Digital Commons Network^™

Incorporating Ontological Information In Biomedical Entity Linking Of Phrases In Clinical Text, Evan French

Theses and Dissertations

Biomedical Entity Linking (BEL) is the task of mapping spans of text within biomedical documents to normalized, unique identifiers within an ontology. Translational application of BEL on clinical notes has enormous potential for augmenting discretely captured data in electronic health records, but the existing paradigm for evaluating BEL systems developed in academia is not well aligned with real-world use cases. In this work, we demonstrate a proof of concept for incorporating ontological similarity into the training and evaluation of BEL systems to begin to rectify this misalignment. This thesis has two primary components: 1) a comprehensive literature review and 2) …

Biotic Characteristics Of Managed And Unmanaged Coastal Dunes In The Outer Banks, North Carolina, Andrew E. White

Theses and Dissertations

Under future climate change and sea level rise scenarios, Natural and Nature-Based Features (e.g., dunes) that protect coastal habitat and infrastructure will be exposed to increased wave energy and storm surge. Understanding how these forces will impact coastal dunes is necessary for their continued use as protective features. Coastal dunes develop through feedback between vegetation and sediment deposition, a process complicated by species-specific growth rates and responses to burial. Wave flume studies have tested the effects of dune vegetation on erosion and found multiple plant organs across several functional types to be important for resisting erosion. Although dune building and …

Artificial Intelligence-Powered Chronic Wound Management System: Towards Human Digital Twins, Salih Sarp

Theses and Dissertations

Artificial Intelligence (AI) has witnessed increased application and widespread adoption over the past decade. AI applications to medical images have the potential to assist caregivers in deciding on a proper chronic wound treatment plan by helping them to understand wound and tissue classification and border segmentation, as well as visual image synthesis.

This dissertation explores chronic wound management using AI methods, such as Generative Adversarial Networks (GAN) and Explainable AI (XAI) techniques. The wound images are collected, grouped, and processed. One primary objective of this research is to develop a series of AI models, not only to present the potential …

Effect Of Viscoelasticity On Cellular Morphology And Activity, Thomas J. Petet Jr

Theses and Dissertations

It has been well established that there is a link between substrate stiffness and cellular activities such as proliferation, migration, and differentiation. Less characterized is the link between the time-dependent viscosity of a substrate with those cellular activities. To explore this, PDMS substrates were created with predictably tunable stiffness and viscosity parameters. A simulated model was also developed in parallel to explore the potential effects of viscosity in a computationally predictive way. It was found that the inclusion of viscosity caused a major paradigm shift to a non-zero substrate equilibrium that was sensitive to increases in the substrate stiffness. Finally, …

Self- And Socially-Regulated Learning In Middle School Science Classrooms: A Multiple Case Study, Lauren Cabrera

Theses and Dissertations

Students must employ self-regulated learning (SRL) and socially-regulated learning (soRL) in the science classroom, which includes a wide array of independent and collaborative learning activities. However, little is known about how student SRL and soRL co-occur in students’ learning and how the classroom teacher influences that regulation in situ (Cabrera et al., in preparation; Panadero et al., 2015). This explanatory, sequential case study analyzes classroom video data from six middle school science classrooms. The study uses an integrated coding scheme that captures SRL and soRL behaviors, soRL modes, and targets of regulation (Greene & Azevedo, 2009; Hadwin et al., 2018; …

Behavioral Screening And Chiral Bioanalysis Of Emerging Stimulant-Type Drugs In Rats, Tyson R. Baird

Theses and Dissertations

The epidemic of drug use in the United States and elsewhere in the world has resulted in tragic loss of life and substantial economic costs. Novel psychoactive substances (NPS) are one of the contributors to this problem, and the lack of information about many of these drugs compounds their risk. This dissertation proposes a strategy to use intracranial self-stimulation (ICSS) as a behavioral screening tool to assess emerging drugs of abuse for their abuse potential in order to generate a proactive threat assessment. A series of stimulant-type drugs including methcathinone, α-pyrrolidinohexanophenone (α-PHP), cocaine, and the phenyltropane analogs of cocaine WIN35428 …

