Detecting Methane Ebullition In Winter From Alaskan Lakes Using Synthetic Aperture Radar Remote Sensing

Thesis (Ph.D.) University of Alaska Fairbanks, 2012Methane (CH4) is a greenhouse gas with a high radiative forcing attribute, yet large uncertainties remain in constraining atmospheric CH4 sources and sinks. While freshwater lakes are known atmospheric CH4 sources, flux through ebullition (bubbling) is difficult to quantify in situ due to uneven spatial distribution and temporally irregular gas eruptions. This heterogeneous distribution of CH4 ebullition also creates error when scaling up field measurements for flux estimations. This thesis reviews estimates of CH4 contribution to the atmosphere by freshwater lakes presented in current literature and identifies knowledge gaps and the logistical difficulties in sampling CH 4 flux via ebullition (bubbling). My research investigates various imaging parameters of space-borne synthetic aperture radar (SAR) to constrain current CH4 emissions from northern lakes. In a GIS spatial analysis of lakes on the northern Seward Peninsula, Alaska, comparing field data of ebullition to SAR, I found that SAR L-band backscatter from lake ice was high from lakes with CH4 bubbles trapped by lake ice and low from lakes with low ebullition activity. The 'roughness' component of a Pauli polarimetric decomposition of quad-pol SAR showed a significant correlation with the percentage of lake ice area containing CH4 bubbles and with CH4 ebullition flux. This indicates that the mechanism of SAR scattering from ebullition bubbles trapped by lake ice is single bounce. I conclude that SAR remote sensing could improve our ability to quantify lake ebullition at larger spatial scales than field measurements alone, could offer between-lake comparison of CH 4 ebullition activity, and is a potential tool for developing regional estimations of lake-source CH4

Sagavanirktok River Spring Breakup Observations 2015

Alaska’s economy is strongly tied to oil production, with most of the petroleum coming from the Prudhoe Bay oil fields. Deadhorse, the furthest north oil town on the Alaska North Slope, provides support to the oil industry. The Dalton Highway is the only road that connects Deadhorse with other cities in Interior Alaska. The road is heavily used to move supplies to and from the oil fields. In late March and early April 2015, the Dalton Highway near Deadhorse was affected by ice and winter overflow from the Sagavanirktok River, which caused the road’s closure two times, for a total of eleven days (four and seven days, respectively). In mid-May, the Sagavanirktok River at several reaches flooded the Dalton from approximately milepost (MP) 394 to 414 (Deadhorse). The magnitude of this event, the first recorded since the road was built in 1976, was such that the Dalton was closed for nearly three weeks. During that time, a water station and several pressure transducers were installed to track water level changes on the river. Discharge measurements were performed, and water samples were collected to estimate suspended sediment concentration. Water levels changed from approximately 1 m near MP414 to around 3 m at the East Bank station, located on the river’s east bank (about MP392). Discharge measurements ranged from nearly 400 to 1560 m3/s, with the maximum measurement roughly coinciding with the peak. Representative sediment sizes (D50) ranged from 10 to 14 microns. Suspended sediment concentrations ranged from a few mg/L (clear water in early flooding stages) to approximately 4500 mg/L. An analysis of cumulative runoff for two contiguous watersheds—the Putuligayuk and Kuparuk—indicates that 2014 was a record-breaking year in both watersheds. Additionally, an unseasonable spell of warm air temperatures was recorded during mid-February to early March. While specific conditions responsible for this unprecedented flood are difficult to pinpoint, runoff and the warm spell certainly contributed to the flood event.ABSTRACT ..................................................................................................................................... i LIST OF FIGURES ....................................................................................................................... iii LIST OF TABLES .......................................................................................................................... v ACKNOWLEDGMENTS AND DISCLAIMER .......................................................................... vi CONVERSION FACTORS, UNITS, WATER QUALITY UNITS, VERTICAL AND HORIZONTAL DATUM, ABBREVIATIONS, AND SYMBOLS ............................................ vii ABBREVIATIONS, ACRONYMS, AND SYMBOLS ................................................................ ix 1 INTRODUCTION ................................................................................................................... 1 2 STUDY AREA ........................................................................................................................ 5 3 METHODOLOGY AND EQUIPMENT ................................................................................ 9 3.1 Ice Elevations Prior to Breakup (GPS Surveys)............................................................. 10 3.2 X-Band SAR Analysis ................................................................................................... 11 3.3 Water Levels .................................................................................................................. 12 3.4 Acoustic Doppler Current Profiler ................................................................................. 14 3.5 Discharge Measurements ............................................................................................... 15 3.6 Suspended Sediments ..................................................................................................... 17 4 RESULTS .............................................................................................................................. 18 4.1 Air Temperature ............................................................................................................. 18 4.2 Annual Precipitation ....................................................................................................... 20 4.3 Cold Season Precipitation .............................................................................................. 22 4.4 Warm Season Precipitation ............................................................................................ 23 4.5 Surface Water Hydrology............................................................................................... 27 4.5.1 Ice Elevations .......................................................................................................... 28 4.5.2 X-Band SAR Analysis ............................................................................................ 31 4.5.3 Water Levels ........................................................................................................... 37 4.5.4 Discharge Measurements ........................................................................................ 43 4.5.5 Additional Field Observations ................................................................................ 49 4.5.6 Cumulative Volumetric Warm Season Runoff ....................................................... 59 4.5.7 Suspended Sediment ............................................................................................... 63 5 CONCLUSIONS ................................................................................................................... 66 6 REFERENCES ...................................................................................................................... 68 7 APPENDICES ....................................................................................................................... 72 ii

