Digital Commons Network^™

Interrogating Antagonistic Differences Among Pseudomonas Aeruginosa Cdia Alleles, Haotian Yang

Master's Theses

Bacteria are complex social organisms that live within mixed communities where microorganisms compete for limited resources. We studied Contact-Dependent Growth Inhibition (CDI), a particular type of competition mediated by a type 5b, or two-partner, secretion system that is widely spread among Gram-negative bacteria. CdiB and CdiA make up the two-partner secretion system that mediates CDI. CdiB translocates CdiA to the cell surface, and CdiA delivers its C-terminal toxin domain to the target cell. The C-terminal toxin (Tox) domain of CdiA is highly diverse. We studied Tox domains of various Pseudomonas aeruginosa clinical isolates. We found different strains that contain unique …

Removing Soluble Phosphorus From Tertiary Municipal Wastewater Using Phosphorus- Deprived, Filamentous Microalgae, Aloysia Ahern

Master's Theses

Harmful algal blooms (HABs) can be detrimental to ecosystems, human health, and economies. The low levels of phosphorus remaining in the effluent of municipal wastewater treatment plants can contribute to HAB formation. To achieve more complete phosphorus removal, an effluent treatment method has been proposed that uses phosphorus-deprived, filamentous microalgae to quickly assimilate soluble phosphorus to low concentrations. This study investigated two parameters that influence the feasibility of such a system: (1) the biomass growth productivity of algal cultures during the phosphorus deprivation period and (2) the correlation between the duration of this period and the phosphorus uptake rate by …

Cofermentation, Post-Alcoholic, And Post-Malolactic Fermentation Blending Of Malbec, Merlot And Petite Sirah Wines, Armando Arturo Vega-Osorno

Master's Theses

A two-year study was conducted to assess the effects of cofermentation on red wine varietals. During the winemaking process, wines can be made from two or more varieties by picking, crushing and fermenting them together, a practice known as cofermentation. They can also be blended either after the completion of alcoholic fermentation or after malolactic fermentation. In the first year of the study, two grape varieties, Merlot (Mer), and Malbec (Mal) were cofermented. On the second year, a third varietal, Petite Sirah (PS) was also studied. Cofermented wines containing every possible binomial combination of the varietals was made and one …

Analysis Of Current And Future Flood Hazard In The Sacramento-San Joaquin Delta, Nicholas L. Mcguire

Master's Theses

The primary motivation of this study is to estimate the current and future flood hazard throughout the Sacramento-San Joaquin Delta in the context of sea-level rise. I also analyzed the effects of storm surge and river flow on extreme events to better understand how these events originate and vary spatially and in time. To address this goal, I combined digital water level records (primarily 1983-present) with archival data collected by the California Department of Water Resources (1929-1983) to reevaluate flood hazard in the Delta and investigate the possible sensitivity of the region different sea-level rise projections. Available archival records from …

Design And Analysis Of A Discrete, Pcb-Level Low-Power, Microwave Cross-Coupled Differential Lc Voltage-Controlled Oscillator, Pavin Singh Virdee

Master's Theses

Radio Frequency (RF) and Microwave devices are typically implemented in Integrated Circuit (IC) form to minimize parasitics, increase precision and tolerances, and minimize size. Although IC fabrication for students and independent engineers is cost-prohibitive, an abundance of low-cost, easily accessible printed circuit board (PCB) and electronic component manufacturers allows affordable PCB fabrication.

