79717 research outputs found
Sort by
Unrealized Economic Benefits in the West Coast Non-Whiting Groundfish Trawl Fishery
Get PDFIn Oregon, commercial fishing is estimated to contribute 67 million was not attained, nearly three times the actual landings of 55.4 million pounds, which were worth $36.4 million in ex-vessel revenue. Increasing attainments of underutilized fish stocks could help diversify, stabilize, and enhance income, jobs, and overall community benefits. The “non-whiting” groundfish trawl fleet only catches 25% or less of their annual quotas of flatfish, rockfish, roundfish, cartilaginous fish, and other species. There are complex issues keeping this fleet from reaching its allocations including geopolitical market constraints, bycatch issues, inflexible regulations and lack of processing and port infrastructure. This research focused on estimating the significance of these unrealized economic benefits, in terms of jobs and income, of the “non-whiting” groundfish trawl fishery’s unutilized quota. This research estimates the potential unrealized economic benefits of full attainment of trawl quotas to West Coast coastal communities. The goal of this research is to serve as catalyst to strengthen collaboration between regulators, NGO’s, industry, and researchers so that they might work together to better address issues in this fishery
Using Stable Isotopes to Estimate the Mean Recharge Elevation of Water Sources in the Central America Region
Get PDFKnowledge of the mean recharge elevation (MRE) of water resources is
important for informing conservation and protection practices where water security is threatened by population growth, urban expansion, and land and climate changes. In this study a Bayesian approach was developed and applied to determine the MRE of 682 surface water samples collected from the Central America region, where Pacific and Caribbean draining basins are characterized by distinct precipitation regimes, based on stable isotope comparisons between surface water samples and interpolated catchment precipitation. Different patterns in MRE were identified for Pacific and Caribbean samples: those collected from the Pacific slope are generally recharged at higher elevations relative to the sample mean catchment elevation (MCE), while those on the Caribbean slope are largely recharged at elevations lower than the sample MCE. The relationships between MRE and MCE for each slope were quantified as: MREP = 1.072 (MCE) + 45.65 and MREC = 0.9493 (MCE) – 28.24 (r2 = 0.93, MAE = 150 m (Pacific) and r2 = 0.76, MAE = 216 m (Caribbean)), and can be used to estimate the MRE of other regional water sources. Including catchment size and surface water site elevation (SWSE) as predictor variables improves MRE estimations because these variables influence the MRE:MCE relationships, especially on the Pacific slope (p <0.001 (Pacific) and < 0.05 (Caribbean) for both catchment size and SWSE). MRE, SWSE, and MRE-SWSE differences are generally greater on the Pacific slope, which hosts the majority of the region’s population and urban centers, corroborating the need to establish protections for the mountainous areas
Investigation of Nematocyst Discharge in Parasitic Cnidarians (Myxozoa)
Get PDFMyxozoans are an enigmatic group of obligately parasitic, microscopic cnidarians. They diverged from their free-living relatives over 600 million years ago and have highly reduced genomes. However, they have retained nematocyst stinging cells which characterize the phylum Cnidaria. Free-living cnidarians utilize this cellular weaponry for defense and predation whereas the myxozoans use it to anchor to their hosts as the first step to infection. In this thesis, I explore similarities and differences in the structure and function of nematocysts from myxozoans and free-living cnidarians via a “double-bladed” approach consisting of wet-lab techniques and bioinformatic analyses. In chapter 2, I report my results from two wet-lab assays that I developed to test the effect of chemical treatments on nematocyst discharge and infection, using the model myxozoan Myxobolus cerebralis. I found that Na+ significantly increased discharge and reduced infection to rainbow trout. This finding aligned with prior work using free-living Cnidaria, suggesting divalent cations bound to poly-gamma glutamate inside the nematocyst can be exchanged with monovalent ions from the environment through the capsule wall to promote discharge. In Appendix A, I report my initial results from bioinformatic analyses of proteomic and transcriptomic datasets from the myxozoan Ceratonova shasta, in searches for genes for voltage-gated ion channels. In free-living Cnidarians, these channels play a role in signaling nematocyst discharge and exocytosis of Ca2+. I found that in C. shasta, genes for these channels were co-expressed with nematocyst-specific genes during sporogenesis in the fish host. Taken together, the results of my wet-lab and computational “double-bladed” approach demonstrate structural and functional homologies between the nematocysts of myxozoans and their free-living cnidarian relatives
Towards a Better Understanding of How the Dietary Supplement Xanthohumol Can Improve Health