Learning Robot Motion From Creative Human Demonstration, Charles C. Dietzel

Theses and Dissertations

This thesis presents a learning from demonstration framework that enables a robot to learn and perform creative motions from human demonstrations in real-time. In order to satisfy all of the functional requirements for the framework, the developed technique is comprised of two modular components, which integrate together to provide the desired functionality. The first component, called Dancing from Demonstration (DfD), is a kinesthetic learning from demonstration technique. This technique is capable of playing back newly learned motions in real-time, as well as combining multiple learned motions together in a configurable way, either to reduce trajectory error or to generate entirely …

Smart City Management Using Machine Learning Techniques, Mostafa Zaman

Theses and Dissertations

In response to the growing urban population, "smart cities" are designed to improve people's quality of life by implementing cutting-edge technologies. The concept of a "smart city" refers to an effort to enhance a city's residents' economic and environmental well-being via implementing a centralized management system. With the use of sensors and actuators, smart cities can collect massive amounts of data, which can improve people's quality of life and design cities' services. Although smart cities contain vast amounts of data, only a percentage is used due to the noise and variety of the data sources. Information and communication technology (ICT) …

Role Of Inhibition And Spiking Variability In Ortho- And Retronasal Olfactory Processing, Michelle F. Craft

Theses and Dissertations

Odor perception is the impetus for important animal behaviors, most pertinently for feeding, but also for mating and communication. There are two predominate modes of odor processing: odors pass through the front of nose (ortho) while inhaling and sniffing, or through the rear (retro) during exhalation and while eating and drinking. Despite the importance of olfaction for an animal’s well-being and specifically that ortho and retro naturally occur, it is unknown whether the modality (ortho versus retro) is transmitted to cortical brain regions, which could significantly instruct how odors are processed. Prior imaging studies show different …

Computational Analysis Of Drug Targets And Prediction Of Protein-Compound Interactions, Sina Ghadermarzi

Theses and Dissertations

Computational prediction of compound-protein interactions generated a substantial amount of interest in the recent years owing to the importance of the knowledge of these interaction for drug discovery and drug repurposing efforts. Research suggests that the currently known drug targets constitute only a fraction of a complete set of drug targets, limiting our ability to identify suitable targets to develop new drugs or to repurpose current drugs for new diseases. These efforts are further thwarted by our limited knowledge of protein-drug (and more generally protein-compound) interactions, where only a subset of drug targets is typically known for the currently used …

Asymmetric Cuh-Catalyzed Reductive Coupling Of Alleneamides With Carbonyl Electrophiles And The Mechanistic Investigation Into The Suzuki-Miyaura Cross-Couplings Of Electron-Deficient Systems, Samantha L. Gargaro

Theses and Dissertations

Most natural products and other biologically active small molecules contain multiple stereogenic heteroatoms throughout their carbon scaffold. As a result, methods to install these multi-heteroatom functionalities efficiently are highly desirable. Reductive coupling reactions have been studied extensively, and reductive allylation has been a key method for generating chiral secondary and tertiary allylic alcohols. This work focuses on utilizing naturally abundant and inexpensive Cu for the asymmetric reductive coupling of alleneamides with carbonyl electrophiles to access highly functionalized multi-heteroatom scaffolds that are difficult to produce via traditional methods. Described herein are methods for these asymmetric reductive coupling reactions. Chapter 1 describes …

The Derivation Of Geologic Ecosystem Services From Geodiversity In The Black Hills Region Of South Dakota And Wyoming, James Campbell Cooke

Dissertations and Theses

The ecosystem services approach seeks to recognize the benefits that people obtain from ecosystems, in order to highlight society’s dependence on natural systems. Ecosystem services fall into four categories: provisioning, regulating, cultural, and supporting services. Most of the ecosystem services research literature is focused on services that arise from biotic components of ecosystems. Ecosystems are dynamic complexes of biotic communities and their physical, non-living environment, interacting as a functional unit. The emphasis on biotic ecosystem services leaves understudied and undervalued the role of the abiotic, physical environment, especially in providing geologic ecosystem services. Geologic ecosystem services have been the focus …

Ecological Changes Of The Lower Niobrara River Valley And Lewis And Clark Lake Delta From Past To Present, Madalyn Christine Bollig

Dissertations and Theses

Over half of the world’s large river systems are impacted by dams. These may prevent sediment flow downstream, resulting in accumulation in the upstream reservoir. On the Missouri River, deltas and associated backwater-affected areas occur in nine locations across six reservoirs. One of these, the Lewis and Clark Lake delta-backwater, is influenced by sediment inputs from both the Missouri River and the Niobrara River. While the extension of the prograding delta into the reservoir has been well documented, there has been little research on upstream (backwater) effects of the delta on the lower Niobrara River. This study examined ecological changes …

