Digital Commons Network^™

Developing Field And Spaceflight Microscopy, Nikki Johnston

Dissertations and Theses

Designing for spaceflight favors the reduction of unnecessary features and cost-cutting, whether thisbe computation, hardware, or procedure. Resources are spent toward fortification and mission success over convenience. Such design goals paired with the relatively smaller budgets of academia lead us to do as much as we can in-house and use open-source as much as we can without compromising mission success. We also believe that thoroughly testing technology in extreme environments on earth is necessary for the success of a flight instrument. We focus on microscopy for life detection. I have spent my time here learning methods of hand-building microscopes to …

Effects Of Wetting Events On Mass Timber Surface Microbial Communities And Voc Emissions: Implications For Building Operation And Occupant Well-Being, Gwynne Á. Mhuireach, Susan Collins, Leslie Dietz, Patrick Finn Horve, Aurélie Laguerre, Dale Northcutt, Jason Stenson, Kevin Van Den Wymelenberg, Elliott Gall, Mark Fretz

Mechanical and Materials Engineering Faculty Publications and Presentations

IntroductionHumans have used wood as a construction material throughout history. Currently, mass timber products, such as cross-laminated timber (CLT), are becoming more popular as a structural material, since they are renewable and have a lower carbon footprint than concrete or steel. Nonetheless, some building types, such as healthcare, veterinary, and food manufacturing, avoid using structural mass timber due to concerns about microbial growth in the event of wetting. One solution is to use protective coatings on mass timber products to increase moisture resistance, although the coatings themselves may generate concerns about volatile organic compound (VOC) emissions. Natural uncoated wood also …

Increased Thermal Stability And Retained Antibacterial Properties In A Sulbactam And Amantadine Salt: Towards Effective Antibacterial-Antiviral Combination Therapies, Josephine Bicknell, Ivan Bondarenko, Alice Colatrella, Elani J. Cabrera-Vega, Jesus Daniel Loya, Delbert S. Botes, Jay L. Mellies, Gonzalo Campillo-Alvarado

Chemistry Faculty Publications and Presentations

A clinically relevant multidrug solid comprising sulbactam (β-lactamase inhibitor) and amantadine (antiviral) displays enhanced thermal stability and sustained antibacterial activity compared to starting materials.

We describe the formation of a multidrug salt comprising sulbactam (SUL, β-lactamase inhibitor) and amantadine (AMNH, antiviral). Physicochemical investigation of the SUL·AMNH salt revealed enhanced thermal stability compared to pristine starting materials. In vitro studies found that salt formation in SUL·AMNH does not disrupt antibacterial activity against model organisms Escherichia coli and Staphylococcus epidermidis. To our knowledge, we show the first β-lactamase inhibitor-antiviral salt where both components have been approved by the U.S. Food and Drug …

Introducing Isomad, A Compilation Of Isotopic Datasets For Madagascar, Sean W. Hixon, Ricardo Fernandes, Antonin Andriamahaihavana, Andrea L. Baden, Marina B. Blanco, Guillaume Caulier, Melanie Dammhahn, Igor Eeckhaut, Timothy M. Eppley, Natalie Vasey, Multiple Additional Authors

Anthropology Faculty Publications and Presentations

Abstract We present the first open-access, island-wide isotopic database (IsoMad) for modern biologically relevant materials collected on Madagascar within the past 150 years from both terrestrial and nearshore marine environments. Isotopic research on the island has increasingly helped with biological studies of endemic organisms, including evaluating foraging niches and investigating factors that affect the spatial distribution and abundance of species. The IsoMad database should facilitate future work by making it easy for researchers to access existing data (even for those who are relatively unfamiliar with the literature) and identify both research gaps and opportunities for using various isotope systems to …

Differentiating Dynamic System Outcomes In Cam Photosynthesis Through Sonification, Duncan Turley

Civil and Environmental Engineering Undergraduate Honors Theses

Sonification is a powerful tool that is harnessed by modern engineers to represent information through audio, and is beginning to be used to interpret more complex data sets. Sonification can be used to facilitate the listeners' ability to grasp microscopic or complex changes in the state of a system. This study uses the assigning of sound patterns to model outputs that indicate chaotic or non-chaotic systems in Crassulacean acid metabolism photosynthesis. Using sound allows the interpretation of chaotic data without the more time intensive processes typically used, such as of Fast Fourier Transformations. Based on past research, it is known …

Fluorescence Microscopy With Deep Uv, Near Uv, And Visible Excitation For In Situ Detection Of Microorganisms, Noel Case, Nikki Johnston, Jay Nadeau

