• Airborne hyperspectral imaging for wetland mapping in the Yukon Flats, Alaska

      Graham, Patrick Ryan; Prakash, Anupma; Rosselló, Jordi Cristóbal; Gens, Rudiger (2020-05)
      This study involved commissioning HySpex, a hyperspectral imaging system, on a single-engine Bush Hawk aircraft; using it to acquire images over selected regions of the Yukon Flats National Wildlife Refuge; establishing a complete processing flow to convert raw data to radiometrically and geometrically corrected hypercubes, and further processing the data to classify wetlands. Commissioning involved designing a customized mount to simultaneously install two-camera systems, one operating in the visible and near infrared region, and the other operating in the shortwave infrared region. Flight planning incorporated special considerations in choosing the flight direction, speed, and time windows to minimize effects of the Bidirectional Reflection Distribution Function (BRDF) that are more dominant in high latitudes. BRDF effects were further minimized through a special processing step, that was added to the established hyperspectral data processing chain developed by the German Space Agency (DLR). Instrument commissioning included a test flight over the University of Alaska Fairbanks for a bore-sight calibration between the HySpex system's two cameras, and to ensure the radiometric and geometric fidelity of the acquired images. Calibration resulted in a root mean square error of 0.5 pixels or less for images acquired from both cameras at 1-meter spatial resolution for each geometrically corrected flight line. Imagery was radiometrically corrected using the ATCOR-4 software package. No field spectra of the study areas were collected due to logistics constraints. However, a visual comparison between current spectral libraries and acquired hyperspectral image spectra was used to ensure spectral quality. For wetlands mapping, a 6-category legend was established based on previous United States Geological Survey and United States Fish and Wildlife Service information and maps, and three different classification methods are used in two selected areas: hybrid classification, spectral angle mapper, and maximum likelihood. Final maps were successfully classified using a maximum likelihood method with high Kappa values and user's and producer's accuracy are more than 90% for nearly all categories. The maximum likelihood classifier generated the best wetland classification results, with a Kappa index of about 0.90. This was followed by the SAM classifier with a Kappa index of about 0.57 and lastly by the hybrid classifier that achieved a Kappa index of only 0.42. Recommendations for future work include using higher-accuracy GPS measurements to improve georectification, building a spectral library for Alaskan vegetation, collection of ground spectral measurements concurrently with flight image acquisition, and acquisition of LiDAR or RGB-photo derived digital surface models to improve classification efforts.
    • Alaska Shorefast Ice: Interfacing Geophysics With Local Sea Ice Knowledge And Use

      Druckenmiller, Matthew L.; Eicken, Hajo (2011)
      This thesis interfaces geophysical techniques with local and traditional knowledge (LTK) of indigenous ice experts to track and evaluate coastal sea ice conditions over annual and inter-annual timescales. A novel approach is presented for consulting LTK alongside a systematic study of where, when, and how the community of Barrow, Alaska uses the ice cover. The goal of this research is to improve our understanding of and abilities to monitor the processes that govern the state and dynamics of shorefast sea ice in the Chukchi Sea and use of ice by the community. Shorefast ice stability and community strategies for safe hunting provide a framework for data collection and knowledge sharing that reveals how nuanced observations by Inupiat ice experts relate to identifying hazards. In particular, shorefast ice break-out events represent a significant threat to the lives of hunters. Fault tree analysis (FTA) is used to combine local and time-specific observations of ice conditions by both geophysical instruments and local experts, and to evaluate how ice features, atmospheric and oceanic forces, and local to regional processes interact to cause break-out events. Each year, the Barrow community builds trails across shorefast ice for use during the spring whaling season. In collaboration with hunters, a systematic multi-year survey (2007--2011) was performed to map these trails and measure ice thickness along them. Relationships between ice conditions and hunter strategies that guide trail placement and risk assessment are explored. In addition, trail surveys provide a meaningful and consistent approach to monitoring the thickness distribution of shorefast ice, while establishing a baseline for assessing future environmental change and potential impacts to the community. Coastal communities in the region have proven highly adaptive in their ability to safely and successfully hunt from sea ice over the last 30 years as significant changes have been observed in the ice zone north of Alaska. This research further illustrates how Barrow's whaling community copes with year-to-year variability and significant intra-seasonal changes in ice conditions. Hence, arctic communities that have coped with such short-term variability may be more adaptive to future environmental change than communities located in less dynamic environments.
    • Alaska's shrinking glaciers: integrated glaciological research for hydrological, ecological, and environmental education applications

