• Earthquake source mechanisms and three-dimensional wavefield simulations in Alaska

      Silwal, Vipul; Tape, Carl; Christensen, Douglas; West, Michael; Ruppert, Natalia; Freymueller, Jeffrey (2018-08)
      This thesis presents: (1) a set of earthquake source mechanism catalogs for Alaska and (2) a threedimensional seismic velocity model of Alaska. The improved earthquake sources are used within the velocity model for generating synthetic seismograms, which are then compared with recorded seismograms to assess the quality of the velocity model. An earthquake source mechanism can be modeled as a moment tensor, which is a 3 × 3 symmetric matrix. We estimate the moment tensor for earthquakes by comparing observed waveforms (body waves and surface waves) with synthetic waveforms computed in a layered model. The improved moment tensor solutions are obtained by utilizing both the body waves and surface waves at as many broadband stations as possible. Further improvement in the inversion technique is obtained by (1) implementation of L1 norm in waveform misfit function and (2) inclusion of first-motion polarity misfit in the misfit function. We also demonstrate a probabilistic approach for quantifying the uncertainty in a moment tensor solution. Moment tensors can be used for understanding the tectonics of a region. In the Cook Inlet and Susitna region, west of Anchorage, we determined moment tensor solutions for small-tointermediate magnitude (M ≥ 2.5) crustal earthquakes. Analyzing these small earthquakes required us to modify the misfit function to include first-motion polarity measurements, in addition to waveform differences. The study was complemented with the probabilistic hypocenter estimation of large historical earthquakes (Mw ≥ 5.8) to assess their likelihood of origin as crustal, intraslab, or subduction interface. The predominance of thrust faulting mechanisms for crustal earthquakes indicate a compressive regime within the crust of south-central Alaska. Wavefield simulations are performed in three regions of Alaska: the southern Alaska region of subduction, the eastern Alaska region with the accreting Yakutat microplate, and the interior Alaska region containing predominantly strike-slip faulting, including the Minto Flats fault zone. Our three-dimensional seismic velocity model of Alaska is an interpolated body-wave arrival time model from a previous study, embedded with major sedimentary basins (Cook Inlet, Susitna, Nenana), and with a minimum shear wave velocity threshold of 1000 m/s. Our comparisons between data and synthetics quantify the misfit that arises from different parts of each model. Furtherwork is needed to comprehensively document the regions within each model that give rise to the observed misfit. This would be a step toward performing an iterative adjoint tomographic inversion in Alaska.
    • Ecogeographic, Adaptive, And Phylogenetic Variations In The Crested Duck (Lophonetta Specularioides) And Their Hemoglobins In The Andes

      Bulgarella, Mariana; McCracken, Kevin; Takebayashi, Naoki; Tubaro, Pablo L.; Winker, Kevin S. (2010)
      Tolerance to high-altitude hypoxia in animals varies widely and is a key factor in determining survival at high elevation. The Andean Cordillera of South America, which spans large elevational and latitudinal gradients, enables the study of native highland populations and the characteristics of hemoglobin proteins that are locally adapted for high-altitude respiration. The waterfowl populations of South America are understudied, little data on demographics and behavior are currently available, and only recently have they been investigated using molecular tools. We studied population genetics, phylogeography, and ecogeographic variation in the crested duck ( Lophonetta specularioides). The crested duck is a dabbling duck, and it comprises two subspecies endemic to highland and lowland regions of South America. The primary objective of this study was to investigate the genetic differentiation between highland and lowlands populations of crested ducks using molecular markers with varying modes of inheritance and rates of substitution. The second objective was to evaluate morphological differences between the subspecies to better understand the forces shaping morphology in the two different environments. A third objective was to provide additional information on the taxonomic relationships and natural history of the crested duck. First, we examined the population genetics of the three adult hemoglobins (alphaD, alphaA, betaA), six autosomal introns, and mtDNA. This multi-locus analysis revealed a significant pattern of differentiation between highland and lowland populations. Four hemoglobin amino acid replacements were found in crested duck that may play a role in influencing high-altitude respiration. The lack of evidence for gene flow for hemoglobin alleles between highland and lowland populations and the biochemical properties of the amino acid substitutions themselves are consistent with the effects of selection acting on these loci. Overall body size was larger for the highland subspecies, body size was intermediate in mid-elevation environments, and smaller individuals were found in the lowlands of Patagonia. We also performed a multi-locus phylogenetic analysis to determine the relationships of Lophonetta within the South American duck clade. Finally, we determined the proportion of genes expressed in bone marow of adult crested duck finding mostly genes related to hemopoietic and immune function.
    • Ecological And Physiological Adaptations Of The Porcupine To Winter Alaska