Physics Faculty Publications and Presentations

We report a simple, inexpensive design of a fluorescence microscope with light-emitting diode (LED) excitation for detection of labeled and unlabeled microorganisms in mineral substrates. The use of deep UV (DUV) excitation with visible emission requires no specialized optics or slides and can be implemented easily and inexpensively using an oblique illumination geometry. DUV excitation (<280 >nm) is preferable to near UV (365 nm) for avoidance of mineral autofluorescence. When excited with DUV, unpigmented bacteria show two emission peaks: one in the near UV ∼320 nm, corresponding to proteins, and another peak in the blue to green range, corresponding to …

Multicolor Dye-Based Flow Structure Visualization For Seal-Whisker Geometry Characterized By Computer Vision, Ondřej Ferčák, Kathleen Lyons, Christin T. Murphy, Kristina M. Kamensky, Raul Bayoan Cal

Mechanical and Materials Engineering Faculty Publications and Presentations

Pinniped vibrissae possess a unique and complex three-dimensional topography, which has beneficial fluid flow characteristics such as substantial reductions in drag, lift, and vortex induced vibration. To understand and leverage these effects, the downstream vortex dynamics must be studied. Dye visualization is a traditional qualitative method of capturing these downstream effects, specifically in comparative biological investigations where complex equipment can be prohibitive. High-fidelity numerical simulations or experimental particle image velocimetry (PIV) are commonplace for quantitative high-resolution flow measurements, but are computationally expensive, require costly equipment, and can have limited measurement windows. This study establishes a method for extracting quantitative data …

Instructors At A Crossroad: Perceptions Of Collaboration And Support Intersect With Intentions To Implement A Cure, Justin Berl

Dissertations and Theses

An ongoing crisis of student drop-off from undergraduate science, technology, engineering and mathematics (STEM) education has led to a sustained call over the last 15+ years for the increased implementation of updated practices in undergraduate STEM education. Though over the past few decades many researchers have developed and analyzed the efficacy of various evidence-based teaching practices (EBTPs) designed to improve the state of undergraduate STEM education throughout the country, the rate at which these EBTPs are implemented in undergraduate STEM classrooms remains low.

In order to better understand the specific factors that affect individual instructors' efforts to implement EBTPs, we …

Autofluorescence Microscopy: Identifying Bacterial Signals On Rock Samples, Noel Case

University Honors Theses

One common method for identifying microbes present in fluid and non-fluid samples is fluorescent dye staining, in which samples are stained with a fluorophore - a molecule excited by an external light source that re-emits energy as higher-wavelength light. The excitation wavelength used greatly impacts the observability of microbes in the resulting fluorescence images, and deep ultraviolet excitation (200-280 nm) seems to provide the highest signal-to-noise ratio of any excitation range. By inoculating rock samples (gypsum and marble) with B. subtilis, staining with SYTO 9, Acridine Orange and FM 1-43 dyes, and imaging with deep UV (275 nm), near …

A Survey Of The Solitary Native Bees Of The Leach Botanical Garden, And Their Floral Associations, Joshua Page

Biology Undergraduate Honors Theses

Solitary native bees are known to be diverse, but are not well studied in Oregon. In order to identify the bee genera present in the Leach Botanical Garden, and their floral usage, a survey was conducted over 2020 and 2021. Biweekly sampling was used to collect bees on flowers, in order to obtain floral usage data. Bees were identified to genus with published taxonomic keys. In total, 19 genera of bees were found. Bee abundance fit a normal distribution, and peaked in July. Ceratina and Lasioglossum were a significant proportion of the population, and were present in the garden from …

Experiences Of Undergraduates And Graduate Teaching Assistants In Biology Course-Based Undergraduate Research Experiences, Emma Crystal Goodwin

Dissertations and Theses

Evidence of positive student outcomes from course-based undergraduate research experiences (CUREs) has sparked implementation of CUREs in introductory biology laboratory courses, as one approach to boosting student engagement in research. In a CURE, students collaborate with other students and instructors on a research project, where they conduct novel scientific research that has relevance to a local or scientific community. However, previous research rarely considers that graduate teaching assistants (GTAs) often teach introductory labs. The classroom role of GTAs expands in a CURE--they no longer need to simply teach a lab class, but also to serve as research mentors. GTAs, who …

Short- And Long-Term Impacts Of A Deliberative Pedagogy In Introductory Biology And Chemistry Courses, Liz Rain-Griffith

