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The Role Of Gli3 In Inflammation, Stephan Josef Matissek

Doctoral Dissertations

Inflammation is an important and healthy mechanism that our body uses for wound-healing and fighting off infections by utilizing molecular pathways of immune and non-immune cells. However, when inflammation is persistent or chronic it can have severe consequences that can lead to auto-immune diseases or cancer. Pathogen-associated molecular patterns (PAMPs), such as Lipopolysaccharide (LPS), present on gramnegative bacteria, or double-stranded RNA (dsRNA), present in RNA-viruses, were shown to be potent inducers of inflammation. These PAMPs are known ligands of Toll like receptor 4 (TLR4), activated by LPS and Toll-like receptor 3 (TLR3), activated by dsRNA which are carried on the …

Utilizing Extended Continental Shelf (Ecs) And Ocean Exploration Mapping Data For Standardized Marine Ecological Classification Of The U.S. Atlantic Margin, Derek C. Sowers

Doctoral Dissertations

Accurate maps of ocean bathymetry and seafloor habitats are needed to support effective marine ecosystem-based management (EBM) approaches. The central premise of this thesis was to synthesize geomorphological elements of large regions of the deep ocean seafloor to establish standards of characterization for ecosystem-based classification. The approach was to apply semi-automated characterization techniques on seafloor bathymetric data that were originally collected for other purposes. The purpose of generating these maps is ultimately to apply to informing ecosystem-based management for large marine regions. While seafloor classification techniques for habitat classification have been applied in shallow water and generally over more local …

Quantifying The Effects Of Land Use And Flow Regime On Metabolism In New England Streams, Daniel R. Bolster

Master's Theses and Capstones

Metabolism in aquatic ecosystems influences food webs and water quality but is potentially altered by changes in land use and flow regime. The interacting effects of storms and land use on stream metabolism are largely understudied. The goal of this study was to understand how flow variability and land use interact to affect biogeochemical cycling in headwater streams. In situ measurements of stage, water temperature, and dissolved oxygen (DO) were made in three headwater streams draining different land uses (urban, forest, and mixed) and one larger river site from July 2017 to January 2018. All streams were located in the …

Effects Of Transmission Side Lobe Interference On Multibeam Echosounder Phase Ramps, Jonathan Hamel

Master's Theses and Capstones

Many multibeam echosounders use split-aperture correlators to generate phase ramps and, subsequently, form bottom detection estimates. The noise present within the phase ramp couples directly into bottom detection estimates. This results in increased bottom detection estimate uncertainty. Known sources of phase ramp noise are additive random noise and baseline decorrelation. Anecdotally, these known sources of noise do not appear sufficient to explain phase ramp noise in several(though not all, e.g. the Simrad ME70) bottom mapping multibeam echosounders. The goal of this thesis was to explore a hypothesis for where additional phase ramp noise might be generated. In pursuit of this …

Potential For Non-Conventional Use Of Split-Beam Phase Data In Bottom Detection, Leonardo Gomes De Araujo

Master's Theses and Capstones

Because the safety of the navigation depends on accurate knowledge of the submerged features, any improvements in the ability to resolve those features are of major interest. Ultimately this reflects the bottom detection performance of the bathymetric measuring system (most commonly multibeam sonar) utilized. To this end, different algorithms for the detection of the seafloor or other targets have previously been developed, all presenting advantages and disadvantages. The two most common techniques are designed around time-series or angle-series analysis, although by far the most focus has been on time-series. The option of recording both amplitude and phase data of the …

White Discipline, Black Rebellion: A History Of American Race Riots From Emancipation To The War On Drugs, Jordan C. Burke

Doctoral Dissertations

This dissertation is a comparative analysis of American race riots, within and across historical eras, from Emancipation (1863) to the War on Drugs (1972). I argue that changes in the status of African-American citizenship produced different forms of race rioting. Examining riot events across eras reveals how ethical principles at the core of democracy are undermined in specific socio-historical contexts—especially equality of participation in collective self-governance. Congressional testimony, state-sponsored riot investigations, and archival data indicate that riots have been used historically to structure racial inequality in both political institutions and economic relations. While race riots have proven instrumental in maintaining …

Analysis Of The Population Dynamics Of Placida Dendritica And Codium Fragile In The Gulf Of Maine And A Theoretical Discussion Of Invasive Species, Seth Goodnight