While nearly all microwave voltage-controlled oscillator (VCO) designs are IC-based, this study presents a discrete PCB-level cross-coupled, differential LC VCO to demonstrate this more affordable and accessible approach. This thesis presents a 65 mW, discrete component VCO PCB with industry-comparable RF performance. A phase noise of -103.7 dBc/Hz …

A Study Of Pressure Probe Response In Steady And Unsteady Flows, Michael T. Charonnat

Master's Theses

The objective of this thesis is two-fold: to analyze the directional calibration of a 3-hole probe in steady flow and to develop a method for the interpretation of measurements recorded with a novel, fast-response Pitot-type probe in unsteady, turbulent flow. Calibration data for the 3-hole probe’s two side ports was taken in the steady, non-turbulent region of a free jet and was evaluated for symmetry. In addition, data that was recorded using one side port in two independent calibration runs was compared to study repeatability. Misalignment was found between the nominally symmetric data sets, which may be the result of …

Mechanisms Of Substrate Selectivity And Transport By Escherichia Coli Atp- Binding Cassette (Abc) Transporter Metni, Yuchun Chen

Master's Theses

ABC transporters are central in many cellular functions including nutrient uptake, signal transduction membrane assembly, and cellular detoxification. Both structural and functional studies have revealed insights into the high-affinity uptake mechanism of the MetNI methionine ABC transporter. Using the energy from ATP binding and hydrolysis, the MetNI-Q system can import L-Met, D-Met, and other methionine derivatives against concentration gradients. Many mechanistic studies of ABC transporter propose a model in which cognate binding proteins sequester substrates in the periplasm and deliver them to the transporter. In contrast, recent in vivo and crystallographic studies of MetNI-Q suggest that some substrates may be …

Smart Spine Tape: Active Wearable Posture Monitoring For Prevention Of Low Back Pain And Injury, Samuel J. Borda

Master's Theses

Back pain and injury are a global health issue and are a leading cause of work and activity absence. Prevention would not only save those affected from the burden of pain and discomfort, but would also save people from loss of over 290 million workdays annually and save the healthcare system billions of dollars in expenses per year. Successful research and development of a wearable technology capable of comprehensively monitoring spinal postures that are leading causes of back pain and injury can result in prevention of mild to severe back pain and injury for high-risk people. To accomplish this, the …

Machine Learning And Software Solutions For Data Quality Assessment In Cern’S Atlas Experiment, Cary Randazzo

Master's Theses

The Large Hadron Collider (LHC) is home to multiple particle physics experiments designed to verify the standard model and push our understanding of the universe to its limits. The ATLAS detector is one of the large general-purpose experiments that make use of the LHC and generates a significant amount of data as part of its regular operations. Prior to physics analysis, this data is cleaned through a data assessment process which involves significant operator resources. With the evolution of the field of machine learning and anomaly detection, there is great opportunity to upgrade the ATLAS Data Quality Monitoring Framework to …

Examining Introductory Computer Science Student Cognition When Testing Software Under Different Test Adequacy Criteria, Austin Shin

Master's Theses

The ability to test software is invaluable in all areas of computer science, but it is often neglected in computer science curricula. Test adequacy criteria (TAC), tools that measure the effectiveness of a test suite, have been used as aids to improve software testing teaching practices, but little is known about how students respond to them. Studies have examined the cognitive processes of students programming and professional developers writing tests, but none have investigated how student testers test with TAC. If we are to improve how they are used in the classroom, we must start by understanding the different ways …

Digital Pastoral, Rebecca Holifield

Master's Theses

Digital Pastoral is a collection of original poems and a creative nonfiction essay, accompanied by a critical introduction.

Upland Migration Of Coastal Marshes As A Response To Sea Level Rise And Fire Management: Past, Present, And Predicted, Devin Jen

Master's Theses

Coastal marshes are one of the most productive and intensively used ecosystems in the world. However, they are under threat due to natural and anthropogenic stressors, such as sea level rise (SLR). SLR can cause marshes to drown, converting them to open water. Marshes can respond to SLR through landward migration when suitable habitat is available. My research focuses on the landward migration pattern and mechanisms. I evaluated the historical land cover changes at the Grand Bay National Estuarine Research Reserve and the Pascagoula River delta over two-time intervals since 1955 and focused on the forest-marsh dynamics. I found that …

Investigation Of Dead Ocean Quahogs (Arctica Islandica) Shells On The Mid-Atlantic Bight Continental Shelf, Alyssa Leclaire

