Physical Sciences and Mathematics Commons^™

Two Fields, One Pellet: Combining Demographics And Population Genetics Through Non-Invasive Sampling Of Snowshoe Hare Fecal Pellets In Michigan., Genelle Nicole Uhrig

Theses and Dissertations

As climate continues to change at a rapid rate, species are increasingly vulnerable to the resulting environmental changes. This is especially true for species whose fitness is closely linked to climate-associated environmental conditions. One of these vulnerable species is snowshoe hare, Lepus americanus, who depends on the timing and duration of snowfall to provide camouflage when they go through seasonal pelage changes from brown in the summer to white in the winter. Whereas snowshoe hare are stable across the core of their range, populations along the southern range edge are experiencing declines due to climate driven environmental changes that cause …

Image Encryption And Stegenography Based On Computational Single Pixel Imaging, Hossein Ghanbari Ghalehjoughi

Theses and Dissertations

Multiple layers of information security are introduced based on computational ghost imaging (CGI). We show, in the first step, that it is possible to design a very reliable image encryption scheme using 3D computational ghost imaging with two single-pixel detectors sending data through two channels. Through the Normalized Root Mean Square scale, it is then shown that a further level of security can be achieved by merging data-carrying channels into one and using a coded order for their placement in the sequence of bucket data carried by the single channel. Yet another layer of security is introduced through hiding the …

A Game Modeling Of A Closed-Loop Supply Chain In A Water-Energy Nexus: Technology Advancement, Market Competition And Capacity Limit, Nabeel Hamoud

Theses and Dissertations

Water and energy are two scarce and concerning resources interconnected in the water-energy nexus. In the nexus, production of energy needs water, and production of water needs energy. For better management of these resources in the nexus, this research considers a supply chain that consists of water suppliers, power suppliers, and consumers of these commodities. In the chain, water suppliers purchase power from power suppliers, and power suppliers purchase water from water suppliers. Other consumers can also buy these resources at the water and power markets. Each firm tries to maximize its own profit. The suppliers of water and power …

Quantifying The Variability In Heavy Metal Concentrations In Produce Grown In Metals-Rich Soil, Harris Lowell Byers

Theses and Dissertations

Childhood Pb exposure is associated with a multitude of poor health outcomes. In food-insecure areas, growing fresh produce in residential backyard gardens is one option for parents; however, commonly grown crops are known to accumulate Pb in consumable tissues when grown in metals-rich soils. A variety of produce representing a continuum of consumable tissues were grown in soils collected from two residential vegetable gardens, a former metal foundry, and commercial topsoil purchased from a local hardware store. The concentrations of heavy metals in crop tissues were measured with custom wavelength dispersive X-ray Fluorescence (WD-XRF) spectroscopy and portable energy dispersive X-ray …

The Dynamics And Speciation Of Arsenic In Drinking Water Wells In Eastern Wisconsin, Evvan Plank

Theses and Dissertations

Arsenic typically develops in Eastern Wisconsin groundwater as a result of oxidation of sulfide bearing minerals in the limestone bedrock (Schreiber et al. 2000). Naturally occurring arsenic exists in groundwater as oxyanions which have two oxidation states, As(III) and As(V). Under ambient pH conditions As(V) is primarily present as an anion (i.e., H2AsO4-) while As(III) tends to be uncharged (i.e., H3AsO3), making it much more difficult to remove through the existing treatment techniques such as adsorption and reverse osmosis (RO). Although many studies exist establishing arsenic concentrations across Wisconsin, there is a lack of investigations into the concentrations of each …

Seasonal Offshore/Inshore Migration Of Round Gobies, Erik Carlson

Theses and Dissertations

Since the invasion of round gobies (Neogobius melanostomus) in Lake Michigan, they have become integrated into both the nearshore and offshore food webs. Round gobies can be found in shallower water (<20 m) during the summer, but they disappear from these depths in early fall. They have been collected, occasionally, offshore in depths greater than 70 m during fall and early spring. These observations and other anecdotal evidence indicate that round goby migrate offshore during the fall and return in the spring. To study this, a large remotely operated vehicle (ROV) was used to conduct video transects offshore at various depths. The offshore sampling showed that round gobies migrated away from nearshore habitat in early October and were almost exclusively found deeper than 20 m by November. The round gobies remained offshore (>30 m) until mid-May, when they began the return to nearshore habitat. The cues to start the offshore and return migrations were not the focus of this project, but the fall offshore migrations coincided with decreasing temperatures nearshore in the fall, and in spring, the offshore movement of the thermal bar. The offshore migration in fall provide an increase in forage opportunity for deep, cold-water predators such as …

