Life Sciences Commons^™

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 …

Understanding Rare Species In California: An Assessment Of Camatta Canyon Amole (Hooveria Purpurea Var. Reducta) And A Meta-Analysis Of California Rare Plants In Literature, Kieran N. Althaus

Master's Theses

California is currently in the midst of a biodiversity crisis. There are approximately 5,000 native species of plants in California, a quarter of which are considered rare. Determining threats to these rare plants is often times difficult. Despite California's botanical resources, we still know very little about much of California’s rare plants. San Luis Obispo County is home to 2,000 of California’s native plant taxa, one- third of which are rare or endemic to the county. These species are of great local and environmental concern.

In Chapter 1, we attempted to assess the impact of non native species on a …

Efficacy Of Chemical And Biological Stump Treatments For The Control Of Heterobasidion Occidentale Infection Of California Abies Concolor, Adrian Luis Poloni

Master's Theses

We conducted an experimental evaluation of treatments to limit Heterobasidion occidentale infection of white fir (Abies concolor) stumps and wounds in California mixed conifer forests. We tested the efficacy of urea, borate, and a mixture of two locally collected Phlebiopsis gigantea strains in preventing pathogen colonization of fir stumps and separately, urea and borate as infection controls on experimental stem wounds. These were paired with a laboratory test on ~100 g wood blocks with and without a one-week delay between inoculation and treatment. Urea, borates, and Phlebiopsis treatments all significantly reduced the stump surface area that was colonized …

The Effects Of Cofermentation Of Cider And Apple Pomace On Cider Attributes, Abigail D. Affonso

Master's Theses

Phenolics are critical to the sensory attributes and health benefits of hard cider due to their contribution to the flavor, mouthfeel, and antioxidant activity. With the increase in demand for cider, the use of dessert apple varieties has become more common leaving ciders lacking in phenolics. However, a promising method to increase their phenolic content is through maceration with apple pomace. This study evaluated the effect maceration with apple pomace during cider fermentation on the extraction of phenolic compounds, as well as its effect on the sensory properties of the final product. For this study, ciders were fermented with 0% …

A Comparative Study Of The Effects Of Microalgae On Poultry Production, Taylor Kaitlyn O'Lear Reid

Master's Theses

Research has shown Spirulina to be a viable feedstuff in poultry production. Other species of microalgae are being studied to determine their effects on poultry production. This project compared four microalgaes: Hydrodictyon, Vaucheria, Uronema, and Spirulina and was broken down into three trials. The first experiment investigated the digestibility of an algae species, Spirulina, in broiler chicken diets. Eighty, 25-day-old Ross 708 broiler chicks were sorted into 20 metabolism cages and received one of two diets: Control Diet or Test Diet (75% basal diet + 25% Spirulina). The apparent ileal amino acid digestibility (AIAAD) of lysine, methionine, cysteine, threonine, isoleucine, …

Developing A Miniature Smart Boat For Marine Research, Michael Isaac Eirinberg

Computer Engineering

This project examines the development of a smart boat which could serve as a possible marine research apparatus. The smart boat consists of a miniature vessel containing a low-cost microcontroller to live stream a camera feed, GPS telemetry, and compass data through its own WiFi access point. The smart boat also has the potential for autonomous navigation. My project captivated the interest of several members of California Polytechnic State University, San Luis Obispo’s (Cal Poly SLO) Marine Science Department faculty, who proposed a variety of fascinating and valuable smart boat applications.

Aged 539 Graduate Internship Report-Golden Valley High School, Madison R. Zittel

Agricultural Education: Graduate Internship Reports

This internship and project report includes documentation required in meeting the quality criteria for secondary-level programs of instruction in agriculture. The documents are concurrently used for the Agriculture Incentive Grant review process at Golden Valley High School conducted by representatives of the California Department of Education. The supporting material includes information to receive state and local funding, outline the goals and objectives of the program, along with an overview of Golden Valley High School, the agriculture program and the community.

