Physical Sciences and Mathematics Commons^™

An Examination Of The Current Knowledge Of Contaminants In Mangroves: Hawaii And Globally, Geoffrey Szafranski

Environmental Science and Management Professional Master's Project Reports

The geographic range of mangrove forests is shifting quickly as they expand poleward in response to climate change while simultaneously being removed from their native extent to clear space for anthropogenic land-uses. Mangrove forests are also known to be sinks for anthropogenic contamination. Yet contamination research is under-researched in mangrove ecosystems, specifically the environmental fate, effect on biodiversity, and risk to human populations from contamination in the context of these changing conditions requires further research. The goal of this thesis is to address this data gap through analysis of contamination in the literature and through an investigational survey of mangrove …

Studies On Bonding, Syntheses, And Applications Of Diarylhalonium Compounds, Shubhendu Karandikar

Dissertations and Theses

Organic compounds containing functionalized benzenoid rings have found tremendous applications in pharmaceuticals, agrochemicals, commodity chemicals, and beyond. As a result, development of methods for the synthesis of functionalized benzenoid rings has gained much attention from the synthetic community. Although many transition-metal mediated methods to functionalize benzenoid rings are known, there has been an upsurge of activity in developing protocols for decoration of benzenoid cores promoted by p-block elements. This excitement stems from the sustainability of earth-abundant elements and unique reactivity patterns observed within the p-block. Among these, transformations promoted by hypervalent halogen compounds, and especially, the diarylhalonium salts are very …

7-Deazaguanines In Dna: Functional And Structural Elucidation Of A Dna Modification System, Samanthi Herath Gedara, Andrew Gustafson, Dirk Iwata-Reuyl, Multiple Additional Authors

Chemistry Faculty Publications and Presentations

The modified nucleosides 2′-deoxy-7-cyano- and 2′-deoxy-7-amido-7-deazaguanosine (dPreQ₀ and dADG, respectively) recently discovered in DNA are the products of the bacterial queuosine tRNA modification pathway and the dpd gene cluster, the latter of which encodes proteins that comprise the elaborate Dpd restriction–modification system present in diverse bacteria. Recent genetic studies implicated the dpdA, dpdB and dpdC genes as encoding proteins necessary for DNA modification, with dpdD–dpdK contributing to the restriction phenotype. Here we report the in vitro reconstitution of the Dpd modification machinery from Salmonella enterica serovar Montevideo, the elucidation of the roles of each protein and the X-ray …

Toward Efficient Rendering: A Neural Network Approach, Qiqi Hou

Dissertations and Theses

Physically-based image synthesis has attracted considerable attention due to its wide applications in visual effects, video games, design visualization, and simulation. However, obtaining visually satisfactory renderings with ray tracing algorithms often requires casting a large number of rays and thus takes a vast amount of computation. The extensive computational and memory requirements of ray tracing methods pose a challenge, especially when running these rendering algorithms on resource-constrained platforms, and impede their applications that require high resolutions and refresh rates. This thesis presents three methods to address the challenge of efficient rendering.

First, we present a hybrid rendering method to speed …

Tools For Quantifying Bacterial Motility Using Digital Holographic Microscopy As Applied To Studying The Simulated Microgravity Environment, Jacqueline Marie Acres

Dissertations and Theses

Digital holographic microcopy (DHM) is a label-free technique that has gained attention in recent years as a tool for volumetric imaging. One application of DHM is for the study of microbial motility with the advantage being that organisms may freely move within their environment. Images created from DHM are in the form of holograms. Holograms are time recordings showing XY information with the Z information contained within. Z information can be retrieved from the holograms directly through a variety of numerical techniques or through reconstruction. Datasets generated from DHM are large and processing remains a challenging task. Here, we show …

Microbial Motility At The Bottom Of North America: Digital Holographic Microscopy And Genomic Motility Signatures In Badwater Spring, Death Valley National Park, Carl Snyder, Jakob P. Centlvre, Shrikant Bhute, Jay Nadeau, Multiple Additional Authors

Physics Faculty Publications and Presentations

Motility is widely distributed across the tree of life and can be recognized by microscopy regardless of phylogenetic affiliation, biochemical composition, or mechanism. Microscopy has thus been proposed as a potential tool for detection of biosignatures for extraterrestrial life; however, traditional light microscopy is poorly suited for this purpose, as it requires sample preparation, involves fragile moving parts, and has a limited volume of view. In this study, we deployed a field-portable digital holographic microscope (DHM) to explore microbial motility in Badwater Spring, a saline spring in Death Valley National Park, and complemented DHM imaging with 16S rRNA gene amplicon …