Get PDFXanthohumol, a prenylated flavonoid found in hops and beer, possesses a long-standing reputation to improve health. Xanthohumol’s cytotoxicity to a wide variety of cancer cell lines is well-established. Herein we provide further insight into the cytotoxicity of not only xanthohumol, but also its non-estrogenic derivatives, to a number of colonic and hepatic carcinoma cell lines. Furthermore, xanthohumol improves health in mouse models of diet-induced obesity. In these models, xanthohumol changes the composition of the intestinal microbiota. Therefore, we hypothesized the intestinal microbiota is required for xanthohumol to mediate its benefits. To test this hypothesis, we developed a novel mouse model of diet-induced obesity suitable for both conventional (in the presence of the microbiota) and germ-free (in the absence of the microbiota) studies of diet-induced obesity, using male Swiss Webster mice. We found the intestinal microbiota is required to mediate xanthohumol’s benefits, and that these benefits resulted in a decrease of plasma insulin, improved Homeostatic Model Assessment of Insulin Resistance, and improved glucose clearance. The results of 16S rRNA fecal gene sequencing revealed xanthohumol supplementation increases the relative abundance of Akkermansia muciniphila, Parabacteroides goldsteinii, and Alistipes finegoldii compared to the high-fat diet. Given this evidence, we hypothesized these bacteria perform xanthohumol biotransformation reactions. We found evidence A. muciniphila may convert xanthohumol into 6-prenylnaringenin but is likely not a major contributor to overall production by the intestinal microbiota. In general terms, we discovered xanthohumol changes the composition of the intestinal microbiota and drastically changes its predicted functional capacity. Most importantly, we developed a new mouse model of diet-induced obesity suitable for investigating the relationship between dietary compounds, the intestinal microbiota and obesity. We successfully show the intestinal microbiota are important in mediating the benefits of xanthohumol in treatment of diet-induced obesity
Examining School-Day Physical Activity Opportunities and the Influence of Physical Activity at School on Weight Status in Rural Oregon Elementary School Children
Get PDFThere is a known relationship between total physical activity (PA) and weight status in children; however, there is a paucity of data examining the prospective relationship between school day PA and obesity among rural elementary school children. A large number of cross-sectional studies have demonstrated that higher levels of PA are inversely associated with overweight and obesity in children. Longitudinal studies examining the prospective relationship between PA and weight status typically rely upon PA and weight data collected through the use of proxy measures (e.g., self-report), not objectively measured data. The majority of children spend around half of their waking hours in the school environment and as such, it is critical to understand how and when children are active at school. A review of school-based policies identified physical education (PE), classroom-based PA (CBPA), and recess as three of the primary intervention categories for increasing PA in children. It has been shown that rural children have greater odds of being obese and yet there is a lack information on how children in rural schools are accruing PA. The research presented in this dissertation narrows the identified research gaps about our understanding of the relationship between the rural school environment, PA, and children’s weight status.
To address the first aim in this dissertation, we assessed the prospective relationship between baseline PA and future weight status in rural elementary school children. Objectively measured height and weight data were collected with pedometer data in 866 rural elementary school children. Linear models were used to evaluate the association between baseline PA and future BMI. Our results indicated that baseline BMI is the strongest predictor of future BMI whereas there is no association between baseline PA and future BMI after controlling for baseline BMI. This relationship did not vary by age, sex, or school.
To address the second aim, we quantified school-day activity levels during various PA opportunities (i.e. CBPA, recess, PE) and evaluated the relationship between PA opportunities and children’s PA levels during the school day. Children from 1st, 3rd, and 5th grade were invited to participate and accelerometer data was collected on 230 children. Classroom schedules were provided by teachers and timestamped data from accelerometers were matched to the classroom schedules. Children accrued a mean of 27.5 minutes of moderate to vigorous PA (MVPA) during the school day and boys were more active than girls in our sample. We observed an interaction between PA domain and grade as the percentage of time in MVPA across domains varied by grade. Children were not meeting the recommended percentage of time in MVPA for PE or recess (≥ 50%). Only 10% of time during CBPA opportunities was spent in MVPA.
