Physical Sciences and Mathematics Commons^™

Draft - Sieve Study Report December 2022, Appendices, Ramboll

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Sequence-Based Bioinformatics Approaches To Predict Virus–Host Relationships In Archaea And Eukaryotes, Yingshan Li

School of Computing: Dissertations, Theses, and Student Research

Viral metagenomics is independent of lab culturing and capable of investigating viromes of virtually any given environmental niches. While numerous sequences of viral genomes have been assembled from metagenomic studies over the past years, the natural hosts for the majority of these viral contigs have not been determined. Different computational approaches have been developed to predict hosts of bacteria phages. Nevertheless, little progress has been made in the virus-host prediction, especially for viruses that infect eukaryotes and archaea. In this study, by analyzing all documented viruses with known eukaryotic and archaeal hosts, we assessed the predictive power of four computational …

Eco-Dystopian Novels Written By Women: Second, Third, And Fourth Wave Feminism, Trystyn Cox

Department of Environmental Studies: Undergraduate Student Theses

The project is thematic; analysis of eco-dystopian novels written by American female authors in the 20th and 21st centuries in order to determine if the different waves of feminism experienced in the United States had any influence over the books. By doing an analysis of eco-dystopian novels the study identifies if there were any outside societal movements or issues going on at the time that may have influenced how the book was created or if a particular book was able to open innovative ideas to the society at the time it was published. I researched the second, third, and fourth …

Identifying How Summer Camp Experiences Affect Children’S Environmental Literacy, Quinn Kimbell

Department of Environmental Studies: Undergraduate Student Theses

Ensuring that children are prepared for environmental issues in the future can be aided by building the skill of environmental literacy. A key factor in building this skill is having natural experiences and creating one’s connection and perception of the environment. This paper aims to identify if summer camps increase children’s perception of the environment. This was completed by testing children with an environmental perception survey (Children’s Environmental Perception Scale) before and after attending a summer camp and assessing environmental pollution knowledge through drawing (modified Draw-An-Environment Test). The rural Nebraska summer camp subjected the children to many outdoor experiences, including …

Folic Acid – Carbon Dots – Doxorubicin Nanoparticles As Cancer Theranostic, Michael Tetteh

Electronic Theses and Dissertations

This work focused on engineering bi-functionalized nanoparticles (NPs) based on carbon dots (CDs) to improve early cancer detection and treatment. Therefore, using folic acid (FA) as a targeting agent, the CDs were prepared to deliver high concentrations (HC) of doxorubicin (DOX) and gemcitabine (GEM) covalently and non-covalently to cancer cells. The prepared FA-CDs-DOX/GEM-HC NPs were characterized using ultraviolet-visible spectroscopy, fluorescence spectroscopy, and Fourier transform infrared spectroscopy. Assessment of the drug loading capacity (DLC) and drug loading efficiency (DLE) indicated that the non-covalent NPs have low DLC but high DLE compared to the relatively low DLE and high DLC of covalent …

Biomolecular Effects Of Dance And Dance/Movement Therapy: A Review, Ivana Lopez-Nieves, Charles E. Jakobsche

Chemistry

The positive health impacts of dance and dance/movement therapy can be seen all the way down to the molecular level. This narrative-style review illustrates this connection by presenting a collection of clinical and preclinical studies that evaluate the effects of dance activities on hormones and other small-molecule metabolites within the human body. The results of these studies show that dance activities can increase levels of nitric oxide, serotonin, estrogen hormones, and HDL cholesterol, while they can decrease levels of dopamine, serum glucose, serum triglycerides, and LDL cholesterol. Levels of cortisol can either be increased or decreased, depending on the type …

Molecular Dynamics Simulations Of The Adenylate Kinase Enzyme And Its Mutant States, Beata Izabella Dulko Smith

