Other Mathematics Commons^™

Identifying Textual Predictors Of Early Termination In Clinical Trials In Medicine: An Explainable Machine-Learning Study, Rohan Ramnarain

Dissertations, Theses, and Capstone Projects

About one in five clinical trials in medicine ends early, wasting valuable resources and reducing the evidence available for developing life-saving medical treatments. This project uses a method called Trial2Vec, which is a self-supervised machine-learning method that converts clinical trial documents into dense numerical representations that capture their key design and clinical characteristics, to turn each proposed clinical trial’s written protocol into a compact numerical profile (a process referred to as embedding). These profiles are then paired with a predictive machine learning models to identify the words and phrases in the trial documents that can signal a higher risk of …

Robustness Of Network Inference Algorithms Under Network Class Misspecification, Roberto Ceja

Electronic Theses, Projects, and Dissertations

Inferring phylogenies in the presence of hybridization remains a difficult problem. As a result, many current methods for reconstructing phylogenetic networks are restricted to a simple class of networks known as level-1. This restriction arises from theoretical considerations rather than empirical evidence, with real data possibly arising from complex networks. In this work, we evaluate the robustness of two level-1 network inference methods, SNaQ and NANUQ+, through a simulation study, when the input data originates from a more complex network. Specifically, we investigate whether these methods can accurately recover important features of the true species network, such as the circular …

Mixed Uncertainty Analysis On Pumping By Peristaltic Hearts Using Dempster-Shafer Theory, Yanyan He, Nicholas A. Battista, Lindsay D. Waldrop

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

In this paper, we introduce the numerical strategy for mixed uncertainty propagation based on probability and Dempster–Shafer theories, and apply it to the computational model of peristalsis in a heart-pumping system. Specifically, the stochastic uncertainty in the system is represented with random variables while epistemic uncertainty is represented using non-probabilistic uncertain variables with belief functions. The mixed uncertainty is propagated through the system, resulting in the uncertainty in the chosen quantities of interest (QoI, such as flow volume, cost of transport and work). With the introduced numerical method, the uncertainty in the statistics of QoIs will be represented using belief …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Integrating Quantitative Skills Into Biology Courses, Kathleen Hoffman, Sarah Leupen, Hannah Pie, Michelle Starz-Gaiano, Patricia Turner, Tory Williams

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Discovering Dune: Essays On Frank Herbert’S Epic Saga., Edited By Dominic J. Nardi And N. Trevor Brierly, G. Connor Salter

Mythlore: A Journal of J.R.R. Tolkien, C.S. Lewis, Charles Williams, and Mythopoeic Literature

G. Connor Salter reviews Discovering Dune: Essays on Frank Herbert’s Epic Saga, edited by Dominic J. Nardi and N. Trevor Brierly, considering its new contributions to studies of Frank Herbert's work. Essays included fit into four categories (Politics and Power, History and Religion, Biology and Ecology, and Philosophy, Choice and Ethics) and range from Herbert's use of ecology in Dune to how game theory may help explain certain characters' apparent ability to see the future. Discovering Dune also includes an appendix which contains the only up-to-date bibliography of Herbert's work (primary and secondary sources).

Exploding Haystacks: Solutions For Fermi Questions, March 2023, John Adam

Mathematics & Statistics Faculty Publications

No abstract provided.

Estimating Glutamate Transporter Surface Density In Mouse Hippocampal Astrocytes, Anca R. Radulescu, Annalisa Scimemi

Biology and Medicine Through Mathematics Conference

No abstract provided.

Optimal Time-Dependent Classification For Diagnostic Testing, Prajakta P. Bedekar, Paul Patrone, Anthony Kearsley

Biology and Medicine Through Mathematics Conference

No abstract provided.

Graph-Theoretic Partitioning Of Rnas And Classification Of Pseudoknots-Ii, Louis Petingi

Publications and Research

Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called blocks and determine whether each block contains a pseudoknot or not. As pseudoknots can not be contained into two different blocks, this characterization allow us to efficiently isolate smaller RNA fragments and classify them as pseudoknotted or pseudoknot-free regions, while keeping these sub-structures intact. Moreover we have extended the partitioning algorithm by classifying a pseudoknot as either recursive or non-recursive in order to continue with our research …

Understanding The Effect Of Adaptive Mutations On The Three-Dimensional Structure Of Rna, Justin Cook

Undergraduate Research and Scholarship Symposium

Single-nucleotide polymorphisms (SNPs) are variations in the genome where one base pair can differ between individuals.¹ SNPs occur throughout the genome and can correlate to a disease-state if they occur in a functional region of DNA.¹According to the central dogma of molecular biology, any variation in the DNA sequence will have a direct effect on the RNA sequence and will potentially alter the identity or conformation of a protein product. A single RNA molecule, due to intramolecular base pairing, can acquire a plethora of 3-D conformations that are described by its structural ensemble. One SNP, rs12477830, which …

