2020-

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Now showing 1 - 20 of 2010

Open Access
Pruning and acceleration of deep neural networks
(Colorado State University. Libraries, 2020) Thivagara Sarma, Janarthanan, author; Pouchet, Louis-Noël, advisor; Rajopadhye, Sanjay, committee member; Pasricha, Sudeep, committee member; Anderson, Chuck, committee member
Deep neural networks are computational and memory intensive applications. Many network pruning and compression solutions has been introduced to deploy inference of large trained models in limited memory and time critical systems. We proposed a new pruning methodology that assigns significance rank to the operations in the inference program and for a given capacity and operation budget, generate only the important operations to do the inference. Our approach has shown that, in many classical feed forward classification networks we can maintain almost the same accuracy as the original inference by executing less than half of the operations in the original program. We also proposed a methodology to improve the effective implementation of the output sparse computation, controllable by a threshold variable.
Open Access
Cofilin-actin rods, a hippocampal pathology in mouse models of human dementias, form from different inducers through a common molecular pathway
(Colorado State University. Libraries, 2020) Babcock, Isaac W., author; Bamburg, James R., advisor; Di Pietro, Santiago M., committee member; Zabel, Mark D., committee member
To view the abstract, please see the full text of the document.
Open Access
Analysis of simulated dilute anode tail-gas combustion characteristics on a CFR engine
(Colorado State University. Libraries, 2020) Balu, Alexander, author; Olsen, Daniel, advisor; Windom, Bret, committee member; Baker, Daniel, committee member
Recent innovations in metal-supported solid oxide fuel cells (MS-SOFC) have increased the longevity and reliability of fuel cells. These innovations drive the desire to create power generating systems that combine different ways of extracting power from a fuel to increase overall fuel conversion efficiency. This investigation assesses the feasibility of operating an internal combustion engine (ICE) with the anode tail-gas, which is a blend of H2, CO, CO2, H2O, and CH4, exhausted by a metal-supported solid oxide fuel cell (MS-SOFC). This engine would be used to support the fuel cell balance of plant equipment, including a compressor and expander, and produce excess electrical power. Seven variations of the expected anode tail-gas blends were determined by varying the dewpoint temperature of the fuel. In three of the test blends, CO2 replaced the water content of the fuel to allow for initial feasibility testing without the capital investment required to simulate the tail-gas with steam injection. Gas blends are tested by combining separate flows of each constituent, and combustion is tested using a Cooperative Fuel Research (CFR) engine. Compression ratio (CR), spark timing, intake manifold temperature (IMT), and boost pressure were manipulated to obtain optimal operating conditions. All test blends produced power and reached stable engine operation. Response surface method (RSM) optimization was used to experimentally optimize operating parameters and determine the maximum achievable efficiency utilizing the CFR engine. Initial feasibility testing performed on test blends with CO2 in place of water showed that all combinations successfully produced power in the engine. The mixture with the highest levels of CO2 was problematic and required an increased CR of 14.4:1, advanced timing of 40° before top dead center (BTDC), and an increased IMT of 70℃. All CO2 test blends operated at brake efficiencies ranging from 12-17% during initial testing. After the feasibility of this project was determined, a steam generator and steam flow meter were installed and used to fully simulate the anode tail-gas blends with steam injection. All fully simulated anode tail-gas blends produced power in the engine, although the blend with the most water content caused operational problems with the CFR engine test stand. These problems were caused by large amounts of water entering the engine lube oil system. RSM optimization was performed on the most viable test blends which had steam injection to 40℃ and 90℃ fuel dewpoint temperatures. During optimization, the 40℃ and 90℃ dewpoint temperature blend brake efficiency increased from 20% to 22.2%, and 17% to 22.3%, respectively. This study determined that ICE operation on dilute anode tail-gas is possible. Anode tail-gas combustion data was collected and used to inform engine and combustion models to facilitate prototype engine development for further testing.
Open Access
Synthesis of monolayer MoS₂ via chemical vapor deposition
(Colorado State University. Libraries, 2020) Varra, Travis, author; Sambur, Justin, advisor; Prieto, Amy, committee member; Yourdkhani, Mostafa, committee member
Two-dimensional materials, specifically transition metal dichalcogenides (TMDs), have emerged as ideal candidates for lightweight and flexible optoelectronic applications. Unlike bulk solids, single layer TMDs exhibit a direct bandgap that makes next-generation device applications possible. This work describes the synthesis of single layer MoS2 via chemical vapor deposition (CVD). This method involves thermal vaporization of MoO3 and S precursors in a tube furnace. The influence of reaction conditions (e.g., temperature, pressure, reaction holding time, carrier gas flow rate, and precursor separation distance) on MoS2 sample morphology was quantified using optical microscopy. Isolated equilateral triangles with 11 μm-long edge lengths were reproducibly grown on Si/SiO2 substrates. The layer thickness was determined using Raman and photoluminescence spectroscopy.