Cloud Based Iot Architecture, Nathan Roehl

Theses and Dissertations

The Internet of Things (IoT) and cloud computing have grown in popularity over the past decade as the internet becomes faster and more ubiquitous. Cloud platforms are well suited to handle IoT systems as they are accessible and resilient, and they provide a scalable solution to store and analyze large amounts of IoT data. IoT applications are complex software systems and software developers need to have a thorough understanding of the capabilities, limitations, architecture, and design patterns of cloud platforms and cloud-based IoT tools to build an efficient, maintainable, and customizable IoT application. As the IoT landscape is constantly changing, …

An Implementation Of Fully Convolutional Network For Surface Mesh Segmentation, Taiyu Zhang

Theses and Dissertations

This thesis presents an implementation of a 3-Dimensional triangular surface mesh segmentation architecture named Shape Fully Convolutional Network, which is proposed by Pengyu Wang and Yuan Gan in 2018. They designed a deep neural network that has a similar architecture as the Fully Convolutional Network, which provides a good segmentation result for 2D images, on 3D triangular surface meshes. In their implementation, 3D surface meshes are represented as graph structures to feed the network. There are three main barriers when applying the Fully Convolutional Network to graph-based data structures.

• First, the pooling operation is much harder to apply to …

Chemical Self-Assembly Strategies Toward The Design Of Molecular Electronic Circuits, Dustin Olson

Theses and Dissertations

The field of molecular electronics is generally divided into one of two major categories, the first focusing on the unique functionalization of single molecules to produce electronic behavior, the other utilizing large assemblies of molecules to produce electronic behavior. The former approach is largely attributed to the seminal paper by Aviram and Ratner in which they proposed a molecular donor-bridge-acceptor (D-B-A) type architecture could lead to single molecule rectification producing electronic effects similar to conventional semiconductor based diodes. Extensive research has been carried out in both fields as it is foreseen that new approaches to electronics miniaturization will be necessary …

The Curious Case Of Nad-Cleaving Nudix Hydrolases, Atreyei Ray

Theses and Dissertations

Nudix proteins are members of a large family of homologous enzymes that hydrolyze nucleoside diphosphates linked to other compounds (x). These enzymes have catalytic activity on a wide range of substrates such as dNTPs (both canonical and their oxidized forms), nucleotide sugars, alcohols, dinucleoside polyphosphates, dinucleotide cofactors, and nucleoside diphosphates linked to RNA. The bacterial genome encodes around 13, while the human genome encodes for 22 such nudix proteins.

The E. coli genome encodes for a mutT mutator gene, the progenitor of the family expressing the MutT pyrophosphohydrolase (NudA) protein (Treffers et al., 1954; Bhatnagar et al., 1988). The enzyme …

Scatter Reduction By Exploiting Behaviour Of Convolutional Neural Networks In Frequency Domain, Carlos Ivan Jerez Gonzalez

Theses and Dissertations

In X-ray imaging, scattered radiation can produce a number of artifacts that greatly

undermine the image quality. There are hardware solutions, such as anti-scatter grids.

However, they are costly. A software-based solution is a better option because it is

cheaper and can achieve a higher scatter reduction. Most of the current software-based

approaches are model-based. The main issues with them are the lack of flexibility, expressivity, and the requirement of a model. In consideration of this, we decided to apply

Convolutional Neural Networks (CNNs), since they do not have any of the previously

mentioned issues.

In our approach we split …

Probing The Early Steps In The Catalytic Reduction Of Nitrite To Ammonia, Catalyzed By Cytochrome C Nitrite Reductase, Md Mahbbat Ali

Theses and Dissertations

Cytochrome c Nitrite Reductase (ccNiR) is a periplasmic, decaheme homodimeric enzyme that catalyzes the six-electron reduction of nitrite to ammonia. Under standard assay conditions catalysis proceeds without detected intermediates, and it’s been assumed that this is also true in vivo. However, this report demonstrates that in vitro it’s possible to trap putative intermediates by controlling the electrochemical potential at which reduction takes place. Such experiments provide valuable insights regarding ccNiR-catalyzed nitrite ammonification.

