Physical Sciences and Mathematics Commons^™

Sers For The Detection Of Trace Materials, Omari Kirkland

Dissertations, Theses, and Capstone Projects

In this dissertation are presented three projects that contribute to the body of research on SERS in the forensic, heritage, and semiconductor fields. The first project, Charge-Transfer mapping on GaN/Ag, a silver-decorated nanopillar semiconductor substrate fabricated from the GaN is used with the Raman probe Rhodamine 6 G (R6G) to map the effect of the nanofeatures on the CT resonance. The second project, in collaboration with Marco Leona from the Metropolitan Museum of Art, explores the use of AgNIFs to identify colorants used on textile fiber samples from four 19th century works of Japanese art. The final project analyzes the …

Untangling The Nature And Timescales Of Magmatic Processes Driving Eruptions At Quiescent Volcanoes: Examples From Momotombo, Nicaragua, And Cumbre Vieja, Canary Islands, Samantha Tramontano

Dissertations, Theses, and Capstone Projects

Across all scales of human relationships (i.e. person-to-person, country-to-country, etc.), qualms can take the form of long-standing wars, quick and intense bouts, or petty exchanges. While our understanding of human behavior is ever increasing, reactions and behaviors of self and others may still come as a surprise. Expressions of disagreement can occur suddenly or following years to centuries of accumulated grievances. The solid earth is also a system that behaves (like human emotion) predictably at times and unpredictably at other times. Some volcanoes, a tangible surface expression of solid earth processes, exhibit precursory signals prior to eruption (e.g. the bulging …

Pedagogical Prisms: Toward Domain Isomorphic Analogy Design For Relevance And Engagement In Computing Education, Briana Christina Bettin, Linda Ott

Michigan Tech Publications

Analogy is a frequently leveraged pedagogical tool used across many disciplines, with computing being no exception. Computing education researchers, however, have raised concerns regarding the limitations of analogy. One obvious concern is the relevance of any given analogy to learners. Designing relevant analogies can greatly increase student engagement with the problem space by centering examples on their lived experiences. Relevant analogies can also facilitate learners in building appropriate connections as they explore novel concepts. Designing relevant analogies is an ongoing process which requires understanding the learners' context. It is unlikely that any given analogy will be "universally"relevant across learners, problems, …

Comparative Analyses Define Differences Between Bhd-Associated Renal Tumour And Sporadic Chromophobe Renal Cell Carcinoma, Young-Seok Ju, Hwajin Lee, Kyungsik Ha, Woojeung Song, Youngwook Kim, Yuki Okawa, Shota Sasagawa, Yuki Kanazashi, Masashi Fujita, Seiya Imoto, Taku Mitome, Shinji Ohtake, Go Noguchi, Sachi Kawaura, Yasuhiro Iribe, Kota Aomori, Tomoyuki Tatenuma, Mitsuru Komeya, Hiroki Ito, Yusuke Ito, Kentaro Muraoka, Mitsuko Furuya, Ikuma Kato, Satoshi Fujii, Haruka Hamanoue, Tomohiko Tamura, Masaya Baba, Toshio Suda, Tatsuhiko Kodama, Kazuhide Makiyama, Masahiro Yao, Brian M Shuch, Christopher J Ricketts, Laura S Schmidt, W Marston Linehan, Hidewaki Nakagawa, Hisashi Hasumi

Faculty, Staff and Student Publications

BACKGROUND: Birt-Hogg-Dubé (BHD) syndrome, caused by germline alteration of folliculin (FLCN) gene, develops hybrid oncocytic/chromophobe tumour (HOCT) and chromophobe renal cell carcinoma (ChRCC), whereas sporadic ChRCC does not harbor FLCN alteration. To date, molecular characteristics of these similar histological types of tumours have been incompletely elucidated.