Use Of Lymesim 2.0 To Assess The Potential For Single And Integrated Management Methods To Control Blacklegged Ticks (Ixodes Scapularis; Acari: Ixodidae) And Transmission Of Lyme Disease Spirochetes, Shravani Chitineni, Elizabeth R. Gleim, Holly D. Gaff

Undergraduate Honors Theses

Annual Lyme disease cases continue to rise in the U.S. making it the most reported vector-borne illness in the country. The pathogen (Borrelia burgdorferi) and primary vector (Ixodes scapularis; blacklegged tick) dynamics of Lyme disease are complicated by the multitude of vertebrate hosts and varying environmental factors, making models an ideal tool for exploring disease dynamics in a time- and cost-effective way. In the current study, LYMESIM 2.0, a mechanistic model, was used to explore the effectiveness of three commonly used tick control methods: habitat-targeted acaricide (spraying), rodent-targeted acaricide (bait boxes), and white-tailed deer targeted acaricide (4-poster …

Introduction To Neutrosophic Genetics, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

Neutrosophic Genetics is the study of genetics using neutrosophic logic, set, probability, statistics, measure and other neutrosophic tools and procedures. In this paper, based on the Neutrosophic Theory of Evolution (that includes degrees of Evolution, Neutrality (or Indeterminacy), and Involution) – as extension of Darwin’s Theory of Evolution, we show the applicability of neutrosophy in genetics, and we present within the frame of neutrosophic genetics the following concepts: neutrosophic mutation, neutrosophic speciation, and neutrosophic coevolution.

Ethnomathematics: Art, Culture, And Social Justice, John R. Jungck

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Modeling Control Methods To Manage The Sylvatic Plague In Black-Tailed Prairie Dog Towns, David C. Elzinga, Shelby R. Stowe, Leland Russell

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Color Space Standardization And Image Analysis For High-Throughput Phenotyping Of Sorghum Bicolor, Alexandria A. Pokorny

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

The Impact Of Truncating Data On The Predictive Ability For Single-Step Genomic Best Linear Unbiased Prediction, Jeremy T. Howard, Thomas A. Rathje, Caitlyn E. Bruns, Danielle F. Wilson-Wells, Stephen D. Kachman, Matthew L. Spangler

Department of Animal Science: Faculty Publications

Simulated and swine industry data sets were utilized to assess the impact of removing older data on the predictive ability of selection candidate estimated breeding values (EBV) when using single-step genomic best linear unbiased prediction (ssGBLUP). Simulated data included thirty replicates designed to mimic the structure of swine data sets. For the simulated data, varying amounts of data were truncated based on the number of ancestral generations back from the selection candidates. The swine data sets consisted of phenotypic and genotypic records for three traits across two breeds on animals born from 2003 to 2017. Phenotypes and genotypes were iteratively …

Mental Models And Neutrosophic Cognitive Maps (Modelos Mentales Y Mapas Cognitivos Neutrosóficos), Maykel Leyva-Vazquez, Rebeca Escobar-Jara, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

In this work, elements related to mental models elicitation and analysis are addressed through causal models. Issues related to the need to include indeterminacy in causal relationships through neutrophic cognitive maps are discussed. A proposal for static analysis in neutrosophic cognitive maps is presented. The following activities are included in the proposal: Calculate, measures of centrality, Classify nodes, De-neutrosification, and Ranking nodes. As future works, the incorporation of new metrics of centrality in neutrosophic cognitive maps is proposed. The inclusion of scenario analysis to the proposal is another area of future work.

Revolution In Ideology: Crafting A Holistic Scientific Dialectic, Nathan Neill

Dialogue & Nexus

Ideology drives scientific research far more than is acknowledged. Since science itself is conducted by individuals, each scientist has a biased conception of themselves and their surroundings relative to the rest of the universe, even if it is never explicated. This sense of relation to the greater universe is what defines the ideology of the individual. It is this sense of relation and self that creates the individual, who goes on to investigate the natural world by the scientific method. In this paper I will examine extant scientific ideology, particularly in Western science, and propose changes that could be helpful.

Sensitivity Analysis Of Wolf Restoration In Yellowstone Nation Park Using Omnivory Models, Derek Fields

Theses, Dissertations and Capstones

In the ever-changing world of ecology, species survival often depends on approximations and measurements taken by biologists. These approximations help to ensure and predict the future of that given species. Our ecological community of interest involves wolves, elk, and berry producing shrubs within Yellowstone National Park. We use two different systems of ordinary differential equations, each increasing in complexity to model our community. In each model the predator (wolves) and consumers (elk) compete for a common resource, berry producing shrubs. We call this consumption of resources, from more than one trophic level, omnivory. We approximate each system with parameter values …

General Equations For Natural Selection Under Complete Dominance, Kasthuri Kannan, Adriana Heguy

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Extracting Biochemical Parameters From Protein Distributions Of Vascular Cells, Partha Srinivasan

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Population Projection And Habitat Preference Modeling Of The Endangered James Spinymussel (Pleurobema Collina), Marisa Draper