Open Access
Forest soil C and N responses to salvage logging and belowground C inputs in bark beetle infested stands
(Colorado State University. Libraries, 2020) Avera, Bethany N., author; Cotrufo, M. Francesca, advisor; Rhoades, Charles, committee member; Rocca, Monique, committee member; van Diepen, Linda, committee member
Managing forest ecosystems in this era of global change requires a fundamental understanding of forest soil properties and processes. Forest disturbance events are projected to increase in severity and frequency, requiring a better understanding of how post-disturbance management will impact ecological processes such as soil nutrient dynamics and stocks of soil carbon (C). The research in this dissertation focused on areas of widespread mortality in lodgepole pine (Pinus contorta var. latifolia) in northern Colorado due to the most recent outbreak of the endemic mountain pine beetle (MPB; Dendroctonus ponderosae Hopkins). The goal of this research was to examine soil nitrogen (N) stocks, plant N uptake, and changes in forest soil C stocks in soil organic matter (SOM) due to tree mortality and subsequent salvage logging and from different belowground C inputs. To achieve this aim, I compared the three most prevalent management options: 1) uncut beetle-infested lodgepole pine stands and clear-cut salvage logged areas with either 2) post-harvest residue retention or 3) post-harvest residue removal. To determine the impacts of MPB-infestation and salvage logging on ecosystem N stocks and plant N uptake, I implemented an experimental field study by adding 15N-labeled ammonium sulfate to research plots centered over lodgepole pine seedlings. Measuring N stocks and 15N recovery in soil and vegetation pools over two growing seasons highlighted the coupled nature of forest C and N cycling between plant and soil forest ecosystem compartments. The majority of the 15N label was recovered in the soil and was not impacted by the management treatments. In contrast, the N uptake by lodgepole pine seedlings was driven primarily by the amount of C fixation and the patterns of C fixation, in turn, related to other environmental factors modulated by the management treatment, such as available light. An observational field study sought to quantify changes in forest soil C stocks in the bulk soil and SOM fractions and detect any changes in C chemistry as a result of management that may impact C persistence. In the dry, high elevation forests studied, soil C increased with salvage logging likely due to mixing of surface residues and O horizon C into the mineral soil during logging. The distribution of C stocks among the mineral soil fractions and the chemistry of those fractions indicated that root C accumulation in the particulate organic matter (POM, >53 μm) is an important mechanism of soil C accumulation in these forest soils. A mechanistic laboratory incubation evaluated the efficiency of mineral-associated organic matter (MAOM, <53 μm) formation from root and hyphal necromass inputs with different C chemistries. This study showed that rye root necromass with more labile and less structural C than pine roots, was processed most in the 38-day incubation and contributed much more efficiently to the formation of MAOM than did the pine roots. Despite less processing, the arbuscular and ectomycorrhizal fungal necromass both contributed as efficiently as rye roots to MAOM formation. These results indicate that both C chemistry and C/N ratio exert controls on residue processing and MAOM formation. Together, this dissertation work showed that salvage logging stimulated the growth of lodgepole pine seedlings, resulting in increased storage of both C and N in the plant biomass above- and belowground. As this pine root biomass turns over, the root necromass will contribute C to the POM fraction, the largest pool of soil C in this system. The net increase of forest soil C with salvage logging found in this study is notable as it suggests that the MPB-infested lodgepole pine forests of Colorado can be salvage logged with a low risk of significant soil C loss. Additionally, the highest recovery of the N label was in the soil, thus the high soil N recovery with higher soil C supports SOM is a sink of N reducing N losses. Finally, pine seedling colonization by ectomycorrhizal fungi may further aid with nutrient retention and the efficient formation of MAOM during regeneration.
Open Access
From Sacrificial Lands to reciprocity: art and social engagement
(Colorado State University. Libraries, 2020) Thornton, Janine, author; Lundberg, Thomas, advisor; Kissell, Kevin, committee member; Moore, Emily, committee member; Plastini, Johnny, committee member
Oh I would touch with this love each wounded place - Anita Barrows, "Psalm" My thesis artworks focus on interconnection and on the Western cultural perception of a separation between humans and nature. This perception developed during the nineteenth-century Westward Expansion, which viewed nature as a source of resources to be utilized and tamed. Within this separation is an assumed hierarchy in which nature is viewed as lesser or expendable when compared to humans. Land continues to be sacrificed for human wants with no regard for the impacts that this land use has on nature and humans, or on our delicate ties of interconnection. The word interconnection is very broad with many meanings and interpretations. In this work, interconnection refers to relationships, especially from an environmental perspective, in which individual behaviors affect other life forms and natural systems. This interconnection is a web of cause and effect, in which actions of individuals have impacts that ripple out into the world. It is often difficult to understand the effects that individual actions have on others, as it requires a heightened awareness of our world and its issues – awareness that can be challenging to achieve. I believe more discussion and action are needed to help expand awareness and sensitivity towards environmental threats. The questions guiding my research ask, a) how I visually represent the concept of human/nature interconnection, b) how I express the environmental necessity of relationship and reciprocity in our actions, and c) how social engagement can help to expand awareness and discussion. I included social engagement in my thesis because I believe a greater depth of understanding can be encouraged through collaborative works with artists and other disciplines. I explored ideas of human/nature interconnection and relationship through studies of materials, place and the environment. Materials such as fibers, cement and plastic connote relationship, culture, consumption and waste. Fibers are reminders of everyday consumer items such as clothing and housewares, which also can provide a sense of status through the brands selected. Plastics link to consumer product consumption, and to trends, which lead to waste when the item is no longer of value. Plastic is another manufactured material used for packaging and consumer product integrity. My use of plastic ties back to product consumption and waste, as most plastics become landfill. Cement is a manufactured material most frequently seen in construction projects, which aligns with urban development and shifting relationships with nature. Following my work with materials, I looked to my relationship with place, focusing on where I live. This included developing a better understanding of how I relate to the land and wildlife around me, and impacts I make by living there. By making the subject matter of my work more personal, I am better able to see my particular relationship with nature and the impacts of decisions I make. Next, I expanded my personal perspective from my locale to a larger view of the rural environment through the collaborative development of the Sacrificial Lands exhibit, which includes my artwork along with work of other artists, poets, and scientists. The Sacrificial Lands project showcases individual perspectives, creativity, and research from a variety of fields. The objectives are to encourage expanded discussion of environmental topics and to promote collaborative endeavors that seek greater environmental awareness and restoration.