Assessing Black Rat Population Abundance And Persistence At The Oceano Dunes State Vehicular Recreation Area, Mars Lu, Julia Kristina Perez

Biological Sciences

The black rat, Rattus rattus, is considered one of the most destructive and widespread invasive species around the world, with the ability to damage crops, kill native species, and spread disease. The Oceano Dunes State Vehicular Recreation Area (ODSVRA) is home to numerous at-risk species such as the Western Snowy plovers (Charadrius nivosus nivosus) and California Least Tern (Sternula antillarum browni). Black rats have been detected at the ODSVRA in studies conducted in 2015 and 2018, and may be a potential threat to nesting seabirds like the plover and the tern. In addition, they may …

Biomass Estimation Of Marine Biofilms On Plastic Surfaces, Kian Banihashemi, Fernando Javier Gil

Biological Sciences

Plastics have become a major source of marine pollution, which threatens food safety and quality, human health, and marine ecosystems. Due to the drastic negative effects of plastics in a marine environment, alternative biodegradable plastics are being generated that are more eco-friendly and have less environmental impact. Though some of these plastics are known to biodegrade, the process of degradation for bioplastics has not been heavily studied in a marine environment. This pilot project sought to both quantify the process of biodegradation and compare across different methods for effectiveness of biomass estimation, which serves as an indicator of biodegradation. Plastics …

Distribution And Ecological Function Of Pacific Lamprey In The San Luis Obispo Creek Watershed, Parker Kalan

Master's Theses

Pacific lamprey (Entosphenus tridentatus) is an endemic species to coastal watersheds along the Pacific Rim in North America and Asia. The species' geographic distribution is retracting and has not been mapped precisely, and the ability for the species to provide ecosystem services, such as water filtration, for supporting watershed management has not been tested. The San Luis Obispo Creek watershed, California, USA is at the southern end of Pacific lamprey’s retracting distribution, and the San Luis Obispo watershed is impacted by degraded water quality, making investigation of Pacific lamprey in the San Luis Obispo Creek watershed of direct …

Seed Longevity And Climatic Tolerance Of San Joaquin Wooly-Threads (Monolopia Congdonii; Asteraceae) An Endangered Plant From The San Joaquin Desert, California, Paul Excoffier

Master's Theses

San Joaquin wooly-threads (Monolopia congdonii; Asteraceae) is a federally-listed, endangered annual plant species from the desert areas of the San Joaquin Valley. Its limited range puts it at risk of extinction if the climate changes in such a way as to hinder its growth and reproduction. The primary aims of the study were to 1) determine how long-lived the seeds of the M. congdonii are, a key determinant of survival of desert annual plant populations through long droughts and 2) determine how severely hotter, drier conditions impact the ability of emerged plants to grow and reproduce. Secondarily, I …

Effect Of Vine Age And Selected Winemaking Techniques On The Sensory Profile Of Central Coast Red Wines, Isabelle Lomonaco

Master's Theses

Descriptive sensory analysis is essential to understanding how differing varietals, viticultural techniques, enological techniques, vintage, regions, etc. impact the sensory characteristics found in wines. These studies analyzed the sensory impacts of vine age, whole cluster and stem addition influences, the frequency of cap management regimes, and selected fermentation variables, on 2019 Zinfandel, 2020 Syrah, 2020 Tannat, 2020 Cabernet Sauvignon, and 2021 Graciano wines respectively, from the Central Coast of California, USA. The investigation of Old vine Zinfandel indicated that these wines were defined as complex due to the wide variety of descriptors used to characterize them, having high color saturation …

Fate Of Listeria Monocytogenes On Two Salad Blends At Ideal And Abusive Temperatures, Taran Virdi

Master's Theses

The consumption of ready-to-eat (RTE) foods has increased with popular RTE salad blends including non-traditional ingredients such as shredded Brussels sprouts, kale, red and green cabbage, chicory, and broccoli stalk. Concurrently, there has been an increase in the number of foodborne illnesses and outbreaks associated with leafy greens. The potential risk associated with these ingredients must be addressed as they have not typically been consumed raw, especially since L. monocytogenes continues to be a leading cause of foodborne illnesses and outbreaks. This study evaluated the survival of L. monocytogenes on two RTE salad blends at refrigeration, mildly abusive, and abusive …