Doctoral Dissertations

This dissertation examines several aspects of the biology and ecology of Codium fragile and Placida dendritica in the Gulf of Maine. Scientific interest in nonindigenous species was examined to determine if any patterns were evident that might indicate a change in the status of an invasive species. Interest in C. fragile had waned in recent years, the timing of which coincides with the decreased ecological dominance and apparent naturalization of the alga. Laboratory and field studies were combined to quantify the dynamics in the population of C. fragile and in the recruitment dynamics of P. dendritica. Results of laboratory research …

Examining The Overlooked Complexities Of School Lunch: An Investigation Into The Juncture Of Food, Schooling, And The Developing Adolescent, Eleanor Kane

Doctoral Dissertations

School lunch is a universal experience for students everywhere and yet remains largely understudied by educational researchers. This dissertation explores school lunch through the lens of adolescent identity theory, with the purpose of investigating the unarticulated and overlooked complexities inherent in the lunch block, from issues of the developing sense of self, to social and cultural meanings surrounding food, and consequences for social reproduction. I used a combination of ethnographic observations and narrative interviews at a rural New England high school, focusing on participants’ daily habits, food practices, and choices during the lunch block. Through this, I established the normative …

Characterizing Student Engagement In A Post-Secondary Developmental Mathematics Class And Exploring The Reflexivity Between Social And Sociomathematical Norms, David Fifty

Doctoral Dissertations

Traditionally, post-secondary developmental mathematics courses aspire to equip students with mathematical content knowledge needed to succeed in calculus and subsequent STEM courses. The literature shows that this goal alone is insufficient, as the emphasis on content acquisition often comes at the expense of developing higher-order skills such as argumentation, reasoning, and flexibility in mathematics problem solving (Chiaravalloti, 2009; Partanen & Kaasila, 2014; Star et al., 2015). Redesigning curricula with these additional objectives in mind requires providing students with opportunities to engage with mathematics in ways that may contrast with their past experiences or expectations. It requires changing patterns of classroom …

Magnetoelastic Excitations In Chiral Magnets, Christopher Libby

Doctoral Dissertations

Emergence of quasiparticles is a central concept in condensed matter physics. As an example, in solids, lattice vibrations lead to quantized phonon excitations, which gives rise to many exotic phenomena, including superconductivity. Things become richer in magnetic systems. Collective fluctuations about a magnetic ground state induce the spin wave excitation, whose quantized quasiparticle is dubbed as the magnon. A fundamental question is how phonon and magnon, as two separate degrees of freedom, can be coupled together. More importantly, certain symmetry, such as spatial inversion symmetry, can be broken in novel magnetic textures. It is interesting to explore whether broken symmetry …

Search For An A' Resonance In The Heavy Photon Search 2.3 Gev Data Set, Samantha Katherine Mccarty

Doctoral Dissertations

The Heavy Photon Search (HPS) experiment is based out of the Thomas Jefferson National Accelerator Laboratory in Newport News and is designed to test the potential existence of a new particle, the "heavy photon" or "A'," which has the potential to mediate interactions between dark forces and the Standard Model. HPS is designed to detect the decay of an A' particle into e⁺e⁻ pairs utilizing an electromagnetic calorimeter and a silicon-strip tracking detector. If the theory is correct, the A' could be generated using the Jefferson Lab high-luminosity electron beam incident upon a tungsten target.

In 2016, HPS collected 10.6 …

Computational Studies Of Small Molecule Transport And Binding, Yong Liu

Doctoral Dissertations

In this thesis, I have studied two classes of systems using molecular dynamics (MD) simulations as a primary approach. The first class of systems is responsible for transport of small molecules. Specically, I have investigated diffusion pathways of inhibitory gas CO within the enzyme FeFe-hydrogenase as well as water transport in articial water channels. The second class of systems are biological proteins and their interactions with ligands. I have focused on Regulators of G-protein Signaling (RGS) proteins and their binding to thiadiazolidinone (TDZD) based small-molecule inhibitors as well as phosphosdiesterase 6 (PDE6) binding with cyclic guanosine monophosphate (cGMP).