METHODS: To elucidate renal tumourigenesis of BHD-associated renal tumours and sporadic renal tumours, we conducted whole genome sequencing (WGS) and RNA-sequencing (RNA-seq) of sixteen BHD-associated renal tumours from nine unrelated BHD patients, twenty-one sporadic ChRCCs and seven sporadic oncocytomas. We then compared somatic mutation profiles with FLCN variants and RNA expression profiles between BHD-associated …

The Integrative Studies On The Functional A-To-I Rna Editing Events In Human Cancers, Xiaobo Zhou

Faculty, Staff and Student Publications

Adenosine-to-inosine (A-to-I) RNA editing, constituting nearly 90% of all RNA editing events in humans, has been reported to contribute to the tumorigenesis in diverse cancers. However, the comprehensive map for functional A-to-I RNA editing events in cancers is still insufficient. To fill this gap, we systematically and intensively analyzed multiple tumorigenic mechanisms of A-to-I RNA editing events in samples across 33 cancer types from The Cancer Genome Atlas. For individual candidate among ∼ 1,500,000 quantified RNA editing events, we performed diverse types of downstream functional annotations. Finally, we identified 24,236 potentially functional A-to-I RNA editing events, including the cases …

Rapid-Query For Fast Identity By Descent Search And Genealogical Analysis

Faculty, Staff and Student Publications

MOTIVATION: Due to the rapid growth of the genetic database size, genealogical search, a process of inferring familial relatedness by identifying DNA matches, has become a viable approach to help individuals finding missing family members or law enforcement agencies locating suspects. A fast and accurate method is needed to search an out-of-database individual against millions of individuals. Most existing approaches only offer all-versus-all within panel match. Some prototype algorithms offer one-versus-all query from out-of-panel individual, but they do not tolerate errors.

RESULTS: A new method, random projection-based identity-by-descent (IBD) detection (RaPID) query, is introduced to make fast genealogical search possible. …

Community Perspectives On Ai/Ml And Health Equity: Aim-Ahead Nationwide Stakeholder Listening Sessions, Katie Stinson, Toufeeq Ahmed Syed

Faculty, Staff and Student Publications

Artificial intelligence and machine learning (AI/ML) tools have the potential to improve health equity. However, many historically underrepresented communities have not been engaged in AI/ML training, research, and infrastructure development. Therefore, AIM-AHEAD (Artificial Intelligence/Machine Learning Consortium to Advance Health Equity and Researcher Diversity) seeks to increase participation and engagement of researchers and communities through mutually beneficial partnerships. The purpose of this paper is to summarize feedback from listening sessions conducted by the AIM-AHEAD Coordinating Center in February 2022, titled the "AIM-AHEAD Community Building Convention (ACBC)." A total of six listening sessions were held over three days. A total of 977 …

A Novel Integrated Approach To Predicting Cancer Immunotherapy Efficacy, Weiling Zhao, Xiaobo Zhou

Faculty, Staff and Student Publications

Immunotherapies have revolutionized cancer treatment modalities; however, predicting clinical response accurately and reliably remains challenging. Neoantigen load is considered as a fundamental genetic determinant of therapeutic response. However, only a few predicted neoantigens are highly immunogenic, with little focus on intratumor heterogeneity (ITH) in the neoantigen landscape and its link with different features in the tumor microenvironment. To address this issue, we comprehensively characterized neoantigens arising from nonsynonymous mutations and gene fusions in lung cancer and melanoma. We developed a composite NEO2IS to characterize interplays between cancer and CD8+ T-cell populations. NEO2IS improved prediction accuracy of patient responses to immune-checkpoint …

Diverged Landscape Of Restaurant Recovery From The Covid-19 Pandemic In The United States, Siqin Wang, Xiao Huang, Bing She, Zhenlong Li

Geosciences Faculty Publications and Presentations

The COVID-19 pandemic has imposed catastrophic impacts on the restaurant industry as a crucial socioeconomic sector that contributes to the global economy. However, the understanding of how the restaurant industry was recovered from COVID-19 remains underexplored. This study constructs a spatially explicit evaluation of the effect of COVID-19 on the restaurant industry in the US, drawing on the attributes of +200,000 restaurants from Yelp and +600 million individual-level restaurant visitations provided by SafeGraph from 1st January 2019 to 31st December 2021. We produce quantitative evidence of lost restaurant visitations and revenue amid the pandemic, the changes in the customers’ origins, …