      Coltrane, Jessica A.; Barboza, Perry; Spalinger, Donald E.; Farley, Sean; Barnes, Brian M. (2012)
      Understanding the ecology and physiology of wildlife is paramount to conservation and management of species. North American porcupines (Erethizon dorsatum) are mammalian herbivores that occupy a diverse array of habitats across a broad geographical range. However, few studies have explored the ecology and physiology of porcupines. I used captive and free ranging porcupines to 1) identify the physiological abilities that enable them to survive on low quality winter forage when thermoregulatory demands are high, 2) determine responses of porcupines to winter conditions, and 3) determine how winter conditions influence habitat selection and home range size at the northern limits of their range. My research revealed that the persistence of porcupines at the northern limits of their range is due to plasticity of food intake, as well as physiological tolerance of low-quality diets and low ambient temperatures. Captive porcupines gained mass when high quality diets were available. However, porcupines decreased their dry matter intake throughout winter, indicating a seasonal decrease in metabolic rate. Low requirements for energy and nitrogen minimized the loss of body mass when intakes were low, while plant toxins increased urinary losses of energy and nitrogen. Free-ranging porcupines conserved lean body mass in winter by catabolizing fat stores. Proportional fat loss was correlated positively with total fat mass at the start of winter. Fat losses were minimized by lowering rates of energy expenditure. Water turnovers were slow in wild porcupines and body temperatures were not reduced to save energy. In order to survive winter on a low quality diet of white spruce (Picea glauca ) needles and cambium and paper birch (Betula papyrifera ) cambium, porcupines maintained large home ranges comprised primarily of mixed conifer/hardwood forests. Occupying a mixed forest habitat allowed porcupine to switch their diet between two forage tree species, potentially alleviating saturated detoxification pathways. Overall, porcupines possess the physiological abilities of a specialist herbivore during winter; however, they rely on abundant high quality summer forages to replenish their stores of fat and protein for reproduction and survival in the subsequent winter.
    • Ecological And Social Influences On Population Dynamics And Genetics Of Moose In Alaska

      Schmidt, Jennifer Irene; McCracken, Kevin (2007)
      I examined social and ecological influences on moose (Alces alces gigas) in Alaska, USA, with respect to hunting success, antler size, and population genetic structure. Catch per unit effort (CPUE) is frequently used to assess hunter success; thus I hypothesized that landscape characteristics and moose density would affect success. Using hunter harvest tickets returned to the Alaska Department of Fish and Game, I modeled CPUE with Weibull regression. I determined success is significantly predicted by hunt location, mode of transportation, hunting regulations, use of commercial services (i.e., guides), year, road density, hunter-to-moose ratio, moose density, and hunter residency status. Antler size is an important factor for hunters and for mating potential in male moose. I hypothesized that moose density, habitat, and use of guides would correlate with antler size of harvested moose. I also predicted that guides would harvest moose with larger antlers and avoid areas where the hunter-to-moose ratio is high compared to nonguided hunters. Results indicated that antler size decreases with increases in moose density and harvest intensity due to density-dependent processes and a younger age structure in heavily harvested areas. Guided hunts tended to harvest larger antlered bulls and avoided areas of high hunter-to-moose ratios. In addition to age and nutrition, genetics influences antler size. I used eight microsatellites and five sample areas to resolve whether population structure exists among moose in Alaska. I hypothesized that population structure does exist given the intense harvest rates, polygynous mating style of moose, and heterogeneous landscape present in Alaska. Dispersal and gene flow between populations was proposed to occur via isolation-by-distance (IBD) with a positive linear relationship between geographic and genetic distance. Results indicated weak but significant population structure for moose in Alaska, and IBD was supported. Pairwise comparisons between populations indicated that moose have established separate populations except for between Tanana Flats and Koyukuk and Koyukuk and the Seward Peninsula. Lastly, I hypothesized incorporation of landscape characteristics and subsequent least-cost path would strengthen the significance of IBD. With an additional population, Tetlin, the significance of IBD as a mechanism for dispersal/gene flow for moose in Alaska was improved.
    • Ecological drivers of mercury accumulation in threespine stickleback fish