Open Access
Optical detection methods for microfluidic devices
(Colorado State University. Libraries, 2020) Koepke, Marina M., author; Lear, Kevin L., advisor; Wilson, Jesse, committee member; Gustafson, Daniel, committee member
Optical technology is a common tool integrated onto microfluidic devices to aid in data collection and counting for biological and chemical research. In this study, a simple optical technique was investigated as a detection method for microfluidic impedance cytometry (MIC) devices. The MIC devices were designed to characterize size and structure of parasite eggs through electrical impedance measurements. This data could directly benefit the medical and veterinary communities by providing information to aid in addressing helminth infections in humans and animals. The current MIC device and instrumentation does not provide a robust way to validate which impedance changes correlate to parasite eggs passing through the electrodes. To address this, an optical detection method was designed, implemented and tested on two different types of microfluidic devices: a glass device and printed circuit board (PCB) device. The optical hardware was accompanied by a trigger circuit that was used to process and manipulate the detected light signal. The circuit was designed with a sensitivity that would detect small changes in light from strongyle-type eggs flowing through the microfluidic channel. The trigger circuit was composed of multiple stages of signal amplification and oscillation suppression techniques so the changes in light could clearly be detected by the electronics. This method proved to be successful in detecting voltage changes ranging from 1.7 mV to 6.8 mV which resulted from strongyle egg sized particles (63-75 μm in diameter) flowing through the microfluidic channel. Adaptations for the optics, bench set-up and microfluidic device design were investigated to transfer this method to different laboratory settings. This study outlines the process of utilizing basic lab tools and components to create an easy to implement optical detection method for a variety of chip designs and laboratory set-ups.
Open Access
In-vehicle validation of energy consumption modeling and simulation
(Colorado State University. Libraries, 2020) DiDomenico, Gabriel, author; Bradley, Thomas, advisor; Quinn, Jason, committee member; Pasricha, Sudeep, committee member
The Colorado State University (CSU) Vehicle Innovation Team (VIT) participated in the first Department of Energy (DOE) Advanced Vehicle Technology Competitions (AVTC) in 1988. Since then, it has participated in the next iterations of the competition as well as other advanced vehicle technology projects. This study aims to validate the team's mathematical modeling and simulation of electrical energy consumption of the EcoCAR 3 competition (academic years 2014-2018) as well as the testing methods used for validation. First, baseline simulation results are obtained by simulating a 0-60 mph wide open throttle (WOT, or 100% APP) acceleration event (AE) with the product being the electrical energy economy in Wh/mi. The baseline model (representing the baseline control strategy and vehicle parameters) is also simulated for 0-40 mph and 0-20 mph AEs. These tests are replicated in the actual vehicle, a 2016 P2 PHEV Chevrolet Camaro entirely designed and built by CSU's VIT. Next, the same AEs are again tested with a changed acceleration rate due to the APP being limited to 45%. The velocity profiles from these tests are used as feedback for the model and the tests are replicated in simulation. Finally, the baseline model is altered in 3 additional ways in order to understand their effect on electrical energy consumption: the mass is increased, then the auxiliary low voltage (LV) load is increased and then the transmission is restricted to only 1 gear. These simulations are again replicated in-vehicle in order to validate the model's capability in predicting changes in electrical energy consumption as certain vehicle parameters are changed. This study concludes that model is able to predict these changes within 6.5%, or ±30.2 Wh/mi with 95% confidence.
Open Access
Do participants with chronic pain have improved self-efficacy after completing the MY-Skills intervention?
