Physical Sciences and Mathematics Commons^™

Probing Conformational Landscapes And Mechanisms Of Allosteric Communication In The Functional States Of The Abl Kinase Domain Using Multiscale Simulations And Network-Based Mutational Profiling Of Allosteric Residue Potentials, Keerthi Krishnan, Hao Tian, Peng Tao, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

In the current study, multiscale simulation approaches and dynamic network methods are employed to examine the dynamic and energetic details of conformational landscapes and allosteric interactions in the ABL kinase domain that determine the kinase functions. Using a plethora of synergistic computational approaches, we elucidate how conformational transitions between the active and inactive ABL states can employ allosteric regulatory switches to modulate intramolecular communication networks between the ATP site, the substrate binding region, and the allosteric binding pocket. A perturbation-based network approach that implements mutational profiling of allosteric residue propensities and communications in the ABL states is proposed. Consistent with …

Closing The Concern-Action Gap Through Relational Climate Conversations: Insights From Us Climate Activists, Julia Coombs Fine

Environmental Studies Faculty Publications

Several studies have found that relational climate conversations can be an effective method of increasing conversational participants’ concern about the climate crisis and encouraging them to take collective action. However, little work has yet examined how such conversations are practiced by climate activists, a group with expertise in relational organizing. Drawing on surveys and semi-structured interviews with climate activists across the USA, this analysis finds that activists frequently have climate conversations with friends and family, most of whom are politically progressive and somewhat to very concerned about the climate crisis. These findings might seem to suggest that climate activists only …

Predicting The Outcomes Of Internet-Based Cognitive Behavioral Therapy For Tinnitus: Applications Of Artificial Neural Network And Support Vector Machine, Hansapani Rodrigo, Eldré W. Beukes, Gerhard Andersson, Vinaya Manchaiah

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

Purpose:

Internet-based cognitive behavioral therapy (ICBT) has been found to be effective for tinnitus management, although there is limited understanding about who will benefit the most from ICBT. Traditional statistical models have largely failed to identify the nonlinear associations and hence find strong predictors of success with ICBT. This study aimed at examining the use of an artificial neural network (ANN) and support vector machine (SVM) to identify variables associated with treatment success in ICBT for tinnitus.

Method:

The study involved a secondary analysis of data from 228 individuals who had completed ICBT in previous intervention studies. A 13-point reduction …

Artificial Intelligence In The Medical Field: Medical Review Sentiment Analysis, Nicholas Podlesak

Honors Capstones

In this research project, natural language processing techniques’ ability to accurately classify medical text was measured to reinforce the relevance of artificial intelligence in the medical field. Sentiment analyses (analyses to determine whether the text was positive or negative) were performed on the prescription drug reviews in an open-source dataset using four different models: lexical, a neural network, a support vector machine, and a logistic regression model. Each model’s effectiveness was gauged by its ability to correctly classify unlabeled drug reviews (i.e., a percentage representing accuracy). The machine learning models were able to accurately classify the text, while the lexical …

Ideals Of Functions With Compact Support In The Integer-Valued Case, Themba Dube, Oghenetega Ighedo, Batsile Tlharesakgosi

Mathematics, Physics, and Computer Science Faculty Articles and Research

For a zero-dimensional Hausdorff space X, denote, as usual, by C(X, ℤ) the ring of continuous integer-valued functions on X. If f ∈ C(X, ℤ), denote by Z(f) the set of all points of X that are mapped to 0 by f. The set C_K(X; ℤ) = {f ∈ C(X; ℤ) | cl_X(X \ Z(f)) is compact} is the integer-valued analogue of the ideal of functions with compact support in C(X). By first working in the category of locales and then interpreting …

Algorithms For Compression Of Electrocardiogram Signals, Yuliyan Velchev

Books

The study is dedicated to modern methods and algorithms for compression of electrocardiogram (ECG) signals. In its original part, two lossy compression algorithms based on a combination of linear transforms are proposed. These algorithms are with relatively low computational complexity, making them applicable for implementation in low power designs such as mobile devices or embedded systems. Since the algorithms do not provide perfect signal reconstruction, they would find application in ECG monitoring systems rather than those intended for precision medical diagnosis.