Decadal-scale hotspot methane ebullition within lakes following abrupt permafrost thaw

Thermokarst lakes accelerate deep permafrost thaw and the mobilization of previously frozen soil organic carbon. This leads to microbial decomposition and large releases of carbon dioxide (CO2) and methane (CH4) that enhance climate warming. However, the time scale of permafrost-carbon emissions following thaw is not well known but is important for understanding how abrupt permafrost thaw impacts climate feedback. We combined field measurements and radiocarbon dating of CH4 ebullition with (a) an assessment of lake area changes delineated from high-resolution (1–2.5 m) optical imagery and (b) geophysical measurements of thaw bulbs (taliks) to determine the spatiotemporal dynamics of hotspot-seep CH4 ebullition in interior Alaska thermokarst lakes. Hotspot seeps are characterized as point-sources of high ebullition that release 14C-depleted CH4 from deep (up to tens of meters) within lake thaw bulbs year-round. Thermokarst lakes, initiated by a variety of factors, doubled in number and increased 37.5% in area from 1949 to 2009 as climate warmed. Approximately 80% of contemporary CH4 hotspot seeps were associated with this recent thermokarst activity, occurring where 60 years of abrupt thaw took place as a result of new and expanded lake areas. Hotspot occurrence diminished with distance from thermokarst lake margins. We attribute older 14C ages of CH4 released from hotspot seeps in older, expanding thermokarst lakes (14CCH4 20 079 ± 1227 years BP, mean ± standard error (s.e.m.) years) to deeper taliks (thaw bulbs) compared to younger 14CCH4 in new lakes (14CCH4 8526 ± 741 years BP) with shallower taliks. We find that smaller, non-hotspot ebullition seeps have younger 14C ages (expanding lakes 7473 ± 1762 years; new lakes 4742 ± 803 years) and that their emissions span a larger historic range. These observations provide a first-order constraint on the magnitude and decadal-scale duration of CH4-hotspot seep emissions following formation of thermokarst lakes as climate warms

Lack of clinical AIDS in SIV-infected sooty mangabeys with significant CD4+ T cell loss is associated with double-negative T cells