      Willacker, James J.; O'Hara, Todd; von Hippel, Frank; Buck, Loren; Welker, Jeffrey; Wipfli, Mark (2013-12)
      I utilized the ecological diversity displayed in the Cook Inlet adaptive radiation of threespine stickleback (Gasterosteus aculeatus species complex, hereafter 'stickleback') to examine the drivers of intra- and inter-population variation in total mercury (THg) concentrations. I examined the importance of sex, trophic position (TP), and habitat-specific foraging (measured as the proportion of the diet derived from benthic sources; a) in stickleback from Benka Lake, Alaska, a lake with both benthic and limnetic ecotypes. The results demonstrate that both sex and habitat-specific foraging are important determinants of THg concentrations in this threespine stickleback population. Specifically, male stickleback and stickleback foraging in limnetic habitats had higher THg concentrations than females or benthic foraging individuals. Further, I found that the relationships between THg concentration, TP, and a differed between the sexes such that TP and a were of approximately equal importance in female fish but TP was more important than a in male fish. I assessed the relative importance of these same factors in determining THg concentrations of stickleback from six lakes spanning a range of trophic ecologies. Across populations, I found sex and TP to be more important determinants of THg concentrations than reliance on benthic prey; however, there was substantial variation in the relative importance of these parameters in individual lakes. Across lakes I also found a positive correlation between THg concentrations in stickleback and the reliance on benthic prey, and my data suggest that differences in the bioavailability of Hg in the lakes were responsible for this relationship. I investigated temporal variation in the THg concentrations of Benka Lake stickleback. The temporal patterns observed in stickleback likely result from numerous physiological and ecological processes. I found that the importance and magnitude of these factors acting upon THg concentrations varied between sexes, ecotypes, or both, though the directions of the relationships were consistent across groups. Despite this variation, TP was consistently the most important determinant of Hg concentrations. Collectively, the results of this dissertation demonstrate that the ecological factors driving THg concentrations in stickleback are complex, likely integrate multiple confounding interactions, and often vary by sex, ecotype, and population (lake). To improve our understanding of the mechanisms underlying Hg bioaccumulation, future research should utilize experimental studies and larger numbers of wild populations to examine the independent effects of these variables within the context of varying physiologies and ecologies.
    • Ecological effects of invasive European bird cherry (Prunus padus) on salmonid food webs in Anchorage, Alaska streams

      Roon, David A.; Wipfli, Mark; Prakash, Anupma; Wurtz, Tricia (2011-08)
      Invasive species are a concern worldwide as they can displace native species, reduce biodiversity, and disrupt ecological processes. European bird cherry (Prunus padus) (EBC) is an invasive ornamental tree that is rapidly spreading and possibly displacing native trees along streams in parts of urban Alaska. The objectives of this study were to: 1) map the current distribution of EBC along two Anchorage streams, Campbell and Chester creeks, and 2) determine the effects of EBC on selected ecological processes linked to stream salmon food webs. Data from the 2009 and 2010 field seasons showed: EBC was widely distributed along Campbell and Chester creeks; EBC leaf litter in streams broke down rapidly and supported similar shredder communities to native tree species; and EBC foliage supported significantly less terrestrial invertebrate biomass relative to native deciduous tree species, and contributed significantly less terrestrial invertebrate biomass to streams compared to mixed native vegetation, but riparian EBC did not appear to affect the amount of terrestrial invertebrate prey ingested by juvenile coho salmon (Oncorhynchus kisutch). Although ecological processes did not seem to be dramatically affected by EBC presence, lowered prey abundance as measured in this study may have long-term consequences for stream-rearing fishes as EBC continues to spread over time.
    • The ecological genetics of gynodioecy in Silene acaulis L. (Caryophyllaceae): spatial sex structure and inbreeding depression

