Physical Sciences and Mathematics Commons^™

Creating Synthetic Analogs Of Fluorescent Speleothems In Wind Cave As An Astrobiological Model Cave, Teresa Feldman

Honors Program Theses

The wind cave system represents a unique environment on Earth where the direct interplay of organic chemistry on the surface can possibly be traced to extremophiles living hundreds of meters below the surface. In many cases, minerals and organics from the surface become trapped in calcite formations creating fluorescent minerals. To understand the environment giving rise to the fluorescent minerals in Wind Cave, laboratory analogs of the calcite crystals found within the Wind Cave National Park cavern were synthesized and analyzed using SEM and fluorescence spectroscopy. This data was compared to the fluorescence and XRF data collected from speleothems in …

Estimating Heading From Optic Flow With Neural Networks, Natalie T. Maus

Honors Theses

Humans have a remarkable ability to estimate their direction of self-motion, or heading, based on visual input stimulus (optic flow). Machines, on the other hand, have a difficult time with this task, especially when flow is introduced that is inconsistent with the motion of the observer. For example, when moving objects enter the field of view, their motion provides inconsistent flow data which often disrupts heading estimates of current heading estimation models. We investigate the ability of neural networks to estimate heading from optic flow data and the limitations of these models when different variations of inconsistent flow are introduced. …

Thermally Driven Topology And The Topological Hall Effect In Chiral Magnets, Tan Dao

Honors Theses and Capstones

No abstract provided.

Using Sentiment Analysis To Find The Public's Opinion On Iowa's Three State Schools, Alexa Ryan Bullock

Honors Program Theses

The purpose of this project was to create my own sentiment analysis that would allow me to analyze reviews of the three Iowa state schools: University of Iowa, Iowa State, and University of Northern Iowa, and organize them in a way that showed the strong and weak points of each university. I accomplished this by researching how sentiment analysis works, applying that to the construction of my own sentiment analysis, and then using it on reviews about these three schools. The goal of this project was to give my audience a greater understanding of how sentiment analysis works by creating …

Hybrid Models As Transdisciplinary Research Enablers, Andreas Tolk, Alison Harper, Navonil Mustafee

Computational Modeling & Simulation Engineering Faculty Publications

Modelling and simulation (M&S) techniques are frequently used in Operations Research (OR) to aid decision-making. With growing complexity of systems to be modelled, an increasing number of studies now apply multiple M&S techniques or hybrid simulation (HS) to represent the underlying system of interest. A parallel but related theme of research is extending the HS approach to include the development of hybrid models (HM). HM extends the M&S discipline by combining theories, methods and tools from across disciplines and applying multidisciplinary, interdisciplinary and transdisciplinary solutions to practice. In the broader OR literature, there are numerous examples of cross-disciplinary approaches in …

Electroosmotic Mixing Of Non-Newtonian Fluid In A Microchannel With Obstacles And Zeta Potential Heterogeneity, Lanju Mei, Defu Cui, Jiayue Shen, Diganta Dutta, Willie Brown, Lei Zhang, Ibibia K. Dabipi

Computational Modeling & Simulation Engineering Faculty Publications

This paper investigates the electroosmotic micromixing of non-Newtonian fluid in a microchannel with wall-mounted obstacles and surface potential heterogeneity on the obstacle surface. In the numerical simulation, the full model consisting of the Navier–Stokes equations and the Poisson–Nernst–Plank equations are solved for the electroosmotic fluid field, ion transport, and electric field, and the power law model is used to characterize the rheological behavior of the aqueous solution. The mixing performance is investigated under different parameters, such as electric double layer thickness, flow behavior index, obstacle surface zeta potential, obstacle dimension. Due to the zeta potential heterogeneity at the obstacle surface, …

Biolability Of Fresh And Photodegraded Pyrogenic Dissolved Organic Matter From Laboratory-Prepared Chars, K. W. Bostick, A. R. Zimmerman, A. I. Goranov, S. Mitra, P. G. Hatcher, A. S. Wozniak