Optimal Domain-Partitioning Algorithm For Real-Life Transportation Networks And Finite Element Meshes, Jimesh Bhagatji, Sharanabasaweshwara Asundi, Eric Thompson, Duc T. Nguyen

Civil & Environmental Engineering Faculty Publications

For large-scale engineering problems, it has been generally accepted that domain-partitioning algorithms are highly desirable for general-purpose finite element analysis (FEA). This paper presents a heuristic numerical algorithm that can efficiently partition any transportation network (or any finite element mesh) into a specified number of subdomains (usually depending on the number of parallel processors available on a computer), which will result in “minimising the total number of system BOUNDARY nodes” (as a primary criterion) and achieve “balancing work loads” amongst the subdomains (as a secondary criterion). The proposed seven-step heuristic algorithm (with enhancement features) is based on engineering common sense …

2023 Residential Metals Abatement Program (Rmap) Field Sampling Plan (Fsp) – Interior Soils - Silver Bow Montessori, Environmental Resource Management (Erm)

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Cpsrp43 Is Both Highly Flexible And Stable: Structural Insights Using A Combined Experimental And Computational Approach, Mitchell Benton, Mercede Furr, Vivek Govind Kumar, Adithya Polasa, Feng Gao, Colin David Heyes, Thallapuranam Krishnaswamy Suresh Kumar, Mahmoud Moradi

Chemistry & Biochemistry Faculty Publications and Presentations

The novel multidomain protein, cpSRP43, is a unique subunit of the post-translational chloroplast signal recognition particle (cpSRP) targeting pathway in higher plants. The cpSRP pathway is responsible for targeting and insertion of light-harvesting chlorophyll a/b binding proteins (LHCPs) to the thylakoid membrane. Upon emergence into the stroma, LHCPs form a soluble transit complex with the cpSRP heterodimer, which is composed of cpSRP43 and cpSRP54. cpSRP43 is irreplaceable as a chaperone to LHCPs in their translocation to the thylakoid membrane and remarkable in its ability to dissolve aggregates of LHCPs without the need for external energy input. In previous studies, cpSRP43 …

The Alternating Access Mechanism In Mammalian Multidrug Resistance Transporters And Their Bacterial Homologs, Shadi A. Badiee, Ugochi H. Isu, Ehsaneh Khodadadi, Mahmoud Moradi

Chemistry & Biochemistry Faculty Publications and Presentations

Multidrug resistance (MDR) proteins belonging to the ATP-Binding Cassette (ABC) transporter group play a crucial role in the export of cytotoxic drugs across cell membranes. These proteins are particularly fascinating due to their ability to confer drug resistance, which subsequently leads to the failure of therapeutic interventions and hinders successful treatments. One key mechanism by which multidrug resistance (MDR) proteins carry out their transport function is through alternating access. This mechanism involves intricate conformational changes that enable the binding and transport of substrates across cellular membranes. In this extensive review, we provide an overview of ABC transporters, including their classifications …

Generalizing Graph Neural Networks Across Graphs, Time, And Tasks, Zhihao Wen

Dissertations and Theses Collection (Open Access)

Graph-structured data are ubiquitous across numerous real-world contexts, encompassing social networks, commercial graphs, bibliographic networks, and biological systems. Delving into the analysis of these graphs can yield significant understanding pertaining to their corresponding application fields.Graph representation learning offers a potent solution to graph analytics challenges by transforming a graph into a low-dimensional space while preserving its information to the greatest extent possible. This conversion into low-dimensional vectors enables the efficient computation of subsequent graph algorithms. The majority of prior research has concentrated on deriving node representations from a single, static graph. However, numerous real-world situations demand rapid generation of representations …

Stability Of Retinol In Liposomes As Measured By Fluorescence Lifetime Spectroscopy And Flim, Louis Sumrall, L. Smith, Elmukhtar Ehmed Alhatmi, Yekaterina G. Chmykh, D. Mitchell, Jay Nadeau