Assessing Dietary Nutrient Adequacy And The Effects Of Season-Long Training On Body Composition And Metabolic Rates Of Men's Division I Collegiate Basketball Player, Morgan M. Nishisaka

Master's Theses

The success of performance in basketball may rely on both optimal body composition and nutrient intake. To our knowledge this is the first study to examine dietary intake adequacy and season-long effects on body composition and metabolism. The purpose of this study was to examine seasonal changes in body composition (BC), resting metabolic rate (RMR) and respiratory quotient (RQ), while also examining the dietary intake adequacy of NCAA DI male basketball players. BC, RMR and RQ were assessed during pre-season, in-season, and post-season (September, December, and March), while dietary assessment was collected in September and February. Results of this study …

Value-Added Opportunities For Tomato And Peach Seeds, Valerie Michelle Lavenburg

Master's Theses

The food industry is increasingly concerned with operational sustainability and food waste reduction. In the United States, the tomato industry was worth $1 billion in 2020, and tomatoes are currently ranked second as the most consumed vegetable after potatoes. Tomato processors have striven to valorize pomace by-products, which contain seeds with valuable compounds such as 45% fiber, 30% oil, and 26% protein. The U.S. peach industry, which was worth $599 million in 2017, is also looking for alternative ways to utilize their seeds, made up of 52% oil. Both tomato and peach seeds are rich in bioactive compounds such as …

Backcountry Equestrian Camping Online Course, Gillian Larson

Agricultural Education: Graduate Internship Reports

This AGED 539 project describes the creation of a Backcountry Equestrian Camping online course, including the goals of the course, an outline of the topics, and a summary description of the module contents. The course itself consists of material designed to provide participants with the necessary information to successfully travel and camp overnight on backcountry trips with a horse or mule, which is presented in a series of modules that include videos, written material, and downloadable PDFs. There is also an evaluation and acknowledgments segment.

Mytrials: Clinical Trial Application Concept, Katie Hollister

Graphic Communication

A clinical trial’s success is dependent upon whether a patient attends their highly-structured clinical trial visit schedule, which may include both in-person clinic visits and virtual check-in visits. MyTrials is a clinical trial journey app prototype that enables patients to schedule, reschedule, and attend join their in-person or virtual clinic visits. This product seeks to reduce the burden that scheduling places on the patient, and provides trial-provided resources and a daily and weekly timeline to help patients navigate their clinical trial journey.

Lytic Bacteriophages And Lactic Acid As Processing Aids Against Salmonella Spp. And Escherichia Coli O157:H7 On Marinated And Tenderized Pork Loins, Sherita Li

Master's Theses

Within the last decade, pork consumption has steadily increased and continues to be the most consumed meat globally. However, pathogenic bacterial strains resistant to antibiotics have also been increasingly found in pig farms, animals, and the environment. Bacterial food poisoning cases due to Salmonella spp. and Escherichia coli (E. coli) O157:H7 appear to be linked with a variety of pork products. The meat industry has recognized that research is needed to combat the multi-drug resistance in foodborne pathogens with alternative methods of control. This study evaluated the effects of both E. coli- and Salmonella-specific lytic bacteriophages and …

Strategies To Promote Responsive Bottle-Feeding In Wic Predict Less Frequent Use Of Food To Soothe And Healthier Weight Status For Infants With Negative Temperaments, Alison K. Ventura, Shannon E. Whaley

Kinesiology and Public Health

Background: Infants with greater temperamental negative affectivity are at higher risk for overfeeding and excess weight gain.

Objective: To examine whether strategies to promote responsive bottle-feeding within WIC promoted healthier maternal feeding practices and infant weight status among infants with greater negative affectivity.