Chemistry & Biochemistry Faculty Publications

Pyrogenic dissolved organic matter (pyDOM) is known to be an important biogeochemical constituent of aquatic ecosystems and the carbon cycle. While recent studies have examined how pyDOM production, composition, and photolability varies with parent pyrogenic solid material type, we lack an understanding of potential microbial mineralization and transformation of pyDOM in the biogeosphere. Thus, leachates of oak, charred at 400 °C and 650 °C, as well as their photodegraded counterparts were incubated with a soil‐extracted microbial consortium over 96 days. During the incubation, significantly more carbon was biomineralized from the lower versus higher temperature char leachate (45% vs. 37% lost, …

Synthesis And Self-Assembling Properties Of Peracetylated Β-1 Triazolyl Alkyl D Glucosides And D-Galactosides, Pooja Sharma, Anji Chen, Dan Wang, Guijun Wang

Chemistry & Biochemistry Faculty Publications

Carbohydrate-based low-molecular-weight gelators (LMWGs) are useful classes of compounds due to their numerous applications. Among sugar-based LMWGs, certain peracetylated sugar beta-triazole derivatives were found to be effective organogelators and showed interesting self-assembling properties. To further understand the structural influence towards molecular assemblies and obtain new functional materials with interesting properties, we designed and synthesized a library of tetraacetyl beta-1-triazolyl alkyl-D-glucosides and D-galactosides, in which a two or three carbon spacer is inserted between the anomeric position and the triazole moiety. A series of 16 glucose derivatives and 14 galactose derivatives were synthesized and analyzed. The self-assembling properties of these new …

Fine-Tuning Of Molecular Structures To Generate Carbohydrate Based Super Gelators And Their Applications For Drug Delivery And Dye Absorption, Jonathan Bietsch, Mary Olson, Guijun Wang

Chemistry & Biochemistry Faculty Publications

Carbohydrate-based low molecular weight gelators (LMWGs) exhibit many desirable properties making them useful in various fields including applications as drug delivery carriers. In order to further understand the structural connection to gelation properties, especially the influence of halide substitutions, we have designed and synthesized a series of para-chlorobenzylidene acetal protected D-glucosamine amide derivatives. Fifteen different amides were synthesized, and their self-assembling properties were assessed in multiple organic solvents, as well as mixtures of organic solvents with water. All derivatives were found to be gelators for at least one solvent and majority formed gels in multiple solvents at concentrations lower than …

Hidden Markov Model And Cyber Deception For The Prevention Of Adversarial Lateral Movement, Md Ali Reza Al Amin, Sachin Shetty, Laurent Njilla, Deepak K. Tosh, Charles Kamhoua

Computational Modeling & Simulation Engineering Faculty Publications

Advanced persistent threats (APTs) have emerged as multi-stage attacks that have targeted nation-states and their associated entities, including private and corporate sectors. Cyber deception has emerged as a defense approach to secure our cyber infrastructure from APTs. Practical deployment of cyber deception relies on defenders' ability to place decoy nodes along the APT path optimally. This paper presents a cyber deception approach focused on predicting the most likely sequence of attack paths and deploying decoy nodes along the predicted path. Our proposed approach combines reactive (graph analysis) and proactive (cyber deception technology) defense to thwart the adversaries' lateral movement. The …

A Global Ecological Classification Of Coastal Segment Units To Complement Marine Biodiversity Observation Network Assessments, Roger Sayre, Kevin Butler, Keith Van Graafeiland, Sean Breyer, Dawn Wright, Charlie Frye, Deniz Karagulle, Madeline Martin, Jill Cress, Tom Allen, Rebecca J. Allee, Rost Parsons, Bjorn Nyberg, Mark J. Costello, Peter Harris, Frank E. Muller-Karger

Political Science & Geography Faculty Publications

A new data layer provides Coastal and Marine Ecological Classification Standard (CMECS) labels for global coastal segments at 1 km or shorter resolution. These characteristics are summarized for six US Marine Biodiversity Observation Network (MBON) sites and one MBON Pole to Pole of the Americas site in Argentina. The global coastlines CMECS classifications were produced from a partitioning of a 30 m Landsat-derived shoreline vector that was segmented into 4 million 1 km or shorter segments. Each segment was attributed with values from 10 variables that represent the ecological settings in which the coastline occurs, including properties of the adjacent …