      Young, Joanna; Pettit, Erin; Arendt, Anthony; Conner, Laura; Hood, Eran (2020-05)
      As air temperatures in Alaska are rising, glacier melt is accelerating and affecting hydrological resources and downstream ecosystem function. The extent to which glacier loss may change hydrological regimes in coastal climates, and how that may impact nearshore marine conditions, is uncertain. Moreover, from a social-ecological standpoint, many citizens today are disconnected from these types of environmental changes, in part due to isolation from visible climate change impacts. This dissertation addresses the dual need for examining recent Alaska glacier changes and resulting hydrological and marine impacts, and for exploring education strategies that leverage glacier changes for environmental identity development. In Chapter One, I present a conceptual framework that links the physical and social sciences research herein as equal components of a social-ecological system. In Chapter Two, I use a glacio-hydrological model to uncover that coastal glaciers of the Juneau Icefield have yet to pass `peak water' delivery. I also find that between 1980 to 2016, glacier ice melt increased annually (+10%, p = 0.14) and in spring (+16%, p = 0.05), leading to changing freshwater composition. In Chapter Three, I compare modeled Mendenhall River discharge to nearshore oceanographic measurements, finding that salinity and density in the upper 15 m are strongly glacially-inuenced (10 to 30 PSU and 1010 to 1023 kg m⁻³), and that glacier runoff exerts a stronger control (r² = 0.66) than total runoff. Large, signicant trends are also detected for 1997 to 2016 August modeled glacier runoff (p = 0.02, + 15%) and observed salinity (p = 0.01, -3.2 PSU), linking these phenomena and revealing ongoing changes. Finally, in Chapter Four, I analyze social science data from youth participants in a science outreach program in a climate-impacted glacier landscape. I find that better understanding ecosystem linkages and seeing the scale of glacier loss first-hand promote environmental identity development by building relatedness and pro-environmental motivation. Together, the glaciological and environmental education research herein provides diverse perspectives on improving both scientic and citizen understanding of glacier mass loss in a changing climate.
    • Alexander Archipelago Wolves: Ecology And Population Viability In A Disturbed, Insular Landscape

      Person, David Karl; Bowyer, R. Terry (2001)
      The Alexander Archipelago wolf (Canis lupus ligoni) occupies Southeast Alaska, a region undergoing intensive harvest of timber. Sitka black-tailed deer (Odocoileus hemionus sitkensis) are the primary prey of these wolves. We conducted a telemetry study of 23 wolves on Prince of Wales and adjacent islands in Southeast Alaska between September 1992 and October 1995. We examined home range, habitat use, reproduction, mortality, and dispersal of wolves in logged landscapes and those that were relatively unlogged. We used those data to parameterize a wolf-deer model to predict long-term effects of timber harvest on the wolf-deer system on Prince of Wales and adjacent islands. Home ranges of 7 wolf packs averaged 259 km2 in winter but only 104 km2 during pup-rearing season (15 April--15 August). Home-range size was positively correlated to pack size, and area per individual wolf was inversely related to the proportion of winter habitat for deer within the home range. Radiocollared wolves were classified as residents, extraterritorials, and dispersers. Annual mortality was 64% for extraterritorial and dispersing wolves and 31% for residents. Eighty-two percent of mortality was human caused. Radiocollared wolves were located mostly at low elevations (<250 m) regardless of time of year, and selected for old-growth forest habitat during pup-rearing season. Wolves generally avoided second-growth forests and clearcuts, and their use of those habitats occurred mostly at night. Density of roads was positively correlated with rate of harvest of wolves. Simulations from our wolf-deer model indicated that deer and wolf populations on Prince of Wales and adjacent islands likely have declined since initiation of industrial-scale logging. Nonetheless, risk that the population of wolves will no longer be viable is low. Our predictions indicate that deer will decline disproportionately to decline of carrying capacity (K). Thus, a small change in K may precipitate large, long-term changes in deer numbers. The most important management strategy for the conservation of wolves in Southeast Alaska is to maintain high-quality habitat for deer. We believe that managing human access by closing roads for motorized use and limiting construction of new roads are also measures necessary to conserve wolves.
    • Alpine thermal dynamics and associated constraints on the behavior of mountain goats in Southeast Alaska

      Frederick, Jeffrey Hébert; Hundertmark, Kris; Pyare, Sanjay; Brinkman, Todd; White, Kevin (2015-08)
      Alpine Caprinae, including mountain goats (Oreamnos americanus), have been described to be sensitive to temperature changes within their summer range and consequently may be forced to select habitats that allow for the maintenance of a stable core temperature on warm days. Survival may be inhibited if warm ambient temperatures cause mountain goats to reduce time foraging or if too much time is spent on thermoregulatory habitat selection. I investigated mountain goat behavioral activity budgets across alpine temperature gradients in Southeast Alaska using focal animal sampling and scan sampling techniques. I tested the effects of temperature on mountain goat activity and mountain goat elevation. Coupled with the behavioral investigations, I simultaneously monitored elevational temperature gradients using an array of passive thermistors. By monitoring hourly temperatures and deriving near-surface lapse rates, I demonstrate the utility of downscaled, region-specific temperature-elevation profiles for ecological applications rather than making inferences based on broad spatial models. Except in winter, lapse rates within the study area were between -0.3°C 100m⁻¹ and -0.4°C 100m⁻¹, and were not inclusive of the global mean environmental lapse rate (-0.65°C 100m⁻¹). Mountain goats within the study area demonstrated behavioral conservation of their activity budgets by altering their orientation through space and time, rather than incurring thermal and/or nutritional deficits. In addition, the animals took advantage of cooler temperatures at high elevations to bolster thermoneutrality. I highlight the need for behavioral ecology research that links physiological mechanisms and mammalian life history in an effort to predict the fate of a sentinel wildlife species as it copes with a changing environment. Indeed, such indicator species are invaluable to understanding the dynamics of change in ecosystem structure, function, and phenology. Given current warming trends and projections of changing climate regimes being more pronounced at higher latitudes, there is a marked need to better understand thermoregulatory constraints on faunal behavior and the effect of changing landscapes on the distributions and survival of wildlife populations in Alaska.
    • An Interdisciplinary Computational Study Of Magnetosphere-Ionsphere Coupling And Its Visual And Thermal Impact In The Auroral Region