Specically, I …

Data Analysis For A Balloon Borne Compton Polarimeter, Sambid Kumar Wasti

Doctoral Dissertations

The Gamma RAy Polarimeter Experiment (GRAPE), a balloon borne Compton polarimeter for 50-500 keV gamma rays, was successfully flown for the second time in 2014. GRAPE uses events in which a photon scatters between 2 detector elements to measure the polarization of the measured photons. GRAPE consists of 24 collimated polarimeter modules. Each module is made up of 64 rectangular scintillators elements in a grid of 8 × 8 (36 plastic scintillators surrounded by 28 CsI scintillators). GRAPE was flown from Fort Sumner, New Mexico on the morning of September 26th 2014. The experiment was at float altitude for 14.4 …

Bacterial Genome And Population Dynamics With Implications For Public Health, Cooper John Park

Doctoral Dissertations

Bacterial populations are extraordinarily heterogeneous. Despite growing clonally, these populations are often composed of multiple lineages distinguished by both phenotypic and genetic differences that are caused by both allelic and whole gene variation. Such genomic mosaicism and within-species variation can significantly impact a species’ response to selective pressures from antibiotic use, vaccination, immune responses and host environment. One important process that contributes to this phenomenon is recombination, the exchange of very similar DNA sequences between strains which can result to either the addition or replacement of homologous genes. Current models of microbial recombination incorporate the null expectation that recombination is …

Does Money Really Grow On Trees? A Case Study Of The Economic And Ecosystem Outcomes Of Timber Stand Improvement In New Hampshire, Mackenzie Kalp

Master's Theses and Capstones

Timber stand improvement (TSI) is one silviculture method that landowners can apply to their forest to enhance timber quality as well as ecosystem services, such as deadwood in the form of standing deadwood, snags, and coarse woody debris (CWD). There are few studies on the economic effectiveness of TSI as a forest management practice. This research uses data collected on land owned by the Blue Hills Foundation, in Strafford, New Hampshire, to present a case study examining economic and ecosystem outcomes of TSI. Because interest rates and market prices are constantly fluctuating, we evaluated outcomes at various interest rates. We …

Automating The Boring Stuff: A Deep Learning And Computer Vision Workflow For Coral Reef Habitat Mapping, Jordan Patrick Pierce

Master's Theses and Capstones

High-resolution underwater imagery provides a detailed view of coral reefs and facilitates insight into important ecological metrics concerning their health. In recent years, anthropogenic stressors, including those related to climate change, have altered the community composition of coral reef habitats around the world. Currently the most common method of quantifying the composition of these communities is through benthic quadrat surveys and image analysis. This requires manual annotation of images that is a time-consuming task that does not scale well for large studies. Patch-based image classification using Convolutional Neural Networks (CNNs) can automate this task and provide sparse labels, but they …

Physiological And Predicted Metagenomic Analysis Of Soil Aggregate Microbial Communities Under Different Tillage Regimes, Lukas Bernhardt

Master's Theses and Capstones

Soils are spatially heterogeneous environments, and the distribution of microorganisms and carbon is organized at the scale of millimeters in soil aggregates. The physio-chemical environment within macroaggregates and microaggregates differ, which may lead to the selection of microbial communities with different survival and growth strategies- here termed life history strategies. Using an aggregate scale survey of microbial communities in agricultural soils, I show that soil aggregates harbor distinct communities with life history characteristics that align with the Yield, Acquisition, Stress tolerator framework (Y-A-S). Soils collected from an eight- year tillage experiment were isolated into four aggregate size classes and physiological …

Evaluating The Performance Of A Multi-Tile Macroalgae Cultivation Structure Using Physical And Numerical Modeling, Zachary John Davonski

Master's Theses and Capstones

A scaled physical-model of a macroalgae cultivation structure was constructed and tested in the UNH wave tank. The physical-model was a 3x3 tile array, consisting of horizontal kelp-growing longlines, node buoys, and mooring lines. The model was scaled by Froude number to a 1:180 length scale. Deployment in the UNH wave tank allowed for evaluation of the design’s performance during wave and current conditions. The model was subjected to waves and simulated currents in order to investigate its response to dynamic loading conditions, as well any anomalous behaviors such as snap loading or component interaction. The motion of the system …

Taking Nitrogen By Storm: Spatial And Temporal Controls On Nitrogen Processing In A Small Reservoir, Eliza Balch