Chemistry & Biochemistry Dissertations - Archive

Adenylate kinase (AK) is a small, monomeric enzyme present across all domains of life. It is responsible for maintaining homeostasis of an intracellular adenylate pool and catalyzes a reversible transfer of the phosphoryl group from NTP (nucleoside triphosphate) to NMP producing two NDP molecules. While most known isoforms take ATP as phosphate donor, AK3 present in mitochondrial matrix employs GTP. Crystallographic investigations revealed that the basis for its selectivity for GTP over ATP came from an additional hydrogen bond between guanosine’s O6 and backbone nitrogen of threonine is responsible for recognition of GTP. Molecular dynamics (MD) simulations have demonstrated that …

Development Of Colorimetric And Fluorescent Antibiotic Biosensors And Synthesis Of Drug-Related Biomimetic Molecules For Calcium Carbonate Polymorph Control And Stabilization, Shan Hazoor

Chemistry & Biochemistry Dissertations - Archive

Polydiacetylene (PDA) polymers are conjugated macromolecules with desirable sensing properties. The presence of alternate double and triple bonds (en-yne subunits) generates electron delocalization in the PDA backbone, yielding a characteristic blue color, which changes to red upon environmental perturbations to the conjugated backbone structure. In chapter 1 PDA polymers containing a functional monomer 10,12- pentacosadiynoic acid-vancomycin conjugate (PCDA-Van) were prepared. Syntheses of different monomers containing different polar head groups were carried out to investigate a compatible monomer with PCDA-van stability. Gram-positive bacterial cell wall sequencing oligopeptides (OP) D-Ala-D-Ala and L-Lys-D-Ala-D-Ala were synthesized as a model for bacterial sensing. The PCDA-Van …

Probing Short-Range Structural Distortion Of Stereochemically Active Lone Pairs In Extended Solid-State Materials, Uyen Phuong Dang

Chemistry & Biochemistry Dissertations - Archive

The structural and electronic effects of the lone pairs play an important role in magnetic, photocatalytic, and semiconducting behaviors of materials. Investigating the role of stereochemically active ns2 lone pairs derived from p-block cations in solid-state materials is important to phenomena associated with polarizable bonding, e.g., ferroelectricity. The effect of lone pairs in ferroelectric polarization has been studied on the lead metaniobate in which the covalency between Pb and O stabilizes the in-plane polarization which leads to orthorhombic symmetry. PbTiO3 has been widely studied for ferroelectric polarization associated with the off-centering of Ti in TiO6 due to the characteristic 6s2 …

Intelligent Fluorescence Image Analysis Of Giant Unilamellar Vesicles Using Convolutional Neural Network, Il Hyung Lee, Sam Passaro, Selin Ozturk, Juan Ureña, Weitian Wang

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

Background: Fluorescence image analysis in biochemical science often involves the complex tasks of identifying samples for analysis and calculating the desired information from the intensity traces. Analyzing giant unilamellar vesicles (GUVs) is one of these tasks. Researchers need to identify many vesicles to statistically analyze the degree of molecular interaction or state of molecular organization on the membranes. This analysis is complicated, requiring a careful manual examination by researchers, so automating the analysis can significantly aid in improving its efficiency and reliability. Results: We developed a convolutional neural network (CNN) assisted intelligent analysis routine based on the whole 3D z-stack …

Transcriptomic Profiling Of Trypanosoma Congolense Mouthpart Parasites From Naturally Infected Flies, Sara Silva Pereira, Kawira Mathenge, Daniel Masiga, Andrew Jackson

All Peer-Reviewed Publications

Background: Animal African trypanosomiasis, or nagana, is a veterinary disease caused by African trypanosomes transmitted by tsetse flies. In Africa, Trypanosoma congolense is one of the most pathogenic and prevalent causes of nagana in livestock, resulting in high animal morbidity and mortality and extensive production losses. In the tsetse fly, parasites colonise the midgut and eventually reach the mouthparts, from where they can be transmitted as the fly feeds on vertebrate hosts such as cattle. Despite the extreme importance of mouthpart-form parasites for disease transmission, very few global expression profile studies have been conducted in these parasite forms. Methods: Here, …