This monograph consists of abstract, preface, five chapters and conclusion. The chapters are as follows: Chapter 1 — Introduction …

Synthesis And Surface Modification Of Azide Decorated Silver Nanoclusters, Alexander H. Stöckli

Electronic Thesis and Dissertation Repository

In nanocluster research, easy modification of the cluster surface while maintaining the cluster core remains a key challenge. Herein we report the synthesis, structure, and properties of four targeted Ag₂₀ nanoclusters (NCs) with surface azide moieties, two of which have 8 azide moieties, [CO₃@Ag₂₀(S^tBu)₁₀(m-N₃-C₆H₄COO)₈(DMF)₄] and [CO₃@Ag₂₀(S^tBu)₁₀(p-N₃-C₆H₄COO)₈(DMF)₄], and two of which have 6 azide moieties, [CO₃@Ag₂₀(S …

Sturgeon Chub Distributional Patterns And Habitat Use And Benthic Fish Assemblage Structure In Missouri River Tributaries Of South Dakota, Mitchell R. Magruder

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

Native species of the Missouri River drainage inhabiting benthic habitats dominate state and federal lists of species at risk. Sicklefin Chub Macrhybopsis meeki and Sturgeon Chub Macrhybopsis gelida are two native Missouri River benthic minnows that are currently under review for federal listing under the Endangered Species Act (ESA) due to extensive population declines and local extirpations within their native range. Substantial alterations to the Missouri River threaten Macrhybopsis spp. and other benthic fishes; however, large, less impacted tributaries in South Dakota may act as refugia for native species. The extent of Sicklefin Chub and Sturgeon Chub populations is largely …

Demographic Groups Differ In Urban Recreational Behavior, Brandon Barlow

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

Urban recreational behavior is an essential component to understanding both how our recreational opportunities will be utilized and how they can be further improved. By improving recreational opportunities, we can ensure safe and reliable emotional and physical outlets for users. As urban areas continue to expand both in geographic area and in population size, urban recreational opportunities will also see growth in the number of recreational users. Demographics provide the opportunity to further understand and predict recreational behavior, producing a variety of decision management tools. Our goal was to understand differences in urban recreational behavior among demographic groups. To address …

The History Of The Enigma Machine, Jenna Siobhan Parkinson

History Publications

The history of the Enigma machine begins with the invention of the rotor-based cipher machine in 1915. Various models for rotor-based cipher machines were developed somewhat simultaneously in different parts of the world. However, the first documented rotor machine was developed by Dutch naval officers in 1915. Nonetheless, the Enigma machine was officially invented following the end of World War I by Arthur Scherbius in 1918 (Faint, 2016).

Wrack Lines Volume 22, Number 2, Fall-Winter 2022-2023, Nancy C. Balcom, Juliana Barrett, Judy Benson, Ben Crnic, Sto Len

Wrack Lines

With the theme, "Looking Ahead: People and Projects Shaping the Future," the Fall-Winter 2022-2023 leads with the first in what will be a series of articles about offshore wind development impacting Connecticut. That is followed by the inspiring story of how a dying forest was replanted for climate resilience. Next, a profile of longtime marine educator Tim Visel tells about his lasting impact on Connecticut schools and students. Lastly, the complex challenge of dealing with Contaminants of Emerging Concern is examined, with descriptions of how Sea Grant is involved and the particularly troublesome group of substances called PFAS.

2022 - The Third Annual Fall Symposium Of Student Scholars

Symposium of Student Scholars Program Books

The full program book from the Fall 2022 Symposium of Student Scholars, held on November 17, 2022. Includes abstracts from the presentations and posters.

A Human Oral Fluid Assay For D- And L- Isomer Detection Of Amphetamine And Methamphetamine Using Liquid-Liquid Extraction, Brian Robbins, Rob E. Carpenter, Mary Long, Jacob Perry

Human Resource Development Faculty Publications and Presentations

Medical providers are increasingly confronted with clinical decision-making that involves (meth)amphetamines. And clinical laboratories need a sensitive, efficient assay for routine assessment of D- and L-isomers to determine the probable source of these potentially illicit analytes. This paper presents a validated method of D- and L-isomer detection in human oral fluid from an extract used for determination of a large oral fluid assay (63 analytes) on an older AB SCIEX 4000 instrument. Taken from the positive extract, D- and L-analytes were added. The method for extraction included addition of internal standard and a 2-step …