A Simple In Situ Method For Optimizing Settings For The Einzel Lens Elements In A Focused Ion Beam, Rich Swinford, Erik Sanchez

Physics Faculty Publications and Presentations

Ion beams have had an incredible impact on research in the past couple of decades. One major reason for this is the continued development of systems having optimal beam currents that allows one to image more clearly at different spot sizes to include higher currents that allow for faster milling. The advancements for Focused ion beam (FIB) columns have developed rapidly due to the computational optimization of lens designs. However, once a system has been produced, the optimal column settings for these lenses may change or simply become obscure. Our work involves regaining this optimization with the newly applied values …

Thin Film Deposition Of Mop, A Topological Semimetal, Robert Browning, Paul Plachinda, Raj Solanki

Physics Faculty Publications and Presentations

MoP is a topological semimetal which has drawn attention due to its unique electrical and optical properties resulting from massless electrons. In order to utilize these properties for practical applications, it is necessary to develop a technique to produce high-quality, large-scale thin films of this 2D material. We report below our initial results of growth of MoP thin films using atomic layer deposition (ALD), where the film grows layer-by-layer. These films were grown on 5 cm × 5 cm silicon oxide coated Si wafers. Resistivity versus temperature measurements show that these films are metallic and includes a partial superconducting phase. …

Picture Gorge Basalt: Internal Stratigraphy, Eruptive Patterns, And Its Importance For Understanding Columbia River Basalt Group Magmatism, Emily Bogdan Cahoon, Martin J. Streck, Anthony A.P. Koppers

Geology Faculty Publications and Presentations

The Picture Gorge Basalt (PGB) of the Columbia River Basalt Group (CRBG) has been previously thought to be limited in its eruptive volume (<3000 >km³) and thought to not extend far from its type locality. At present, PGB represents only 1.1 vol% of the CRBG with a relatively limited spatial distribution of ~10,000 km². New age data illustrate that the PGB is the earliest and longest eruptive unit compared to other main-phase CRBG formations and that some dated basaltic flows reach far (~100 km) beyond the previously mapped extent. This study focuses on extensive outcrops of …

Systems Thinking Activities Used In K-12 For Up To Two Decades, Diana Fisher, Systems Thinking Association

Complex Systems Faculty Publications and Presentations

Infusing systems thinking activities in pre-college education (grades K-12) means updating precollege education so it includes a study of many systemic behavior patterns that are ubiquitous in the real world. Systems thinking tools include those using both paper and pencil and the computer and enhance learning in the classroom making it more student-centered, more active, and allowing students to analyze problems that have been heretofore beyond the scope of K-12 classrooms. Students in primary school have used behavior over time graphs to demonstrate dynamics described in story books, like the Lorax, and created stock-flow diagrams to describe what was needed …

Long-Term Phosphorus Reduction And Phytoplankton Responses In An Urban Lake (Usa), Yuan Xiao Grund, Yangdong Pan, Mark Rosenkranz, Eugene Foster

Environmental Science and Management Faculty Publications and Presentations

Eutrophication is one of the primary factors causing harmful cyanobacteria blooms in freshwater lakes. This study investigated the long-term changes in water quality and summer phytoplankton assemblages in Oswego Lake, OR, USA, in relation to phosphorus reduction through hypolimnetic aeration and alum applications. Both water quality and phytoplankton assemblages were sampled biweekly during the summers from 2001 to 2013. The concentrations of total phosphorus, soluble reactive phosphorus, and total nitrogen decreased 66%, 93% and 31%, respectively, in response to the hypolimnetic aeration and alum treatments since 2005. Summer phytoplankton assemblages showed a 62% reduction of cyanobacteria biovolume and a …

Columbia River Rhyolites: Age-Distribution Patterns And Their Implications For Arrival, Location, And Dispersion Of Continental Flood Basalt Magmas In The Crust, Martin J. Streck, Vanessa M. Swenton, William C. Mcintosh, Matt Heizler

