Digital Commons Network^™

Using Bivalves As An Indicator For Fecal Bacteria, Kamala Chuss

Honors Scholar Theses

This project focuses on the integration of fecal bacteria from warm-blooded animals into bivalve tissue, and the utilization of bivalves as an indicator for fecal bacteria in waterways. Bivalves may give a more representative long-term average of fecal bacteria in water as compared to direct water testing. The primary objective is to create a standard operating procedure to use bacterial testing of bivalves as a proxy for bacteria concentration in the water. This method can be used in places where bivalves do not already exist by adding them to a body of water, or by collecting bivalves that already exist …

Invasion Stress Mitigates Climate Stress In A Brackish Marsh Amphipod, Lorna E. Haworth, Sarah Nancollas, Susie N. Landa, Anne E. Todgham, Richelle L. Tanner

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

1. Organisms in coastal brackish ecosystems face not only highly variable environmental conditions, but the intensity and stochasticity of these environmental conditions are anticipated to increase due to climate change. While environmental changes are often presented unilaterally as stressors, there are some anthropogenic environmental transformations, such as the introduction of habitat forming plant species, that may mitigate physiological stress imposed by warming. In Suisun Marsh in the California Delta, native plant canopies allow light and heat to penetrate to the understory yet the canopies of the introduced Phragmites australis reed block out sunlight and heat for organisms living below.
2. We set …

Brain Endothelial Permeability, Transport, And Flow Assessed Over 10 Orders Of Magnitude Using The In Situ Brain Perfusion Technique, Quentin R. Smith, Haritha Mandula, Jagan Mohan R. Parepally, Jun Oki, Fancy Thomas, Helen R. Thorsheim, Abraham J. Al‑Ahmad, Thomas J. Abbruscato, Per Ask, David S. Hage, Peter J. Robinson

David Hage Publications

Background Cerebral blood flow normally places a limit on the magnitude of brain vascular permeability (P) that can be measured in vivo. At normal cerebral blood flow, this limit falls at the lower end of lipophilicity for most FDAapproved CNS drugs. In this study, we report on two methods that can be used to overcome this limitation and measure brain vascular permeability values that are up to ~1000 times higher using the in situ brain perfusion technique.

Methods Rat brain was perfused with physiological saline at increased flow rate and in the presence of various concentrations of plasma protein, serum …

Phytoplankton As A Bioindicator For Evaluation Of The Irrigation Water Quality Near A Metal-Coating Factory, Mimatun Nasihah, Ardyati Ardyati, Dian Siswanto, Catur Retnaningdyah

Makara Journal of Science

The irrigation water quality in Plosowahyu village, Lamongan District, Indonesia, has declined because of industrial waste disposal in irrigation canals. Specifically, waste from a metal-coating factory considerably threatens the aquatic ecosystem. To assess the impact, we evaluated water quality on the basis of phytoplankton diversity and various phys-icochemical parameters. We collected water and phytoplankton samples from four locations in Plosowahyu village: before the wastewater treatment plant (WWTP) outlet of the metal-coating factory, at this outlet, and from two sites in Wahyu River, with three repetitions at each site. The study measured several physicochemical parameters, including total dissolved solids (TDS), total …

Analysis Of Dense Metals Accumulation In Shikaripara Stone Mines, Gopinath Gorai, Nirajan Kumar Mandal

Makara Journal of Science

This study aimed to measure the amount of dangerous substances in the cultivated area of the Shikaripara stone mines in Jharkhand, India, which are well known for their stone quarrying. Sixteen soil samples were collected at varying dis-tances from the Shikaripara stone mines in the Dumka District of Jharkhand. The metals found in these samples in-clude Pb, As, Zn, Mn, Cd, Cu, Fg, and Fe. The combined amount of the elements was calculated by inductively coupled plasma mass spectrometry. Enrichment factor, accumulation index, contamination factor, pollution load index (PLI), Nemerow index, and ecological risk index (RI) were employed to assess …

Comparing Multivalent Cross-Linked Sodium Alginate/ Montmorillonite Beads Containing Curcumin Or Cayenne Pepper As Drug Carriers And Their Antimicrobial Resistance, Shionainn Traynor, Shubham Sharma