Results from these studies suggest that baseline school day PA is not associated with future BMI and that baseline BMI is the best predictor of future BMI. PA patterns during school day PA opportunities varies by sex and grade with boys being more active than girls across all domains. Although results from this dissertation help fill in research gaps, additional exploration of 1) casual effects of weight change in rural elementary school children, and 2) identifying strategies to increase MVPA during the school day PA opportunities are warranted
Simulation Automation for the Evaluation of Formula Student Aerodynamic Concepts
Get PDFThe design of a competition-winning aero package must consider multiple vehicle attitudes. Aerodynamic concepts simulated in heave, pitch, roll, high-speed yaw, and low-speed yaw to design a stable and predictable aero package. The methodology automates the simulation setup process of five vehicle attitudes. The overall and subsystem force coefficients are calculated and evaluated using a weighted sum with a bias toward yaw conditions. Turbulence models are tested against coast-down test data to select the appropriate turbulence model for the application. The results presented are a combination of multiple simulation parameters to evaluate the GFR2021 vehicle. The results presented can be used to tune the aero package or inform geometric changes to increase aerodynamic performance and vehicle stability
Using Computational and Statistical Methods as an Aid to Study Environmentally Relevant Organic Molecules
Get PDFIn this report, three studies are presented that utilize computations to predict transformations, identities, and properties of environmental organic molecules. Each study shows how computations can lead to models of chemical behavior. The importance of this research is rooted in the need for understanding how human behavior and health intersect with environmental systems.
The first study investigates different methods for predicting the regioselective reaction of polycyclic aromatic hydrocarbons (PAHs) with atmospheric oxidants, resulting in transformation products (PAH-TPs). As by-products of fossil fuel combustion, PAHs are important environmental molecules that have been shown to have toxic or mutagenic effects on human health, with some transformation products showing increased toxicity. Four approaches are compared to experimentally observed PAH-TP formation; these four approaches are: 1) Clar’s aromatic resonance structures, 2) Gibbs free energy of reaction to form a hydroxylated PAH intermediate, 3) computed atomic charges, and 4) average local ionization energy (ALIE). Both thermodynamic stability of the hydroxylated adduct and ALIE are found to most accurately predict the observed reactive site.
The second study evaluates infrared multiphoton dissociation (IRMPD) spectroscopy as a means of determining the identity of molecules in a complex mixture of secondary organic aerosols (SOA) formed from the ozonolysis of a-pinene. IRMPD requires a very small sample amount compared to other characterization methods such as nuclear magnetic resonance (NMR) or infrared (IR) spectroscopy. This is especially valuable as large samples are difficult to gather from atmospheric filters. The results herein show that IRMPD has good overlap with standards and computed spectra, yielding detailed structural information of isolated molecules.
The final study explores oxidative potential (OP) of PAHs and PAH-TPs found in the environment. These compounds, when inhaled as a component of particulate matter, contribute to the formation of reactive oxygen species in biological systems. The Gibbs free energy of reaction (∆G) to form a radical anion is used to predict the oxidation potential of 135 PAHs. Electron density is evaluated using the GINI method to determine shared electron inequality as it relates to OP. A dithiothreitol (DTT) assay used to quantify OP in biological systems is evaluated by Dr. Amber Kramer; individual OPs are then combined to predict behavior of mixtures. This study found that ∆G shows statistically significant correlations with structural components, electron density, molecular mass, and substituents on PAH molecules. It is shown that mixtures do not follow an additive model effect
Thermal Ecology and Population Dynamics of Female Greater Sage-Grouse Following Wildfire in the Trout Creek Mountains of Oregon and Nevada
Get PDFThe greater sage-grouse (Centrocercus urophasianus; hereafter, sage-grouse) is a ground nesting gallinaceous bird that requires large contiguous patches of sagebrush. Sage-grouse populations have declined, especially in the Great Basin where changes in wildfire regimes and the invasion of annual grasses have contributed to habitat loss and fragmentation. During the last 35 years, wildfire activity has increased in the Great Basin and this shift has been linked to decreased populations in sage-grouse. The effect of fire on sage-grouse populations is strongly linked to the reduction of sagebrush cover within their seasonal ranges that occurs after fire. Even at low intensities, fire kills most sagebrush species. Furthermore, the response of vegetation after fire is highly variable both spatially and temporally, and strongly influenced by environmental characteristics as well as pre- and post-fire land management practices. However, high elevation mountain big sagebrush communities are more resilient and recover more quickly than low elevation Wyoming big sagebrush communities. In cases where invasive annual grasses become dominant, the loss of vegetation structural complexity can increase predation risks and reduce thermal heterogeneity for sage-grouse. Thermal variation allows animals to select areas with temperatures that efficiently regulate physiological process. In addition to contributing to general space use patterns, seeking thermal refuge can increase an animal’s nest success and annual survival. There is limited knowledge regarding the short-term (<6 yrs) effects of fire on sage-grouse demographics and their thermal environments. My research builds on a study that began in March 2013 after the Holloway fire burned ~187,000 ha during the summer of 2012 in the Trout Creek Mountains of southeastern Oregon and northwest Nevada.