Geology Faculty Publications and Presentations

Columbia River province magmatism is now known to include abundant and widespread rhyolite centers even though the view that the earliest rhyolites erupted from the McDermitt Caldera and other nearby volcanic fields along the Oregon–Nevada state border has persisted. Our study covers little-studied or unknown rhyolite occurrences in eastern Oregon that show a much wider distribution of older centers. With our new data on distribution of rhyolite centers and ages along with literature data, we consider rhyolites spanning from 17.5 to 14.5 Ma of eastern Oregon, northern Nevada, and western Idaho to be a direct response to flood basalts of …

Looking Backward And Forward: Volcanology In The Years 2000, 2010, 2020, And Beyond, Jonathan Fink, Katharine Cashman

Geology Faculty Publications and Presentations

Figuring out how volcanoes work is one of the geoscience’s most complex puzzles. Clues of all sizes, shapes, and colors are scattered across every continent, the bottom of the ocean, in the atmosphere, and on the surfaces of other planets. Generations of geologists, geophysicists, geodesists, and geochemists have used field observations, laboratory measurements, and theory to fill gaps left by their predecessors. Yet critical uncertainties remain. Why do eruptions begin? What determines their intensity? What controls their frequency and style of activity? What causes them to end? These unsolved issues leave society increasingly vulnerable to volcanic disruptions. Hundreds of published …

Nanoscale Hafnium Metal-Organic Frameworks Enhance Radiotherapeutic Effects By Upregulation Of Type I Interferon And Tlr7 Expression, Eunseo Choi, Madeleine R. Landry, Nathan Pennock, Katherine Weinfurter, Multiple Additional Authors

Chemistry Faculty Publications and Presentations

Recent preclinical and clinical studies have highlighted the improved outcomes of combination radiotherapy and immunotherapy. Concurrently, the development of high-Z metallic nanoparticles as radiation dose enhancers has been explored to widen the therapeutic window of radiotherapy and potentially enhance immune activation. In this study, we evaluate folate-modified hafnium-based metal-organic frameworks (HfMOF-PEG-FA) in combination with imiquimod, a TLR7 agonist, as a well-defined interferon regulatory factor (IRF) stimulator for local antitumor immunotherapy. The enhancement of radiation dose deposition by HfMOF-PEG-FA and subsequent generation of reactive oxygen species (ROS) deregulates cell proliferation and increases apoptosis. HfMOF-PEG-FA loaded with imiquimod (HfMOF-PEG-FA@IMQ) increases DNA double-strand …

Cementation And Groundwater Chemistry In Pleistocene Paleodune Deposits Of The Central Oregon Coast, Adrienne Lynn Stephens

Dissertations and Theses

Pleistocene paleodune deposits occur along the Oregon coast, underlying coastal towns, roadways, and associated power and water infrastructure(s). Secondary cementation within these deposits provides some stability, allowing for near-vertical sea cliffs and roadcut outcrops. Yet, slope instability is a prevalent hazard observed within the paleodune deposits. Weakening of cementing agents via changes to groundwater conditions due to altered vegetation, climate change, or contamination, for example, could promote slope instability, threatening lives and infrastructure. This study aims to investigate the variability in the type and degree of cementation and to determine how they are affected by changes in groundwater conditions.

To …

Organizational Readiness Assessment For Fraud Detection And Prevention: Case Of Airlines Sector And Electronic Payment, Sultan Ayed Alghamdi

Dissertations and Theses

Payment processing systems have advanced significantly in the airline business. Because e-payments are easy, they have captured the attention of many companies in the aviation industry and are quickly becoming the dominant means of payment. However, as technology advances, fraud grows at a comparable rate. Over the years, there has been a surge in payment fraud incidents in the airline sector, reducing the platform's trustworthiness. Despite attempts to eliminate e-payment fraud, decision-makers lack the technical expertise required to use the finest fraud detection and prevention assessments; this research recognizes the lack of an established decision model as a hurdle and …

Teaching Routines And Student-Centered Mathematics Instruction: The Essential Role Of Conferring To Understand Student Thinking And Reasoning, Eva Thanheiser, Kathleen Melhuish