Safe Sharing For Sensitive Data, Kristi Thompson

Western Libraries Presentations

This workshop focused on the question of when and how human subjects' data can be safely shared. It introduced the basics of data anonymization and discussed how to tell if a dataset has been de-identified. Case studies of successful anonymization and some spectacular failures were shared

An Empirical Study On The Classification Of Python Language Features Using Eye-Tracking, Jigyasa Chauhan

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Python, currently one of the most popular programming languages, is an object-
oriented language that also provides language feature support for other programming
paradigms, such as functional and procedural. It is not currently understood how
support for multiple paradigms affects the ability of developers to comprehend that
code. Understanding the predominant paradigm in code, and how developers classify
the predominant paradigm, can benefit future research in program comprehension as
the paradigm may factor into how people comprehend that code. Other researchers
may want to look at how the paradigms in the code interact with various code smells.
To investigate how …

On A Guiding Of Whistler-Mode Waves By Density Gradients, Anatoly V. Streltsov

Publications

Observations from satellites demonstrate that in the magnetosphere, VLF whistler-mode waves are frequently detected in the narrow transition regions, where the plasma density changes its magnitude over a short distance across the ambient magnetic field. These observations suggest that the small-scale, isolated density gradients can guide the VLF whistler-mode waves along the field. We investigate the guiding of the whistler-mode waves by the transverse density gradients with a size much less than the characteristic perpendicular size of the wave. We found analytical solutions describing these waves in the plasma with a sharp density discontinuity between two homogeneous regions, and confirm …

2022 Draft Final Blacktail Creek Groundwater Hydraulic Control System Remedial Design Work Plan, Stantec Consulting Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Medical Monitoring Working Group Meeting Minutes, Mike Mcanulty

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

2022 Draft Final Blacktail Creek Groundwater Hydraulic Control System Remedial Design Work Plan, Stantec Consulting Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

The Contribution Of Non-Tropical Cyclone Vortices To The Rainfall Of The Philippines, Lyndon Mark P. Olaguera, Jun Matsumoto, John A. Manalo

Physics Faculty Publications

Weaker disturbances than tropical cyclones (TCs) such as tropical depressions and cold surges can significantly induce heavy rainfall and flooding events over the Philippines. However, the analysis of these disturbances including their rainfall contributions are often neglected in previous studies. As the first attempt to address this research gap, this study investigates the rainfall contribution of non-TC vortices over the Philippines from 1979 to 2020. Only those rainfall-producing non-TC vortices that formed and appeared within a 500-km radius from the Philippine coastline were examined in this study. A total of 7,686 non-TC vortex days (50% of the total days during …

Stabilization Of Zero-Energy Skin Modes In Finite Non-Hermitian Lattices, Cem Yuce, Hamidreza Ramezani

Physics and Astronomy Faculty Publications and Presentations

The zero energy of a one-dimensional semi-infinite non-Hermitian lattice with nontrivial spectral topology may disappear when we introduce boundaries to the system. While the corresponding zero-energy state can be considered as a quasi-edge state for the finite lattice with a long survival time, any small disruption (noise) in the initial form of the quasi-edge state can significantly shorten the survival time. Here, by tailoring the couplings at one edge we form an exceptional point allowing for a topological phase transition and the stabilization of the quasi-edge state in a finite-size lattice with open edges. Such a small modification in the …

Improving Adjacency List Storage Methods For Polypeptide Similarity Analysis, Arianna Swensen

Honors Theses

Protein design is a complex biomolecular and computational problem. Working on increasingly large protein folding problems requires an improvement in current analysis methods available. This work first discusses various methods of protein design, including de novo protein design, which is the primary focus of this thesis. Then, a new approach utilizing a B+ tree to effectively store and query a graph of keys and vertices is proposed in order to store the number of times two polypeptides are considered to be similar. This approach is found to have a reduction in time complexity from current mapping methods and thus provides …

Scaling Epa-Rimm With Multicore System Management Interrupt Handlers, Alexander K. Freed

Dissertations and Theses

Continuous runtime integrity measurement mechanisms (RIMMs) can be used for timely detection of kernel and hypervisor rootkits. Researchers have proposed running RIMMs in privileged execution environments, such as the x86 architecture’s System Management Mode (SMM), to detect interference from rootkits that have gained control of the host operating system. However, the extended amount of time in SMM required to perform inspections can cause severe disruption to the host. A previously proposed RIMM design called EPA-RIMM addresses this by decomposing long inspections across multiple System Management Interrupts (SMI), the interrupt used to invoke SMM.