      Keller, Stephen Robert (2002-12)
      Gynodioecy, the co-occurrence of females and hermaphrodites, is considered an intermediate step in the evolution of separate sexes in flowering plants. Highly variable female frequencies among populations suggest structuring of sex determining genes and differences in the relative fitness of females and hermaphrodites as seed parents. I investigated spatial variability in sex ratio and the effects of inbreeding on offspring quality in Silene acaulis. Female frequencies varied among populations from 0.32 to 0.69, and most were at temporal equilibrium. Females were significantly clumped within two of six populations. Females produced from 4 to 27 times as many fruits as hermaphrodites. Self-pollination of hermaphrodites reduced offspring survivorship and growth by an average of 67% compared to outcrosses. Overall, spatial variation in female frequency suggests a role of founder events and local seed dispersal. Low fruit production and reduced quality of inbred offspring suggest hermaphrodites may be functioning primarily as pollen donors.
    • Ecological mechanisms and effectiveness of bioremediation in Alaska

      Leewis, Mary-Cathrine Christina Elaine; Leigh, Mary Beth; O'Hara, Todd; Ruess, Roger; Taylor, D. Lee (2014-05)
      What drives microbial community structure and function is a fundamental question of microbial ecology. Soil microbial communities have wide ranging metabolic capabilities, which include performing oxidation-reduction reactions responsible for cycling of nutrients and organic compounds and biodegradation of pollutants. One major determinant of microbial function in soils is vegetation type. Considering plants are diverse in chemical composition, they impact the quantity and quality of carbon and nutrients available to microbes through root turnover, root leachates, as well as by altering pH and soil microclimate (moisture, temperature). Rhizosphere interactions, in the form of phytoremediation, can be capitalized upon to provide a potentially cost effective method for detoxifying contaminated soils using plants and associated soil microorganisms. The remote locations and cold climate of Alaska provide unique challenges associated with phytoremediation such as finding effective plant species that can achieve successful site clean-up despite the extreme environmental conditions that includes minimal site management. Here we investigate the potential mechanisms and related effectiveness of microbial communities and native boreal vegetation associated with contaminant degradation and biogeochemical cycling. We examined three different soil systems to understand how dominant vegetation type, historical treatment and contamination shape the microbial community structure and functional potential. First, we used stable isotope probing to understand how microbial communities act in concert to biotransform the recalcitrant contaminants, polychlorinated biphenyls. Second, we sought to understand if dominant vegetation type controls microbial community structure and function either through direct impacts of plant root exudates and detritus or indirectly through the influence of plants on soil chemistry, composition, and structure. Finally, we conducted a forensic investigation of a petroleum contaminated site with no active site management for 15 years to assess the long-term effects of phytoremediation on soil petroleum concentrations, microbial community and vegetation colonization. The results of these experiments provide novel insights into the mechanisms of contaminant removal in boreal forest soils and the role of plants in ecosystem resilience to contamination, and demonstrates that phytoremediation using native and local plants can be an effective means to treat petroleum contaminated soils.
    • The ecological niche of storm-petrels in the North Pacific and a global model of dimethylsulfide concentration