The Effect Of Climate Variability In The Efficacy Of The Entomopathogenic Fungus Metarhizium Acridum Against The Desert Locust Schistocerca Gregaria, Samuel F. Kamga, Frank T. Ndjomatchoua, Ritter A. Guimapi, Ingeborg Klingen, Clément Tchawoua, Anne Grete Roer Hjelkrem, Karl H. Thunes, Francois M. Kakmeni

All Peer-Reviewed Publications

Despite substantial efforts to control locusts they remain periodically a major burden in Africa, causing severe yield loss and hence loss of food and income. Distribution maps indicating the value of the basic reproduction number R0 was used to identify areas where an insect pest can be controlled by a natural enemy. A dynamic process-based mathematical model integrating essential features of a natural enemy and its interaction with the pest is used to generate R0 risk maps for insect pest outbreaks, using desert locust and the entomopathogenic fungus Metarhizium acridum (Synn. Metarhizium anisoliae var. acridum) as a case study. This …

Crystal Structures Of (Z)-(Ethene-1,2-Di­Yl)Bis­­(Di­Phenyl­Phosphine Sulfide) And Its Complex With PtIi Dichloride, Brain Rawls, Jeremy Cunningham, John E. Bender, Richard J. Staples, Shannon Biros

Open Access Publishing Support Funded Articles

The crystal structures of (Z)-(ethene-1,2-di­yl)bis­(di­phenyl­phosphine sulfide), C₂₆H₂₂P₂S₂ (I), along with its complex with Pt^II dichloride, di­chlorido[(Z)-(ethene-1,2-di­yl)bis­(di­phenyl­phosphine sulfide)-κ²S,S′]platinum(II), [PtCl₂(C₂₆H₂₂P₂S₂)] (II), are described here. Compound I features P=S bond lengths of 1.9571 (15) and 1.9529 (15) Å, with a torsion angle of 166.24 (7)° between the two phosphine sulfide groups. The crystal of compound I features both intra­molecular C—H⋯S hydrogen bonds and π–π inter­actions. Mol­ecules of compound I are held together …

Cover Cropping And Organic Amendments To Improve Sandy Soils Under Organic Vegetable Production, Charles Williamson

All Theses

Coastal Plain soils in the Southeastern USA are typically sandy with poor soil structure, low soil organic carbon (SOC) content, and meager soil fertility that pose challenges to organic agriculture. Adding organic inputs is a strategy to improve these soils' physical, chemical, and biological characteristics. Here, we aim to investigate the impacts of Cover Cropping (CC) and manure inclusions on sandy soils under organic vegetable production. The experiment design was a randomized complete block with two treatments of manure application (with and without) and four CC treatments of cereal rye (Secale cereale), hairy vetch (Vicia villosa), …

Learning To Reason About Code With Assertions: An Exploration With Two Student Populations, Sarah Blankenship

All Theses

Code tracing is fundamental to students’ understanding of a program, and symbolic reasoning that entails learning to use assertions with abstract input and output values, as opposed to concrete values, enhances that understanding. Symbolic reasoning teaches students valuable abstraction and logic skills that will serve them well in all aspects of programming and their software
development careers.
We use lessons integrated into an online educational tool to supplement classroom instruction to help students learn symbolic reasoning. We explore two ways for students to learn about assertions: Writing assertions to capture the behavior of given code and solving Parsons-style problems in …

Mysteerio: Multi-Regional Environmentally Extended Input-Output Model For United States, Yash Srivastava

All Theses

This research work titled My State Environmentally Extended Regional Input-Output (MYSTEERIO) is based on the concept of multi-regional environmentally extended input-output (MREEIO), which is a combination of lifecycle thinking and economics principles. Numerous studies have highlighted the advantages of using this methodology to determine the environmental impacts associated with economic activities for a region. However, no prior attempt has been made to conduct a state-level analysis for the US. This research work thus tries to estimate the impacts embodied due to the consumption of goods and services at the state level by using the MREEIO principles. Extensive coverage of the …

Oam-Based Wavelets In A High Speed Optical Probing System For Measuring The Angular Decomposition Of The Environment, Justin Free