SURE Journal: Science Undergraduate Research Experience Journal

The aim of the following work was to investigate and compare curcumin and cayenne pepper in microbeads composed of sodium alginate (SA) crosslinked with montmorillonite (MMT) to act as drug carriers and their antimicrobial resistance. The microbeads were prepared through ion-exchange in multivalent solutions of CaCl₂, MgCl₂ and AlCl₃. The microbeads were characterized by Scanning Electron Microscopy (SEM), Energy Dispersive X-ray analysis (EDX) and the time required for intercalation of curcumin and cayenne pepper with MMT. Simulated intestinal fluid (pH 7.3) and gastric fluid (pH 1.2) at 37°C were used for comparison in swelling studies. …

Editorial - Sure Journal Vol 6, Anne M. Friel, Eva Campion, Sinead Loughran

SURE Journal: Science Undergraduate Research Experience Journal

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The Mathematical Laws Of Morphology And Biomechanics Through Ontogeny, Wijesooriya Kisal Wijesooriya

The Journal of Purdue Undergraduate Research

No abstract provided.

Performance Prediction For Hub-Based Swarms, Puneet Jain

Theses and Dissertations

Optimization problems lie at the core of improving performance in various tasks, ranging from day-to-day work scheduling to coordinating robots in a warehouse fulfillment center. Distributed swarm systems provide a robust and adaptive solution approach to many optimization problems. Instead of using one really sophisticated agent, multiple smaller less sophisticated agents can provide the flexibility to evaluate more options and still provide a "good" answer. This dissertation uses graphs to model, analyze, and simulate swarm behavior, primarily to predict the time-to-converge (TTC) and success probability. First, we use a bipartite model for the distributed best-of-N problem, and show how the …

Utility Of Immobilized Metal Salens As Electrocatalysts: Fuel Cells And Organic Electrosynthesis, Zachary A. Nguyen, Shelley D. Minteer

Chemistry Faculty Research & Creative Works

There have been significant advancements in the electrosynthesis of fuels and organic molecules, making it an increasingly sustainable and cost-effective alternative to traditional chemical redox reagents. Early versions of these systems faced challenges in chemo selectivity due to high applied overpotentials, which have been mitigated with the introduction of molecular electrocatalysts, like metal salens (MSalens). These MSalens reduce the required overpotentials, increase turnover numbers (TON), and have simple modularity within their ligand structure allowing for tunable selectivity. While these MSalen electrocatalysts are typically used homogeneously for engineering simplicity, downstream separations are often costly and time-consuming. Immobilization of MSalens addresses these …

Effect Of Temperature And Rhenium Content In Precipitates On Dispersion Hardening Of Tungsten, Yulia R. Sharapova, Arseny M. Kazakov, Elena A. Korznikova, Alexandr Zinovev, Dmitry Terentyev, Sergey V. Dmitriev

Karbala International Journal of Modern Science

Tungsten (W) is being developed as a plasma-facing material for fusion reactors, where it is subjected to MeV neutron irradiation, low-energy helium isotope particles, and high temperatures. These conditions lead to the formation of point defects, dislocation loops, voids, and transmutation into rhenium (Re) and osmium (Os), which form precipitates that significantly impact dislocation motion and increase hardness. This study uses molecular dynamics modeling to examine the interaction between an edge dislocation and Re-rich particles of various stoichiometries, specifically coherent bcc-phase particles and noncoherent σ-phase precipitates. Results show that shear stress increases by approximately 20-40% with larger particle size (3-5 …

Key Epigenetic And Signaling Factors In The Formation And Maintenance Of The Blood-Brain Barrier, Jayanarayanan Sadanandan, Sithara Thomas, Iny Elizabeth Mathew, Zhen Huang, Spiros L Blackburn, Nitin Tandon, Hrishikesh Lokhande, Pierre D Mccrea, Emery H Bresnick, Pramod K Dash, Devin W Mcbride, Arif Harmanci, Lalit K Ahirwar, Dania Jose, Ari C Dienel, Hussein A Zeineddine, Sungha Hong, Peeyush Kumar T

Faculty, Staff and Student Publications

The blood-brain barrier (BBB) controls the movement of molecules into and out of the central nervous system (CNS). Since a functional BBB forms by mouse embryonic day E15.5, we reasoned that gene cohorts expressed in CNS endothelial cells (EC) at E13.5 contribute to BBB formation. In contrast, adult gene signatures reflect BBB maintenance mechanisms. Supporting this hypothesis, transcriptomic analysis revealed distinct cohorts of EC genes involved in BBB formation and maintenance. Here, we demonstrate that epigenetic regulator's histone deacetylase 2 (HDAC2) and polycomb repressive complex 2 (PRC2) control EC gene expression for BBB development and prevent Wnt/β-catenin (Wnt) target genes …