      Styers, John; Newby, Greg (2012)
      A three-dimensional, three-fluid simulation (ions, electrons, and neutrals) was explicitly parallelized, facilitating the study of small-scale magnetospheric-ionospheric (M-I) coupling processes. The model has ionization and recombination, self-consistently (semi-empirically) determined collision frequencies, and a height resolved ionosphere. Inclusion of ion inertial terms in the momentum equation enables the propagation of Alfven waves. Investigation at small scales required large system domains, and thus fast parallel computers. The model was explicitly parallelized---enabling investigations of M-I coupling processes on very small temporal and spatial scales. The generation, reflection, and propagation of Alfven waves is of importance to the understanding of M-1 coupling processes---it is, in fact, the primary means of communication of physical processes in the coupled system. Alfvenic reflections were modeled for two different boundary conditions, and it was shown that the deformation of the current layer was Alfvenic in character. Visualizations of the data obtained appear to be consistent with the visual characteristics of actual discrete aurora in nature. The model reproduces qualitatively, and semi-quantitatively, in a self-consistent manner, some the behaviors of the formation and time-evolution of discrete arcs. These include the narrowness of arcs; electric fields extending parallel outward from the arcs; and fast (plasma) flows in the region of discrete arcs. Large-scale models---due to inevitable limitations of computational resources---need to make large-scale averages of computed properties. In regions of active small-scale structure, significant under-representation of the Joule heating occurs. It has been shown that the under-representation of the Joule heating in the region of active aurora can be as large as a factor of 8. This work includes a computer-based study of a quantitative approximation of this underrepresentation of the Joule heating by global, large-scale models and experimental observations.
    • An Investigation Into Argon-40/Argon-39 Radiogenic Dating And X-Ray Analysis Of Shales And Clays From Northern Alaska

      Munly, Walter Campbell; Layer, Paul (2004)
      In this thesis I develop a new 40Ar/39Ar dating technique for measuring ages and estimating cooling histories of potassium-bearing minerals within shales and clays. To overcome problems of argon recoil, small shale or clay flakes (possessing diameters less than 2 mm) were encapsulated within microampoules under vacuum. Encapsulation ensures that argon that recoils from tiny crystals during irradiation in a nuclear reactor cannot escape and will therefore be detected during 40Ar/39Ar laser step-heating. The step heating method is effective in differentiating between, and dating neoformed and detrital illite components. My use of this method has revealed a significant age difference across the Toyuk thrust, Brooks Range, northern Alaska. Devonian shales from south of the thrust yield relatively flat age spectra indicative of a younger illitic component, and argon retention ages around 225 Ma. Shale samples from north of the thrust yield staircase age spectra indicative of a detrital illite component, and older retention ages (233--391 Ma). Modeling of these spectra across the Toyuk also suggests that argon loss and subsequent cooling occurred at about 140 Ma. Retention ages across the Toyuk thrust may reflect differences in depths of tectonic burial, or differing ages of crystallization of neoformed illite during initial deposition and burial. 40Ar/39Ar age spectra from the Colville basin, North Slope, Alaska, illites are generally dominated by detrital illite, yielding high temperature step-heat ages up to 475 Ma. Illite crystallization ages from the NPRA (National Petroleum Reserve in Alaska) range between 205 and 225 Ma. These ages are older than depositional ages and therefore suggest that this illite was transported from outside the Colville basin, perhaps from the Brooks Range. The Colville basin samples also reveal argon loss at ~45 Ma. Paleocene samples from the Exxon Alaska State A-1 well yield illite crystallization ages of about 205 Ma, and argon loss ages around 40 Ma. X-ray diffraction of the Colville basin samples indicates the presence of multiple clay phases, including detrital and neoformed illite. This complex mineralogy precluded estimating when the host shales were within the oil generation window.
    • An investigation of the dynamics of the mesopause: Fabry-Perot observations of winds and temperatures from nightglow emissions