Anticipating And Adapting To The Future Impacts Of Climate Change On The Health, Security And Welfare Of Low Elevation Coastal Zone (Lecz) Communities In Southeastern Usa, Thomas Allen, Joshua Behr, Anamaria Bukvic, Ryan S.D. Calder, Kiki Caruson, Charles Connor, Christopher D'Elia, David Dismukes, Robin Ersing, Rima Franklin, Jesse Goldstein, Jonathon Goodall, Scott Hemmerling, Jennifer Irish, Steven Lazarus, Derek Loftis, Mark Luther, Leigh Mccallister, Karen Mcglathery, Molly Mitchell, William Moore, Charles Reid Nichols, Karinna Nunez, Matthew Reidenbach, Julie Shortridge, Robert Weisberg, Robert Weiss, Lynn Donelson Wright, Meng Xia, Kehui Xu, Donald Young, Gary Zarillo, Julie C. Zinnert

Political Science & Geography Faculty Publications

Low elevation coastal zones (LECZ) are extensive throughout the southeastern United States. LECZ communities are threatened by inundation from sea level rise, storm surge, wetland degradation, land subsidence, and hydrological flooding. Communication among scientists, stakeholders, policy makers and minority and poor residents must improve. We must predict processes spanning the ecological, physical, social, and health sciences. Communities need to address linkages of (1) human and socioeconomic vulnerabilities; (2) public health and safety; (3) economic concerns; (4) land loss; (5) wetland threats; and (6) coastal inundation. Essential capabilities must include a network to assemble and distribute data and model code to …

Characterizing Seagrass Effects On Hydrodynamics Of Waves And Currents Through Field Measurements And Computational Modelling, Ramin Familkhalili, Navid Tahvildari

Civil & Environmental Engineering Faculty Publications

Low-lying coastal and estuarine areas are among the most populated regions globally, have high economic significance, and are increasingly threatened by climate change, sea level rise, nuisance flooding, and extreme storms. Nature-based coastal protections are sustainable and sea-level resilient alternatives compared to traditional solutions such as dikes and seawalls. Submerged aquatic vegetation (SAV) or seagrasses can provide coastal flood and erosion protection by attenuating storm wave and current energy and stabilizing seabed sediments. However, more research is needed to understand the interactions between flow, SAVs, and sediments. These dynamic interactions affect flow at different scales and seagrass productivity. In this …

Efficient Algorithms For Identifying Loop Formation And Computing Θ Value For Solving Minimum Cost Flow Network Problems, Timothy Michael Chávez, Duc Thai Nguyen

Computational Modeling & Simulation Engineering Faculty Publications

While the minimum cost flow (MCF) problems have been well documented in many publications, due to its broad applications, little or no effort have been devoted to explaining the algorithms for identifying loop formation and computing the value needed to solve MCF network problems. This paper proposes efficient algorithms, and MATLAB computer implementation, for solving MCF problems. Several academic and real-life network problems have been solved to validate the proposed algorithms; the numerical results obtained by the developed MCF code have been compared and matched with the built-in MATLAB function Linprog() (Simplex algorithm) for further validation.

The Enlightening Role Of Explainable Artificial Intelligence In Chronic Wound Classification, Salih Sarp, Murat Kuzlu, Emmanuel Wilson, Umit Cali, Ozgur Guler

Engineering Technology Faculty Publications

Artificial Intelligence (AI) has been among the most emerging research and industrial application fields, especially in the healthcare domain, but operated as a black-box model with a limited understanding of its inner working over the past decades. AI algorithms are, in large part, built on weights calculated as a result of large matrix multiplications. It is typically hard to interpret and debug the computationally intensive processes. Explainable Artificial Intelligence (XAI) aims to solve black-box and hard-to-debug approaches through the use of various techniques and tools. In this study, XAI techniques are applied to chronic wound classification. The proposed model classifies …

Spatio-Temporal Modelling Of Tick Life-Stage Count Data With Spatially Varying Coefficients, Thabo Lephoto, Henry Mwambi, Oliver Bodhlyera, Holly Gaff