Methods: Secondary analysis of data from a matched-pair cluster randomized trial. Policy, systems and environmental change (PSE) strategies to promote responsive bottle-feeding were implemented at three WIC clinics; these clinics were compared with three matched control clinics. Linear mixed models tested whether infant negative affectivity interacted with PSE strategies to predict feeding and weight outcomes when infants …

Effects Of Intertidal Position On The Capacity For Anaerobic Metabolism And Thermal Stress Response In The Common Acorn Barnacle, Balanus Glandula, Kyra Anderson

Master's Theses

Intertidal habitats are characterized by dynamic, tidally-driven fluctuations in abiotic and biotic factors. Many of the environmental stressors that vary across the intertidal (e.g., temperature, oxygen, food availability, predation pressure) are strong drivers of metabolic rate in ectotherms. As such, we predicted that there may be pronounced differences in the metabolic and stress physiology of conspecific sessile invertebrates occupying at different relative tidal heights. The common acorn barnacle Balanus glandula represents an ideal model organism in which to investigate the possibility of tidal height-dependent physiological differences, owing to their wide distribution in the intertidal zone and their eurytolerant nature. In …

Synthetic Design And Anisotropic Conductivities Of Polymeric Mixed Ion- Electron Conductors, Nika Bondar, Abigail Slimp, Patrick Gruoner, Jason Lin

Baker/Koob Endowments Awarded Projects

Our project documented, in extensive detail, the liquid crystalline (LC) assembly pathway from solution to solid state in the supramolecular complexes of the mixed ionic-electronic conducting polymers (MIECPs) prepared from carboxylated poly(3-alkylthiophene) and ionic liquid surfactant. Using UV-visible spectroscopy we have shown that the complexation is accompanied by the surfactochromism showing colorimetric response and conformational transitions as a function of the IL surfactant mole ratio. Additionally, we have demonstrated via Polarized Optical Microscopy (POM), that the equimolar solution exhibits rodlike conformation and its hydrogel spontaneously forms a 2D smectic LC mesophase with a lamellar periodicity. Defect-free LC domains were produced …

Associations Between Mothers’ Use Of Food To Soothe, Feeding Mode, And Infant Weight During Early Infancy, Megan K. Hupp, Peggy C. Papathakis, Suzanne Phelan, Alison K. Ventura

Kinesiology and Public Health

Weight status and rate of weight gain in the first six months postpartum are strong predictors of later obesity; thus, infant feeding practices are an important target for obesity prevention efforts. The use of food to soothe (FTS) is associated with less-favorable eating habits and weight outcomes for older infants and children. However, few studies have examined correlates of use of FTS during early infancy. The primary aim of this cross-sectional study was to explore associations between use of FTS and infant weight status in the first 6 months postpartum. A secondary aim was to identify the combination of maternal …

Evaluation Of Heat Tolerant Cauliflower Varieties On California’S Central Coast, Lauren Booke

Master of Science in Environmental Sciences and Management Projects

Heat tolerant trials of vegetable crops will help to improve food security when it becomes affected by rising temperatures due to climate change. By having heat tolerant vegetable crops, we can ensure the well-being of individuals in our society—nutritionally, economically, and socially. California is responsible for 90% of the cauliflower production in the United States. This research aims to determine the overall productivity of three heat tolerant cauliflower varieties (Bishop, Mardi, Flame Star) during the summer months (July- September) on California’s central coast. Stomatal conductance and chlorophyll fluorescence were measured throughout the growing cycle to evaluate plant stress and photosynthetic …

Pitch Canker In The Año Nuevo Monterey Pine Stand: A Retrospective Analysis, Davis Harrison

Master of Science in Environmental Sciences and Management Projects

Monterey pine (Pinus radiata) is a closed cone conifer tree native to California. Although it is an ecologically and economically valuable tree, there are only five remaining native populations, including, the Año Nuevo stand along California’s central coast. All the remaining native populations have faced threats to their survival, none more than the non-native disease pitch canker (Fusarium circinatum). This fungal infection causes lesions, dead branches, tree top death, and can be potentially fatal to infected trees. This paper is a continuation of a study beginning in 2001, aimed at evaluating the impact of silvicultural management practices on pitch canker …