      Conner, James F.; Smith, R. W. (1994)
      This work is a study of the behavior of tidal and planetary waves in the upper-middle atmosphere near the geographic south pole. This is accomplished with a characterization of the dynamic state of these motions. I used ground-based Fabry-Perot Spectrometer (FPS) measurements of the multiple-line, $P\sb1$(2)$\sb{c,d}$, nightglow emissions from the X$\sp2$II band of the neutral OH* molecule. I developed analytical techniques to determine a space and time distribution of spectral amplitudes and phases for the dynamic parameters of kinetic temperature and neutral wind in the OH* layer. Spectral analysis of the variations in this layer indicate the existence of two groups: a planetary wave group (periods of ${\sim}$1-10 days), with eastward phase progression, and a near semi-diurnal group (periods of ${\sim}$8-13 hours), with westward phase progression. Specific periods vary slightly for different years; this is most likely due to remote propagation conditions. Further separation of each group shows the wind oscillations exhibit wave-number one behavior with associated wave-number zero temperature oscillations, (with a few exceptions). The periodicities in the planetary group neutral wind motions are consistent with the model results of Salby, 1984, for propagation to high latitudes through realistic mean flows. The characterization of the dynamics of this layer has led to the discovery of a basic azimuthal asymmetry in the distribution of spectral amplitude for a given oscillation, that is, preferred azimuths. These preferred azimuths appear to be associated with changes in the direction, not the amplitude, of a cross-polar mean wind. This finding, in conjunction with the evanescence of some features, uncovered two cases of planetary wave dissipation. These occur when oscillations attempt to maintain their preferred alignment with a changing mean wind direction resulting in a decay of wind amplitude and a burst of thermal oscillation. Both cases occur at the same time. Coincident with these decays are enhancements in the wind and thermal energy of other, longer period, oscillations which share the same azimuthal preferences. Also coincident is an acceleration of the mean wind.
    • Analysis and interpretation of volcano deformation in Alaska: Studies from Okmok and Mt. Veniaminof volcanoes

      Fournier, Thomas J.; Freymueller, Jeffrey; Larsen, Jessica; Cervelli, Peter; Christensen, Douglas; McNutt, Stephen (2008-12)
      Four studies focus on the deformation at Okmok Volcano, the Alaska Peninsula and Mt. Veniaminof. The main focus of the thesis is the volcano deformation at Okmok Volcano and Mt. Veniaminof, but also includes an investigation of the tectonic related compression of the Alaska Peninsula. The complete data set of GPS observations at Okmok Volcano are investigated with the Unscented Kalman Filter time series analysis method. The technique is shown to be useful for inverting geodetic data for time dependent non-linear model parameters. The GPS record at Okmok from 2000 to mid 2007 shows distinct inflation pulses which have several months duration. The inflation is interpreted as magma accumulation in a shallow reservoir under the caldera center and approximately 2.5km below sea level. The location determined for the magma reservoir agrees with estimates determined by other geodetic techniques. Smaller deflation signals in the Okmok record appear following the inflation pulses. A degassing model is proposed to explain the deflation. Petrologic observations from lava erupted in 1997 provide an estimate for the volatile content of the magma. The solution model VolatileCalc is used to determine the amount of volatiles in the gas phase. Degassing can explain the deflation, but only under certain circumstances. The magma chamber must have a radius between ~1and 2km and the intruding magma must have less than approximately 500ppm CO2. At Mt. Veniaminof the deformation signal is dominated by compression caused by the convergence of the Pacific and North American Plates. A subduction model is created to account for the site velocities. A network of GPS benchmarks along the Alaska Peninsula is used to infer the amount of coupling along the mega-thrust. A transition from high to low coupling near the Shumagin Islands has important implications for the seismogenic potential of this section of the fault. The Shumagin segment likely ruptures in more frequent smaller magnitude quakes. The tectonic study provides a useful backdrop to examine the volcano deformation at Mt. Veniaminof. After being corrected for tectonic motion the sites velocities indicate inflation at the volcano. The deformation is interpreted as pressurization occurring beneath the volcano associated with eruptive activity in 2005.
    • Analysis of composition and chronology of dome emplacement at Black Peak Volcano, Alaska utilizing aster remote sensing data and field-based studies

      Adleman, Jennifer Nicole (2005-05)
      Black Peak volcano is a 3̃.5km-diameter caldera located on the Alaska Peninsula that formed 4̃,600 years ago in an eruption that excavated>km³ of material. The caldera floor is occupied by at least a dozen overlapping dacitic to andesitic lava domes and flows. Examination of XRF results and observations of the domes in and around the caldera reveals a range of 57-65wt% SiO₂ and variations in amphibole content. Evidence for magma mixing includes vesicular enclaves and geochemical trends that indicate involvement of a more mafic magma into a dacitic reservoir. The purpose of this study is to investigate if, and how, these differences in composition and mineralogy are detectable in satellite emissivity and TIR data (ASTER) and compare the results to ground-based field observations to discern changes in the mineralogical and chemical properties of the domes. This study incorporates the use of decorrelation-stretch image processing techniques and the deconvolution of laboratory emissivity spectra to assess the viability of discriminating variations in the lithologies observed at Black Peak volcano. Compositional results from XRD and electron microprobe analyses are comparable to those obtained through deconvolution processing. Surfaces of <10% amphibole and SiO₂ of 60-65wt% and those that correspond to>1̲0% and <61 wt% SiO₂ are distinguishable in the ASTER data.
    • Analysis of GNAC Volleyball using the Bradley-Terry Model