Biological Sciences Faculty Publications

There is a vast amount of geo-referenced data in many fields of study including ecological studies. Geo-referencing is usually by point referencing; that is, latitudes and longitudes or by areal referencing, which includes districts, counties, states, provinces and other administrative units. The availability of large geo-referenced datasets for modelling has necessitated the development and application of spatial statistical methods. However, spatial varying coefficients models exploring the abundance of tick counts remain limited. In this study we used data that was collected and prepared by researchers in the Department of Biological Sciences from the Old Dominion University, Virginia, USA. We modelled …

Contrasting Heat Stress Response Patterns Of Coral Holobionts Across The Red Sea Suggest Distinct Mechanisms Of Thermal Tolerance, Christian R. Voolstra, Jacob J. Valenzuela, Serdar Turkarslan, Anny Cárdenas, Benjamin C.C. Hume, Gabriela Perna, Carol Buitrago-López, Katherine Rowe, Monica V. Orellana, Nitin S. Baliga, Suman Paranjape, Guilhem Banc-Prandi, Jessica Bellworthy, Moaz Fine, Sarah Frias-Torres, Daniel J. Barshis

Biological Sciences Faculty Publications

Corals from the northern Red Sea, in particular the Gulf of Aqaba (GoA), have exceptionally high bleaching thresholds approaching >5℃ above their maximum monthly mean (MMM) temperatures. These elevated thresholds are thought to be due to historical selection, as corals passed through the warmer Southern Red Sea during recolonization from the Arabian Sea. To test this hypothesis, we determined thermal tolerance thresholds of GoA versus central Red Sea (CRS) Stylophora pistillata corals using multi-temperature acute thermal stress assays to determine thermal thresholds. Relative thermal thresholds of GoA and CRS corals were indeed similar and exceptionally high (~7℃ above MMM). However, …

Use Of Response Shift To Improve Agreement Between Patient-Reported And Performance-Based Outcomes In Knee Patients, Shelby Baez, Johanna M. Hoch, Carl Mattacola, Philip Gribble, Jennifer S. Howard

Clinical Practice in Athletic Training

The purpose of this study was to determine whether the implementation of performance-based tasks (PBTs) prior to completion of patient-reported outcome measures (PROs) would create a change, or a response shift, in PROs in patients with knee injuries. A randomized controlled trial was implemented to examine the effectiveness of a response-shift based interventions to enhance the correlation between PBTs and PROs. Participants (n=20) were knee-injured patients who were removed from activity for a minimum of 1-week. Participants were randomly assigned to complete PBTs (intervention) or to watch videos detailing an injury prevention program (control). The International Knee Documentation Committee Subjective …

A Multi-Resolution Graph Convolution Network For Contiguous Epitope Prediction, Lisa Oh

Dartmouth College Master’s Theses

Computational methods for predicting binding interfaces between antigens and antibodies (epitopes and paratopes) are faster and cheaper than traditional experimental structure determination methods. A sufficiently reliable computational predictor that could scale to large sets of available antibody sequence data could thus inform and expedite many biomedical pursuits, such as better understanding immune responses to vaccination and natural infection and developing better drugs and vaccines. However, current state-of-the-art predictors produce discontiguous predictions, e.g., predicting the epitope in many different spots on an antigen, even though in reality they typically comprise a single localized region. We seek to produce contiguous predicted epitopes, …

When To Stop Computing And Start Investing, Sean R. Aguilar, Olga Kosheleva

Departmental Technical Reports (CS)

Purpose: The purpose of the study is to analyze when -- while predicting the future price of a financial instrument -- we should stop computations and start using this information for the actual investment.

Design/methodology/approach: We derive the explicit formulas explaining how the resulting gain depends on the duration of computations.

Findings: We provide an algorithm that enables us to decide the computation time that leads to the largest possible gain.