UV/Vis spectropotentiometry showed that nitrite-loaded Shewanella oneidensis ccNiR is reduced in a concerted 2-electron step to generate an {FeNO}7 moiety at the active site, with an associated midpoint …

Optimizing Hydrogen Sulfide Removal And Biogas Production Using The Water Wash Method, Brian Leightner

Theses and Dissertations

Biogas forms from decomposing organic material in agricultural digesters, landfills, and wastewater treatment plant digesters. Biogas is mostly composed of methane, and can be used as a carbon-based fuel. Microorganisms that consume organics in these waste streams also produce hydrogen sulfide (H2S) as part of the biogas, in varying trace amounts. H2S is corrosive to engines and pipes for machinery, a human health hazard when inhaled, and an aquatic hazard when dissolved in water. Water washing is an absorption process that dissolves hydrogen sulfide and other water soluble compounds in this process and carries it away from the gas, thereby …

Part I: A Concise Asymmetric Synthesis Of Microtubule Inhibitor Tryprostatin B Part Ii: Synthesis And Biological Assessment Of Histone Deacetylase (Hdac) Inhibitors Part Iii: Acid Catalyzed Reactions Of Aromatic Ketones With Ethyl Diazoacetate, Md Mizzanoor Rahaman

Theses and Dissertations

PART I: A CONCISE ASYMMETRIC SYNTHESIS OF MICROTUBULE INHIBITOR TRYPROSTATIN B

Tryprostatin (TPS) A and B, microtubule inhibitor, are the members of a family of prenylated Trp-Pro diketopiperzine alkaloids. These two natural products were isolated in 1995 from the fermentation broth of Aspergillus fumigatus BM939 by Osada and coworkers. TPS and related diketopiperazine containing compounds such as phenylahistins, spirotryprostatins, and cyclotryprostatins are inhibitors of the mammalian cell cycle. They prevent cell cycle progression at the G2/M phase through a unique mechanism consisting of inhibiting the interaction between microtubule assisted proteins (MAP-2) and the C-terminal end of tubulin. TPS A and …

Controlling And Manipulating Microscopic Particles In Solution By Using Various Electric Field Geometries, Xavier Sacro Udad

Theses and Dissertations

Progress in micro- and nanotechnologies depends on our capability of manipulating and interacting with microscopic particles and nanosize material. A promising approach towards this goal is the use of electric fields, which are the dominant forces at the molecular length scale. One technique for trapping nanoparticles in solution uses an externally controlled electric field, generated by two electrode pairs, to counteract the Brownian motion of a single, selected particle. Unlike other trapping tools, such as optical tweezers or magnetic tweezers, this approach scales favorably with particle size, down to the level of a single molecule. However, it depends on real-time …

Conditional Survival Analysis For Concrete Bridge Decks, Azam Nabizadeh, Habib Tabatabai, Mohammad A. Tabatabai

Civil and Environmental Engineering Faculty Articles

Bridge decks are a significant factor in the deterioration of bridges, and substantially affect long-term bridge maintenance decisions. In this study, conditional survival (reliability) analysis techniques are applied to bridge decks to evaluate the age at the end of service life using the National Bridge Inventory records. As bridge decks age, the probability of survival and the expected service life would change. The additional knowledge gained from the fact that a bridge deck has already survived a specific number of years alters (increases) the original probability of survival at subsequent years based on the conditional probability theory. The conditional expected …

Effects Of Stormwater Green Infrastructure On Watershed Outflow: Does Spatial Distribution Matter?, Benjamin Fahy, Heejun Chang

International Journal of Geospatial and Environmental Research

Green Stormwater Infrastructure (GSI) has become a popular method in urban stormwater management. We examined how spatial distribution of GSI affected rainfall-runoff relationships in a recently developed neighborhood in Gresham, Oregon, USA for the 2017-2018 water year. Runoff ratio, peak discharge, and flashiness were compared under four precipitation scenarios (of differing intensity and duration) and different spatial arrangements of GSI. Distributed GSI reduced runoff ratio (10 - 20%), peak discharge (26 - 68%), and flashiness index (56 - 70%). Distributed GSI outperformed centralized structures for all metrics, reducing runoff ratio (22 - 32%), peak discharge 67 to 69%, and flashiness …

Loop Currents And Anomalous Hall Effect From Time-Reversal Symmetry-Breaking Superconductivity On The Honeycomb Lattice, P.M.R. Brydon, D.S.L. Abergel, Daniel Agterberg, Victor M. Yakovenko