All Theses

This thesis presents the theoretical development of orbital angular momentum (OAM) based wavelets for the analysis of localized OAM information in space. An optical probing system for generating and detecting these wavelets is demonstrated; individual wavelets can scan the environment in 10µs or less. The probing system was applied to a three-dimensional atmospheric turbulence distribution to obtain a continuous wavelet transform of the angular information of the turbulent propagation path about a fixed radius. An entire continuous wavelet transform was measured in 3.8ms; the measurements are much faster than the turbulence and give insight into the short time scale of …

Scaling Investment In Renewable Energy Generation To Achieve Sustainable Development Goals 7 (Affordable And Clean Energy) And 13 (Climate Action) And The Paris Agreement: Roadblocks And Drivers, Mithatcan Aydos, Perrine Toledano, Martin Dietrich Brauch, Ladan Mehranvar, Theodoros Iliopoulos, Sunayana Sasmal

Columbia Center on Sustainable Investment

The zero-carbon energy transition is the solution to the 2022 energy crisis and a fundamental part of the solution to the global climate crisis. Yet, there are relatively low levels of investment in renewable energy in developing countries, hindering their achievement of the Sustainable Development Goals (SDGs) and contribution to the Paris Agreement goals.

In 2021, the Asia–Pacific region (excluding China) accounted for less than 8% of investments in energy transition technologies, Latin America and the Caribbean for less than 4%, and Africa and the Middle East for less than 2%. Annual investment in zero-carbon energy in developing economies other …

Conflicts Between Ghg Accounting Methodologies In The Steel Industry, John Biberman, Perrine Toledano, Baihui Lei, Max Lulavy, Rohini Ram Mohan

Columbia Center on Sustainable Investment

Accurate, verifiable, and comparable greenhouse gas (GHG) emissions data throughout supply chains in the materials sector are necessary to drive decarbonization. This is particularly the case for the steel supply chain, a major source of GHG emissions with untapped potential for reduction. However, emissions accounting methods used by the steel industry suffer from gaps and misalignment, resulting in significant differences in reported GHG emissions. The result is a patchwork reporting landscape vulnerable to manipulation and miscommunication, generating little actionable data for policymakers, producers, customers, and investors. These shortcomings highlight the need for a harmonized carbon accounting framework for the steel …

Scaling Investment In Renewable Energy: Roadblocks And Drivers – Executive Summary, Mithatcan Aydos, Perrine Toledano, Martin Dietrich Brauch, Ladan Mehranvar, Theodoros Iliopoulos, Sunayana Sasmal

Columbia Center on Sustainable Investment

The zero-carbon energy transition is the solution to the 2022 energy crisis and a fundamental part of the solution to the global climate crisis. Yet, there are relatively low levels of investment in renewable energy in developing countries, hindering their achievement of the Sustainable Development Goals (SDGs) and contribution to the Paris Agreement goals.

In 2021, the Asia–Pacific region (excluding China) accounted for less than 8% of investments in energy transition technologies, Latin America and the Caribbean for less than 4%, and Africa and the Middle East for less than 2%. Annual investment in zero-carbon energy in developing economies other …

Authigenic Clay Mineral Evidence For Restricted, Evaporitic Conditions During The Emergence Of The Ediacaran Doushantuo Biota, Shujun Han, Stefan C. Lӧhr, April N. Abbott, Andre Baldermann, Martin Voigt, Bingsong Yu

Marine Science

The Ediacaran Period witnessed major environmental change and an expansion of eukaryotic life following the Marinoan glaciation. The Doushantuo Formation of south China has furnished much of our understanding of Earth System and biosphere evolution during this period, but its depositional setting–marine or non-marine–is still debated. Here we conduct mineralogical, petrographic and geochemical analyses of samples from the lower Doushantuo Formation in order to determine the origin of saponite clay minerals which are abundant in this interval. We find that the morphology and distribution of the saponite clays suggest they are of pre-compaction, authigenic origin. We infer that the lower …