Biodiversity In Residential Yards For Sustainability In Small Cities: Understanding Public Attitudes, Opportunities And Limitations In Vermillion, Sd, Rina Thapa

Dissertations and Theses

As urban areas are expanding with the growing size of human population, it is increasingly important to understand the role that residential yards can play in biodiversity conservation because they often comprise a large proportion of green spaces in cities. Most of the research performed to date on the role of residential yards in biodiversity conservation has been conducted in large cities. The role of residential yards in biodiversity conservation in small cities is still largely unknown. In this research, I discuss the relationship between biodiversity and the structure of green space, public attitudes towards the presence of wildlife, public …

Medication Errors: Causes, Theories And Interventions, Tuyba Karim

Master of Science in Nursing Family Nurse Practitioner

Rationale, aims and objectives: Following heart disease and cancer, medication errors rank third as the leading cause of death in the United States. For the primary care provider, the root causes of medication errors stem from multiple factors. To improve positive learning outcomes for primary care providers in reducing medication errors, this project sets out to examine the utility of educational interventions in improving the present standard of care as it relates to medication error safety and patient outcomes.

Methods: A literature review was conducted analyzing recent studies that examined the use of educational interventions in promoting positive learning outcomes …

Estimating The Ecosystem Service Of Aleutian Cackling Goose Droppings On Pastures, Brian G. Fagundes

Cal Poly Humboldt theses and projects

The Aleutian cackling goose (Branta hutchinsii leucopareia) experienced a population low of 790 geese in 1974 and has recovered to the current estimate of 186,100 geese in 2021. Private livestock producers view geese as pasture competitors and use hazing and hunting to scare geese from private lands to adjacent public lands. I investigated if geese provide an ecosystem service via dropping fertilizing effects to improve pastures in northern California.

A greenhouse experiment was conducted from February-August 2019 at Cal Poly Humboldt, divided into two experiments: freshly sown ryegrass pasture and established plant and soil communities removed intact from …

Drought Responses Across Diverse Conifer Species, Habitats, And Competitive Gradients In Northern California, Gabriel J. Roletti

Cal Poly Humboldt theses and projects

Frequent and intense drought events are rapidly altering stand dynamics in western North American forests. Climate, competition, and site characteristics can affect the growth responses of individual trees to drought stress. The ecological and geographical diversity of northern California provides a unique opportunity to measure these responses across species, habitat types, and levels of competitive pressure. This study used dendrochronological techniques and linear mixed-effects models to assess growth responses to drought in four montane and two coastal conifer species across 54 study sites (nine sites per species and 540 trees total) in northern California. Growth was evaluated from 2002-2018 and …

Carnivore And Ungulate Responses To Cattle In A Grazed Forest Ecosystem, Rebecca Carniello

Cal Poly Humboldt theses and projects

Habitat disturbance, a leading threat to biological diversity, comes in many forms and can alter the behavior of wildlife and reduce the amount of suitable habitat. Livestock grazing, a form of habitat disturbance, is the most widespread influence on native ecosystems of western North America. Research on the impacts of introduced domestic herbivores on wild carnivores and ungulates varies, and the degree to which wildlife species are affected is often species-specific. I used remote trail cameras to compare the activity patterns of black bears (Ursus americanus), coyotes (Canis latrans), bobcats (Lynx rufus), mountain lions …

Factors Affecting The Production Of Berries Of The Red Huckleberry Plant In The Redwood Experimental Forest, Kagat G. Mcquillen

Cal Poly Humboldt theses and projects

Vaccinium parvifolium (red huckleberry) is a culturally and commercially valued food for different coastal tribes of northwestern California.

Today some tribes are regaining access to ancestral lands, and Indigenous researchers are working to document information about culturally significant plant species and their management to reclaim traditional ecological knowledge and restore food sovereignty.