Dissertations and Theses

There have been multiple national calls for curricular reform in college-level science, technology, engineering, and mathematics (STEM), including a need to instill democratic skills in students. Democratic skill building can be embedded in STEM classrooms through intentional "deliberative pedagogies" which include skills in: communication, collaboration, and application. We developed and implemented a deliberative pedagogy, Deliberative Democracy (DD), across introductory majors and non-majors biology courses and a majors chemistry course. In two separate studies, I took a longitudinal, qualitative research approach to understand introductory biology and chemistry students' experiences and perceptions of DD. For the first study, I tracked a cohort …

Undergraduate Biology Education Research Gordon Research Conference: A Meeting Report, Erin L. Dolan, Michelle Borrero, Kristine Callis-Duehl, Miranda M. Chen Musgrove, Joelyn De Lima, Isi Ero-Tolliver, Laci M. Gerhart, Emma Goodwin, Lindsey R. Hamilton, Meredith A. Henry, Jose Herrera, Bethany Huot, Stacey Kiser, Melissa E. Ko, Marcy E. Kravec, Mark Lee, Lisa B. Limeri, Melanie E. Peffer, Debra Pires, Juan S. Ramirez Lugo, Starlette M. Sharp, Nicole A. Suarez

Biology Faculty Publications and Presentations

The 2019 Undergraduate Biology Education Research Gordon Research Conference (UBER GRC), titled “Achieving Widespread Improvement in Undergraduate Education,” brought together a diverse group of researchers and practitioners working to identify, promote, and understand widespread adoption of evidence-based teaching, learning, and success strategies in undergraduate biology. Graduate students and postdocs had the additional opportunity to present and discuss research during a Gordon Research Seminar (GRS) that preceded the GRC. This report provides a broad overview of the UBER GRC and GRS and highlights major themes that cut across invited talks, poster presentations, and informal discussions. Such themes include the importance of …

Despite Similar Perceptions And Attitudes, Postbaccalaureate Students Outperform In Introductory Biology And Chemistry Courses, Erin E. Shortlidge, Liz Rain-Griffith, Chloe Shelby, Gwen Shusterman, Jack Barbera

Biology Faculty Publications and Presentations

Embedding active learning is a common mechanism for meeting science, technology, engineering, and mathematics (STEM) education reform goals. Researchers have identified student benefits from such strategies, yet these benefits may not be universal for all students. We sought to identify how students at a nontraditional university perceive introductory biology and chemistry courses, and whether perceptions relate to course type, performance, or student status. We surveyed students (n = 601) using open-ended prompts regarding their perceptions of factors that impact their learning and interest, and about specific learning strategies. Generally, students did not differ in what influenced their learning or …

Computer-Based Instruction As A Form Of Differentiated Instruction In A Traditional, Teacher-Led, Low-Income, High School Biology Classroom, Cheryl Casey

Dissertations and Theses

In 2015 the U.S. continues to struggle with academic achievement in public schools. Average test scores from 15 year olds taking the Program for International Student Assessment placed the U.S. as 38th out of 71 countries (Drew Devlin, 2017). It is common to discuss elimination of the achievement gap as the single most effective way to improve the U.S.'s mediocre standing among the highest scoring countries in the world in primary and secondary student test scores (McGhee,2004; Flemming 2012). In the broadest sense of the term the "achievement gap" refers to the difference in academic success between different groups of …

Two-Photon Excitation, Fluorescence Microscopy, And Quantitative Measurement Of Two-Photon Absorption Cross Sections, Fredrick Michael Dearmond

Dissertations and Theses

As optical microscopy techniques continue to improve, most notably the development of super-resolution optical microscopy which garnered the Nobel Prize in Chemistry in 2014, renewed emphasis has been placed on the development and use of fluorescence microscopy techniques. Of particular note is a renewed interest in multiphoton excitation due to a number of inherent properties of the technique including simplified optical filtering, increased sample penetration, and inherently confocal operation. With this renewed interest in multiphoton fluorescence microscopy, comes an increased demand for robust non-linear fluorescent markers, and characterization of the associated tool set.