Physics Faculty Articles

We study a tight-binding model on the honeycomb lattice of chiral d-wave superconductivity that breaks time-reversal symmetry. Because of its nontrivial sublattice structure, we show that it is possible to construct a gauge-invariant time-reversal-odd bilinear of the pairing potential. The existence of this bilinear reflects the sublattice polarization of the pairing state. We show that it generates persistent loop current correlations around each lattice site and opens a topological mass gap at the Dirac points, resembling Haldane’s model of the anomalous quantum Hall effect. In addition to the usual chiral d-wave edge states, there also exist electronlike edge …

Light Scattering In Diffraction Limit Infrared Imaging, Ghazal Azarfar

Theses and Dissertations

Fourier Transform Infrared (FTIR) microspectroscopy is a noninvasive technique for chemical imaging of micrometer size samples. Employing an infrared microscope, an infrared source and FTIR spectrometer coupled to a microscope with an array of detectors (128 x 128 detectors), enables collecting combined spectral and spatial information simultaneously. Wavelength dependent images are collected, that reveal biochemical signatures of disease pathology and cell cycle. Single cell biochemistry can be evaluated with this technique, since the wavelength of light is comparable to the size of the objects of interest, which leads to additional spectral and spatial effects disturb biological signatures and can confound …

Development Of Indicators For Human Fecal Pollution Using Deep-Sequencing Of Microbial Communities, Shuchen Feng

Theses and Dissertations

The gut microbiome is shaped by both host physiology and environmental factors, which results in unique communities that contain certain members specific to a host. Microbial source tracking (MST) methods that rely on host-specific fecal microorganisms have been applied to detect human fecal pollution over the past two decades. The most common approach uses quantitative polymerase chain reaction (qPCR) to amplify certain sequences of these microorganisms, or human fecal markers. To date, most bacterial human fecal markers have focused on the HF183 cluster within the genus Bacteroides. However, cross-reactions with animals or variable Bacteroides abundance in humans have been found. …

Sedimentological And Geochemical Analysis Of Deep-Water Deposits In The Mojón De Hierro Formation At Arroyo Garrido, Tepuel-Genoa Basin, Patagonia, Argentina, Natalie Beatrice Mcnall

Theses and Dissertations

The Earth has had multiple Phanerozoic glacial intervals but the Late Paleozoic Ice Age (LPIA) was its longest and most extensive, lasting from the Late Devonian (~372 Ma) until the Late Permian (~254 Ma). The LPIA is the last complete climate shift from a greenhouse to icehouse and back to a greenhouse state and the only one to occur on a biologically complex Earth. Therefore, it provides perspectives on deep-time climatic transitions, the parameters controlling them, and the Earth’s physical, chemical and biological responses to such climate changes. Research on mid to high-latitude deposits in Gondwana provides evidence that the …

Unraveling Plague Ecology Through Vector And Host Genetics, Rachael Marie Giglio

Theses and Dissertations

The transmission of vector-borne diseases involves complex interactions between vectors and their host species. These complex host-parasite interactions can be difficult to study with traditional, field-based methods. My dissertation aims to use a population genomics approach to elucidate transmission pathways of plague among prairie dog colonies. Plague is a flea-borne, zoonotic disease caused by the bacterium Yersinia pestis. It is infamous for causing the Black Death (1347-1353), one of the most devastating pandemics in human history. Since its emergence in North America around 1900, plague has spread to native rodents, thus creating a sylvatic cycle. Prairie dogs (Cynomys spp.) are …

Multi-Tap Extended Kalman Filter For A Periodic Waveform With Uncertain Frequency And Waveform Shape, And Data Dropouts, Justin Saboury

Theses and Dissertations

Gait analysis presents the challenge of detecting a periodic waveform in the presence of time varying frequency, amplitude, DC offset, and waveform shape, with acquisition gaps from partial occlusions. The combination of all of these components presents a formidable challenge. The Extended Kalman Filter for this system model has six states, which makes it weakly identifiable within the standard Extended Kalman Filter network. In this work, a novel robust Extended Kalman Filter-based approach is presented and evaluated for clinical use in gait analysis. The novel aspect of the proposed method is that at each sample, the present and several past …

Optimizing Self-Healing Wind Turbine Blades Utilizing Dicyclopentadiene Infused Vascular Networks, Giovanni Lewinski