Master's Theses

Ocean quahogs, Arctica islandica, are a long-lived, widely dispersed, biomass dominate in the Mid-Atlantic; therefore, quahog shells are valuable resources for studying climate change over time. Recently, dead ocean quahog shells were discovered south and inshore of the present biogeographic range of this animal. The presence of ocean quahog shells outside the current range is presumably a consequence of past regressions and transgressions of the Cold Pool, the bottom-trapped, cool body of water that allows boreal animals to live at lower latitudes. Dead ocean quahog shells were collected offshore of the DelMarVa Peninsula then radiocarbon-dated, evaluated for taphonomic condition, …

Effects Of Shoreline Development And Freshwater Discharge On Nekton Assemblage And Trophic Structure In A Northern Gulf Of Mexico Estuary, Glenn Schumacher

Master's Theses

Coastal salt marshes support a diversity of nekton and facilitate critical ecosystem functions but are threatened by shoreline development and climate change. Therefore, coastal ecosystem managers have begun incentivizing the use of living shorelines (LS), erosion control structures incorporating native plantings, to mitigate ecological consequences of marsh loss. However, post-restoration climate changes may shift habitat templates and negate positive effects of ecosystem restoration. I evaluated the ecology nekton along LS, natural marshes, hardened shorelines and greyed shorelines within Biloxi Bay, Mississippi, during a high freshwater discharge (HFD) period by comparing nekton assemblage (using species richness, Shannon-Wiener diversity, and relative abundance), …

Fabrication Of Lab-Scale Polymeric And Silicon Dioxide Nanoparticle-Enabled Thin Film Composite Reverse Osmosis Membranes For Potable Reuse Applications, Timothy J. Dinh

Master's Theses

Reverse osmosis (RO) is widely used for water reclamation and is one of the most feasible technologies for addressing water scarcity around the world. RO membrane fabrication procedures are continually being optimized and modified to enhance the treatment performance and efficacy of the RO process. A review of the existing literature published on membrane fabrication revealed that a detailed and reproducible methodology consistent among prior studies was not available. Therefore, the primary objective of this study was to utilize techniques from prior research to develop a reliable lab-scale membrane fabrication process for studying the potable reuse applications of TFC RO …

Deep Learning For Detecting Trees In The Urban Environment From Lidar, Julian R. Rice

Master's Theses

Cataloguing and classifying trees in the urban environment is a crucial step in urban and environmental planning. However, manual collection and maintenance of this data is expensive and time-consuming. Algorithmic approaches that rely on remote sensing data have been developed for tree detection in forests, though they generally struggle in the more varied urban environment. This work proposes a novel method for the detection of trees in the urban environment that applies deep learning to remote sensing data. Specifically, we train a PointNet-based neural network to predict tree locations directly from LIDAR data augmented with multi-spectral imaging. We compare this …

Reinforcement Actor-Critic Learning As A Rehearsal In Microrts, Shiron Manandhar

Master's Theses

Real-time strategy (RTS) games have provided a fertile ground for AI research with notable recent successes based on deep reinforcement learning (RL). However, RL remains a data-hungry approach featuring a high sample complexity. In this thesis, we focus on a sample complexity reduction technique called reinforcement learning as a rehearsal (RLaR), and on the RTS game of MicroRTS to formulate and evaluate it. RLaR has been formulated in the context of action-value function based RL before. Here we formulate it for a different RL framework, called actor-critic RL. We show that on the one hand the actor-critic framework allows RLaR …

Population Genetics Of Cownose Rays, Rhinoptera Spp. In The Western Atlantic, Helen Weber

Master's Theses

Using molecular tools (e.g., the NADH subunit II mitochondrial gene), this study was the first to document the Brazilian cownose ray, Rhinoptera brasiliensis, within the northwestern Atlantic (NWA), and was the first study to examine population structure in R. brasiliensis within the NWA or northern Gulf of Mexico (GMX), revealing novel insights into the population biology of the animal and extending its range by nearly 1,500 km. This study also examined the sympatrically occurring American cownose ray, R. bonasus, and found population structure between the NWA and the GMX and the NWA and the southwestern Atlantic (SWA). High …