The present study, focused on red huckleberry, Vaccinium parvifolium, took place in the ancestral territory of the Yurok Tribe, currently managed by the US Forest Service as the Redwood Experimental Forest (REF) in Klamath, CA. Geographic Information Systems-based mapping, forest ecological field data collection, and a literature …

Sediment Production From Forest Roads In Areas Affected By The August Complex Fire In Northern California, Zachary J. Gigone

Cal Poly Humboldt theses and projects

Wildfire activity is increasing in California and is an important factor affecting erosion rates. Landscapes recently affected by wildfire, areas that have been salvage logged after a fire, and unpaved forest roads are all major sources of sediment which can impair water quality and negatively impact many aquatic species. Therefore, this study was conducted to quantify erosion rates from native and gravel surfaced forest road segments after the August Complex fire, evaluate the impact of salvage logging activities on sediment production from roads, and understand the effect of soil burn severity on sediment production from these road segments. Finally, this …

Late Quaternary Glacier Fluctuations At Picayune Lake, Northern California, Aidan Patrick Cowan

Cal Poly Humboldt theses and projects

The Klamath Mountains are a 233-km-long (north to south) mountain range located in northern California that shows extensive geomorphic evidence of Pleistocene glaciation. Within the Klamath’s there are many highland lakes, which record evidence of glacial deposition, one of which is Picayune Lake. Lake sediment data collected from Picayune Lake offers insights into the glaciation, and broader depositional history of the Picayune Lake Valley, as well as the climate history of the Klamath Mountains region. I measured magnetic susceptibility, loss on ignition, and grain size in sediment cores and used radiocarbon dating to determine a chronology of glacier fluctuations in …

Comparison Of Environmental Dna And Underwater Visual Count Surveys For Detecting Juvenile Coho Salmon (Oncorhynchus Kisutch) In Rivers, Jason T. Shaffer

Cal Poly Humboldt theses and projects

Environmental DNA (eDNA) has developed into a useful tool for determining the distribution of rare aquatic species, but relatively few studies have directly compared the detection probabilities of this method with other conventional survey techniques. These comparisons can inform which method may be better suited to address study objectives. In this study, the overall goal was to compare the ability of eDNA and underwater visual count (UVC) surveys to detect juvenile coho salmon (Oncorhynchus kisutch), a species of conservation concern at the southern extent of its geographic range. Specifically, I address two objectives: (1) compare the ability of …

The Effect Of Brain Breaks On Student Outcomes Of School-Aged Children In K-12 Classrooms: A Meta-Analysis, Teron H. Schaeffer

Cal Poly Humboldt theses and projects

BACKGROUND: Integrated physical activity in the classroom has been shown to affect K-12 students’ development positively. Students of all abilities benefit from multimodality learning. PURPOSE: This study investigates the relationship between classroom brain breaks and school-aged students' classroom behaviors. METHODS: The Meta-analysis search process consisted of 3 Phases: (1) Screen the titles, (2) Screen the abstracts, and (3) Retrieve the Full Text. Literature searches were conducted in eight electronic academic journal databases: SPORTDiscus, PsycINFO, PsycARTICLES, Cochrane Database, Web of Science/Web of Knowledge, ProQuest, Child Development and Adolescent Studies, and ERIC. Students (N) are enrolled in schools serving students from kindergarten …

Geomorphic Evaluation Of The Goose Lake Fault And Fluvial Terraces At The Yager Creek–Van Duzen River Confluence, Northern Coastal California, Samuel E. Bold

Cal Poly Humboldt theses and projects

Upper-plate deformation in the southern Cascadia subduction zone is dynamic and complex, situated in the transition between northward translation to westward convergence. Rock uplift and incision rates characteristic of this dynamic region are preserved in suites of fluvial and marine terraces. Fluvial terraces at the Yager Creek–Van Duzen River confluence record fluvial incision rates, and are crosscut by the understudied Goose Lake fault, an upper plate structure. In this work, I use high resolution lidar imagery to map terrace surfaces, and use optically stimulated luminescence, radiocarbon, and Beryllium-10 geochronology to bracket terrace ages and calculate incision and slip rates. With …

Copy Number Variations In Patients With Idiopathic Recurrent Pregnancy Loss: An Arraycgh Approach, Onur Yildiz, Fatma Silan, Taner Karakaya, Öztürk Özdemi̇r