Theses and Dissertations

Self-healing wind turbine blades can reduce costs associated with maintenance, repair, and energy compensation. Self-healing is the ability to sustain and recover from damage autonomously. The self-healing presented in this paper uses the reaction of two agents Dicyclopentadiene, DCPD, and Grubbs’ first-generation catalyst, henceforward known as a catalyst to fuel this recovery. DCPD is housed as a liquid isolated from the catalyst until a damaging event occurs, causing the two agents to mix and solidify to form the thermoset Polydicyclopentadiene, PDCPD. We discuss the efforts made to optimize the self-healing properties of wind turbine blades and provide new systems to …

A Pedagogy Of Techno-Social Relationality: Ethics And Digital Multimodality In The Composition Classroom, Kristin M. Ravel

Theses and Dissertations

I bring together the relational ethics of feminist critical theory with approaches of multimodal rhetoric to examine the ethical implications of composing on social media platforms. Most social media platforms are designed to value consumerism, efficiency, quantity of web traffic, and constant synchronous response over concerns of responsible and critical communication. I propose a rhetorical approach of techno-social relationality (TSR) as an intervention against such corporate-minded design. Through this approach, I argue that civil engagement is not limited to people’s social responsibilities but rather is entwined in complex, material-technical contexts. By considering the responsibility of our machines as much as …

Scattering In Infrared Microspectroscopy, Alex James Schofield

Theses and Dissertations

Mid-infrared absorbance spectra obtained from spatially inhomogeneous and finite samples often contain scattering effects that undermine the Beer-Lambert law assumption. Such spectra contain generally non-linear contributions from the scattering material’s complex refractive index, which may result in derivative-like bands with shifted peak positions. It is first shown using Mie theory for spherical scatterers, that these band distortions may be interpreted and accurately modeled by Fano theory when the imaginary part of its complex dielectric function is small and Lorentzian in nature—as is the case for many biological media. By fitting Fano line shapes to isolated absorbance bands, recovery of the …

A Minimal Time Solution To The Firing Squad Synchronization Problem With Von Neumann Neighborhood Of Extent 2, Kathryn Boddie

Theses and Dissertations

Cellular automata provide a simple environment in which to study global behaviors. One example of a problem that utilizes cellular automata is the Firing Squad Synchronization Problem, first proposed in 1957. This paper provides an overview of the standard Firing Squad Synchronization Problem and a commonly used technique in solving it. This paper also provides a statement of a new extension of the Standard Firing Squad Synchronization Problem to a different neighborhood definition - a Von Neumann neighborhood of extent 2. An 8 state 651 rule minimal time solution to the extended problem is described, presented and proven, along with …

Model Augmented Deep Neural Networks For Medical Image Reconstruction Problems, Hongquan Zuo

Theses and Dissertations

Solving an ill-posed inverse problem is difficult because it doesn't have a unique solution. In practice, for some important inverse problems, the conventional methods, e.g. ordinary least squares and iterative methods, cannot provide a good estimate. For example, for single image super-resolution and CT reconstruction, the results of these conventional methods cannot satisfy the requirements of these applications. While having more computational resources and high-quality data, researchers try to use machine-learning-based methods, especially deep learning to solve these ill-posed problems. In this dissertation, a model augmented recursive neural network is proposed as a general inverse problem method to solve these …

A Study In Molecular Recognition: Synthesis Of A Β-Sheet Mimic & Quantitation Of Metal Ions In Aqueous Solutions Through Solid Supported Semi-Selective Chemosensors, Tyler G. Fenske

Theses and Dissertations

From the hydrophobic effect, which is responsible for the organization of amphipathic molecules into cellular membranes, to the highly specific hydrogen binding patterns found in DNA base pairs that keeps our genetic material “zipped up”, non-covalent and reversible interactions are critical to properly functioning biological processes. Molecular recognition is an area of study that seeks to better understand these observed phenomena. In a general sense, association of “Host” and “Guest” molecules are based on ionic forces, hydrophobic interactions, cation-π effects, π-π stacking, conformational restriction, and many others. This dissertation will primarily focus on two projects that have an emphasis on …

Visualization Of Uncertain Boundaries Of Undersea Features, Hyowon Ban, Hyo Hyun Sung

International Journal of Geospatial and Environmental Research

There have been several studies that detect, measure, analyze, and visualize the undersea features by using technologies in multiple disciplines including geography and oceanography. However, definitions of the undersea features often vary among the existing leading literature. Due to this reason the geographical boundary for a certain undersea feature is sometimes not identical among the definitions. In this study, we explore semantic uncertainty in the definitions of some undersea features and apply approaches from fuzzy-set theory and geographic information science on empirical bathymetric data to visualize the uncertain boundaries of the undersea features. Results from this study demonstrate that the …