Social Equity Is Key To Sustainable Ocean Governance, Katherine M. Crosman, Edward H. Allison, Yoshitaka Ota, Andrés M. Cisneros-Montemayor, Gerald G. Singh, Wilf Swartz, Megan Bailey, Kate M. Barclay, Grant Blume, Mathieu Colléter, Michael Fabinyi, Elaine M. Faustman, Russell Fielding, P. Joshua Griffin, Quentin Hanich, Harriet Harden-Davies, Ryan P. Kelly, Tiff Annie Kenny, Terrie Klinger

Honors College Faculty Publications

Calls to address social equity in ocean governance are expanding. Yet ‘equity’ is seldom clearly defined. Here we present a framework to support contextually-informed assessment of equity in ocean governance. Guiding questions include: (1) Where and (2) Why is equity being examined? (3) Equity for or amongst Whom? (4) What is being distributed? (5) When is equity considered? And (6) How do governance structures impact equity? The framework supports consistent operationalization of equity, challenges oversimplification, and allows evaluation of progress. It is a step toward securing the equitable ocean governance already reflected in national and international commitments.

A Multistate Competing Risks Framework For Preconception Prediction Of Pregnancy Outcomes, Kaitlyn Cook, Neil J. Perkins, Enrique Schisterman, Sebastien Haneuse

Statistical and Data Sciences: Faculty Publications

Background: Preconception pregnancy risk profiles—characterizing the likelihood that a pregnancy attempt results in a full-term birth, preterm birth, clinical pregnancy loss, or failure to conceive—can provide critical information during the early stages of a pregnancy attempt, when obstetricians are best positioned to intervene to improve the chances of successful conception and full-term live birth. Yet the task of constructing and validating risk assessment tools for this earlier intervention window is complicated by several statistical features: the final outcome of the pregnancy attempt is multinomial in nature, and it summarizes the results of two intermediate stages, conception and gestation, whose outcomes …

The North Platte River Valley: The Intersectionality Between Water Quality And People, Anni Poetzl

School of Natural Resources: Dissertations, Theses, and Student Research

The North Platte River (NPR) Valley of western Nebraska is a semi-arid watershed with row crop production, livestock production, and urban land use activity and has a population of diverse stakeholders. These land use activities contribute to the enrichment of surface waters, such as streams, which can affect human and ecosystem health, as well as economic development and recreational activities. The project objectives are to: (1) quantify the movement of dissolved inorganic nutrients from the land within the NPR Valley to the NPR via tributaries and canals, (2) identify spatiotemporal variability of nutrient limitation of periphyton growth within the NPR, …

Human And Hydrologic Influences On Nebraska's Endangered Rainwater Basin Wetlands, Sarah Thompson

Department of Earth and Atmospheric Sciences: Dissertations, Theses, and Student Research

Over half of wetlands in North America have been lost or degraded. Rainwater Basin (RWB) wetlands, located in south-central Nebraska, are a primary example of such loss; an estimated 90% have been destroyed by land conversion for agriculture. Remaining RWB wetlands are often embedded in row-crop fields, where they are threatened by altered surface water runoff flow, drainage features, and excess sediment inputs. Efforts at the state and federal level have been made to preserve this wetland complex due to the critical stopover habitat these wetlands provide for migratory birds. Land managers work to maintain sufficient water levels during migratory …

Machine Learning-Based Methods For The Segmentation Of Scanning Electron Microscopy Images Of Fine-Grained Shale Samples, Binqian Yin

Earth & Environmental Sciences Dissertations - Archive

The segmentation of scanning electron microscopy (SEM) images is critical yet time-consuming for geological studies, as it will need to differentiate the boundaries for different mineral objects to facilitate subsequent analyses, such as porosity calculation. Recently, machine learning methods, especially convolutional neural networks (CNNs), have been explored to segment SEM images for fine-grained shale samples. However, existing methods fail to address two critical issues in the segmentation of shale rock images---insufficient labeled data and imbalanced objects. To this end, this dissertation has proposed a machine learning pipeline that consists of supervised, semi-supervised, and active learning stages to reduce manual efforts …