      Humphries, Grant R. W. (2010-05)
      Ecological niche modeling techniques were used to create global, monthly predictions of sea surface dimethylsulfide (DMS) concentrations, and breeding season distribution of Leach's Storm-Petrel (Oceanodroma luncorhoa) and Fork-Tailed Storm-Petrel (O. furcata) in the North Pacific. This work represents the first attempt to model DMS concentrations on a global scale using ecological niche modeling, and the first models of Storm-Petrel distribution for the North Pacific. Storm-Petrels have been shown to be attracted to DMS, and it is therefore likely that a model of sea surface DMS concentration would help explain and predict Storm-Petrel distribution. We have successfully created the most accurate models of sea surface DMS concentrations that we are currently aware of with global correlation (r) values greater than 0.45. We also created Storm-Petrel models with area under the receiver operating characteristic curve (AUC) values of greater than 0.90. Using just DMS as a predictor variable we were also able to create models with AUC values upwards of 0.84. Future conservation efforts on pelagic seabird species may be dependent on models like the ones created here, and it is therefore important that these methods are improved upon to help seabird management on all scales (global, national, regional and local).
    • An ecological-physiology perspective on seabird responses to contemporary and historic environmental change

      Will, Alexis P.; Kitaysky, Alexander; Breed, Greg; Powell, Abby; Springer, Alan (2017-05)
      The chapters included in this dissertation implement an ecological-physiology approach to understanding how long-lived marine organisms, using seabirds as a model, respond to changes in the environment. Many seabird populations are governed by bottom-up processes, yet efforts to connect prey dynamics and parameters such as breeding performance often yield mixed results. Here I examined how individual foraging behavior and nutritional status change at the inter-annual, decadal, and multi-decadal scale. I validated that the concentration of the avian stress hormone in seabird feathers is indicative of their exposure to nutritional stress. I then used this technique to show that young seabirds (Rhinoceros auklets, Cerorhinca monocerata) that experience variable foraging conditions during their prolonged nestling period incurred higher nutritional stress when provisioned with prey that was relatively low in energy content. On the other hand, when examining adult foraging behavior, a signal of environmental variability was lost in the noise of changing diets. Foraging behavior of adults appeared to be highly flexible and less informative in regard to detecting an environmental change. I used stable isotope analysis to re-construct the isotopic niche dynamics (where and at what trophic level seabirds were obtaining prey) and partitioning of food resources for three abundant seabirds (common and thick-billed murres, Uria aalge, and U. lomvia, respectively; and black-legged kittiwakes, Rissa tridactyla) breeding in the southeastern Bering Sea under cold and warm states of the ecosystem. Access to diverse habitat reversed how seabirds partitioned prey during food shortages: seabirds with access to multiple habitats contracted their isotopic niche during food-limited conditions in contrast to the expansion of the isotopic niche observed for seabirds with access to only one type of habitat. Finally, I measured nutritional stress and stable isotope signatures (carbon and nitrogen) in contemporary and historic red-legged kittiwake (Rissa brevirostris) feather samples to examine how birds breeding on St. George Island have responded to changes in summer and winter conditions in the Bering Sea over time. Red-legged kittiwakes were less nutritionally stressed during warm summers and winters. It is not clear, however, whether all seabirds would do well if the Bering Sea were to break with its pattern of oscillating between warm and cold conditions. Prey for these birds may either be negatively affected by continuously warm conditions (murres and black-legged kittiwakes feeding on juvenile pollock, Gadus chalcogrammus) or the conditions that are most beneficial to the prey are not known (red-legged kittiwakes feeding on myctophids). With this work I suggest that measuring nutritional stress in feathers and using stable isotope analysis to characterize foraging niches may document more dynamic responses to changes in the environment than population level parameters such as breeding performance. To do so, however, requires a better understanding of the relationship between these individual-level responses and fitness.
    • Ecology of a reestablished population of muskoxen in northeastern Alaska