(Colorado State University. Libraries, 2020) Kinkel, Charla, author; Schmid, Arlene A., advisor; Atler, Karen E., committee member; Fruhauf, Christine A., committee member
Purpose: The aim of this study was to explore if participants with chronic pain have improved self-efficacy in performing daily activities and managing pain symptoms after completing the Merging Yoga and self-management Skills program (MY-Skills). Method: Care dyads, comprised of caregivers and care-recipients with chronic pain were recruited to complete the 8-week MY-Skills intervention. Twice each week, participants engaged in a one-hour group self-management course followed by a one-hour group yoga session developed for care dyads with chronic pain. Self-efficacy outcomes were collected using the Chronic Pain Self-Efficacy Scale (pain management, physical function, coping with symptoms); the PROMIS® Self-Efficacy for Managing Daily Activities Short Form 4a; and the PROMIS Self-Efficacy for Managing Symptoms Short Form 4a. Data for all participants were analyzed using a paired t-test. A post hoc exploratory analysis of separate caregiver and care-recipient outcomes was conducted using a Wilcoxon signed ranks test. Results: Eight participants completed the study (50.23±14.77 avg. age, 77% female, 69% with pain for > 10 years). The participants reported increased self-efficacy across all measures and domains, with significant improvement found for self-efficacy for physical function (38.97±19.45 vs. 59.10±18.60, p = .004). The post hoc exploratory analysis showed increased self-efficacy in all caregiver outcomes. Care-recipients reported increased self-efficacy in all areas except pain management, which significantly decreased. Conclusion: MY-Skills improved self-efficacy to varying degrees for participants in aggregate. Improvements in self-efficacy related to physical function demonstrated that MY-Skills increased participants' confidence in performing everyday occupations such as running errands, doing chores, working, and socializing. Interventions that improve self-efficacy, like MY-Skills, may help people with chronic pain gain function, problem-solving, and coping skills to reclaim a sense of control and enhance quality of life.
Open Access
Secure CAN logging and data analysis
(Colorado State University. Libraries, 2020) Van, Duy, author; Daily, Jeremy, advisor; Simske, Steve, committee member; Papadopoulos, Christos, committee member; Hayne, Stephen, committee member
Controller Area Network (CAN) communications are an essential element of modern vehicles, particularly heavy trucks. However, CAN protocols are vulnerable from a cybersecurity perspective in that they have no mechanism for authentication or authorization. Attacks on vehicle CAN systems present a risk to driver privacy and possibly driver safety. Therefore, developing new tools and techniques to detect cybersecurity threats within CAN networks is a critical research topic. A key component of this research is compiling a large database of representative CAN data from operational vehicles on the road. This database will be used to develop methods for detecting intrusions or other potential threats. In this paper, an open-source CAN logger was developed that used hardware and software following the industry security standards to securely log and transmit heavy vehicle CAN data. A hardware prototype demonstrated the ability to encrypt data at over 6 Megabits per second (Mbps) and successfully log all data at 100% bus load on a 1 Mbps baud CAN network in a laboratory setting. An AES-128 Cipher Block Chaining (CBC) encryption mode was chosen. A Hardware Security Module (HSM) was used to generate and securely store asymmetric key pairs for cryptographic communication with a third-party cloud database. It also implemented Elliptic-Curve Cryptography (ECC) algorithms to perform key exchange and sign the data for integrity verification. This solution ensures secure data collection and transmission because only encrypted data is ever stored or transmitted, and communication with the third-party cloud server uses shared, asymmetric secret keys as well as Transport Layer Security (TLS).
Open Access
Calcium, telomere length, and parasitism in passerines nesting at high elevation
(Colorado State University. Libraries, 2020) Rodriguez, Marina D., author; Huyvaert, Kathryn P., advisor; Doherty, Paul F., Jr., advisor; Bailey, Susan M., committee member
Most organisms are exposed to numerous environmental stressors at various points throughout life, and, through natural selection, organisms' responses to such stressors have been optimized by natural selection for the best fitness outcomes. During the breeding season, wild vertebrates often make a trade-off between current reproduction and self-maintenance when dealing with environmental stressors. The total cost of reproduction is made up of all of the resources and energy that go into activities related to reproduction (e.g., nest building, finding a mate, foraging for food and nutrients related to offspring production, parental care) that do not go into self-maintenance. The cost of these activities can vary depending on resource availability, where limited resources can increase the cost associated with breeding due to increased energy associated with foraging and competing for the resource. In birds, calcium is a critical resource due to its importance in egg production and offspring development, and low calcium availability often leads to decreased reproductive success. In my first chapter, I used an experimental approach to assess the effects of supplemental calcium on reproductive parameters of Tree Swallows (Tachycineta bicolor) in a high elevation environment. Calcium-supplemented birds in my study area laid more, larger eggs, and had higher hatching success compared to control females. These results provide evidence that calcium availability is a constraint on breeding Tree Swallows at high elevation, perhaps due to the harsh conditions and concomitantly higher metabolic costs that force a costlier and more intense trade-off between foraging for food or for calcium. The increase in reproductive parameters for calcium supplemented nests in Chapter 1 highlights a cost associated with calcium foraging that constrains reproduction. For my second chapter, I aimed to better understand how calcium availability affects the cost of reproduction in mother Tree Swallows and offspring by using telomere shortening as a proxy of life stress and lifespan. Telomeres are terminal features of chromosomes consisting of repetitive DNA sequences that shorten with age and stress, and whose length is positively correlated with survival. I used telomere shortening as a proxy for the costs associated with reproduction to better