      Karwoski, Daniel; Short, Margaret; Goddard, Scott; McIntyre, Julie; Barry, Ron (2020-05)
      Ranking is the process by which a set of objects is assigned a linear ordering based on some property that they possess. Not surprisingly, there are many different methods of ranking used in a wide array of diverse applications; ranking plays a vital role in sports analysis, preference testing, search engine optimization, psychological research, and many other areas. One of the more popular ranking models is Bradley-Terry, which is a type of aggregation ranking that has been used mostly within the realm of sports. Bradley-Terry uses the outcome of individual matchups (paired-comparisons) to create rankings using maximum-likelihood estimation. This project aims to briefly examine the motivation for modeling sporting events, review the history of ranking and aggregation-ranking, communicate the mathematical theory behind the Bradley-Terry model, and apply the model to a novel volleyball dataset.
    • Analysis Of Methods For Solar Wind Propagation From Lagrangian Point L1 To Earth

      Jensen, Poul F.; Bristow, William; Newman, David; Nielsen, Hans; Otto, Antonius; Smith, Roger (2013)
      The Lagrangian point L1 is situated about 1.5 million kilometers sunwards from Earth and provides a unique orbiting point for satellites, placing them constantly upstream in the solar wind, allowing for prediction of solar wind conditions impacting Earth's magnetosphere. Short-term forecasting of geomagnetic activity requires extrapolation of solar wind data from L1 to Earth (typical propagation time around 1 hour), as does any research in interactions between the solar wind and the magnetosphere during intervals when no Earth-orbiting satellites are in the solar wind. To accurately predict propagation delays it is necessary to take the geometry of incoming solar wind structures into account. Estimating the orientation of solar wind structures currently has to be done using single satellite measurements, which will likely remain the case for another decade or more, making it important to optimize single satellite techniques for solar wind propagation. In this study a comprehensive analysis of 8 different single satellite propagation methods was performed, each involving several variable parameters. 4 of these used electric field calculations and had not previously been tested for solar wind propagation. Large amounts of data were propagated from a satellite near L1 to target satellites near Earth for comparison to measured data, using specific test scores to evaluate relative performance between methods and parameter values. Electric field methods worked well for continuous data but did not predict arrival time of discontinuities (abrupt transitions) as accurately as methods based on magnetic field data, one of which delivered the best results on all accounts. This method had also been found to give best results in a previous study, but optimal parameter values were significantly different with the larger data set used here. Propagating 6,926 discontinuities it was found that on average they arrive about 30 seconds later than predicted (about 1% of the propagation time). Barring a systematic error in velocity data or delay calculations the offset suggests an asymmetry in the geometry of solar wind structures. While this idea is physically plausible it was not unambiguously supported by the data.
    • Analysis Of Model And Observation Data For The Development Of A Public Pm2.5 Air-Quality Advisories Tool (Aquat)

      Tran, Huy Nguyen Quang; Molders, Nicole; Bhatt, Uma; Cahill, Catherine F.; Grell, Georg A.; Kramm, Gerhard (2012)
      An air-quality advisory tool (AQuAT) that combines mobile measurements of particulate matter less than or equal to 2.5mum in diameter (PM2.5) with air-quality simulations performed with the Alaska adapted version of the Community Multiscale Air Quality (CMAQ) model was developed to interpolate PM2.5-measurements into unmonitored neighborhoods in Fairbanks, Alaska. AQuAT was developed as traditional interpolation methods of interpolating the mobile measurements were unsuccessful. Such a spatially differentiated air-quality advisory is highly desired in Fairbanks due to health concerns of PM2.5, and the need to improve the quality of life. The accuracy of AQuAT depends on the accuracy of the air-quality simulations used for its database. Evaluation of these simulations showed that they captured the observed relationships between PM2.5-concentrations and major meteorological fields (e.g., wind-speed, temperature, and surface-inversions) well. Skill scores for simulated PM2.5-concentrations fell in the range of modern models. The AQuAT database can include information on the nonlinear impacts of various emission sources on PM2.5-concentrations. This benefit was illustrated by investigating the impacts of emissions from point sources, uncertified wood-burning devices, and traffic on the distribution of PM 2.5-concentrations in the neighborhoods. Sensitivity studies on the effects of wood-burning device changeouts on the PM2.5-concentrations suggested that the emission inventory should be updated as soon as possible to capture recent changes in the emission situation in response to the changeout program. The performance of AQuAT was evaluated with PM2.5-measurements from mobile and stationary sites, and with simulated PM2.5-concentrations of winter 2010/2011 which were assumed to be "grand-truth" data. These evaluations showed that AQuAT captured the magnitudes and temporal evolutions of the PM 2.5-measurements and the "grand-truth" data well. The inclusion of wind-speed, wind-direction, and temperature in AQuAT did not improve its accuracy. This result may be explained by the fact that the relationships between meteorology and PM2.5-concentrations were already captured by the database. AQuAT allows quick spatial interpolation after the mobile measurements were made and provides error bars. It also allows for any route within the area for which a database of simulated concentrations exists. It was shown that AQuAT can be easily transferred for applications in other regions.
    • Analysis of structure and function of the serotonin type-3 receptor using site directed mutagenesis, structure activity relationship and chimeric constructs