Turkish Journal of Medical Sciences

Background/aim: It is not always possible to determine the causative basis of pregnancy losses and even today it has been reported that 50% of cases with recurrent pregnancy loss (RPL) have no reason to be detected. In our study, it is aimed to reveal the copy number variations (CNVs) of the genes which presumably have a potential effect in individuals with RPL and contribute to subsequent functional studies in the follow-up. Materials and methods: We retrospectively evaluated the array-comparative genomic hybridization (aCGH) data of cytogenetically 64 normal individuals (21 couples, 11 unrelated women, and 11 unrelated men) who had applied …

Interaction Effects Of Age And Body Weight Losses During Moulting On The Performance Ofcommercial Laying Hens, Mian Mubashar Saleem, Jibran Hussain, Usman Elahi, Ehsaan Ullah Khan, Muhammad Usman, Syed Ghulam Mohayudin Hashmi, Sohail Ahmad

Turkish Journal of Veterinary & Animal Sciences

This study evaluated the interaction effects of different age groups and body weight losses during moulting on the productive performance, egg quality, and immune response of commercial laying hens. In total 324 Lohmann Selected Leghorn Lite laying hens of 80 and 108 weeks old were studied. A completely randomized experimental design in factorial arrangement, with 6 treatments of 6 replicates with 9 hens each, was applied. Treatments consisted of 2 production cycles (80 and 108 weeks) and three body weight losses during moulting (20%, 25%, and 30%). Productive performance (body weight, feed intake, egg weight, production percent, egg mass, feed …

A Game Theoretic Approach To Design Mating Programs For Livestock, Ebru Ergüneş Berki̇n, Hasan Önder, Özgür Hakan Aydoğmuş

Turkish Journal of Veterinary & Animal Sciences

In this study, we proposed a new game theoretic method to design a mating program. The index and game theoretic methods were applied with calculated breeding values using pedigree on two different data sets whose economic traits consist of negative (milk yield and fat percentage) and positive (birth and weaning weight) genetic correlated data. For the negative genetic correlated data set, even if total expected benefits were equal for two methods, mating programs were changed, and the coefficient of variation obtained using the game theoretic method was smaller than that of the index method. This result showed that the expected …

Productive Performance, Egg Quality, And Hatching Traits Of Japanese Quail Lines Selectedfor Higher Body Weight And Egg Number, Abdur Rehman, Jibran Hussain, Athar Mahmud, Khalid Javed, Abdul Ghayas, Sohail Ahmad

Turkish Journal of Veterinary & Animal Sciences

The present study evaluated the effect of selection for higher body weight (weight based selection = WBS) and egg numbers (egg based selection = EBS) on productivity, egg quality, and hatching traits of Japanese quail for three generations. From a base population of 1125 day-old chicks of Japanese quail, best performing families were allowed to propagate for getting next generation. WBS in G3 presented higher values of feed intake, egg weight, hatching weight. However, egg production and feed conversion ratio were better in EBS during G3. The incidence of embryonic mortality was also lower in the WBS line. In the …

Comparison Of M, Mm And Lts Estimators In Linear Regression In The Presence Of Outlier, Cem Tirink, Hasan Önder

Turkish Journal of Veterinary & Animal Sciences

In this study, it was aimed to evaluate the performance of different estimators that will be used in regression analysis, which is one of the multivariate statistical methods in the presence of outliers in the data set. Sixth month live weight was estimated with various body measurements for Saanen kids taken from a private farm. In the data set, the use and performance of robust estimators were evaluated because the least squares method did not provide reliable results in the case of outliers. M (for Huber and Tukey bisquare) estimator, MM estimator and LTS estimator were used as robust used …

Investigating Genetic Diversity Of Indonesian Native Cattle Breeds Using Mitochondrialdna 16s Rrna Gene, Restu Misrianti, Sony Hartono Wijaya, Cece Sumantri, Jakaria Jakaria

Turkish Journal of Veterinary & Animal Sciences

This study aimed to estimate the genetic diversity and phylogenetic relationships of Indonesian native and local cattle breeds using 16S rRNA mitochondrial DNA. The study analyzed 93 DNA samples from six cattle breeds. The polymerase chain reaction was conducted using two primer pairs to sequence the complete 16S rRNA gene. The number of the polymorphic site (S), pairwise nucleotide differences (K), haplotype diversity (Hd), and nucleotide diversity (?) were estimated using DnaSP 6 software. PopART v. 1.7 software was employed for the median-joining network analysis, while a neighbor-joining tree was reconstructed based on the Kimura 2-parameter model using MEGA X …