understand life history trade-offs of Tree Swallows at high elevation sites. Similar to Chapter 1, I found that Tree Swallows supplemented with calcium had higher reproductive success, although I also found that supplemented nests had more telomere shortening compared to birds at control nests. These results provide evidence that Tree Swallows supplemented with calcium experience higher reproductive output at the cost of lower expected survival in the form of more telomere shortening. While investing resources in reproduction may lead to higher reproductive output for the current breeding season, this increase in reproductive success can come with a cost to survivorship. One way that resource allocation can shape survivorship is through investment in immune function. In many systems, however, more species-level and individual-level research is needed on host-parasite relationships before trade-offs between immune function and reproduction can be assessed. For my third chapter, I conducted a survey of avian Haemosporida: blood parasites that include those that cause avian malaria. I surveyed an avian community for haemosporidian parasites in the Colorado Rocky Mountains in order to estimate prevalence and diversity of blood parasites and to find species-level and individual-level characteristics that influence infection prevalence. I found that open cup nesters have higher blood parasite prevalence than cavity or open cup nesters. Additionally, male Ruby-crowned Kinglets, White-crowned Sparrows, and Wilson's Warblers had a higher prevalence of haemosporidian parasites compared to the other species analyzed, as did Red-breasted Nuthatches, which, like Ruby-crowned Kinglets, have a high body condition index. This chapter presents baseline knowledge of avian blood parasite presence, prevalence, and diversity across avian species in the Colorado Rocky Mountains and adds to our knowledge of host-parasite relationships of blood parasites and their avian hosts.
Open Access
Detection and relocation of earthquakes in the sparsely instrumented Mackenzie Mountains region, Yukon and Northwest Territories, Canada
(Colorado State University. Libraries, 2020) Heath, David C., author; Schutt, Derek L., advisor; Aster, Richard C., committee member; Wald, David J., committee member; Cheney, Margaret, committee member
The Mackenzie Mountains are an actively uplifting and seismogenic arcuate thrust belt lying within the Northwest Territories and Yukon, Canada. Seismic activity in the region is poorly constrained due to a historically sparse seismograph distribution. In this study, new data are analyzed from the 40-station, ~875 km-long Mackenzie Mountains temporary network (Baker et al., 2020) crossing the Cordillera-Craton region adjacent to and within the Mackenzie Mountains, in conjunction with Transportable Array and other sparsely distributed arrays in the region. Data from approximately August 2016 – August 2018 are processed and compared to the sparse-network earthquake catalog records maintained by the USGS and Natural Resources Canada. Using algorithms developed by Kushnir et al. (1990), Rawles and Thurber (2015), and Roecker et al. (2006), signals are identified and subsequently associated across the network to note potential events, estimate phase onsets, and resolve hypocenter locations. This study improves the regional earthquake catalog by detecting smaller-magnitude earthquakes and lowering the regional magnitude of completeness from Mc = 2.5 to 1.9. Within the Mackenzie Mountains and immediately surrounding areas we find 524 new events and additionally recommend an updated location for 185 previously cataloged events. Our b-value computation for the updated catalog (0.916 ± 0.08) likely indicates a relatively high level of regional differential stress. We identify the spatial distribution of earthquakes in the Mackenzie Mountains as diffuse, and offer far-field stress transfer as a mechanism for producing widespread reverse faulting observed in the region. Further, we associate regional seismicity with tectonic activity in the context of known faults and orogenic provinces such as the Richardson Mountains.
Open Access
Patents, knowledge creation, and spillovers in genetics for agriculture and natural resources
(Colorado State University. Libraries, 2020) Samad, Ghulam, author; Graff, Gregory D., advisor; Maskus, Keith E., committee member; Weiler, Stephan, committee member; Hooten, Mevin, committee member
Increasing food, energy, and resource demand by growing global population is putting unprecedented pressure on agriculture and natural resource systems. Innovation in agriculture, energy, and other resource intensive industries contributes enormously to productivity and sustainability gains. Innovation in genetic resources and biological systems is a particularly promising yet controversial area of such innovation. Generally, it has been observed that regional clustering (economies of agglomeration) plays an important role in driving innovation. To what extent do we observe regional clustering to play a role in innovation in these industries? Especially given that production is highly diffused geographically, and research and technology are seen as highly globalized (global public goods vs. global monopolies by MNCs). The overarching questions address by this study are the following: (1) What do patents reveal about geographic patterns of knowledge creation and spillovers? (2) What economic and policy factors drive invention activity at the regional scale? And indirectly, (3) What is the role of regional clustering in driving innovations for food security and sustainability? To address these overarching objectives this study is mainly separated into three parts. The first part delves into three related questions: (1) How have biological inventions for use in primary resource-intensive industries been spatially distributed across the United States? And, in particular, to what degree have they been geographically concentrated? (2) What are the time-space dynamics of biological inventions for these industries? To what extent does the concentration of previous inventions effect where new inventions arise? And, (3) based on these insights, can we identify primary innovation clusters in the U.S. for these industries? This study draws on detailed information on inventor address from about 34,000 patented inventions as indicators of innovation and entrepreneurship in three closely related industries: (1) agriculture, (2) bioenergy, and (3) environmental management. To address these questions three approaches are used mapping, Moran I and regression analysis. Results indicate these biological inventions are distributed across the U.S, but highly concentrated clusters are formed in urban regions. Moreover, a