SIV infection of natural host species such as sooty mangabeys results in high viral replication without clinical signs of simian AIDS. Studying such infections is useful for identifying immunologic parameters that lead to AIDS in HIV-infected patients. Here we have demonstrated that acute, SIV-induced CD4+ T cell depletion in sooty mangabeys does not result in immune dysfunction and progression to simian AIDS and that a population of CD3 +CD4-CD8- T cells (double-negative T cells) partially compensates for CD4+ T cell function in these animals. Passaging plasma from an SIV-infected sooty mangabey with very few CD4 + T cells to SIV-negative animals resulted in rapid loss of CD4 + T cells. Nonetheless, all sooty mangabeys generated SIV-specific antibody and T cell responses and maintained normal levels of plasma lipopolysaccharide. Moreover, all CD4- low sooty mangabeys elicited a de novo immune response following influenza vaccination. Such preserved immune responses as well as the low levels of immune activation observed in these animals were associated with the presence of double-negative T cells capable of producing Th1, Th2, and Th17 cytokines. These studies indicate that SIV-infected sooty mangabeys do not appear to rely entirely on CD4+ T cells to maintain immunity and identify double-negative T cells as a potential subset of cells capable of performing CD4+ T cell-like helper functions upon SIV-induced CD4+ T cell depletion in this species

Expanding the Repertoire of Modified Vaccinia Ankara-Based Vaccine Vectors via Genetic Complementation Strategies

nkara (MVA) is a safe, highly attenuated orthopoxvirus that is being developed as a recombinant vaccine vector for immunization against a number of infectious diseases and cancers. However, the expression by MVA vectors of large numbers of poxvirus antigens, which display immunodominance over vectored antigens-of-interest for the priming of T cell responses, and the induction of vector-neutralizing antibodies, which curtail the efficacy of subsequent booster immunizations, remain as significant impediments to the overall utility of such vaccines. Thus, genetic approaches that enable the derivation of MVA vectors that are antigenically less complex may allow for rational improvement of MVA-based vaccines. during infection, and that the processes governing the generation of antiviral antibody responses are more readily saturated by viral antigen than are those that elicit CD8+ T cell responses. deletion, enables the generation of novel replication-defective MVA mutants and expands the repertoire of genetic viral variants that can now be explored as improved vaccine vectors

CD4saurus Rex &HIVelociraptor vs. development of clinically useful immunological markers: a Jurassic tale of frozen evolution

One of the most neglected areas of everyday clinical practice for HIV physicians is unexpectedly represented by CD4 T cell counts when used as an aid to clinical decisions. All who care for HIV patients believe that CD4+ T cell counts are a reliable method to evaluate a patient immune status. There is however a fatalistic acceptance that besides its general usefulness, CD4+ T cell counts have relevant clincal and immunological limits. Shortcomings of CD4 counts appear in certain clinical scenarios including identification of immunological nonresponders, subsequent development of cancer on antiretroviral teatment, failure on tretment simplification. Historical and recently described parameters might be better suited to advise management of patients at certain times during their disease history. Immunogenotypic parameters and innate immune parameters that define progression as well as immune parameters associated with immune recovery are available and have not been introduced into validation processes in larger trials. The scientific and clinical community needs an effort in stimulating clinical evolution of immunological tests beyond "CD4saurus Rex" introducing new parameters in the clinical arena after appropriate validatio

A Novel CCR5 Mutation Common in Sooty Mangabeys Reveals SIVsmm Infection of CCR5-Null Natural Hosts and Efficient Alternative Coreceptor Use In Vivo

In contrast to HIV infection in humans and SIV in macaques, SIV infection of natural hosts including sooty mangabeys (SM) is non-pathogenic despite robust virus replication. We identified a novel SM CCR5 allele containing a two base pair deletion (Δ2) encoding a truncated molecule that is not expressed on the cell surface and does not support SIV entry in vitro. The allele was present at a 26% frequency in a large SM colony, along with 3% for a CCR5Δ24 deletion allele that also abrogates surface expression. Overall, 8% of animals were homozygous for defective CCR5 alleles and 41% were heterozygous. The mutant allele was also present in wild SM in West Africa. CD8+ and CD4+ T cells displayed a gradient of CCR5 expression across genotype groups, which was highly significant for CD8+ cells. Remarkably, the prevalence of natural SIVsmm infection was not significantly different in animals lacking functional CCR5 compared to heterozygous and homozygous wild-type animals. Furthermore, animals lacking functional CCR5 had robust plasma viral loads, which were only modestly lower than wild-type animals. SIVsmm primary isolates infected both homozygous mutant and wild-type PBMC in a CCR5-independent manner in vitro, and Envs from both CCR5-null and wild-type infected animals used CXCR6, GPR15 and GPR1 in addition to CCR5 in transfected cells. These data clearly indicate that SIVsmm relies on CCR5-independent entry pathways in SM that are homozygous for defective CCR5 alleles and, while the extent of alternative coreceptor use in SM with CCR5 wild type alleles is uncertain, strongly suggest that SIVsmm tropism and host cell targeting in vivo is defined by the distribution and use of alternative entry pathways in addition to CCR5. SIVsmm entry through alternative pathways in vivo raises the possibility of novel CCR5-negative target cells that may be more expendable than CCR5+ cells and enable the virus to replicate efficiently without causing disease in the face of extremely restricted CCR5 expression seen in SM and several other natural host species