Originality/value: To the best of our knowledge, this is the first solution to the problem. Following our recommendations will allow investors to select the computation time for which the …

How To Gauge Reliability Of A Binary Classification Result: A Simple Case, Olga Kosheleva, Vladik Kreinovich

Departmental Technical Reports (CS)

In many practical situations, we need to make a binary decision based on the available data: whether an incoming email is a spam or not, whether to give a bank loan to a company, etc. In many such situations, we can (and do) use machine learning to come up with such a decision. The problem is that while the results of a machine learning model are not 100% reliable, the existing machine learning algorithms do not allow us to decide how reliable is each result. In this paper, for simple examples, we provide a technique for gauging this reliability.

Validation Of Hplc Method For The Determination Of Chemical And Radiochemical Purity Of A 68ga-Labelled Euk-Sub-Kf-(3-Iodo-Y-) Dotaga, Ayşe Uğur, Şükrü Gökhan Elçi̇, Doğangün Yüksel

Turkish Journal of Chemistry

The prostate-specific membrane antigen (PSMA) represents an ideal biomarker for molecular imaging. Various PSMA-targeted radioligands are available for prostate cancer imaging. In this study, labeling of PSMA I&T with 68Ga, as well as validation of the radiochemical purity of the synthesis product by reverse phase radio high-performance liquid chromatography (HPLC) method are intended. Since the standard procedure for the quality control (QC) was not available, definition of chemical and radiochemical purity of 68Ga-PSMA I&T was carried out according to the Q2 (R1) ICH guideline. The standard QC tests were analyzed with Scintomics 8100 radio-HPLC system equipped with a radioactivity detector. …

Integrated 3d-Qsar, Molecular Docking, And Molecular Dynamics Simulation Studies On 1,2,3-Triazole Based Derivatives For Designing New Acetylcholinesterase Inhibitors, Khalil El Khatabi, Ilham Aanouz, Reda El-Mernissi, Atul Kumar Singh, Mohammed Aziz Ajana, Tahar Lakhlifi, Shashank Kumar, Mohammed Bouachrine

Turkish Journal of Chemistry

Alzheimer's disease (AD) is a multifactorial and polygenic disease. It is the most prevalent reason for dementia in the aging population. A dataset of twenty-six 1,2,3-triazole-based derivatives previously synthetized and evaluated for acetylcholinesterase inhibitory activity were subjected to the three-dimensional quantitative structure-activity relationship (3D-QSAR) study. Good predictability was achieved for comparative molecular field analysis (CoMFA) (Q2 = 0.604, R2 = 0.863, rext2 = 0.701) and comparative molecular similarity indices analysis (CoMSIA) (Q2 = 0.606, R2 = 0.854, rext2 = 0.647). The molecular features characteristics provided by the 3D-QSAR contour plots were quite useful for designing and improving the activity of …

Central Equatorial Pacific Cooling During The Last Glacial Maximum, Minda Moriah Monteagudo, Jean Lynch-Stieglitz, Thomas M. Marchitto, Matthew W. Schmidt

OES Faculty Publications

Establishing tropical sea surface temperature (SST) during the Last Glacial Maximum (LGM) is important for constraining equilibrium climate sensitivity to radiative forcing. Until now, there has been little data from the central equatorial Pacific in global compilations, with foraminiferal assemblage‐based estimates suggesting the region was within 1°C of modern temperatures during the LGM. This is in stark contrast to multi‐proxy evidence from the eastern and western Pacific and model simulations which support larger cooling. Here we present the first estimates of glacial SST in the central equatorial Pacific from Mg/Ca in Globigerinoides ruber. Our results show that the central Pacific …

Pore Water Exchange-Driven Inorganic Carbon Export From Intertidal Salt Marshes, Joeseph J. Tamborski, Meagan Eagle, Barret L. Kurylyk, Kevin D. Kroeger, Zhaoihui Aleck Wang, Paul Henderson, Matthew A. Charette

OES Faculty Publications

Respiration in intertidal salt marshes generates dissolved inorganic carbon (DIC) that is exported to the coastal ocean by tidal exchange with the marsh platform. Understanding the link between physical drivers of water exchange and chemical flux is a key to constraining coastal wetland contributions to regional carbon budgets. The spatial and temporal (seasonal, annual) variability of marsh pore water exchange and DIC export was assessed from a microtidal salt marsh (Sage Lot Pond, Massachusetts). Spatial variability was constrained from ²²⁴Ra : ²²⁸Th disequilibria across two hydrologic units within the marsh sediments. Disequilibrium between the more soluble ²²⁴Ra …