      Reynolds, Patricia Claire Embry (1998)
      The restoration of muskoxen (Ovibos moschatus) to regions of former range in northeastern Alaska presented an opportunity to study population dynamics, seasonal patterns, and dispersal in an expanding population of ungulates. Muskoxen were returned to the Arctic National Wildlife Refuge (Arctic NWR) in 1969-70 after an absence of $>$100 years. In 1982-97, I used annual censuses, counts by sex and age, radio and satellite telemetry, and data from Landsat-TM maps to determine rates of population growth, changes in production, survival, and group size over time, seasonal habitat use, activity patterns, and dispersal of mixed-sex groups. In 1982-86, mixed-sex groups of muskoxen occupied the same regions as in 1977-81, but annual rates of increase and calf production declined (1977-81: rate = 0.24, 87 calves/100 adult females; 1982-86: rate = 0.14, 61 calves/100 adult females). In 1987-95, numbers of muskoxen in regions first occupied declined and stabilized at $<$300 animals as calf production continued to decline and mixed-sex groups dispersed into unoccupied regions. Survival of calves and yearlings did not decline over time. By 1995, about 800 muskoxen were distributed between the Itkillik River west of Prudhoe Bay, Alaska, and the Babbage River in northwestern Canada. In summer, female muskoxen occupied large core areas $(\bar x=223$ km$\sp2),$ and had high rates of movement $(\bar x=2.6$ km/day) and activity $(\bar x=18.9$ counts/min). In winter muskoxen remained in small core areas (mid-winter $\bar x=25$ km$\sp2)$ and reduced movements (mid-winter $\bar x=1.4$ km/day) and activity (mid-winter $\bar x=11.8$ counts/min.) possibly as a strategy to conserve energy. Muskoxen selected (use $>$ availability) riparian and moist sedge vegetation along rivers in all seasons. Dispersal of mixed-sex groups occurred infrequently through periodic pulses. Population density likely influenced patterns of dispersal through social interactions and habitat change. Weather conditions that affected the length of the growing season and availability of winter forage were major factors in the dynamics, distribution, and dispersal patterns of this reestablished population of muskoxen.
    • Ecology of mountain sheep: effects of mining and precipitation

      Oehler, Michael William (1999-12)
      We examined effects of mining on mountain sheep (Ovis canadensis nelsoni) in California. Size of home range, forage quality, and diet did not differ between populations in mined and nonmined areas. During summer, we observed the greatest disparity in time spent feeding and diet quality. Because of their dependence on a spring adjacent to the mine, sheep may have spent more time vigilant, and less time feeding. Reducing mining during summer may benefit sheep. We also compared ecology of two female mountain sheep populations from different areas (xeric vs. mesic) in the Mojave Desert. The more xeric Panamint Range was typified by more bare ground, less shrubs, less grass, and larger home ranges than at Old Dad Peak. Females from Old Dad foraged on grasses, whereas those from the Panamints consumed shrubs. We concluded that sheep from the Panamints required larger home ranges because of lower-quantity and quality of forage.
    • Ecology of Prince of Wales spruce grouse

      Nelson, Aleya R. (2010-12)
      Recently, spruce grouse on Prince of Wales Island (POW) in southeast Alaska have been proposed as a separate subspecies. Furthermore, life-history of spruce grouse on POW, which is temperate coastal rainforest, varies sufficiently from birds in mainland areas, mostly boreal forest, to warrant specific management. Therefore, I examined the ecology of spruce grouse on POW to determine how timber harvest influences their survival and habitat selection and ultimately to provide recommendations for their conservation. During 2007-2009, we found that the greatest variation in survival probability was attributed to breeding status. The annual survival of non-breeding birds was 0.72±0.082 (S±) while for breeding birds it was 0.08±0.099. Logging did not adequately predict survival, with no differences among habitats. Conversely, I found differences in selection among habitats. At the watershed scale, spruce grouse preferred unharvested forest. At both watershed and homerange scales, spruce grouse avoided edges and preferred roads. Road-related mortality was the largest known source of death. POW spruce grouse and mainland subspecies exhibit sufficiently different survival rates and habitat preference to warrant specific management. We recommend limited road closures during periods when POW spruce grouse are most vulnerable due to the high rates of mortality associated with this preferred habitat.
    • Edge detection using Bayesian process convolutions