spatial clustering pattern clearly exists. In term of concentration of biological inventions for these industries, a rural-urban division exists. Inventions do not tend to concentrate near production activities but tend to concentrate in urban area. The number of inventions in an area in prior years has a significant impact on the number of current year inventions. This relationship represents the localized spillover phenomenon. While we do see inventions in rural areas, rural areas do not appear to be the hotspots of innovation in agricultural, energy, or environmental biotechnologies. The second part of this dissertation explores the covariates of regional concentration of these biological inventions for agriculture, energy, and environment in the United States. First, the geographic patterns of these inventions are analyzed using negative binomial panel regression of patented inventions by region, to identify the density of inventions overall as well as the space-time dynamics of invention cumulativeness. We find that inventions have been spatially concentrated in about 30 major metropolitan clusters, and that spatial distribution has remained remarkably stable over time. Factors of population, earnings, and farm income are correlated with their invention counts. As a first rule, these inventions are created in higher population urban regions. Although, among regions of similar population inventions are more likely closer to agricultural production. Results clearly show the emergence of largely urban innovation clusters in agriculture and resource industries. The third part of this dissertation broadens the scope to explore the spatial distribution and covariates of regional invention activity across Organization for Economic Cooperation and Development (OECD) countries. Three approaches are used mapping, Moran I and regression analysis to analyse the spatial distribution and covariates across OECD. The results showed that while inventions are distributed across the OECD, there again appear to be concentrated clusters in larger urban regions (another broader set of top 30 clusters). Moreover, the number of inventions made in prior years has significant explanatory power on the number of current year inventions, by region. This represents the localized spillover phenomenon. In addition, region size (as measured by population) and level of economic activity (as measured by regional income) do not appear to be related to the count of inventions for these industries. R&D expenditures (regional) and an IP index (which is national in nature but is applied to regions for this study) are strongly related to biotech invention activity for these industries. A rural-urban division does appear to exist. Finally, these invention counts appear to be negatively correlated with gross value added of agriculture by region across OECD countries.
Open Access
Impacts of Arctic warming and sea ice loss on the Northern Hemisphere mid-latitude large-scale circulation
(Colorado State University. Libraries, 2020) Ronalds, Bryn, author; Barnes, Elizabeth A., advisor; Thompson, David, committee member; Randall, David A., committee member; Eykholt, Richard, committee member
The consequences of the rapid warming of the Arctic and associated sea ice loss on the Northern Hemisphere atmospheric circulation is still largely debated. The uncertainty in the circulation response stems from a poor understanding of the underlying physical mechanisms of the remote response, regional and seasonal differences, differences between models and experimental set-ups, the large internal variability of the system, and the short observational record. This research seeks to address some of this uncertainty, specifically the uncertainty related to the physical mechanisms, regionality, and modeling differences. The wintertime Northern Hemisphere eddy-driven jet streams over the North Pacific and North Atlantic basins exhibit differing responses to Arctic warming and sea ice loss in a fully coupled climate model. In the North Atlantic the jet weakens, narrows along the poleward flank, and shifts slightly equatorward. This response is similar to previous studies examining the Northern Hemisphere zonal mean jet response. In contrast, the North Pacific jet strengthens and extends eastward in response to Arctic sea ice loss, with no change in latitude, and narrows slightly along the poleward flank. In both cases, there are high latitude anomalous easterlies in the region of sea ice loss, where the local surface temperature gradients are weakening. This can lead to changes in locations and frequency of wave-breaking, thus leading to changes in the mean zonal winds further south, in the vicinity of the jet. This work relates the differing changes in the North Pacific and North Atlantic to these changes in wave-breaking in a simplified atmospheric model, and posits that the location of the jet relative to the region of Arctic sea ice loss is a dominant factor in determining the mean jet response to the sea ice loss and local warming. Changes in the mean wintertime Northern Hemisphere midlatitude zonal winds are found to be indicative of changes to the sub-seasonal variability of the wintertime zonal winds. The sub-seasonal circulation patterns over the ocean basins are closely linked with continental weather regimes, including changes in temperature and precipitation. While establishing a causal link between Arctic sea ice loss and changes to remote weather regimes in the observational record remains difficult, the Polar Amplification Model Intercomparison Project (PAMIP) provides insight into possible relationships and consequences. The design of the project eliminates differences in experimental set-ups across models and aids in addressing the uncertainty in regional responses. Across four climate models, Arctic sea ice loss leads to a strengthened and extended North Pacific jet in the January-February mean. This mean change is also associated with changes to the sub-seasonal, wintertime North Pacific zonal wind variability. All four models show an increase in strengthened and extended North Pacific eddy-driven jet stream events and a decrease in weakened, retracted and equatorward-shifted North Pacific jet events in January-February. Previous work has also established the relationships between North Pacific jet stream variability and downstream, North American weather regimes, and changes to the former are expected to impact the latter. Again, there is model agreement in an increase of a warm west/cold east temperature dipole over North America, associated with the strengthened and extended jet events. There is also a decrease in cold air temperature anomalies over North America, associated with weakened and equatorward-shifted jet events.