Physics Faculty Publications and Presentations

Retinol shows complex photophysical properties that make it potentially useful as an exogenous or endogenous probe of membrane microenvironment, but it has not been fully explored. In this study, we use bulk fluorescence lifetime measurements and fluorescence lifetime imaging microscopy (FLIM) to examine the stability of retinol in phosphatidylcholine (PC) multilamellar and unilamellar vesicles with and without cholesterol. We find that both light and exposure to ambient temperature and oxygen contribute to retinol degradation, with the addition of an antioxidant such as butylated hydroxytoluene (BHT) essential to provide stability, especially in the absence of cholesterol. With exposure to ultraviolet light …

Solitary Waves In A Quantum Droplet-Bearing System, Garyfallia Katsimiga, Simeon I. Mistakidis, G. N. Koutsokostas, D. J. Frantzeskakis, R. Carretero-González, P. G. Kevrekidis

Physics Faculty Research & Creative Works

We Unravel The Existence And Stability Properties Of Dark Soliton Solutions As They Extend From The Regime Of Trapped Quantum Droplets Towards The Thomas-Fermi Limit In Homonuclear Symmetric Bose Mixtures. Leveraging A Phase-Plane Analysis, We Identify The Regimes Of Existence Of Different Types Of Quantum Droplets And Subsequently Examine The Possibility Of Black And Gray Solitons And Kink-Type Structures In This System. Moreover, We Employ The Landau Dynamics Approach To Extract An Analytical Estimate Of The Oscillation Frequency Of A Single Dark Soliton In The Relevant Extended Gross-Pitaevskii Model. Within This Framework, We Also Find That The Single Soliton Immersed …

Earth Steward: Will Steffen's Contributions To Earth System Science, Governance And Law, W.J. Boonstra, P. Magalhães, B. J. Preston, J. Taylor Rockström

Research Collection Yong Pung How School Of Law

In January 2023, the world lost one of its most influential environmental scientists, Will Steffen. Recognised by his peers as the ‘Father of Earth System Science’, Steffen exemplified the ethic of planetary stewardship (Stockholm Resilience Centre 2023; Fig. 1). This ethic was especially evident, not only in Steffen’s scholarship, but also in his contributions to creating institutions that respect the reality of a single integrated Earth System and aim to govern human behaviour accordingly (Steffen 2016). This article commemorates Will Steffen’s scientific work in Earth System Science, and places it in the larger context of his contributions to governance and …

Law Smells: Defining And Detecting Problematic Patterns In Legal Drafting, Corinna Coupette, Dirk Hartung, Janis Beckedorf, Maximilian Bother, Daniel Martin Katz

Research Collection Yong Pung How School Of Law

Building on the computer science concept of code smells, we initiate the study of law smells, i.e., patterns in legal texts that pose threats to the comprehensibility and maintainability of the law. With five intuitive law smells as running examples—namely, duplicated phrase, long element, large reference tree, ambiguous syntax, and natural language obsession—, we develop a comprehensive law smell taxonomy. This taxonomy classifies law smells by when they can be detected, which aspects of law they relate to, and how they can be discovered. We introduce text-based and graph-based methods to identify instances of law smells, confirming their utility in …

Artificial Intelligence Cad Tools In Trauma Imaging: A Scoping Review From The American Society Of Emergency Radiology (Aser) Ai/Ml Expert Panel, Zhaoyong Feng, J Stephen Spann, Nathan Sarkar, Yunting Fu

Faculty, Staff and Student Publications

BACKGROUND: AI/ML CAD tools can potentially improve outcomes in the high-stakes, high-volume model of trauma radiology. No prior scoping review has been undertaken to comprehensively assess tools in this subspecialty.

PURPOSE: To map the evolution and current state of trauma radiology CAD tools along key dimensions of technology readiness.

METHODS: Following a search of databases, abstract screening, and full-text document review, CAD tool maturity was charted using elements of data curation, performance validation, outcomes research, explainability, user acceptance, and funding patterns. Descriptive statistics were used to illustrate key trends.