The Implementation Of Artificial Intelligence In University Classrooms: Perspective And Applications, Erika Grodzki, Gary Carlin, Stefanie Powers, Hung Chum Kao

Faculty and Staff Publications & Presentations

This study examined the integration of Artificial Intelligence (AI) in university classrooms, focusing on its benefits, challenges, and the diverse perspectives of academic faculty. While AI was widely embraced in disciplines like animation and design for enhancing creativity and efficiency, traditional fields remained cautious due to concerns about academic integrity and its impact on critical thinking. By analyzing literature and case studies, the presentation highlighted AI’s transformative potential in higher education, fostering dialogue on its strategic adoption to balance innovation with ethical and pedagogical considerations.

Climate- And Land-Use Change Impacts On Ecosystem Services Provided By Prairie Pothole Wetlands, Alina Mullins

Master's Projects and Capstones

Prairie pothole wetlands are a type of depressional, isolated wetland that can be found in the glaciated landscape of the mid-central United States and portions of southern Canada, also referred to as the Prairie Pothole Region (PPR). The region is consistently recognized for its historic production and support of migratory waterfowl populations among other types of mammals and invertebrates largely due to the variability in pothole wetlands water levels and vegetative structure. Isolated from other waterbodies and lacking surface water connections, the hydrology of prairie pothole wetlands is influenced by the region’s continental climate. Historically, the region receives much of …

Identifying Fecal Contamination Sources In The Grand Bay National Estuarine Research Reserve, Amanda M. Free

Theses and Dissertations

The Grand Bay National Estuarine Research Reserve (GNDNERR) has a history of elevated fecal coliform counts. However, the source of the contamination is not well understood. According to past sanitary surveys, there has been a history of malfunctioning residential septic systems and inadequate wastewater treatment in the upper watershed. Feral hogs (Sus scrofa) and birds are also abundant in the estuary and could be potential contributors to elevated fecal coliform levels. To better understand the temporal and spatial variation of fecal coliforms in the GNDNERR and inform oyster reef management, eight sites within the GNDNERR watershed were sampled monthly for …

Algal Community Investigations: Present Day To Year-2100 For Mississippi Lakes And The Western Mississippi Sound, Emma Madison Tucker

Theses and Dissertations

Algae play a key role in the aquatic environment as primary producers; however, they can form harmful algal blooms that are detrimental to the aquatic environment, people, and even the economy. It is generally believed that climate change will influence future algal blooms. The first study estimated algae community in three freshwater locations in Mississippi, Desoto Lake, White’s Creek Lake, and Columbus Lake, and one saline location, Western Mississippi Sound, using modern and new tools of the autonomous surface vessel, FlowCam, and EcoTaxa. From those results and leading into the second study was the application of four climate scenarios on …

Investigations Of Guayule Resin As A Wood Protectant, Queen Aguma

Theses and Dissertations

Wood products are subject to deterioration by numerous processes, as a biological material. Today, a significant area of preservative development is the utilization of existing plant residues that have water-repelling, antibacterial, antifungal, and insecticidal properties as components of wood protectants. Parthenium argentatum, known as guayule (wy-oo-lee), is a promising wood protectant due to its resin. However, the resin's complicated chemical, physical, and solvent-resistant properties make it difficult to use. The primary goal of this study was to eliminate the use of any solvent and rely on thermal modification only to fractionate usable compounds from guayule resin. Utilizing heated dialysis and …

Deep Learning - Based Automated Detection And Classification Of Foreign Materials In Poultry Using Color And Hyperspectral Imaging, Rohini Maram

Theses and Dissertations

This thesis explores the use of Deep learning for detection and classification of small foreign materials (FMs) in poultry meat using color and hyperspectral imagery (HSI). The study employs You only look once (YOLO) object detection models on color images for precise localization, and one-dimensional convolutional neural network (1D CNN), two-dimensional convolutional neural network (2D CNN) was used on HSI (600 – 1700 nm) for classification. Twelve different FMs commonly known as polymers including PVC, PET, LDPE and HDPE, were examined using 52 color and 52 hyperspectral images. Four YOLO models (v5x, v7x, v8x, v10x) were implemented, trained, tested and …

Investigation Of Real-Time Gaseous Thermal Decomposition Products Of Representative Per- And Polyfluoroalkyl Substances (Pfas), Kateřina Litvanová, Bethany Klemetstrud, Feng Xiao, Alena Kubatova