EPA-RIMM is intended for deployment on server-class …

Methods For Single-Cell And Low-Input Proteomics, Yiran Liang

Theses and Dissertations

Single-Cell Proteomics (SCP) can provide unique insights into biological processes by resolving heterogeneity that is obscured by bulk measurements. Gains in the overall sensitivity and proteome coverage through improvements in sample processing and analysis increase the information content obtained from each cell, particularly for less abundant proteins. In addition to achieving in-depth proteome coverage from single cells, higher throughput measurements enable large-scale and statistically significant features within single cell populations. This dissertation focuses on method development to improve the sensitivity and throughput of SCP based on the nanoPOTS (nanodroplet Processing in One pot for Trace Samples) platform. The methods discussed …

Local Well-Posedness Of The Cauchy Problem For A P -Adic Nagumo-Type Equation, L. F. Chacón-Cortés, C. A. Garcia-Bibiano, Wilson A. Zuniga-Galindo

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

We introduce a new family of p -adic nonlinear evolution equations. We establish the local well-posedness of the Cauchy problem for these equations in Sobolev-type spaces. For a certain subfamily, we show that the blow-up phenomenon occurs and provide numerical simulations showing this phenomenon.

Congruences For Consecutive Coefficients Of Gaussian Polynomials With Crank Statistics, Dennis Eichhorn, Lydia Engle, Brandt Kronholm

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

In this paper, we establish infinite families of congruences in consecutive arithmetic progressions modulo any odd prime ℓ for the function p ( n , m , N ) , which enumerates the partitions of n into at most m parts with no part larger than N . We also treat the function p ( n , m , ( a , b ] ) , which bounds the largest part above and below, and obtain similar infinite families of congruences.

For m ≤ 4 and ℓ = 3 , simple combinatorial statistics called "cranks" witness these congruences. We prove …

Uc-249 Hemorrhage, Daniel M. Respess, Antonio S. Brewer, Kenny Tran, Sandy Li, Rick B. Watson

C-Day Computing Showcase

Hemorrhage is a fast-paced FPS action game with a focus on risky gameplay and dodging enemy attacks. Fight your way through hordes of grotesque creatures and make it to the end! The player starts with limited health but can steal more from killing enemies. Then, you can unleash this stored-up health to deal massive damage to your foes! Will you choose to be an unkillable tank? Or a brutal glass cannon?

Uc-276 Akwaaba Web Server Security Project, Jayland Vann, Ty G. Rogers, Cody Reese, Ronald W. Southern, Taiyeb Choudhury

C-Day Computing Showcase

Our team engaged in a mock cybersecurity drill. Our objective was to take on the roll of cybersecurity consultants and to secure a mock business website. Afterwards, we were to engage in the active defense of the site from another team, while perpetuating attacks on another team's site. Goals: -Secure a business website and then engage in it's active defense. -Perform a successful attack(s) on another team's website. Outcomes: -Developed a comprehensive security policy -Documented site risk and vulnerabilities -Implemented security and configuration changes

Gc-312 Gtri It Service Desk System, Koranna Nwago, Venkata Emani, Venkata Naga Rishita Gopi, Bhavishya Chatrathi, Siphiwindoda Msimanga

C-Day Computing Showcase

This overarching project would be web development, which would entail coding both the back end and the front end. The use of libraries is encouraged, but we must be cautious about licensing and ensure that this project remains as open-source as possible (a good open-source license ensures people can use, modify, redistribute, and sell without worry). This is a free and open-source project.

Uc-268 Buggy - Price Scraper Application, David W. Fitzgerald, John Blake, Anderson F. Guse, Jessica Zardoya, Paul Allen

C-Day Computing Showcase

Buggy is a desktop price scraper application that finds the best deals for users across several major retailers. Retailers include Amazon, Costco, Target, Walmart, and eBay. It simplifies bargain hunting by condensing product information from multiple websites into one, convenient place. Users can save products for future access, track search history, and compare search results with tabs for navigation. When they are ready to buy, they can simply click on the buy button and are directed to the vendor's page to check out.