Open Access
Assessment of novel causes and investigation into the gut microbiome in cats with chronic kidney disease
(Colorado State University. Libraries, 2020) Summers, Stacie, author; Lappin, Michael, advisor; Quimby, Jessica, committee member; Dow, Steve, committee member; Prenni, Jessica, committee member
To view the abstract, please see the full text of the document.
Open Access
Evaluation of controlled end gas auto ignition with exhaust gas recirculation in a stoichiometric, spark ignited, natural gas engine
(Colorado State University. Libraries, 2020) Bayliff, Scott Michael, author; Olsen, Daniel B., advisor; Windom, Bret, committee member; Baker, Daniel, committee member
Many stationary and heavy-duty on-road natural gas fueled engines today operate under stoichiometric conditions with a three-way catalyst. The disadvantage of stoichiometric natural gas engines compared to lean-burn natural gas and diesel engines is lower efficiency, resulting primarily from lower power density and compression ratio. Exhaust gas recirculation (EGR) coupled with advanced combustion controls can enable operation with higher compression ratio and power density, which yields higher efficiency. This also results in engine operation between the limits of knock and misfire. Operation between these limits has been named controlled end gas auto-ignition (C-EGAI) and can be used to improve the brake efficiency of the engine. Various methods of cylinder pressure-based knock quantification were explored to implement C-EGAI. The indicated quantification methods are used for the implementation of a control scheme for C-EGAI with a relation to the fractional heat release due to auto-ignition. A custom EGR system was built and the effect of EGR on the performance of a stoichiometric, spark ignited, natural gas engine is evaluated. C-EGAI is implemented and the optimal parameters are determined for peak performance under EGR and C-EGAI conditions. In this study, knock detection is used for the recognition, magnitude, and location of the auto-ignition events. Cylinder pressure-based knock detection was the primary method for determining the occurrence and location of knock but was also used for implementing the ignition control scheme for controlled end gas auto-ignition. The combustion intensity metric (CIM) enabled parametric ignition timing control which allowed for the creation of a relationship between fractional heat release due to auto-ignition and CIM. Both exhaust gas recirculation and controlled end gas auto-ignition were analyzed with a cooperative fuel research (CFR) engine modified for boosted fuel/air intake. The data was interpreted to provide a proper evaluation of unique analytical methods to quantify the results of C_EGAI and characterize the live auto-ignition events. The control variables for this method of C-EGAI were optimized with EGR conditions to generate the point of peak performance on the CFR engine under stoichiometric, spark ignited, natural gas conditions.
Open Access
The ecological effects of multiple disturbances on subalpine forest structure and recovery in a changing climate
(Colorado State University. Libraries, 2020) Schapira, Zoe, author; Stevens-Rumann, Camille, advisor; Hoffman, Chad, committee member; Rocca, Monique, committee member
Due to the shifting global climate, the severity, size, and frequency of climate-driven disturbances are increasing, inevitably causing disturbances to interact in time and space. Bark beetle epidemics and wildfires have historically shaped the disturbance regimes of western North American forests. Their interactive effects on stand dynamics and recovery are inadequately studied in Engelmann spruce (Picea engelmannii)- subalpine fir (Abies lasiocarpa) dominant forests; understanding these interactions is imperative to the management and health of forested ecosystems. Tree seedling densities and species composition, surface fuel loading, and stand structure characteristics were compared across 80 sites that experienced either high tree mortality from epidemic spruce beetle outbreaks (>50% affected basal area), high-severity wildfire (>90% tree mortality), post-outbreak high-severity wildfire (1-3 years post-outbreak), or no disturbance (control) in northern Colorado and southern Wyoming. The beetle-affected sites span multiple years post-outbreak from 1996-2017, ultimately comprising a chronosequence of beetle-affected stands. Structural changes in subalpine stands following spruce beetle outbreaks include species compositional shifts in overstory trees, and significant increases in fuel loading over time-since-outbreak. Tree seedling densities among outbreak and control sites differ significantly from burned areas, indicating that wildfires override the effects of repeated disturbances on regeneration. While a cursory assessment of post-outbreak regeneration based on height resulted in the appearance of consistent and stable forest recovery, subsequent aging techniques shed additional light on the drivers of subalpine tree establishment. Subalpine tree regeneration may remain suppressed in the understory for over a century; post-outbreak recovery dynamics cannot be fully understood through the use of height as a proxy for seedling age. Given the strong correlation between Engelmann spruce and subalpine fir establishment with cool and moist growing conditions, there remains significant uncertainty about post-disturbance recovery and the persistence of spruce-fir forests in a warming and drying world. It is critical to understand post-disturbance fuel dynamics and stand recovery to identify hazards for subsequent fire suppression, implement treatments to enhance forest resilience, and to understand the potential consequences of climate-induced shifts in disturbance regimes on forest health.