Post-Czu Lightning Complex Regeneration In The Año Nuevo Monterey Pine Stand, Allison Trutna

Master of Science in Environmental Sciences and Management Projects

Climate induced increases in fire frequency and severity along with years of fire suppression and drought are predicted for California. The recent CZU Lightning Complex, a high severity wildfire, burned in the Santa Cruz Mountains on California’s central coast and affected an assortment of vegetation, including the survival and recovery of the native Año Nuevo Monterey pine (Pinus radiata (D. Don)) stand. This stand is partially located in Cal Poly’s Swanton Pacific Ranch and has been monitored for over 20 years for the presence of pitch canker (Fusarium circinatum) fungal disease. This study characterized the survival and initial recovery of …

Apache Science Team, Denise L. Jameson

Agricultural Education: Graduate Internship Reports

Sanger High school has the unique opportunity to offer a wide array of classes and pathways for students to take so that they can meet their educational goals of graduation the move on to higher education or starting a career right out of high school. Students have all these opportunities and benefits to have a strong start out of high school, but ultimately students are unaware of what jobs are related to those choices or pathways that they have decided to take part in. Apache Science Team allows for students to experience and learn about many different careers and opportunities …

Estimating And Modeling Transpiration Of A Mountain Meadow Encroached By Conifers Using Sap Flow Measurements, Simon Joseph Marks

Master's Theses

Mountain meadows in the western USA are experiencing increased rates of conifer encroachment due to climate change and land management practices. Past research has focused on conifer removal as a meadow restoration strategy, but there has been limited work on conifer transpiration in a pre-restoration state. Meadow restoration by conifer removal has the primary goal of recovering sufficient growing season soil moisture necessary for endemic, herbaceous meadow vegetation. Therefore, conifer water use represents an important hydrologic output toward evaluating the efficacy of this active management approach. This study quantified and evaluated transpiration of encroached conifers in a mountain meadow using …

Classifying Electrocardiogram With Machine Learning Techniques, Hillal Jarrar

Master's Theses

Classifying the electrocardiogram is of clinical importance because classification can be used to diagnose patients with cardiac arrhythmias. Many industries utilize machine learning techniques that consist of feature extraction methods followed by Naive- Bayesian classification in order to detect faults within machinery. Machine learning techniques that analyze vibrational machine data in a mechanical application may be used to analyze electrical data in a physiological application. Three of the most common feature extraction methods used to prepare machine vibration data for Naive-Bayesian classification are the Fourier transform, the Hilbert transform, and the Wavelet Packet transform. Each machine learning technique consists of …

Effects Of Nitrogen Management And Cultivar On Strawberry Production Under Disease Pressure, Kamille A. Garcia-Brucher

Master's Theses

Effects of nitrogen management and cultivar on strawberry production under disease pressure

Kamille Garcia-Brucher

California strawberry growers face increasing regulatory pressures to manage nitrogen (N) applications in their production system. Standard practice in the California strawberry industry is to apply a synthetic pre-plant controlled release fertilizer (CRF) to ensure the crop has sufficient N during winter establishment. Some research from the UC Cooperative Extension suggests this practice is not efficient at delivering N to the crop since most of the N is released from CRF before strawberry crop N uptake is significant. Another concern for California strawberry growers is loss …

Fuel Inventory Report For Montana De Oro State Park, Spencer Gordon

Master of Science in Environmental Sciences and Management Projects

Within the last century anthropogenic effects have shifted fire resilient habitats that are adapted to thousands of years of frequent low intensity fires to landscapes that are susceptible to extreme fire behavior which threaten human assets and sensitive natural resources. Entities that manage forests will need to prioritize fuel reduction as a management tool to promote forest health and mitigate hazardous fire conditions. A fuel inventory of a eucalyptus forest at Montana De Oro State Park in Los Osos, CA was collected using a combination of Brown’s 1973 and Brown’s 1982 methods. The fuel inventory revealed the eucalyptus forest yielded …