These factors have led to an experimental …

Toxicant Formation In Dabbing: The Terpene Story, Jiries Meehan-Attrash, Wentai Luo, Robert M. Strongin

Chemistry Faculty Publications and Presentations

Inhalable, noncombustible cannabis products are playing a central role in the expansion of the medical and recreational use of cannabis. In particular, the practice of “dabbing” with butane hash oil has emerged with great popularity in states that have legalized cannabis. Despite their growing popularity, the degradation product profiles of these new products have not been extensively investigated. The study herein focuses on the chemistry of myrcene and other common terpenes found in cannabis extracts. Methacrolein, benzene, and several other products of concern to human health were formed under the conditions that simulated realworld dabbing. The terpene degradation products observed …

Sexual Education Pedagogy In The Global South: Pubmed Data In The Age Of Globalization, Grace A. Walker-Stevenson

University Honors Theses

This systematic review and subsequent analysis examines the harm caused by inadequate sexual education in countries with minimal access to healthcare. This review relies on PubMed as its singular database. PubMed is a free search engine that utilizes the MEDLINE database of references on life sciences and biomedical topics. This database is maintained by The United States Library of Medicine and The National Institutes of Health, therefore it is an authoritative entity on the subject of health research. Assessing the breadth of knowledge represented in PubMed related to this issue can be extrapolated to estimate the current state of salient …

How To Assess Your Cure: A Practical Guide For Instructors Of Course-Based Undergraduate Research Experiences, Erin Shortlidge, Sara Brownell

Biology Faculty Publications and Presentations

Integrating research experiences into undergraduate life sciences curricula in the form of course-based undergraduate research experiences (CUREs) can meet national calls for education reform by giving students the chance to “do science.” In this article, we provide a step-by-step practical guide to help instructors assess their CUREs using best practices in assessment. We recommend that instructors first identify their anticipated CURE learning outcomes, then work to identify an assessment instrument that aligns to those learning outcomes and critically evaluate the results from their course assessment. To aid instructors in becoming aware of what instruments have been developed, we have also …

Currents In Fishery Management, Genevieve Depuy

University Honors Theses

This thesis provides an overview of fishery management policy types and attempts to determine best practices for biological sustainability in terms of species preservation and biomass recovery. Key concepts include biological sustainability, regulatory forces, and fishery management and output trends. The research question investigated is: what are the best policy practices for regulating marine fishery health and biological stability? The research process of this paper included a review of prior literature in the field of marine policy and fishery management, as well as the use of United States data from the Pacific and Atlantic coasts to evaluate management strategies. Based …

Moss In The Classroom: A Tiny But Mighty Tool For Teaching Biology, Erin E. Shortlidge, James R. Hashimoto

Biology Faculty Publications and Presentations

Here we present a mechanism to infuse ecology into the classroom using a broadly adaptable system. We developed a novel moss-based project that introduces research-based experiences for middle school students, and can be modified for integration into K-16 classrooms. The project is ecologically relevant, facilliating opportunities for students to experience intimate interactions with ecosystem subtleties by asking their own questions. We describe and suggest how students can develop, build, test, and assess microcosm experiments of their own design, learning the process of science by “doing science.” Details on project execution, representative examples of distinctive research-question-based projects are presented. We aim …

Applying Gps And Accelerometers To The Study Of African Savanna (Loxodonta Africana) And Asian Elephant (Elephas Maximus) Welfare In Zoos, Matthew Robert Holdgate

Dissertations and Theses

African savanna elephants (Loxodonta africana) and Asian elephants (Elephas maximus) are a focus of welfare research in zoos due to their high intelligence, complex social structure, and sheer size. Due to these challenges, some argue that zoos are inherently incapable of providing appropriate care for elephants, while others believe that zoos can fulfill the needs of these species with improved husbandry. There is a general consensus from both within and outside of zoos, however, that zoos must improve their elephant programs or cease exhibiting these animals altogether. Now more than ever, applied research on zoo elephant welfare is needed to …

Integrating K-W-L Prompts Into Science Journal Writing: Can Simple Question Scaffolding Increase Student Content Knowledge?, Brandon Joel Wagner

Dissertations and Theses

Writing-to-learn strategies have been administered in the past to enrich student learning. The purpose of this study was to see if K-W-L prompts in science journal writing could benefit student content knowledge within biology. Two high school biology classes were provided with learning journals. The journals given to the students during the treatment unit were provided with K-W-L question prompts to guide student learning while during the comparison unit students were given an open ended writing assignment. Pre and posttests were administered to determine student-learning gains. Student motivations and opinions of the treatment were collected through student interviews. The combined …

Associations Between Input And Outcome Variables In An Online High School Bioinformatics Instructional Program, Douglas S. Lownsbery

Dissertations and Theses

Quantitative data from a completed year of an innovative online high school bioinformatics instructional program were analyzed as part of a descriptive research study. The online instructional program provided the opportunity for high school students to develop content understandings of molecular genetics and to use sophisticated bioinformatics tools and methodologies to conduct authentic research. Quantitative data were analyzed to identify potential associations between independent program variables including implementation setting, gender, and student educational backgrounds and dependent variables indicating success in the program including completion rates for analyzing DNA clones and performance gains from pre-to-post assessments of bioinformatics knowledge. Study results …