In chapter 2, I established baseline values and characterized the spatial and temporal thermal variation in 3 dominant sagebrush (Artemisia spp.) communities using a black bulb technique (Tbb), which integrates ambient temperature (Tair), solar radiation, and convective heat transfer. I collected 56,446 Tbb estimates from 144 random points within the breeding range of sage-grouse from 15 April – 23 July in 2017 and 2018. Then, I used linear mixed-effects models where Tbb is a function of Tair to describe differences between unburned and burned sagebrush communities. My findings indicated 1) unburned and burned sagebrush communities exhibited high thermal heterogeneity in Tbb relative to Tair. For example, Tbb varied by 47° C in both unburned and burned communities when Tair was 20° C. 2) Fire altered the thermal environment and reduced the thermal refuge in Wyoming big sagebrush communities (A. tridentata wyomingensis) during low and high Tair more than low sagebrush (A. arbuscula) and mountain big sagebrush communities (A. t. vaseyana). Notably, when Tair was 0° C, unburned Wyoming big sagebrush communities (-12° C) were 7° C warmer than burned communities (-19° C) and when Tair was 35° C, unburned Wyoming big sagebrush communities (55° C) were 9° C cooler than burned communities (64° C). 3) Shrub cover and height were associated with thermal refuge in unburned and burned sagebrush communities. These results elucidate the thermal environment of the sagebrush and associated changes from fire, and illustrate the importance of shrub structure, which can provide thermal refuge for organisms in unburned and burned communities during extreme low and high Tair.
In Chapter 3, I examined sage-grouse nest site selection and nest success with respect to thermal and vegetation characteristics at 77 unburned and 18 burned nest sites as well as 31 unburned and 33 burned random landscape locations. I found that 1) Nest bowls (x̅ = 15.2°C, SD = 9.6, burned and unburned combined) were cooler and had less thermal variation than both nearby microsites (x̅ = 17.5°C, SD = 13.4) and the broader landscape (x̅ = 22.3°C, SD = 14.4). 2) Nest bowls in burned and unburned sagebrush communities more effectively moderated the thermal environment compared to the microsite and landscape. Specifically, nest bowls (burned and unburned combined) remained warmer than the microsite when Tair was 9°C. Similarly, nest bowls were warmer than the landscape when Tair was 16°C. 3) Nest bowls from successful nests (burned and unburned nests combined) buffered Tbb more effectively (β ̂ = 1.28, 95% CI: 1.25 to 1.30) than nest bowls from failed nests (β ̂ = 1.34, 95% CI: 1.32 to 1.36) at higher Tair. For example, Tbb at successful nest bowls was 2°C and 3°C cooler than Tbb at failed nest bowls when Tair was 25°C and 35°C, respectively. 4) Visual obstruction at nest sites has a strong, positive effect on daily nest survival. These findings provide some insight into how the thermal environment influences nest site selection and nest success and identifies the importance of vegetation that remains or reestablishes after fire for sage-grouse during nesting.
In Chapter 4, my objective was to quantify the population response of sage-grouse following the Holloway fire and examine sensitivity in the population growth rate, with respect to vital rates. I developed a stochastic 2-age female population matrix model for yearlings and adults during each year (2013 – 2018) of the study using vital rate estimates developed for each year. I found that 1) Nest survival (1st nests: yearlings: x̅ = 0.54, SD = 0.04; adults: x̅ = 0.31, SD = 0.09; renests: x̅ = 0.39, SD = 0.22) was comparable to nest survival values reported for sage-grouse across their distribution, despite extreme reduction in sagebrush cover at nesting sites. In contrast, chick survival (x̅ = 0.27, SD = 0.07) and female survival (yearlings: x̅ = 0.41, SD = 0.16; adults: 0.48 SD = 0.16) was low compared to other values reported for sage-grouse. 2) Annual estimates of λ indicated that the sage-grouse population on my study area was declining during 5 of 6 years. 3) Variation in λ was driven by female survival and chick survival. Moreover, sensitivity in λ with respect to female survival and chick survival, decreased and increased, respectively, during the 6-years post-fire. These results suggest strong negative effects of fire on important vital rates for sage-grouse population growth and illustrate the potential trade-offs among life histories for the species following fire.