Safety and Reactogenicity of Canarypox ALVAC-HIV (vCP1521) and HIV-1 gp120 AIDSVAX B/E Vaccination in an Efficacy Trial in Thailand

A prime-boost vaccination regimen with ALVAC-HIV (vCP1521) administered intramuscularly at 0, 4, 12, and 24 weeks and gp120 AIDSVAX B/E at 12 and 24 weeks demonstrated modest efficacy of 31.2% for prevention of HIV acquisition in HIV-uninfected adults participating in a community-based efficacy trial in Thailand.Reactogenicity was recorded for 3 days following vaccination. Adverse events were monitored every 6 months for 3.5 years, during which pregnancy outcomes were recorded. Of the 16,402 volunteers, 69% of the participants reported an adverse event any time after the first dose. Only 32.9% experienced an AE within 30 days following any vaccination. Overall adverse event rates and attribution of relatedness did not differ between groups. The frequency of serious adverse events was similar in vaccine (14.3%) and placebo (14.9%) recipients (p = 0.33). None of the 160 deaths (85 in vaccine and 75 in placebo recipients, p = 0.43) was assessed as related to vaccine. The most common cause of death was trauma or traffic accident. Approximately 30% of female participants reported a pregnancy during the study. Abnormal pregnancy outcomes were experienced in 17.1% of vaccine and 14.6% (p = 0.13) of placebo recipients. When the conception occurred within 3 months (estimated) of a vaccination, the majority of these abnormal outcomes were spontaneous or elective abortions among 22.2% and 15.3% of vaccine and placebo pregnant recipients, respectively (p = 0.08). Local reactions occurred in 88.0% of vaccine and 61.0% of placebo recipients (p<0.001) and were more frequent after ALVAC-HIV than AIDSVAX B/E vaccination. Systemic reactions were more frequent in vaccine than placebo recipients (77.2% vs. 59.8%, p<0.001). Local and systemic reactions were mostly mild to moderate, resolving within 3 days.The ALVAC-HIV and AIDSVAX B/E vaccine regimen was found to be safe, well tolerated and suitable for potential large-scale use in Thailand.ClinicalTrials.govNCT00223080

Innovative approach to control of an emulsion loader

In this thesis, the work to develop the vision system for the Emulsion Loading Automation Project (ELAP) is presented. The ELAP project was a collaborative effort among various team members to develop an intelligent system to automate the complex task of an emulsion loader used in underground mining operations. The vision system was tasked with the challenging imaging requirements of locating and identifying drill-holes in the rock face of an underground mine, and to provide visual guidance for the hose guide to load the drill-holes with emulsion. The first part of this thesis outlines the development of image processing algorithms to segment and identify drill-holes present in an image acquired from a video stream. This involved applying thresholding and morphological techniques to preprocess the image to improve contrast, separate touching objects, and fill any holes. A pattern recognition model was then developed using drill-hole feature data to classify segmented objects as either drill-holes or background artifacts. The second part of this thesis presents the work performed for visual guidance to position the robotic boom in front of a drill-hole for loading. Using a camera mounted to the end of a robotic boom, camera and hand-eye calibration routines were developed to transform the drill-hole image object to both the camera and end-effector reference frames. A visual guidance algorithm was then developed using the calibration parameters to visual servo the robotic boom to a drill-hole for loading. Finally, testing performed in an underground mine after the critical subsystems were integrated and operational, verified the vision system operation as designed