Mathematics and Statistics Faculty Publications and Presentations

We compare two lessons with respect to how a teacher centers student mathematical thinking to move instruction forward through enactment of five mathematically productive teaching routines: Conferring To Understand Student Thinking and Reasoning, Structuring Mathematical Student Talk, Working With Selected and Sequenced Student Math Ideas, Working with Public Records of Students’ Mathematical Thinking, and Orchestrating Mathematical Discussion. Findings show that the lessons differ in the enactment of teaching routines, especially Conferring to Understand Student Thinking and Reasoning which resulted in a difference in student-centeredness of the instruction. This difference highlights whose mathematics was being centralized in the classroom and whether …

Native Seed Germination Trials At The Rae Selling Berry Seed Bank, Garbiel E. Campbell, Roxy Olsson, April Hersey, Stephanie Meikle, Kris Freitag

Rae Selling Berry Seed Bank and Plant Conservation Program

This presentation is a summary of germination trials on seeds native to the Pacific Northwest.

Data From: The Geography Of Glaciers And Perennial Snowfields In The American West, Andrew G. Fountain, Bryce Glenn, Hassan J. Basagic

Geology Faculty Datasets

A comprehensive mid-20th century inventory of glaciers and perennial snowfields (G&PS) was compiled for the American West, west of the 100° meridian. The inventory was derived from U.S. Geological Survey 1:24,000 topographic maps based on aerial photographs acquired during 35 years,1955–1990.

Recent Advances In Experimental Design And Data Analysis To Characterize Prokaryotic Motility, Megan M. Dubay, Jacqueline Acres, Max Riekeles, Jay Nadeau

Physics Faculty Publications and Presentations

Bacterial motility plays a key role in important cell processes such as chemotaxis and biofilm formation, but is challenging to quantify due to the small size of the individual microorganisms and the complex interplay of biological and physical factors that influence motility phenotypes. Swimming, the first type of motility described in bacteria, still remains largely unquantified. Light microscopy has enabled qualitative characterization of swimming patterns seen in different strains, such as run and tumble, run-reverse-flick, run and slow, stop and coil, and push and pull, which has allowed for elucidation of the underlying physics. However, quantifying these behaviors (e.g., identifying …

Dependence Among Order Statistics For Time-Transformed Exponential Models, Subhash C. Kochar, Fabio Spizzichino

Mathematics and Statistics Faculty Publications and Presentations

Let (X1, . . . ,Xn) be a random vector distributed according to a time-transformed exponential model. This is a special class of exchangeable models, which, in particular, includes multivariate distributions with Schur-constant survival functions and with identical marginals. Let for 1 ≤ i ≤ n, Xi:n denote the corresponding ith order statistic. We consider the problem of comparing the strength of dependence between any pair of Xi’s with that of the corresponding order statistics. It is proved that for m = 2, . . . , n, the dependence of X2:m on X1:m is more than that of X2 …

Datasets From: Application Of Aerial Insar To Measure Glacier Elevations, Bryce Glenn, Andrew G. Fountain, Delywn Moller

Geology Faculty Datasets

In September 2016 NASA flew an interferometric synthetic aperture radar (GLISTIN) over most of the glacier-covered regions of the coterminous USA for the purpose of mapping the surface elevation of the glaciers. Where multiple passes were flown over the same ground track, the data were mosaiced together to improve data coverage and elevation accuracy. These data are to be used with elevations collected by past and future efforts to calculate volume change of glaciers.

The data were the basis for:

Glenn, Bryce Allen, "Assessing Airborne Radar to Map Glacier Elevations in Alpine Terrain Including Estimated Glacier Volume Change …

An Equivalence Checking Framework For Agile Hardware Design, Yanzhao Wang, Fei Xie, Zhenkun Yang, Pascuale Cocchini, Jin Yang

Computer Science Faculty Publications and Presentations

Agile hardware design enables designers to produce new design iterations efficiently. Equivalence checking is critical in ensuring that a new design iteration conforms to its specification. In this paper, we introduce an equivalence checking framework for hardware designs represented in HalideIR. HalideIR is a popular intermediate representation in software domains such as deep learning and image processing, and it is increasingly utilized in agile hardware design.We have developed a fully automatic equivalence checking workflow seamlessly integrated with HalideIR and several optimizations that leverage the incremental nature of agile hardware design to scale equivalence checking. Evaluations of two deep learning accelerator …

The Role Of Preprocessing For Word Representation Learning In Affective Tasks, Nastaran Babanejad, Heidar Davoudi, Ameeta Agrawal, Manos Papagelis