RESULTS: A total of 4052 records were screened, and 233 full-text …

Attainable And Sustainable Home Building Solutions, Katrina Matthews

Construction Management

Sustainability has fortunately been a recent concern in the construction industry as climate change continues to impose potentially insurmountable threats to the global environment. Although many new methods have been adopted in efforts to lessen the adverse environmental effects of construction-related activities, as a society, we still have much room for growth as the built environment accounts for almost 50% of global emissions. Many changes and standards must be adopted to make these solutions efficiently beneficial. To set industry standards, we must start with the most basic form of construction- residential building. This report covers two attainable framing solutions for …

Exploring The Potential Of Pavegen’S Kinetic Energy Generating Floor For Sustainable Energy Solutions: A Proposal For Cal Poly Slo, Brandon J. Cuneo

Construction Management

This paper proposes the installation of Pavegen's kinetic energy generating floors at Cal Poly’s campus as a sustainable energy solution. Pavegen has developed a pioneering technology that converts footsteps into clean and renewable energy. The versatility of these floors is demonstrated through successful implementations in various settings, such as transportation hubs and public spaces, generating power from foot traffic. Collaborations with Schneider Electric, installation at Dupont Circle, and integration at Heathrow Airport showcase the potential for sustainable urban infrastructure. This paper outlines research conducted on Pavegen and similar solutions, including communication with company representatives and examining proposed installation locations at …

Diffusion-Driven Aggregation Of Particles In Quasi-2d Membranes, Oscar Gullickson Rausis

Physics

Many biological membranes can be modeled as two-dimensional (2D) viscous fluid sheets surrounded by three-dimensional (3D) fluids of different viscosity. Such membranes are dubbed quasi-2D as they exhibit properties of both 2D and 3D fluids. The Saffman length is a parameter that describes the energy exchange between the membrane and bulk fluids and controls the cross-over from 2D to 3D hydrodynamics. We aim to model diffusion-driven aggregation of particles embedded in a quasi-2D membrane. It is known that hydrodynamic interactions between solute particles significantly reduce their aggregation rate in 3D fluids. It is expected that in quasi-2D membranes the reduction …

Optimizing Solid Thermal Storage In Insulated Solar Electric Cookers, Stefan Avramov

Physics

Insulated Solar Electric Cookers, more commonly known by their acronym ISECookers, are an alternative to biomass cooking. The ISECooker in its simplest form is a solar panel connected to a heating element, in contact with a cooking pot in an insulated chamber. An aluminum puck can be heated as solid thermal storage (STS) for increased power and night time cooking. Power was limited to about 500 W by the interface between the STS and cookpot. Powdered graphite and silver were separately applied to increase thermal flow. However, the powdered graphite decreased the thermal flow, while powdered silver decreased the temperature …

Neuroevolution Application To Collaborative And Heuristics-Based Connected And Autonomous Vehicle Cohort Simulation At Uncontrolled Intersection, Frederic Jacquelin, Jungyun Bae, Bo Chen, Darrell Robinette

Michigan Tech Publications

Artificial intelligence is gaining tremendous attractiveness and showing great success in solving various problems, such as simplifying optimal control derivation. This work focuses on the application of Neuroevolution to the control of Connected and Autonomous Vehicle (CAV) cohorts operating at uncontrolled intersections. The proposed method implementation’s simplicity, thanks to the inclusion of heuristics and effective real-time performance are demonstrated. The resulting architecture achieves nearly ideal operating conditions in keeping the average speeds close to the speed limit. It achieves twice as high mean speed throughput as a controlled intersection, hence enabling lower travel time and mitigating energy inefficiencies from stop-and-go …

Supramolecular Design Of 3d-Printable Hydrogels For Functional Materials, Miao Tang