Senior Honors Projects, 2010-2019

The James Spinymussel (Pleurobema collina) is an endangered mussel species at the top of Virginia’s conservation list. The James Spinymussel plays a critical role in the environment by filtering and cleaning stream water while providing shelter and food for macroinvertebrates; however, conservation efforts are complicated by the mussels’ burrowing behavior, camouflage, and complex life cycle. The goals of the research conducted were to estimate detection probabilities that could be used to predict species presence and facilitate field work, and to track individually marked mussels to test for habitat preferences. Using existing literature and mark-recapture field data, these goals were accomplished …

Bioinformatic Game Theory And Its Application To Cluster Multi-Domain Proteins, Brittney Keel

Department of Mathematics: Dissertations, Theses, and Student Research

The exact evolutionary history of any set of biological sequences is unknown, and all phylogenetic reconstructions are approximations. The problem becomes harder when one must consider a mix of vertical and lateral phylogenetic signals. In this dissertation we propose a game-theoretic approach to clustering biological sequences and analyzing their evolutionary histories. In this context we use the term evolution as a broad descriptor for the entire set of mechanisms driving the inherited characteristics of a population. The key assumption in our development is that evolution tries to accommodate the competing forces of selection, of which the conservation force seeks to …

Manipulating The Mass Distribution Of A Golf Putter, Paul J. Hessler Jr.

Senior Honors Projects

Putting may appear to be the easiest but is actually the most technically challenging part of the game of golf. The ideal putting stroke will remain parallel to its desired trajectory both in the reverse and forward direction when the putter head is within six inches of the ball. Deviation from this concept will cause a cut or sidespin on the ball that will affect the path the ball will travel.

Club design plays a large part in how well a player will be able to achieve a straight back and straight through club head path near impact; specifically the …

Clique Topology Reveals Intrinsic Geometric Structure In Neural Correlations, Chad Giusti, Eva Pastalkova, Carina Curto, Vladimir Itskov

Department of Mathematics: Faculty Publications

Detecting meaningful structure in neural activity and connectivity data is challenging in the presence of hidden nonlinearities, where traditional eigenvalue-based methods may be misleading. We introduce a novel approach to matrix analysis, called clique topology, that extracts features of the data invariant under nonlinear monotone transformations. These features can be used to detect both random and geometric structure, and depend only on the relative ordering of matrix entries. We then analyzed the activity of pyramidal neurons in rat hippocampus, recorded while the animal was exploring a 2D environment, and confirmed that our method is able to detect geometric organization using …

Some Effects Of The Human Genome Project On The Erdős Collaboration Graph, Chris Fields

Journal of Humanistic Mathematics

The Human Genome Project introduced large-scale collaborations involving dozens to hundreds of scientists into biology. It also created a pressing need to solve discrete mathematics problems involving tens of thousands of elements. In this paper, we use minimal path lengths in the Erdős Collaboration Graph between prominent individual researchers as a measure of the distance between disciplines, and we show that the Human Genome Project brought laboratory biology as a whole closer to mathematics. We also define a novel graph reduction method and a metric that emphasizes the robustness of collaborative connections between researchers; these can facilitate the analysis of …

Epistasis In Predator-Prey Relationships, Iuliia Inozemtseva

College of Graduate Studies: Theses & Dissertations

Epistasis is the interaction between two or more genes to control a single phenotype. We model epistasis of the prey in a two-locus two-allele problem in a basic predator- prey relationship. The resulting model allows us to examine both population sizes as well as genotypic and phenotypic frequencies. In the context of several numerical examples, we show that if epistasis results in an undesirable or desirable phenotype in the prey by making the particular genotype more or less susceptible to the predator or dangerous to the predator, elimination of undesirable phenotypes and then genotypes occurs.

Random Search Models Of Foraging Behavior: Theory, Simulation, And Observation, Ben C. Nolting

Department of Mathematics: Dissertations, Theses, and Student Research

Many organisms, from bacteria to primates, use stochastic movement patterns to find food. These movement patterns, known as search strategies, have recently be- come a focus of ecologists interested in identifying universal properties of optimal foraging behavior. In this dissertation, I describe three contributions to this field. First, I propose a way to extend Charnov's Marginal Value Theorem to the spatially explicit framework of stochastic search strategies. Next, I describe simulations that compare the efficiencies of sensory and memory-based composite search strategies, which involve switching between different behavioral modes. Finally, I explain a new behavioral analysis protocol for identifying the …

Oyun: A New, Free Program For Iterated Prisoner’S Dilemma Tournaments In The Classroom, Charles H. Pence, Lara Buchak

Faculty Publications

Evolutionary applications of game theory present one of the most pedagogically accessible varieties of genuine, contemporary theoretical biology. We present here Oyun (oy-oon, http://charlespence.net/oyun), a program designed to run iterated prisoner's dilemma tournaments, competitions between prisoner's dilemma strategies developed by the students themselves. Using this software, students are able to readily design and tweak their own strategies, and to see how they fare both in round-robin tournaments and in “evolutionary” tournaments, where the scores in a given “generation” directly determine contribution to the population in the next generation. Oyun is freely available, runs on Windows, Mac, and Linux computers, …