Primed And Cued: Long-Term Acoustic Telemetry Links Interannual And Seasonal Variations In Freshwater Flows To The Spawning Migrations Of Common Snook In The Florida Everglades, Jordan A. Massie, Rolando O. Santos, Ryan J. Rezek, W. Ryan James, Natasha M. Viadero, Ross E. Boucek, David A. Blewett, Alexis A. Trotter, Philip W. Stevens, Jennifer S. Rehage

Marine Science

Background: Spawning migrations are a widespread phenomenon among fishes, often occurring in response to environmental conditions prompting movement into reproductive habitats (migratory cues). However, for many species, individual fish may choose not to migrate, and research suggests that conditions preceding the spawning season (migratory primers) may influence this decision. Few studies have provided empirical descriptions of these prior conditions, partly due to a lack of long-term data allowing for robust multi-year comparisons. To investigate how primers and cues interact to shape the spawning migrations of coastal fishes, we use acoustic telemetry data from Common Snook (Centropomus undecimalis) in Everglades National …

Impact Of The Pacific Sector Sea Ice Loss On The Sudden Stratospheric Warming Characteristics, Jiarong Zhang, Yvan J. Orsolini, Varavut Limpasuvan, Jinro Ukita

Marine Science

The atmospheric response to Arctic sea ice loss remains a subject of much debate. Most studies have focused on the sea ice retreat in the Barents-Kara Seas and its troposphere-stratosphere influence. Here, we investigate the impact of large sea ice loss over the Chukchi-Bering Seas on the sudden stratospheric warming (SSW) phenomenon during the easterly phase of the Quasi-Biennial Oscillation through idealized large-ensemble experiments based on a global atmospheric model with a well-resolved stratosphere. Although culminating in autumn, the prescribed sea ice loss induces near-surface warming that persists into winter and deepens as the SSW develops. The resulting temperature contrasts …

Rapid Detection Of Recurrent Non-Muscle Invasive Bladder Cancer In Urine Using Atr-Ftir Technology, Abdullah I. El-Falouji, Dalia M. Sabri, Naira M. Lofti, Doaa M. Medany, Samar A. Mohamed, Mai Alaa-Eldin, Amr Mounir Selim, Asmaa A. El Leithy, Haitham F. Kalil, Ahmed El-Tobgy, Ahmed Mohamed

Chemistry Faculty Publications

Non-muscle Invasive Bladder Cancer (NMIBC) accounts for 80% of all bladder cancers. Although it is mostly low-grade tumors, its high recurrence rate necessitates three-times-monthly follow-ups and cystoscopy examinations to detect and prevent its progression. A rapid liquid biopsy-based assay is needed to improve detection and reduce complications from invasive cystoscopy. Here, we present a rapid spectroscopic method to detect the recurrence of NMIBC in urine. Urine samples from previously-diagnosed NMIBC patients (n = 62) were collected during their follow-up visits before cystoscopy examination. Cystoscopy results were recorded (41 cancer-free and 21 recurrence) and attenuated total refraction Fourier transform infrared (ATR-FTIR) …

Strong Constraints On New Physics From The Icecube South Pole Neutrino Observatory, Grant Kendrick Parker

Physics Dissertations - Archive

The IceCube Neutrino Observatory, a gigaton-scale ice Cherenkov detector located deep within the Antarctic glacier, has detected hundreds of thousands of atmospheric neutrinos at energies from a few GeV to 100 TeV. Above 100 GeV, where ordinary oscillation effects become vanishingly small, this data sample is particularly sensitive to a wide range of beyond-standard-model (BSM) neutrino oscillation mechanisms. This thesis presents two searches for such BSM physics: flavor-changing nonstandard neutrino interactions (NSI) and neutrino oscillation decoherence (decoherence). The first analysis constrains the mu-tau flavor-changing NSI parameter with eight years of IceCube atmospheric neutrino data ranging from 500 GeV to 1 …