Open Access
Cosmogenic background rejection for the sterile neutrino search with the Short-Baseline Neutrino Program far detector
(Colorado State University. Libraries, 2020) Hilgenberg, Christopher M., author; Wilson, Robert J., advisor; Harton, John, committee member; Toki, Walter, committee member; Zhu, Wen, committee member
As the Short-Baseline Neutrino Program Far Detector, the ICARUS liquid argon time-projection chamber will operate at shallow depth and therefore be exposed to the full surface flux of cosmic rays. This poses a problematic background to the sterile neutrino search. A direct way to reject this background is to surround the cryostat with a detector capable of tagging incident cosmic muons with high efficiency, the Cosmic Ray Tagging System (CRT). I have worked to develop the CRT detector hardware and the simulation and reconstruction software. This system, currently undergoing installation, is approximately 25% commissioned and taking data. I have developed a powerful method for cosmogenic background rejection utilizing the CRT and Photon Detection System. Results from a simulation based study, informed by CRT data, demonstrate the power of the technique in rejecting cosmogenic events with little adverse impact on the neutrino sample.
Open Access
Customer and system impacts of grid support functions for voltage management strategies
(Colorado State University. Libraries, 2020) Giraldez Miner, Julieta, author; Suryanarayanan, Siddharth, advisor; Atadero, Rebecca, committee member; Yang, Liuqing, committee member; Young, Peter, committee member; Zimmerle, Daniel, committee member
This document describes modeling techniques and methods to study the impacts to the utility and to the customer of using DERs such as advanced inverters to provide voltage support in order to maintain voltage within the recommended voltage limits. For this, a method for accurately representing secondary circuits in distribution feeders is proposed and quasi-static-time series (QSTS) simulation techniques are used to study the impact of advance inverter functions to the utility for managing voltage and to the customer in terms of possible generation curtailment. This dissertation looks at factors in medium and low-voltage circuit topology that drive customer voltages with DERs, and investigates where along the distribution feeder are voltage based advance inverter grid support function most effective. The described modeling techniques and methods have informed policy and regulatory type decisions such as updating DER interconnection tariffs and standards.
Open Access
Factors influencing access to higher education in La Rinconada, Peru: an ethnographic case study
(Colorado State University. Libraries, 2020) Busch, AnneLiese M., author; Jennings, Louise, advisor; Lynham, Sue, committee member; Kuk, Linda, committee member; Sagas, Ernesto, committee member
Studies show that there is a large gap in participation in higher education between Peru's poorest members of society and their wealthier counterparts despite the existence of 51 public universities located across Peru that are free of cost. Quantitative studies addressing this topic rely on a culture of poverty paradigm and have argued that this discrepancy is due to a lack of culture that prioritizes higher education among Peru's poor. The purpose of this study was to investigate why it is that the poorest segments of the population in Peru overwhelmingly do not pursue higher education despite the existence of tuition-free public universities, to understand the extent to which culture and systemic factors outside their control explain this phenomenon, and to examine how mining families perceive the role of and access to higher education for their children. This study focused on the community of La Rinconada, Peru for three primary reasons: (a) La Rinconada is representative of many illegal mining communities in not just Peru, but Latin America in that it is perceived as a city where low-skilled workers have an opportunity to generate more income working in the mines than by relying on positions that pay minimum wage (now 930 soles per month, which is equivalent to approximately $284); (b) more than 98% of La Rinconada's population is comprised of individuals belonging to the lowest socioeconomic level of Peruvian society; and (c) the population of La Rinconada has nearly quadrupled within the past decade and continues to grow. This study employed an ethnographic case study approach including recording and documenting observations of La Rinconada and Juliaca, the two sites in which the interviews were conducted, and conducting interviews with three separate groups of study participants including 14 teachers, 17 parents employed in a mining-related industry and 10 students. Field notes of all observations were kept and recorded as well as all interviews and conversations with the interview participants following their consent. The interviews were transcribed in Spanish and were then translated into English. Codes and patterns for each of the three groups of interview participants (teachers, parents employed in a mining-related industry, and students) were identified and were used to identify the three resulting themes. The observations I recorded and documented in La Rinconada demonstrate the harsh conditions of day-to-day life for its residents and highlight the extent to which the parents I interviewed are willing to go in order to provide a better life for their children; a life which for most participants included the pursuit of higher education. In the interviews I conducted I identified three themes: acceptance of harsh conditions for more opportunity, importance of higher education and the obstacles to pursuing it and the perceived role of higher education in future success. My findings indicate that for the parents employed in mining-related industries higher education was a priority because of the perceived financial and personal stability it would enable their children to enjoy and the social status and prestige a bachelor's degree would signify for their children because they would now be considered professional as opposed to a laborer. In general, for residents of La Rinconada, financial constraints and distance from institutions of higher education were identified as being the biggest obstacles to accessing higher education. My findings show that despite the fact that half of the individuals I interviewed had not pursued higher education themselves, all of the participants stated that they valued higher education and viewed it as essential to achieving financial and personal stability and they emphasized their desire for their children to pursue higher education.