Pressure Disturbance Upstream Of The Boundary Layer Data System, Michelle S. Leclere

Master's Theses

The primary objective for this work was to evaluate the reliability of computational fluid dynamics (CFD) tools in the prediction of upstream surface pressure disturbance and pressure drag of various instrument excrescence shapes for a small aircraft flight test device called the Boundary Layer Data System (BLDS). Insights on pressure disturbance will serve as a guide for the placement of BLDS probes/sensors, and pressure drag can be used to ensure sufficient adhesive is used to install BLDS instrumentation. The Mach number for all CFD cases was 0.12 and the Reynolds number based on excrescence height varied from 4 x 10 …

Changes In The Morphology Of Widgeon Grass (Ruppia Maritima) With The Onset Of Reproduction And Impacts On Fish Assemblages At The Chandeleur Islands, La, Matthew Byrnes

Master's Theses

Seagrasses are important submerged coastal habitats that support nearshore communities. Ruppia maritima (widgeon grass) is a widespread species whose leaves branch extensively when reproductive. The goal of this study was to understand use of reproductive and non-reproductive R. maritima by fishes, recognizing the morphological change undergone by the plant when flowering. During the peak reproductive season in August and September 2021, R. maritima meadows at the Chandeleur Islands, LA were sampled to describe the spatial distribution and morphology of reproductive plants and investigate habitat use by fish assemblages. We assessed spatial trends in R. maritima presence and occurrence of reproduction …

Sedimentary Characteristics And Associated Carbon And Nutrients Of Overbank Sediments Deposited During The 2018, 2019, And 2020 Floods In Embanked Floodplains Along The Lower Mississippi River Near Natchez, Mississippi, Rachel Kelk

Master's Theses

The Lower Mississippi River (LMR) experienced major floods in 2018, 2019, and 2020. Sediment deposition in the embanked floodplains during floods represent important storage and sequestration opportunities for carbon and nutrients from ~40% of the continental USA. This research aims to compare depositional thicknesses, organic matter (OM), carbon (C), nitrogen (N), phosphorous (P) concentrations, and grain sizes in floodplain sediments deposited by the combined 2018-19 floods to the 2020 flood along the LMR near Natchez, Mississippi. Greater depositional thicknesses in 2018-19 are best explained by their combined flood durations; the 2019 flood was the longest in recorded history. Slightly higher …

Psychosocial Maturity And Alcohol Outcomes: The Mediating Role Of Alcohol Protective Behavioral Strategies, Skyler Hoover

Master's Theses

The present study evaluated the mediating role of alcohol protective behavioral strategies on the relationship between temperance, responsibility, perspective (i.e., the facets of psychosocial maturity) and alcohol use outcomes. Potential invariant paths among graduate and undergraduate students were also explored. All participants were undergraduate and graduate students at the University of Southern Mississippi aged 18 to 25. Participants reported demographic information and completed measures of temperance, responsibility, perspective, alcohol use, and alcohol consequences. Results indicated the full mediation model showed poor fit the data; greater temperance predicted greater alcohol protective behavioral strategy use, greater responsibility and perspective predicted less alcohol …

Artist-Configurable Node-Based Approach To Generate Procedural Brush Stroke Textures For Digital Painting, Keavon Chambers

Master's Theses

Digital painting is the field of software designed to provide artists a virtual medium to emulate the experience and results of physical drawing. Several hardware and software components come together to form a whole workflow, ranging from the physical input devices, to the stroking process, to the texture content authorship. This thesis explores an artist-friendly approach to synthesize the textures that give life to digital brush strokes.