Dartmouth College Ph.D Dissertations

Additive manufacturing, more commonly known as 3D-printing, is bringing about a grand technological transformation in material design and fabrication. In contrast to traditional fabrication techniques, 3D-printing features rapid prototyping, complex and customized 3D structural designs, and multi-material integration. Among current 3D-printing systems, direct-ink-writing (DIW) exhibits unique functionalities due to its mild operation conditions and the ability to integrate various organic and inorganic entities. Although supramolecular binding motifs are increasingly utilized in 3D-printing designs, the optimization of 3D-printable inks remains largely empirical. In this thesis, we present two strategies to rationally design supramolecularly crosslinked 3D-printable hydrogels, including (1) micro-crystallization and (2) …

Predicting Hiv Vaccine-Mediated Protection Level To Identify Immune Correlates Using Positive Unlabeled Learning, Shiwei Xu

Dartmouth College Ph.D Dissertations

The development of a vaccine for Human Immunodeficiency Virus type 1 (HIV-1) is a crucial step in preventing the global spread of AIDS. To ensure the progress and effectiveness of this vaccine, it is essential to establish efficient biotechnology platforms and data mining methods. These methods would help identify immune characteristics that distinguish individuals with varying levels of vaccine-induced protection and determine the underlying factors that contribute to protection against HIV acquisition. While previous studies have focused on identifying immune markers associated with infection outcomes among vaccinated patients, it is important to acknowledge the limitations of traditional case-control analytical protocols …

More (Sema|Meta)Phors: Additional Perspectives On Analogy Use From Concurrent Programming Students, Briana Christina Bettin, Linda Ott, Julia Hiebel

Michigan Tech Publications

A concurrent computing course is filled with challenges for upper-level programming students. Understanding concurrency provides deeper insight into many modern computing and programming language behaviors, but the subject matter can be difficult even for relatively proficient students. It can be a challenge to help students navigate and understand these unfamiliar topics. While there is a difference in general programming familiarity, teaching this novel material is not unlike some challenges faced when engaging introductory students with first programming concepts. In this work, we explore the use of analogy by students while learning a novel programming methodology. We investigate perceptions of the …

Assessing Dynamics And Trends Of Co2 Flux On The Louisiana Shelf, Claire Mcguire

Master's Theses

The Gulf of Mexico on an annual timescale acts as a sink for ­CO₂. Previous studies have investigated regional-scale trends in the Gulf based on model output. In our investigation of the northern Gulf of Mexico, and especially the area surrounding the Louisiana delta, we found different trends compared with previous studies of the open ocean Gulf and broader shelf region. Predictions of global patterns of the ocean CO₂ cycle require regional studies of unique areas like the Louisiana Shelf. The Louisiana Shelf is a shallow system, has input from river systems, experiences seasonal hypoxia, and is …

Understanding The Flow Dynamics Of The Pearl River, Ms, Through Hydrodynamic Modeling, Nahruma Mehzabeen Pieu

Master's Theses

The Pearl River brings fresh water and nutrients into Lake Borgne regulating conditions for oyster growth in estuarine waters. However, there are no flow measurement stations installed on East Pearl or West Pearl either at the river outlets or after the upstream bifurcation of the Pearl. This study aims to model the Lower Pearl River to understand the flow dynamics in the major branches, and to determine the final outflow distribution into the Mississippi Sound, aiming to improve river forcing for ocean models studying estuarine dynamics of the Mississippi Sound.

Synthetic meandering bathymetry with updated banks is developed and applied …

Synthesis And Study Of High-Spin Stable Organic Radicals For Electrical Conductors And Mannosamine Nitroxide For Mri Contrast Agents, Shuyang Zhang

Department of Chemistry: Dissertations, Theses, and Student Research

In the first project, we describe the synthesis of an ambient stable high spin organic diradical 4 based on the Blatter moiety. The high-spin (S = 1) organic diradical 4, which consists of two Blatter radical moieties in a conjugated structure, exhibits a nearly exclusive population (88%) on triplet ground state at room temperature as a consequence of a large single-triplet energy gap (ΔEST = 0.5 kcal/mol). The target diradical molecule is synthesized over five steps with structural confirmation by single-crystal X-ray diffraction. The thermogravimetric analysis (TGA) shows the onset of decomposition at ~264 oC, indicating the diradical molecule has …