      Suryanarayanan, Asha; Schulte, Marvin K.; Taylor, Barbara; Drew, Kelly; Kuhn, Thomas B. (2005-05)
      The serotonin type-3 receptor (5-HT₃R) is a cation conducting ligand gated ion channel that mediates fast synaptic transmission. The 5-HT₃R belongs to the Cys loop superfamily of ligand gated ion channels that also includes the nicotinic acetylcholine, glycine and GABAa receptors. The 5-HT₃R has been implicated in several processes such as emesis, gastrointestinal motility, drug abuse, alcoholism and nociception. Studies involving the ligand-binding domain will thus aid in development of new drugs that modulate these physiological and pathophysiological processes. The ligand-binding site of this receptor is comprised of six putative loops, viz. loop A-F. The focus of this thesis was to study the interactions of both agonists and antagonists with the 5- HT₃R. Interactions of two agonists, 5-HT and mCPBG, with the loop C region of the receptor were studied employing biochemical and receptor modeling studies. These studies identify novel determinants of 5-HT and mCPBG interactions with the 5-HT3 receptor. Similar studies involving granisetron, a competitive 5-HT₃R antagonist also reveal novel amino acids that interact with this antagonist. In order to further understand antagonist interactions with this receptor, the approach of structure activity relationship (SAR) studies was also employed to study the functional group interactions of lerisetron, a novel 5-HT₃R antagonist. Taken together with data from loops A, B, D and E, these data reveal an emerging picture of ligand interactions with the 5-HT₃R.
    • Analysis of trinitrophenylated adenosine and inosine using capillary electrophoresis-laser induced fluorescence detection and gamma-cyclodextrin

      Stephen, Terilyn Koehler Lawson; Green, Thomas K.; Duffy, Lawrence K.; Drew, Kelly L. (2016-05)
      Adenosine (Ado) and adenine ribonucleotides are essential in cell metabolism and energy production, cellular signaling, and DNA and RNA synthesis. The biosynthesis of these molecules takes place in both the intracellular and extracellular space via transphosphorylation reactions catalyzed by several distinct kinase enzymes like adenylate kinase. Several analytical detection methodologies have been developed to monitor these molecules in biological tissue, including both liquid chromatography (LC) and capillary electrophoresis (CE) techniques. However, many of these methodologies are limited by separation resolution and sample injection volume requirements. This thesis presents a novel capillary electrophoresis-laser induced fluorescence detection (CE-LIF) method with high separation power to analyze Ado and Inosine (Ino), a metabolite of Ado, by derivatization with 2,4,6-trinitrobenzenesulfonic acid to form fluorescent trinitrophenylated complexes of Ado (TNP-Ado) and Ino (TNP-Ino). The development and validation of the CE-LIF method, optimization of the trinitrophenylation reaction, and fluorescence enhancement of TNP-Ado and TNP-Ino with γ-cyclodextrin will be discussed. Detection limits were 1.6 μM for Ado and 4 μM for Ino in rat brain tissue. Large-volume sample stacking (LVSS) was employed to further enhance the sensitivity of the CE-LIF method, with detections limits of 310 nM and 159 nm for Ado and Ino, respectively. The CE-LIF method offers promise for the analysis of Ado, Ino and potentially other adenine ribonucleotides in small volume generating biological experiments like in vivo microdialysis and single cell metabolomics.
    • An analysis of turbulent sensible heat fluxes within a heterogeneous black spruce boreal forest in Alaska