Master's Theses and Capstones

Nitrate inputs pose a threat to aquatic ecosystems, leading to eutrophication, algal blooms, and habitat loss in downstream coastal marine and estuarine habitats. Rivers and streams can attenuate nitrogen between inputs and coastal outputs, moderating ecosystem harm. While nitrogen dynamics in streams and rivers have been studied for decades, less is known about the wetlands through which they flow, namely small reservoirs. Storms can have a large influence on nitrogen processing in reservoirs through hydrologic changes and introduction of new solute sources, but are poorly understood. To understand the spatial and temporal variability of nitrogen processing in a small reservoir, …

Using Stable Isotopes To Determine Dominant Methane Production Pathways Of Thaw Ponds In A Subarctic Peatland, Kathryn Ann Bennett

Master's Theses and Capstones

Arctic and subarctic ecosystems are currently warming faster than any other region of the globe, accelerating seasonal permafrost thaw. As thaw progresses, small water bodies can form due to slumping of the peatland surface. These ponds emit methane (CH4), a strong, radiatively important trace gas, predominantly through ebullition (bubbling). Two different types of methanogenic Archaea present in these systems produce CH4 through their respective production pathways: acetoclastic and hydrogenotrophic methanogenesis. The acetoclastic pathway forms CH4 using CH3COOH, an organic carbon (C) source while hydrogenotrophic methanogenesis uses CO2, an inorganic C source. Stable isotopes can be used to characterize the relative …

Why Does This Entity Matter? Finding Support Passages For Entities In Search, Shubham Chatterjee

Master's Theses and Capstones

In this work, we propose a method to retrieve a human-readable explanation of how a retrieved entity is connected to the information need, analogous to search snippets for document retrieval. Such an explanation is called a support passage.

Our approach is based on the idea: a good support passage contains many entities relevantly related to the target entity (the entity for which a support passage is needed). We define a relevantly related entity as one which (1) occurs frequently in the vicinity of the target entity, and (2) is relevant to the query. We use the relevance of a passage …

Environmental, Human Health, And Economic Implications Of Landfill Leachate Treatment For Pfas Removal, Danyi Feng

Master's Theses and Capstones

Landfill leachate is commonly treated offsite with municipal wastewater. This offsite leachate treatment may be limited or no longer applicable due to the increasingly stringent regulations and concerns related to PFAS discharge into the environment, resulting in development of full-scale, onsite leachate treatment facilities. To help landfills prepare for the potential shift from offsite to onsite leachate treatment for PFAS compliance, this study analyzed and compared the environmental, human health, and economic performances of a typical onsite and a typical offsite leachate treatment alternative using life cycle assessment (LCA) and life cycle cost assessment (LCCA). Two distinct functional units were …

A Multi-Scale Crystal Plasticity Finite Element Modeling Framework For Predicting Strain-Rate Sensitive Deformation Of Hexagonal Metals, William G. Feather

Master's Theses and Capstones

This work presents improvements to the methods used in crystal plasticity simulations. It shows how these improvements can be used to accurately predict the deformation behavior of two magnesium alloys, WE43, and AZ31. The first improvement to the methodology is guidance on the type of finite elements to use in explicit grain crystal plasticity simulations. This study found that quadratic tetrahedral and linear hexahedral elements are the most accurate element types included in the study. The study also concluded that tetrahedral elements are more desirable due to fast mesh generation and flexibility to describe geometries of grain structures. The second …

Geodermatophilaceae Biofilm Formation And Rock Recolonization, Krista Greengrass

Master's Theses and Capstones

The Geodermatophilaceae genera—Geodermatophilus, Blastococcus, and Modestobacter—live on rock surfaces and create biofilms that deteriorate stone architecture and monuments. Their biofilms increase the rate of weathering and erosion but are not well studied. Recently, thirteen strains were isolated, and their genomes sequenced. These new Geodermatophilaceae isolates along with Modestobacter marinus strain BC501 and Blastococcus saxobsidens strain DD2 were used in this study to evaluate biofilm formation under different environmental factors including temperature, light, and salt and heavy metal exposure. Ten isolates were used for experiments to recolonize back onto the rock substrates from which the isolates were obtained. For most of …

Obtaining A Reference For Calibrating Broadband Multibeam Seabed Backscatter, Ivan Bodra Guimaraes