Computer Science Faculty Publications and Presentations

Affective tasks, including sentiment analysis, emotion classification, and sarcasm detection have drawn a lot of attention in recent years due to a broad range of useful applications in various domains. The main goal of affect detection tasks is to recognize states such as mood, sentiment, and emotions from textual data (e.g., news articles or product reviews). Despite the importance of utilizing preprocessing steps in different stages (i.e., word representation learning and building a classification model) of affect detection tasks, this topic has not been studied well. To that end, we explore whether applying various preprocessing methods (stemming, lemmatization, stopword removal, …

An Improved Lower Bound For Sparse Reconstruction From Subsampled Walsh Matrices, Jaroslaw Blasiok, Patrick Lopatto, Kyle Luh, Jake Marcinek, Shravas Rao

Computer Science Faculty Publications and Presentations

We give a short argument that yields a new lower bound on the number of uniformly and independently subsampled rows from a bounded, orthonormal matrix necessary to form a matrix with the restricted isometry property. We show that a matrix formed by uniformly and independently subsampling rows of an N ×N Walsh matrix contains a K-sparse vector in the kernel, unless the number of subsampled rows is Ω(KlogKlog(N/K)) — our lower bound applies whenever min(K,N/K) > logC N. Containing a sparse vector in the kernel precludes not only the restricted isometry property, but more generally the application of those matrices for …

Rdkg: A Reinforcement Learning Framework For Disease Diagnosis On Knowledge Graph, Shipeng Guo, Kunpeng Liu, Pengfei Wang, Weiwei Dai, Yi Du, Yuanchun Zhou, Wenjuan Cui

Computer Science Faculty Publications and Presentations

Automatic disease diagnosis from symptoms has attracted much attention in medical practices. It can assist doctors and medical practitioners in narrowing down disease candidates, reducing testing costs, improving diagnosis efficiency, and more importantly, saving human lives. Existing research has made significant progress in diagnosing disease but was limited by the gap between interpretability and accuracy. To fill this gap, in this paper, we propose a method called Reinforced Disease Diagnosis on Knowlege Graph (RDKG). Specifically, we first construct a knowledge graph containing all information from electronic medical records. To capture informative embeddings, we propose an enhanced knowledge graph embedding method …

Unequal Trust: Bottled Water Consumption, Distrust In Tap Water, And Economic And Racial Inequality In The United States, Daniel Jaffee

Sociology Faculty Publications and Presentations

Reviewing public health, nutrition, and social science literature, this article examines how bottled water consumption and spending in the United States differ along lines of race, ethnicity, and income, how these consumption patterns have changed in recent years, and how those shifts map onto perceptions of the safety and trustworthiness of tap water supplies, both before and since the Flint water disaster. It also addresses the differential impact of bottled water spending on household income. The findings challenge the truism that bottled water consumption is positively correlated with income, instead showing a bimodal racial and class consumption pattern that reflects …

Machine Learning Predictions Of Electricity Capacity, Marcus Harris, Elizabeth Kirby, Ameeta Agrawal, Rhitabrat Pokharel, Francis Puyleart, Martin Zwick

Complex Systems Faculty Publications and Presentations

This research applies machine learning methods to build predictive models of Net Load Imbalance for the Resource Sufficiency Flexible Ramping Requirement in the Western Energy Imbalance Market. Several methods are used in this research, including Reconstructability Analysis, developed in the systems community, and more well-known methods such as Bayesian Networks, Support Vector Regression, and Neural Networks. The aims of the research are to identify predictive variables and obtain a new stand-alone model that improves prediction accuracy and reduces the INC (ability to increase generation) and DEC (ability to decrease generation) Resource Sufficiency Requirements for Western Energy Imbalance Market participants. This …

Botanical Updates From Psu, Gabriel Campbell

Rae Selling Berry Seed Bank and Plant Conservation Program

These slides summarize the botanical work conducted at PSU in 2022.

Spartina Species Invasive In Coastal Salt Marshes And Mudflats Of The Pacific Northwest, Gabriel E. Campbell, Ashley Newcomb, Jacob Rose

Center for Lakes and Reservoirs Publications and Presentations

Spartina (cordgrass) species are invasive plants that threaten the Pacific Northwest of the United States of America. This document contains a literature review, map of known occurrences, and identification guide of Spartina species invasive in coastal salt marshes and mudflats of the Pacific Northwest.