Chemistry Faculty Publications

The thermal decomposition of per- and poly fluoroalkyl substances (PFAS) is poorly understood. Here, we present an innovative, comprehensive analytical method to investigate their thermal decomposition, including perfluorocarboxylic acids (PFCAs), alcohol, sulfonates, and GenX (acid dimer), focusing on identifying their breakdown products. In this study, evolved gas analysis–mass spectrometry (EGA-MS) was used for fast real-time screening to determine the significant temperatures to be investigated with the thermal desorption-pyrolysis coupled with gas chromatography–mass spectrometry (TD-Py-GC-MS), which provided detailed information about evolved PFAS and their breakdown products. This approach enabled a systematic study of perfluorocarboxylic acids (PFCAs) ranging from C₃ to …

Recovery Of Black Carbon Concentrations In Burned Forests In Wyoming, Usa, Monica Vanesa Zapata Villegas

Dissertations and Theses

Burned forests that remain standing following fire release light-absorbing particles (LAPs), including black carbon (BC), into winter snowpacks, reducing snow surface albedo and accelerating snowmelt timing for decades postfire. Although the role of LAPs in seasonal snow has been extensively studied, the spatiotemporal variability of LAPs' contributions to snowmelt relative to time-since-fire and burn severity remains unknown. This study aimed to quantify the spatiotemporal variability of forest fire effects on LAPs in snow and associated snow albedo in the Triple Divide region of western Wyoming, headwaters of the Colorado, Columbia, and Missouri rivers. Using geochemical analysis and radiative transfer modeling, …

A Survey Of Several Python Libraries Foe Computational Geometry, Meghana Kolluru

Masters Projects

This project delves into computational geometry, a crucial area of computer science, by

implementing algorithms to solve geometric problems using Python libraries like Shapely, SciPy,

and Triangle. It begins with foundational tasks such as creating geometric objects (points, lines,

polygons) and performing operations like calculating distances, intersections, and unions. These

basics lay the groundwork for tackling more advanced applications.

Key implementations include the Convex Hull, which computes the smallest convex

polygon enclosing a set of points, aiding in applications like collision detection and GIS. The

project also explores Voronoi Diagrams, which partition a plane into regions based on proximity,

and …

Sulfhydryl-Containing Compounds And Iron Homeostasis: Mechanisms Of Labile Iron Pool Dysregulation And Consequences For Cellular Health, Steven Lowell Mann Christiansen

Theses and Dissertations

While iron's unique coordination chemistry and redox activity have resulted in its broad incorporation into biological systems, dysfunction in key iron-regulating mechanisms can transform these biochemical advantages into factors that contribute to several pathological conditions. This dissertation explores the complex interactions between iron and sulfhydryl-containing compounds (SCCs), with particular focus on glutathione's (GSH) role in stabilizing iron reactivity juxtaposed with homocysteine's (Hcy) ability to disrupt iron homeostasis and promote disease progression. Through rigorous biochemical analysis and experimentation, we demonstrate that Hcy disrupts iron regulation through several mechanisms: (1) Hcy competitively displaces protective iron-binding molecules in the Labile Iron Pool (LIP), …

Emerging Aquatic Plant Threats To Oregon Waterways, Jacob Rose, Gabriel Campbell

Center for Lakes and Reservoirs Publications and Presentations

This brief presentation provides an overview some of two invasive aquatic plants that pose a threat to the Columbia River, where it borders Oregon and Washington. Flowering rush (Butomus umbellatus) and fragrant waterlily (Nymphaea odorata) threaten aquatic habitats up and down the Columbia River. Staff from the Center for Lakes & Reservoirs promoted a quick, picture-based key for flowering rush and lookalikes. This presentation was given orally at the Oregon Department of Agriculture's Interagency Noxious Weed Symposium to an audience of natural resource practitioners.

Growth And Yield Of Bok Choy (Brassica Rapa L.) Plants In Post-Rock Excavation Soils Provided With Phosphate-Solubilizing Bacteria And Manure, Cecep Hidayat, Yati Setiati Rachmawati, Dhea Rizqi Utami, Sofiya Hasani, Anna Aina Roosda, Windhy Chandria

Jurnal Kultivasi

Elevated sand and gravel mining to meet market needs causes negative impacts on the environment, soil, and biodiversity. The government issued a regulation that requires revegetation as reclamation of mineral and coal mining. The conversion needs to overcome the physical and chemical characteristics of post-rock excavation soil that can be utilized by economic value plants such as bok choy. This experiment aimed to determine the growth and yield of bok choy on post-rock excavation soil by providing phosphate solubilizing bacteria (PSB) and various manure types. The study was conducted in Margasari Village, Buah Batu District, Bandung at an altitude of …