Most painting software provides a limited library of predefined brush textures. They aim to offer styles approximating physical media like paintbrushes, pencils, markers, and airbrushes. Often these are static bitmap textures that are …

Exploring The Impact Of Cognitive Awareness Scaffolding For Debugging In An Introductory Computer Science Class, Jiwon Lee

Master's Theses

Debugging is a significant part of programming. However, a lot of introductory pro- gramming classes tend to focus on writing and reading code than on debugging. They utilize programming assignments that are designed in ways such that students learn debugging by completing these assignments which makes debugging more of an im- plicit goal. In this thesis, we propose a cognitive awareness scaffolding in debugging to help students self-regulate their debugging process. We validate its effectiveness by conducting experiments with students in four sections of a Data Structures course, which is one of the introductory computer science classes at California Polytechnic …

Music Visualization Using Source Separated Stereophonic Music, Hannah Eileen Chookaszian

Master's Theses

This thesis introduces a music visualization system for stereophonic source separated music. Music visualization systems are a popular way to represent information from audio signals through computer graphics. Visualization can help people better understand music and its complex and interacting elements. This music visualization system extracts pitch, panning, and loudness features from source separated audio files to create the visual. Most state-of-the art visualization systems develop their visual representation of the music from either the fully mixed final song recording, where all of the instruments and vocals are combined into one file, or from the digital audio workstation (DAW) data …

A Study Of Grammar-Based Fuzzing Approaches, Ziwei Wu

Master's Theses

Fuzzing is the process of finding security vulnerabilities in code by creating inputs that will activate the exploits. Grammar-based fuzzing uses a grammar, which represents the syntax of all inputs a target program will accept, allowing the fuzzer to create well-formed complex inputs. This thesis conducts an in-depth study on two blackbox grammar-based fuzzing methods, GLADE and Learn&Fuzz, on their performance and usability to the average user. The blackbox fuzzer Radamsa was also used to compare fuzzing effectiveness. From our results in fuzzing PDF objects, GLADE beats both Radamsa and Learn&Fuzz in terms of coverage and pass rate. XML inputs …

Specialized Named Entity Recognition For Breast Cancer Subtyping, Griffith Scheyer Hawblitzel

Master's Theses

The amount of data and analysis being published and archived in the biomedical research community is more than can feasibly be sifted through manually, which limits the information an individual or small group can synthesize and integrate into their own research. This presents an opportunity for using automated methods, including Natural Language Processing (NLP), to extract important information from text on various topics. Named Entity Recognition (NER), is one way to automate knowledge extraction of raw text. NER is defined as the task of identifying named entities from text using labels such as people, dates, locations, diseases, and proteins. There …

Development Of A Dual-Band Radio Repeater To Be Carried By A Fixed-Wing Small Unmanned Aerial System, Carl Recine

Master's Theses

With the continued rise in wildfires in California, and around the world, technological advancements are needed to improve the safety and effectiveness of wildland firefighters. One area that provides an opportunity for such development is the deployment of temporary communications networks. Currently, radio repeaters are set up on mountain tops in the response area; such repeaters do not provide flexibility once installed, still have blind spots, and require the time of valuable assets like helicopters to install.

This thesis will establish the feasibility of airborne radio repeaters for wildland firefighting. In order to successfully demonstrate the feasibility of such an …

Increasing The Effectiveness Of K-12 Stem Worshops Through Targeted Context And Creative Technolgies, Melina Lopez

Master's Theses

Economic projections reveal a need for one million more Science, Technology, Engineering, and Math (STEM) professionals over the next decade than the United States is producing at the current rate. As a result, STEM education is a major focus of recent legislation and funding in Congress as the number of STEM professionals is inadequate to support innovation and the ever-changing economy. In response to the urgent need for more competitive STEM professionals, there has been a widespread implementation of workshops, organizations, and school programs aimed at amplifying K-12 student STEM literacy and interest. Some programs are even created to specifically …

A Course On Advanced Real-Time Embedded Systems, Krista Round

Master's Theses

This thesis discusses the development of an advanced real-time embedded systems course offered at California Polytechnic State University, San Luis Obispo, which aims to prepare students to design modern complex real-time embedded systems. It describes the goals of the real-time embedded systems curriculum, which includes an introductory and advanced course. Finally, this paper discusses the challenges of creating a successful advanced real-time embedded systems course and proposes changes to the current advanced real-time embedded systems course in response to those challenges.