Master's Theses and Capstones

Standard calibration procedures for multibeam sonars currently only address the fidelity of the bathymetric data. Equivalent effort is needed to ensure that the acquired seabed backscatter strength measurements are referenced to a similarly precise level. This thesis presents an operational method for acquiring reference seabed backscatter data utilizing multiple pre-calibrated split beam echo sounders covering a wide range (45-450 kHz) of frequencies. This is needed to cover the full range of frequencies utilized by multi-sector multibeam systems operating in continental shelf depths.The method considers both the frequency and the angle of incidence dependence of the backscatter strength of a homogenous …

Nutrient Solution Effects On Plant Health And Microbial Community Composition In Soilless Strawberry Culture, William Miller Hardesty-Dyck

Master's Theses and Capstones

Holding advantages in efficiency and geographical flexibility, soilless Controlled Environmental Agriculture (CEA) systems have emerged as economically viable and ecologically sound alternatives to field agriculture, especially in high-value fruit and vegetable production. While commercial soilless operations typically use synthetic, mineral-based nutrient solutions for plant nutrition, there is interest in incorporating more ecologically sustainable naturally derived sources. Aquaponics - the linkage of aquaculture with soilless crop production - represents one such alternative. Aquacultural effluents can provide partial to complete plant nutrition following solids removal and nitrifying biofiltration, while the incorporation of solutes into crop biomass reduces the need to discharge culture …

Immunohistochemical Characterization Of A Novel Population Of Reticular Thalamic Neurons Expressing Cholecystokinin And Type 1 Cannabinoid Receptors, Shayna Mallat

Master's Theses and Capstones

The thalamic reticular nucleus (TRN) filters somatosensory stimuli by providing inhibition to the excitatory thalamic relay nuclei, which then communicate with the cortex to appropriately integrate and respond to sensory stimuli. The TRN is also responsible for generating and maintaining sleep spindles, which are important for memory and cognition, and are disrupted in various psychiatric disorders. Previous studies have shown that the TRN is comprised of several neuronal subpopulations that carry out specific functions. These neurons can be distinguished using peptide markers such as parvalbumin (PV), somatostatin (SST), and calbindin (CB). In this thesis, I identified a novel neuronal population …

Experimental Investigation And Plasticity Modeling Of Ss316l Microtubes Under Varying Deformation Paths, Elizabeth Marie Mamros

Master's Theses and Capstones

Results for SS316L microtube experiments under combined inflation and axial loading for single and multi-loading segment deformation paths are presented along with a plasticity model to predict the associated stress and strain paths. The microtube inflation/tension machine, utilized for these experiments, creates biaxial stress states by applying axial tension or compression and internal pressure simultaneously. Two types of loading paths are considered in this paper, proportional (where a single loading path with a given axial:hoop stress ratio is followed) and corner (where an initial pure loading segment, i.e., axial or hoop, is followed by a secondary loading segment in the …

In A Nutshell: Nutritional And Environmental Factors Impacting Small Mammal Seed Selection In Northeastern Forests, Nicholas Bryan Moore

Master's Theses and Capstones

Rodents often play vital roles in their ecosystems as seed predators and dispersers and can significantly influence the succession and assembly of plant communities. We conducted seed tray experiments to assess the nutritional and environmental factors that influence selection and foraging time of three common rodent granivores: the white-footed mouse (Peromyscus leucopus), the deer mouse (Peromyscus maniculatus), and the southern red-backed vole (Myodes gapperi) for three common seeds: American beech (Fagus grandifolia), red maple (Acer rubrum), and eastern hemlock (Tsuga canadensis). This work was conducted at Bartlett Experimental Forest located within White Mountain National Forest in New Hampshire. Using mixed-effects …

Dynamic Dissolved Organic Matter Response To Increases Of Energy Availability In Forested Headwater Streams, Katherine Xiomara Perez-Rivera

Master's Theses and Capstones

Forested headwater streams receive inputs of dissolved organic matter (DOM) that can be transformed by biota as they are transported downstream. Biotic uptake of ambient DOM is difficult to assess through direct experimentation, as the fate of a specific organic compound added to a stream is unlikely to mirror that of the ambient DOM pool. Here we examined the dynamics of DOM by using a hybrid approach that combines uptake metrics of a simple organic compound with a direct assessment of the effects of adding this presumably labile organic carbon source (acetate) on the ambient DOM pool. We proposed that …