My research examined some of the unknown responses of sagebrush communities and sage-grouse following a large wildfire. These findings illustrate how fire effects the thermal environment of sagebrush communities and sage-grouse nest site selection and nest success. Furthermore, my results provide an initial examination into the demographic, population, and life history response of sage-grouse following a large wildfire
Indoor Localization Using Direction of Arrival Approach
Get PDFIn this paper, a Direction of Arrival (DOA) based system is proposed. This method searches the direction relative to the array to find where the signal source is located. The proposed system can achieve sub-meter level accuracy with a near real-time update rate. Also, we introduced several refinement methods including a compact tracking system that is compatible with small items, a DOA accuracy prediction function, a method based on linear prediction to expand antenna array to create a virtual antenna matrix, and a novel method for multipath effect cancellation. Overall, the proposed system achieved sub-meter level accuracy, and the functionality of the refinement methods has been approved in the simulation
Efficacy of Sanitizers at Controlling Listeria spp. and Listeria monocytogenes When Challenged with Variables Commonly Encountered in Food Processing Environments
Get PDFListeria monocytogenes (Lm) is a pathogenic bacterium associated with the foodborne disease listeriosis in humans. Listeriosis affects thousands of people in the U.S. yearly, with neonates, elderly, pregnant women, and immunocompromised persons disproportionately affected. Lm has a high mortality rate in these populations (20 - 30%) with symptoms including septicemia, meningitis, encephalitis, and, in pregnant women, stillbirth and miscarriage. Due to the severity of the disease it causes, the U.S. has a zero-tolerance policy for Lm in ready-to-eat (RTE) food products. Lm is ubiquitous and often associated with food processing facilities, and the food processing environment itself is the main source of contamination in RTE products. Cleaning and sanitation are vital in reducing the presence of Lm in these areas. There are a variety of sanitizers available for use in the food industry. Among these are a widely used class of sanitizers called quaternary ammonium compounds (QUATs). Additionally, the U.S. Environmental Protection Agency (EPA) recently approved seven active ingredients for use in eco-friendly alternatives to traditional sanitizers. Despite these and other control methods, recalls and outbreaks due to Lm continue to occur. The objectives of this thesis were: (i) to determine the minimum bactericidal concentrations (MBCs) of two traditional (TR) sanitizers, including benzalkonium chloride (BAC) and a commercial QUAT (CQAC), and two eco-friendly (EF) sanitizers, including an alcohol-based (ALB) and a citric acid-based (CAB) sanitizer, against Listeria spp. (n=22) at temperatures ranging from 4 – 30oC; (ii) to evaluate the behavior of Lm (n=8) in sub-lethal concentrations of these sanitizers, mimicking unintentional dilution that may occur in processing facilities; and (iii) to assess the efficacy of sanitizers against Lm (n=5) attached to stainless steel (SS) and plastic at 4oC and 30oC for 24 h.
Minimum bactericidal concentrations (MBCs), based on the percentage of the manufacturer recommended concentration (% MRC), were significantly lower for TR sanitizers compared to those of EF sanitizers (P < 0.001; ANOVA). Temperature had a significant impact on MBCs of all sanitizers, with MBCs decreasing as temperature increased (P < 0.05; ANOVA). Similar growth behavior of isolates exposed to sub-lethal EF sanitizers was observed. In contrast, growth in sub-lethal concentrations of TR sanitizers revealed two isolates that were severely inhibited, confirming that differences in the ability of isolates to tolerate QUATs exist in the tested population.
Attachment to surfaces affected tolerance to sanitizers, with attached bacteria more tolerant than those in the planktonic state. All Lm isolates tested had survival rates above 50% when attached to SS and plastic at 30oC and treated with BAC and CAB at their MRC/ET. Incidence of inactivation for all sanitizers tested increased when both Lm attachment and sanitizer treatment occurred at 4oC. Differences in survival on two surface materials was also observed, with higher survival rates occurring with attachment on SS compared to plastic coupons. Scanning electron micrographs revealed greater population of bacteria on coupons when attached at 30oC compared to 4oC. Additionally, micrographs of plastic coupons showed they had a smoother surface compared to SS coupons. Notably, addition of a cleaning step, by scrubbing inoculated coupons (30oC, 24h) with cotton tips soaked in detergent, prior to treatment with sanitizers, decreased the incidence of survival on SS and plastic coupons treated with ALB and CAB; however, it did not significantly reduce survival of Lm on SS or plastic treated with QUATs.
Overall, the response of Lm isolates to sub-lethal concentrations varied the most with QUAT sanitizers, indicating that genetic variation between Lm strains may have a greater effect on the efficacy of these sanitizers. Attachment of Lm isolates on commonly used food contact surface materials greatly reduced the efficacy of all sanitizers tested. Food processing industry should consider cleaning and sanitizing more often than once every 24 h to reduce the risk of surface adherent Lm surviving cleaning and sanitation procedures. Collectively, these findings highlight important variables, such as sanitizer types, temperatures, and surfaces, that need to be carefully considered by food processing facilities when designing and implementing their cleaning and sanitation regimes