      Lang, Yanda; Short, Margaret; Barry, Ron; Goddard, Scott; McIntyre, Julie (2017-05)
      This project describes a method for edge detection in images. We develop a Bayesian approach for edge detection, using a process convolution model. Our method has some advantages over the classical edge detector, Sobel operator. In particular, our Bayesian spatial detector works well for rich, but noisy, photos. We first demonstrate our approach with a small simulation study, then with a richer photograph. Finally, we show that the Bayesian edge detector performance gives considerable improvement over the Sobel operator performance for rich photos.
    • The effect of a low copper diet on muskox calf immune function and health

      Swor, Rhonda Michelle (2002-08)
      Weight loss and ill thrift are common problems encountered in muskox calves raised in captivity. Varied diagnostic results suggest that there is immunosuppression possibly related to trace mineral intake. This experiment evaluates the influence of a single trace element, copper, on muskox calf health and development. Muskox calves consuming a diet containing 5 ppm Cu exhibited lower weight gains, reduced survivability, depleted lymphoid tissue, thinner aortic arches, more muscle wasting and an increased occurrence of diarrhea than a group consuming the same diet but receiving injectable Cu supplementation. This study demonstrates the importance of adequate copper in the diet ensuring proper growth and development of the immune system in muskox calves. Muskox calf health and ultimately survival depends upon careful management to ensure the transition from a milk-based diet to a properly balanced solid diet. This coupled with efforts to minimize exposure to pathogens and environmental bacteria will enhance survival.
    • Effect of filling methods on the forecasting of time series with missing values

      Cheng, Mingyuan (2014-12)
      The Gulf of Alaska Mooring (GAK1) monitoring data set is an irregular time series of temperature and salinity at various depths in the Gulf of Alaska. One approach to analyzing data from an irregular time series is to regularize the series by imputing or filling in missing values. In this project we investigated and compared four methods (denoted as APPROX, SPLINE, LOCF and OMIT) of doing this. Simulation was used to evaluate the performance of each filling method on parameter estimation and forecasting precision for an Autoregressive Integrated Moving Average (ARIMA) model. Simulations showed differences among the four methods in terms of forecast precision and parameter estimate bias. These differences depended on the true values of model parameters as well as on the percentage of data missing. Among the four methods used in this project, the method OMIT performed the best and SPLINE performed the worst. We also illustrate the application of the four methods to forecasting the Gulf of Alaska Mooring (GAK1) monitoring time series, and discuss the results in this project.
    • Effect of oxidative stress on kinetic parameters of cellular actin dynamics

      Kulkarni, Sayali Devdatta (2007-12)
      The integrity and dynamics of the actin cytoskeleton is essential for the morphology and motility of neuronal cells both in developing and adult nervous system. Oxidative modification of actin both as monomers and in filaments alters the kinetics of actin filament dynamics contributing to neurodegeneration and aging. Our objective focused on changes of the kinetic parameters of oxidized actin as opposed to naive actin and its resulting effects on actin filament dynamics. We first validated Surface Plasmon Resonance (SPR) technology for our objective by studying interaction of naive actin with a monoclonal anti-actin antibody and DNase I. For interactions of actin monomers under polymerizing conditions yet below the critical concentration of actin, we determined real time rate constants for actin nucleation steps for the first time. The association rate constant (ka) for the first monomer was 7.5x10³ μM⁻¹sec⁻¹ and the dissociation rate constant (ka) for first monomer was 0.256 sec⁻¹. Whereas Ka for second monomer remained unchanged (6.66x10³ μM⁻¹sec⁻¹), kd for second monomer was significantly decreased (1.82x10⁻³ sec⁻¹). We also found that affinity of oxidized actin to unoxidized actin is significantly (100 fold) reduced. Our findings demonstrate that SPR allows measurement of (kinetic parameters) for unmodified actin monomers.
    • The effect of topography on the seismic wavefield

