), and oxygen reduction reaction (ORR). Many energy conversion devices, such as fuel cells, metal-air batteries, and water-splitting systems, depend on these interactions to function. These technologies have huge potential to meet the increasing need for hydrogen production and renewable energy sources worldwide, which are critical to attaining a sustainable energy future. When compared with noble metal-based catalysts, the FeCo alloy catalyst shows much higher catalytic activity, according to previous studies. Hydrothermal …

Soybean Oil-Derived Acrylate/Methacrylate Ether For High Resolution Additive Manufacturing (3d Printing) Technology, Tanuj Patel

Electronic Theses & Dissertations

Additive Manufacturing is one of the rapidly developing techniques, as industries continue to explore new ways to create prototypes and end-use parts, one of the significant challenges that remains is the reliance on petroleum-based plastics for 3D printing, especially in the production of photocurable resins. that may be used to prototype complex structures and sophisticated geometries that are typically challenging to produce with conventional methods. Thus, replacing petroleum-based plastics with renewable resources is increasingly important for additive manufacturing (3D printing) of photocurable resins. The use of bio-based renewable resources in AM is a feasible alternative to traditional petroleum-based plastics. Henceforth, …

Trade-Off Between Limonene & Geraniol-Based Reprocessable And Non-Reprocessable Epoxy Thermosets: Role Of Aliphatic Diamines In Polymer Networks Design, Priyankkumar Kanubhai Patel

Electronic Theses & Dissertations

The growing demand for sustainable materials, driven by environmental concerns and the rapid depletion of fossil fuels, has garnered significant attention in the fabrication of bio-based epoxy thermosets as renewable alternatives to petroleum-derived thermosetting polymers. The present study focuses on the synthesis and characterization of epoxy prepolymer resins derived from limonene and geraniol via a two-step process, followed by the fabrication of thermally cross-linked flexible epoxy thermoset films using various traditional aliphatic diamine curing agents, namely 1,2-ethylenediamine (EDA), 1,4-butylenediamine (BDA), and 1,6-hexamethylenediamine (HDA). Additionally, the incorporation of cystamine, a disulfide-containing diamine, enabled the formation of a covalent adaptable network through …

Re: Comment Letter For Draft Final Bpsou Unreclaimed Site Anderson Shaft Remedial Action Work Plan (Rawp) (Dated June 14, 2024), Molly Roby

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Effectiveness Of Urban Composting And Waste Management In The San Francisco Bay Area, Elijah Ashiagbor

Master's Projects and Capstones

The increasing food waste epidemic contributes to environmental degradation through amplified GHG emissions, notably CH4, from MSW landfills. Addressing this challenge is essential for public health and environmental sustainability. This research reviews municipal composting initiatives within the San Francisco Bay Area, evaluating effectiveness, efficiency, and sustainability. Utilizing data from CalRecycle and local municipalities, this study analyzes different composting processes, regulatory compliance with California’s Senate Bill 1383, and factors affecting waste diversion rates. Key discoveries indicate that in-vessel composting shows better efficiency and compost quality compared to windrow methods, particularly suitable for urban counties with space limitations. However, participation rates in …

Analyzing Ballast Water Treatments, Invasive Species, And Pathogens, And A Decade-Long Analysis On The San Francisco And Baltimore Ports, Jasmin Ibarra-Cortes

Master's Projects and Capstones

Installation of advanced technologies to treat ballast water on ships is necessary to meet current ballast water management standards and reduce the secondary spread of invasive species during intracoastal voyages. This research includes a literature review on non-native aquatic species, particularly diapausing eggs, and available treatment methods for installation. A comparative analysis from 2014 - 2024 on bulker, tanker, and container vessels arriving coastwise to the ports of San Francisco and Baltimore was performed to evaluate treatment installation trends, traffic patterns, and the effectiveness of treatment(s) on targeting diapausing eggs. Use of ultraviolet (UV) radiation combined with filtration has increased …