Lagrangian Betweenness As A Measure Of Bottlenecks In Dynamical Systems With Oceanographic Examples, Enrico Ser-Giacomi, Alberto Baudena, Vincent Rossi, Mick Follows, Sophie Clayton, Ruggero Vasile, Cristóbal López, Emilio Hernández-García

OES Faculty Publications

The study of connectivity patterns in networks has brought novel insights across diverse fields ranging from neurosciences to epidemic spreading or climate. In this context, betweenness centrality has demonstrated to be a very effective measure to identify nodes that act as focus of congestion, or bottlenecks, in the network. However, there is not a way to define betweenness outside the network framework. By analytically linking dynamical systems and network theory, we provide a trajectory-based formulation of betweenness, called Lagrangian betweenness, as a function of Lyapunov exponents. This extends the concept of betweenness beyond the context of network theory relating hyperbolic …

A Kernel-Based Change Detection Method To Map Shifts In Phytoplankton Communities Measured By Flow Cytometry, Corinne Jones, Sophie Clayton, François Ribalet, E. Virginia Armbrust, Zaid Harchaoui

OES Faculty Publications

1. Automated, ship-board flow cytometers provide high-resolution maps of phytoplankton composition over large swaths of the world's oceans. They therefore pave the way for understanding how environmental conditions shape community structure. Identification of community changes along a cruise transect commonly segments the data into distinct regions. However, existing segmentation methods are generally not applicable to flow cytometry data, as these data are recorded as ‘point cloud’ data, with hundreds or thousands of particles measured during each time interval. Moreover, nonparametric segmentation methods that do not rely on prior knowledge of the number of species are desirable to map community shifts. …

Synoptic Mesoscale To Basin Scale Variability In Biological Productivity And Chlorophyll In The Kuroshio Extension Region, Sophie Clayton, Hilary I. Palevsky, Luanne Thompson, Paul D. Quay

OES Faculty Publications

The Kuroshio current separates from the Japanese coast to become the eastward flowing Kuroshio Extension (KE) characterized by a strong latitudinal density front, high levels of mesoscale (eddy) energy, and high chlorophyll a (Chl). While satellite measurements of Chl show evidence of the impact of mesoscale eddies on the standing stock of phytoplankton, there have been very limited synoptic, spatially resolved in situ estimates of productivity in this region. Here, we present underway measurements of oxygen/argon supersaturation (ΔO2/Ar), a tracer of net biological productivity, for the KE made in spring, summer, and early autumn. We find large seasonal differences in …

Elevating Dissolved Oxygen—Reflections On Developing And Using Long-Term Data, Nancy N. Rabalais

Gulf and Caribbean Research

This prospectus took me about as long to generate as my 36—year record of working on the issue of northern Gulf of Mexico (nGOM) oxygen deficiency, or so I felt. There was so much to cover, but I focused on the issue of hypoxia on the Louisiana continental shelf from the early 1980s to present and my participation in the research and outreach. Not that I was ignoring other aspects of my academic research career (e.g., stone crab populations and their differences in physiology and larval development along the nGOM coast; settlement of crab megalopae, especially blue crabs, on artificial …

See-Trend: Secure Traffic-Related Event Detection In Smart Communities, Stephan Olariu, Dimitrie C. Popescu

Computer Science Faculty Publications

It has been widely recognized that one of the critical services provided by Smart Cities and Smart Communities is Smart Mobility. This paper lays the theoretical foundations of SEE-TREND, a system for Secure Early Traffic-Related EveNt Detection in Smart Cities and Smart Communities. SEE-TREND promotes Smart Mobility by implementing an anonymous, probabilistic collection of traffic-related data from passing vehicles. The collected data are then aggregated and used by its inference engine to build beliefs about the state of the traffic, to detect traffic trends, and to disseminate relevant traffic-related information along the roadway to help the driving public make informed …