      Miller, Ulrika; Tape, Carl; West, Michael; Christensen, Douglas (2014-12)
      Active tectonic settings exhibit deformation manifested by earthquakes and by strong topographic variations due to erosion and uplift. Seismic waves from these earthquakes will clearly be influenced by the topographic variations, but it is challenging to isolate the effects of topography from the effects of variations in 3D seismic wave-speed structure. Here we design a realistic numerical experiment to investigate the effects of topography on the regional seismic wavefield. We choose southern California as a target region. We perform several sets of 3D seismic wavefield simulations for 137 earthquake sources ranging from Mw3.4 to 5.4. We test the influence of topography within a homogeneous model and a layered model, and for each model we establish the shortest resolvable period for each path between a source and station. By examining the path-specific shortest resolvable periods, we are able to make some generalizations. Topography has the strongest influence on surface waves, particularly for waveforms with travel paths that are nodal to the source radiation; in these directions, the wave amplitudes are relatively low, so any multi-pathing or scattering effects due to topography are more easily identified. The topographic effects are stronger for shorter periods and for longer paths. The influence of topography on the seismic waveforms arises from both the change in the topographic surface, but also the change in the wave-speed structure that arises from perturbing the topography for a 1D (or 3D) wavespeed model. These generalizations of the influence of topography provide a basis for further numerical investigations or for where to search within a regional set of observations for the topographic effects. Topography should be included within simulation-based seismic imaging applications, especially those at high frequencies, in order to eliminate the possibility of attributing topographically-caused waveforms to subsurface variations in structure.
    • The effect of varying active layer and soil climate on net nitrogen mineralization and foliar nitrogen in a boreal watershed

      Rohrs-Richey, Jennifer K. (2004-12)
      In the Alaskan boreal forest, black spruce (Picea mariana) is the forest type most severely limited by nitrogen mineralization. Nitrogen cycling in upland black spruce forests of the Interior is affected by the interactions between permafrost, soil climate, and litter quality. Permafrost and soil climate also play a significant role in nitrogen acquisition of shrubs, which are important for biomass turnover and element cycling in the understory. This study took place in a boreal watershed and addressed the question of how variation in soil climate and active layer between north and south-facing aspects affected 1) net nitrogen mineralization rate and 2) foliar nitrogen concentrations in understory shrubs. I hypothesized that south-facing aspects, with warmer, drier soils and deeper active layers would have higher mineralization rates and support deciduous and evergreen shrubs with higher nitrogen status. Contrary to my predictions, net mineralization rate was not explained by active layer or soil climate. In support of my hypothesis, I found shrubs generally had higher foliar N on south-facing aspects. My study concludes that 1) the typical controls of net mineralization do not operate over the small scale of this study and 2) although more favorable soil conditions supported shrubs with higher foliar N, seasonal and spatial differences in foliar N cannot be categorized by growth strategy.
    • Effects of bear viewers and photographers on brown bears (Ursus arctos) at Hallo Bay, Katmai National Park and Preserve

      French, Howard Blair (2007-05)
      We investigated the effects of bear viewing and photography on brown bears (Ursus arctos) that used open habitats at Hallo Bay, Katmai National Park and Preserve (KNPP), Alaska. We also investigated how bear use of the area varied with season, human presence, and time of day. We found that the mean number of bears present varied significantly with season, time of day, and human presence. There were significantly more bears present before the salmon season than during the salmon season; bear numbers increased significantly during the day, and there were significantly more bears when humans were present. Humans at varying distances least affected activity budgets of sows with spring cubs, but foraging efficiency (bites per minute) of sows with spring cubs was significantly lower with humans <50 m away than with humans absent. Fishing success (chases per catch) of large males and single bears was lower when humans were present, but fishing success of sows with spring and older cubs was higher when humans were present. We conclude that humans are affecting brown bears that use Hallo Bay and therefore the Katmai NPP Bear Management Plan is being violated as well as the act establishing the National Park Service. We recommend that managers at KNPP restrict visitor use at Hallo Bay and enforce existing policy.