      Starkenburg, Derek P.; Fochesatto, Gilberto J.; Prakash, Anupma; Kane, Douglas L.; Gens, Rudiger; Cristóbal, Jordi (2015-05)
      Turbulent sensible heat fluxes within the heterogeneous canopy of a black spruce boreal forest in Interior Alaska are evaluated at three different scales in order to assess their spatial variability, and to determine the feasibility of upscaling locally measured flux values to the landscape scale for modeling applications and climate studies. The first evaluation is performed locally at a single micrometeorological tower in an area of the boreal forest with a mean canopy height of 4.7 m. The data were taken across winter, spring and summer of 2012 from two sonic anemometers, one below the canopy at 3 m above ground, and one above the canopy at 12 m above ground. A multiresolution analysis is used to isolate coherent structures from the turbulent temperature time series at both instruments. When mean global statistics of coherent structures are analyzed at the two levels independently, results show an average of 8 structures per period, a mean duration of 85 s, and a mean sensible heat flux contribution of 48%. A spectral version of the Stokes parameters is applied to the turbulent horizontal wind components to show that 31% of the coherent turbulent structures detected at 12 m, and 13% at 3 m, may be complicated by canopy waves due to the prevalence of stable flows at this high latitude location. A most remarkable finding is that less than 25% of the coherent structures detected at these two heights occur synchronously, which speaks robustly to the lack of flow interaction within only 9 vertical meters of the forest, and to the complexity of the vertical aggregation of sensible heat therein. The second evaluation quantifies differences in turbulent sensible heat fluxes horizontally between two micrometeorological towers 600 m apart, one in a denser canopy (DC) and the other in a sparser canopy (SC), but under approximately similar atmospheric boundary layer conditions. Results show that SC is ~ 3°C cooler and more stably stratified than DC during nighttime. This suggests that changes in the height and density of the canopy impact local temperature and stability regimes. Most importantly, the sensible heat flux at DC is greater during midday periods, with that difference exceeding 30% of the measured flux and over 30 W m⁻² in magnitude more than 60% of the time. This difference is the result of higher mechanical mixing due to the increased density of roughness elements at DC. Furthermore, the vertical distribution of turbulent heat fluxes verifies a maximum above the canopy crown when compared with the levels below and well above the canopy. These spatial variations of sensible heat flux result from the complex scale aggregation of energy fluxes over a heterogeneous canopy, and suggest that locally measured fluxes will likely differ from large-scale area averaged values. The third evaluation compares locally measured sensible heat fluxes from a sonic anemometer atop a 24 m micrometeorological tower to those derived from a large aperture scintillometer (LAS) whose beam is centered near the tower at an average height of 36 m above ground, and over a path length of 1423 m. This analysis focuses on unstable daytime periods from June, July and August of 2013. The daytime is defined as 0700-2000 Alaska Standard Time, since local sensible heat flux values derived from the sonic anemometer (HEC) are robust (above 50 W m⁻²) during this time, and since this time also agrees with the minima in the mean diurnal pattern of Cn² from the LAS. For daytime periods with robust sensible heat flux values, HEC and the large-scale flux from the LAS (HLAS) correlate with R² = 0.68, while HEC captures about 82% of HLAS on average. The magnitude of HEC and HLAS are both strongly sensitive to incoming solar radiation, with HLAS having a better correlation and regression slope, suggesting that the local measurements are adjusting also to surface and/or flow conditions above the heterogeneous canopy. Evaluation of the magnitude of the ratio of HEC/HLAS for days with varying amounts of solar radiation suggests that while radiation affects the magnitude of HEC and HLAS independently, it does not affect their ratio. For daytime periods with lower fluxes (HEC between 10 and 50 W m⁻²), HEC captures about 69% of HLAS on average. However, local and large-scale fluxes during this low flux regime correlate poorly with incoming solar radiation (R² = 0.42 for HLAS and R² = 0.15 for HEC), and with one another (R² = 0.27), suggesting that local heterogeneities are not well-integrated into the large-scale flux. Therefore, low flux periods should be considered separately for the purposes of upscaling local to landscape scale flux values in the boreal forest. For the high flux regime, a finer resolution of upscaling can be provided based on the mean diurnal pattern of HEC/HLAS and the Obukhov length (L). Namely, as the boundary layer becomes less unstable in late afternoon, HEC/HLAS increases, supporting that the eddy covariance technique can capture more of the large-scale flux when the boundary layer is more shear-driven (less buoyancy driven).
    • Analysis of uncertainty in simulated exchange of heat and moisture at the land-atmosphere interface

      Jankov, Mihailo (2005-08)
      Land surface models (LSMs) serve to describe the atmosphere-land surface exchange in numerical weather prediction models (NWPMs) and global circulation models (GCMs). The use of empirical soil and vegetation parameters in LSMs introduces uncertainty that propagates and affects predictions of the lower boundary conditions. To statistically assess that uncertainty in predicted evapotranspiration (water transport by direct evaporation from bare ground and canopy and transpiration by the canopy) and ground heat flux for natural ranges of atmospheric soil and vegetation conditions, the Gaussian Error Propagation method is utilized. The assessed uncertainties in direct and canopy water evaporation, transpiration and ground heat flux display prominent diurnal cycles. Prediction of evapotranspiration in desert areas is limited by the uncertainty in the evaporation of water collected on the canopy and transpiration. To improve predictions of evapotranspiration the maximal canopy storage and shielding factor should be determined with higher accuracy. It is found that uncertainty in ground heat flux is particularly great in dry and warm areas covered with sandy clay loam. A better prediction of ground heat flux requires a better parameterization of thermal conductivity and a higher degree of accuracy of the pore size distribution index.
    • An analysis of volcanic ash plume movement and dispersion within the North Pacific