How Does Student Understanding Of A Concept Change Throughout A Unit Of Instruction? Support Toward The Theory Of Learning Progressions, Brian Jay Dyer

Dissertations and Theses

This study documented the changes in understanding a class of eighth grade high school-level biology students experienced through a biology unit introducing genetics. Learning profiles for 55 students were created using concept maps and interviews as qualitative and quantitative instruments. The study provides additional support to the theory of learning progressions called for by experts in the field. The students' learning profiles were assessed to determine the alignment with a researcher-developed learning profile. The researcher-developed learning profile incorporated the learning progressions published in the Next Generation Science Standards, as well as current research in learning progressions for 5-10th grade students …

Bismuth Nanoparticles As Medical X-Ray Contrast Agents: Synthesis, Characterization And Applications, Anna Laura Brown

Dissertations and Theses

Bismuth based nanomaterials have recently attracted attention as heavy element X-ray contrast agents because of the high atomic number and predicted biological compatibility of bismuth. Nanoparticle X-ray contrast agents may enable a number of novel medical imaging applications, including blood pool and site-directed imaging. However these hypothetical applications are hindered by lack of suitable synthetic methods for production of imaging agents. This dissertation describes synthesis of a novel class of bismuth nanoparticles that are aqueously stabilized using poly and monosaccharides. These particles are synthesized using highly biologically compatible reagents and are oxidatively stable in water and in moderately basic buffered …

Ecomorphology And Mating Behavior Of Two Species Of Night-Stalking Tiger Beetles, Omus Audouini And O. Dejeanii, Robert Kent Richardson

Dissertations and Theses

Night-stalking tiger beetles (Cicindelinae: Omus) are among the least studied members of the highly diverse Carabid sub-family Cicindelinae, the tiger beetles. Despite populations of Omus being common in the forest floor habitats of the west coast of North America and their conspicuous predatory role within terrestrial arthropod communities, little is known about the biology and ecology of Omus.

Field studies showed that two species of Omus existed in the forested areas of Powell Butte Nature Park, Portland, Oregon, USA: Omus audouiniand O. dejeanii. The co-occurrence of sympatric, and likely syntopic, species allowed for a comparative approach in examining and analyzing …

Cephalopod Genomics: A Plan Of Strategies And Organization, Caroline B. Albertin, Laure Bonnaud, C. Titus Brown, Wendy J. Crookes-Goodson, Rute R. Da Fonseca, Carlo Di Cristo, Brian P. Dilkes, Eric Edsinger-Gonzales, Robert M. Freeman Jr., Roger T. Hanlon, Kristen M. Koenig, Annie R. Lindgren, Mark Q. Martindale, Patrick Minx, Leonid L. Moroz, Marie-Therese Nödl, Spencer V. Nyholm, Atsushi Ogura, Judit R. Pungor, Joshua J. C. Rosenthal, Erich M. Schwarz, Shuichi Shigeno, Jan M. Strugnell, Tim Wollesen, Guojie Zhang, Clifton W. Ragsdale

Biology Faculty Publications and Presentations

The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, “Paths to Cephalopod Genomics- Strategies, Choices, Organization,” held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an …

Bayesian And Related Methods: Techniques Based On Bayes' Theorem, Mehmet Vurkaç

Systems Science Friday Noon Seminar Series

Bayes' theorem is a simple algebraic consequence of conditional probability. Yet, its consequences are critical to philosophy, society, and technology. Starting from its simple derivation, we will show how its interpretation in terms of base rates (priors) and class-conditional likelihoods illuminates everyday problems in medicine and law, and provides signal processing, communications, machine learning, model selection, and other applications of statistics with powerful classification and estimation tools. Next, we will briefly examine some of the ways in which this theorem can be adopted to include multiple attributes, contexts, hypotheses, and levels of risk. Methods derived from or related to Bayes’ …

Scale Invariant Object Recognition Using Cortical Computational Models And A Robotic Platform, Danny Voils

Dissertations and Theses

This paper proposes an end-to-end, scale invariant, visual object recognition system, composed of computational components that mimic the cortex in the brain. The system uses a two stage process. The first stage is a filter that extracts scale invariant features from the visual field. The second stage uses inference based spacio-temporal analysis of these features to identify objects in the visual field. The proposed model combines Numenta's Hierarchical Temporal Memory (HTM), with HMAX developed by MIT's Brain and Cognitive Science Department. While these two biologically inspired paradigms are based on what is known about the visual cortex, HTM and HMAX …