Current Status And The Significance Of Local Wisdom Biofertilizer In Enhancing Soil Health And Crop Productivity For Sustainable Agriculture: A Systematic Literature Review, Irwandhi, Fiqriah Hanum Khumairah, Emma Trinurani Sofyan, Nadia Nuraniya Kamaluddin, Anne Nurbaity, Diyan Herdiyantoro, Tualar Simarmata

Jurnal Kultivasi

Soil fertility is recognized as a crucial factor in supporting plant growth and productivity. The utilization of biofertilizers as environmentally friendly fertilizers is aimed at enhancing soil fertility and plant productivity. This study aims to explore the potential of local material for developing local wisdom biofertilizers (LWB) for achieving sustainable agriculture. A systematic literature review was conducted using bibliometric analysis, Preferred Reporting Items for Systematic Reviews, and Meta-Analyses (PRISMA) method, employing the Scopus search engine with the keywords "local AND wisdom AND biofertilizer" OR "biofertilizer" OR "local AND microorganism" OR "soil AND health OR crop AND productivity OR sustainable agriculture". …

Environmental Concerns: Thinking Beyond The Traditional Elections, Muhammad Faisal Ali

CBER Conference

A sustainable future is intricately tied to maintaining a sustainable environment, both on a global scale and within individual countries. In 2023, recorded temperatures reached unprecedented highs, signaling a concerning trend toward global warming and prompting widespread alarm. These circumstances have spurred increased global attention and a shift away from intensive emission practices towards more environmentally friendly approaches. This research provides empirical evidence on the monetary value of lost environmental benefits due to the production of massive ballot papers for the elections. Focusing on the environmental impact of the 2024 General Election, the study also considers the environmental implications beyond …

Orbital Thinking: Planetary Orbit As A Model For Neurodivergent Thought Experiences In Animation, Thomas Labow

Honors Projects

As an artist diagnosed with Attention-Deficit/Hyperactivity Disorder, or ADHD, the aim of my research is to artistically explore neurodivergent experiences using gravity-assisted space flight as a visual metaphor for episodic memory and the pivot between correlated ideas. “Orbit of Attention” is a short animated film that visualizes interconnected mental processes through the use of a character-driven narrative. The creative choice of depicting ideas as planets is inspired by the gravity-assisted flight path of the Voyagers’ grand tour of the solar system. In visualizing unconventional thought processes, “orbital thinking” was used to model episodic memory. As a research project, this film …

Antibiotic Resistance Of Laboratory E. Coli Strains, Alexis H. Hart

Honors Projects

Antibiotic resistance is an ongoing global health crisis. The prevalence and distribution of antibiotic resistance in environmental microbial communities have become climactic areas of investigation due to their far-reaching implications for ecosystem health, human well-being, and the sustainability of antimicrobial efficacy.

On The Benefits Of Directness In Virtual Characters For Motivational Interviews, Michael O'Mahony, Cathy Ennis, Robert Ross

Conference papers

Understanding the factors influencing successful engagement with Embodied Conversational Agents (ECAs) remains a significant challenge. This understanding could be used to personalise agents to users to improve interactions. Some studies have shown that simulating personalities in healthcare agents can improve effectiveness and engagement. However, it is not yet well understood how variations of agent personality can be leveraged to improve user engagement with Motivational Interviewing (MI) ECAs. Specifically how the balance between agent warmth and directness can be controlled in an MI agent to improve likeability and engagement. We conducted an online Wizard-of-Oz (WoZ) mediated study of two variants of …

Methods In Environmental Studies, Erika Dunagan, Maya Mendoza, Posey Graber, Alex Cullins, Emma Mcginnis, Ally Nepomuceno, Isabella Buchan

Featured Student Work

This publication is a collection of undergraduate research conducted in the Methods in Environmental Studies course at the University of San Francisco in Fall 2024. The student-led projects explore the intersections of place, policy, ecology, and cultural identity through applied environmental research methodologies. Topics include a decolonial examination of the Forest Park Mound Group and Indigenous resilience in St. Louis; a comparative study of Navajo cosmology and ecological justice; a social and environmental impact assessment of Costa Rica’s National Decarbonization Plan; a psychogeographical analysis of Golden Gate Park and its impact on the psyche, emotions, behaviour, and health of urban …