      Papp, Kenneth R.; Dean, Kenneson; Sharpton, Virgil; Dehn, Jonathan; Schneider, David (2002-08)
      This study analyzes the movement and dispersion of airborne volcanic ash within the North Pacific region by simulating volcanic plumes from 22 volcanoes using the PUFF ash-tracking model. The model is run hourly using archived wind field data between 1994-2001 and the results are analyzed with statistical and GIS software. Maps and statistics are generated revealing the distribution of simulated airborned ash particles at 6 and 24 hr intervals, constraining the likely direcion and distance a volcanic ash cloud may propagate from a given volcano. The results indicate wind field charactistics during and after an eruption may have a larger effect on volcanic cloud growth rate than the eruption dynamics. Wind field and statistical analyses show North Pacific ash cloud distribution is strongly affected by the intensity, migration, and location of the Polar jet stream and associated cyclones. Although often used operationally during an eruption crisis, the PUFF model can also be used as an effective research tool and provide airborne ash hazard mitigation for towns, airports, and air traffic within the North Pacific region.
    • Analyzing tree distribution and abundance in Yukon-Charley Rivers National Preserve: developing geostatistical Bayesian models with count data

      Winder, Samantha; Short, Margaret; Roland, Carl; Goddard, Scott; McIntyre, Julie (2018-05)
      Species distribution models (SDMs) describe the relationship between where a species occurs and underlying environmental conditions. For this project, I created SDMs for the five tree species that occur in Yukon-Charley Rivers National Preserve (YUCH) in order to gain insight into which environmental covariates are important for each species, and what effect each environmental condition has on that species' expected occurrence or abundance. I discuss some of the issues involved in creating SDMs, including whether or not to incorporate spatially explicit error terms, and if so, how to do so with generalized linear models (GLMs, which have discrete responses). I ran a total of 10 distinct geostatistical SDMs using Markov Chain Monte Carlo (Bayesian methods), and discuss the results here. I also compare these results from YUCH with results from a similar analysis conducted in Denali National Park and Preserve (DNPP).
    • Anisotropy in the Alaska subduction zone: shear-wave splitting observations from local and teleseismic earthquakes

      Richards, Cole; Tape, Carl; West, Michael; Freymueller, Jeffrey (2020-05)
      Shear-wave splitting observations can provide insight to mantle flow due to the link between the deformation of mantle rocks and their direction dependent seismic wave velocities. We identify shear-wave anisotropy in the Cook Inlet segment of the Alaska subduction zone by analyzing splitting parameters of S phases from local intraslab earthquakes between 50 and 200 km depths and SKS waves from teleseismic events. These earthquakes were recorded from 2015-2017 (local S) and 2007-2017 (SKS) by stations from SALMON (Southern Alaska Lithosphere and Mantle Observation Network), TA (EarthScope Transportable Array), MOOS (Multidisciplinary Observations Of Subduction), AVO (Alaska Volcano Observatory), and the permanent network. Automatic phase picking (dbshear) of 12095 local earthquakes (Ml ≥ 1.5) recorded at 84 stations yielded 678 high-quality splitting measurements (filtered 0.2-1 Hz). Teleseismic SKS phases recorded at 112 stations with 26,143 event-station pairs resulted in 360 high-quality SKS splitting measurements (filtered 0.02-1 Hz and 0.01-1 Hz). Measurements for both datasets were made using the SC91 minimum eigenvalue method with software package MFAST. We compare local S and SKS splitting patterns both from previous studies and our own analysis and find that they are most similar in the far forearc, at the Kenai Peninsula, below which there is no mantle wedge. Anisotropy in the subducting Pacific lithosphere and subslab asthenosphere is likely here as both S and SKS display plate convergence fast directions and SKS measurements exhibit delay times too long (∼2 s) to be explained solely by lithospheric anisotropy. Large splitting delay times (∼0.5 s) for local measurements that mainly sample slab further indicate that the Pacific slab lithosphere contains significant anisotropy. We also observe anisotropy in the mantle wedge indicated by an increase in delay time as focal depth increases for stations with ray paths dominantly sampling wedge. These measurements display trench-perpendicular and plate convergence fast directions consistent with 2D corner flow in the mantle wedge. Both datasets show trench-parallel splitting directions in select areas of the arc/forearc that overlie parts of the mantle wedge and nose. B-type olivine in the mantle nose, subslab asthenospheric flow, flow around the slab edge, and anisotropy in the Pacific lithosphere all could be invoked to explain this pattern. While we are unable to distill the anisotropy to a single responsible structure, the sharp transition in the local S data splitting pattern from trench-perpendicular in the backarc to trench-parallel across the arc suggests B-type olivine in the mantle nose. For an overall model, we favor 2D corner flow of A-type olivine in the mantle wedge induced by downdip motion of the slab, B-type olivine in the nose, and plate convergence parallel anisotropy in the subslab asthenosphere and subducting Pacific lithosphere to explain the observed splitting patterns. It is clear that the subducting slab's structure and motion are the dominant influence on anisotropy and mantle flow regimes here. The differences in local S and SKS splitting results motivate further study on frequency dependence of splitting measurements and emphasize the need for a better understanding of which earth structures are responsible for the observed splitting patterns globally. This study constitutes the first comprehensive local splitting study in Alaska and refutes the common interpretation of along arc flow in the mantle wedge proposed by many previous splitting studies in Alaska.