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Data Driven Analysis Of Samara Seed Kinematics And Dynamics, Shashwat Sparsh

Master's Theses

Samara Seeds are a class of fruit most famously belonging to the Acer species and are characterized by their single-bladed geometry and their auto-rotation response during descent. This steady-state auto-rotation response is the subject of aerodynamic analysis which aim to quantify the performance. The period prior to the beginning of steady-state auto-rotation is classified as the transition regime and has not been the subject of intense scrutiny.

This thesis employs a data-driven approach to analyzing the kinematic and dynamic response of these seeds during both the transition and auto-rotation stages of flight to quantify the performance with respect to the …

Synthesis Of Sensitive Oligodeoxynucleotides Containing Acylated Cytosine, Adenine, And Guanine Nucleobases, Komal Chillar, Rohith Awasthy, Marina Tanasova, Shiyue Fang

Michigan Tech Publications

Background/Objective: Oligodeoxynucleotides (ODNs) containing base-labile modifications such as N4-acetyldeoxycytidine (4acC), N6-acetyladenosine (6acA), N2- acetylguanosine (2acG), and N4-methyoxycarbonyldeoxycytidine (4mcC) are highly challenging to synthesize because standard ODN synthesis methods require deprotection and cleavage under strongly basic and nucleophilic conditions, and there is a lack of ideal alternative methods to solve the problem. The objective of this work is to explore the capability of the recently developed 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) method for the incorporation of multiple 4acC modifications into a single ODN molecule and the feasibility of using the method for the incorporation of the 6acA, 2acG and 4mcC modifications into ODNs. Methods: …

Development Of Small-Molecule Inhibitors For Bacteroides, Naegleria, And Toxoplasma Microorganisms And Synthesis Of N-Heterocycles From Thiolated Ene-Ynes And Azodicarboxylates, Samuel Kwain

All Dissertations

Humans and microorganisms are intricately interconnected, with microbes constituting an essential component of human biology and ecology. This interdependence necessitates a delicate balance between leveraging beneficial microbes and mitigating the impact of harmful ones. The human gut microbiome, home to trillions of microorganisms, predominantly comprises commensal species that support health. However, dysbiosis within this ecosystem has been linked to serious diseases. For instance, an overrepresentation of Bacteroides species is associated with Type I diabetes mellitus (T1D) and various chronic gut disorders, including ulcerative colitis, inflammatory bowel disease, celiac disease, and colorectal cancer. Similarly, Naegleria fowleri, a free-living amoeba, causes …

Development Of Lineal Energy Spectrum-Based Biological Effects Models For Protons, Joseph M. Decunha, Fada Guan, David Grosshans, Zhongxing Liao, Dragan Mirkovic, Oleg Vassiliev, Radhe Mohan

Dissertations and Theses (Open Access)

In this dissertation, methods are developed and described to allow for the rapid calculation of microdosimetric spectra (specifically, lineal energy) for protons. SuperTrack, a GPU-accelerated tool for calculation of microdosimetric spectra was developed and is capable of computing lineal energy spectra up to 5000x faster than using Geant4 directly. Proton lineal energy spectra generated by SuperTrack are indistinguishable from those generated by Geant4. With SuperTrack, large libraries of lineal energy spectra for monoenergetic protons spanning 0-300 MeV have been developed. The proton lineal energy spectra calculated by SuperTrack have been compared to experimental measurements made by a tissue equivalent proportional …

Nanosecond Pulsed Electric Field And Plasma Jets For Cancer Therapy, Edwin Ayobami Oshin

Biomedical Engineering Theses & Dissertations

Nanosecond pulsed electric field (nsPEF) employs nanosecond-duration, high voltage pulses to induce oxidative stress, leading to temporary or permanent damage to cells or tissue (also known as reversible and irreversible electroporation), and has been considered a promising approach for cancer therapy. In parallel to this, nanosecond pulsed atmospheric pressure plasma jets (ns-APPJs) have also shown to be effective in inactivating cancer cells or increasing sensitivity of cells to electric fields. ns-APPJs are known to generate reactive chemical agents, including reactive oxygen and nitrogen species (RONS) which induces oxidative stress resulting in cell proliferation, apoptosis, and necrosis. In this dissertation, a …

Infrared Laser Ablation Of Biomolecules From Formalin-Fixed Tissue, Blessing Chisom Egbejiogu

LSU Doctoral Dissertations

In the research described in this dissertation, a high-precision infrared laser ablation microsampling method was utilized for spatially resolved proteomic and lipidomic analyses of formalin fixed paraffin embedded (FFPE) tissue, a widely used archival sample in biomedical research. Despite its extensive use, FFPE tissue presents challenges for proteomic analysis due to protein cross-linking and modifications introduced during fixation, which can hinder extraction and identification. Developing a streamlined high-resolution method to recover biomolecules from FFPE samples is critical for advancing biomarker discovery, retrospective studies, and multi-omics research. To address these challenges, this study employs an infrared (IR) laser ablation microdissection system …

A New Water-Soluble Silicon Phthalocyanine That Catalyzes The Photodegradation Of Pollutant Dyes, Damla Nur Kaya, Behi̇ce Sebnem Sesalan

Turkish Journal of Chemistry

The removal of color arising from water-soluble dyes in wastewaters is necessary to counter the threat to health. Because of thedifficulty in elimination of these dyes by conventional methods, their photodegradation using photosensitizers such as phthalocyanines(Pcs) has been employed recently. When compared to peripherally substituted derivatives, silicon Pcs are reported to be morebiocompatible with low toxicity. Thus a new silicon Pc substituted with two quaternized dimethylamino phenoxy units (compound 1)and its quaternized derivative (compound 2) were synthesized to test its photocatalytic ability employing the dyes methylene blue (MB),eosin B (EB), erythrosine (ERB), sulforhodamine B (SRB), and brilliant blue FCF (BRB), …

Taming Biological Complexity Through The Use Of Symmetries, Luis A. Álvarez-García

Dissertations, Theses, and Capstone Projects

The study of biological systems is, inherently, the study of very complex systems. This is essentially due to the fact that they are made up of numerous, often very complicated, interactions between an extensive number of components. Often necessitating an abundance of quantitative parameters and details for a precise description. The human brain for ex- ample, consisting of ∼ 80 billion neurons with ∼ 800 to 100 trillion connections between them, each of them depending on a large set of parameters. Even simpler examples such as bacterial organisms, such as E. coli and B. subtilis, which we focus on …

Chemistry Of Metalloguanines: An Overview Of Their Synthesis Routes And Their Implementations For The Period 2000-2024, Farah Saadoon Jaafar, Mahasin F. Alias

Karbala International Journal of Modern Science

Guanine has a variety of roles in chemistry, from its basic function in the storing and transferring genetic information to its usages in synthetic chemistry and other fields. Because of its distinct structure and biological importance, it is a fundamental component of contemporary study in organic chemistry and molecular biology.

In this review, we focused on covering the synthetic pathways of various derivatives of guanine from the year 2000 until the present. As a result of the guanine molecule containing multiple functional groups, this gives us the ability to prepare several guanines such as O⁶-alkylating guanines, O^{6 …}

Gompertz Distribution On Time Scales, Wasiu Sule

Theses, Dissertations and Capstones

We shall investigate Gompertz dynamic equations within the context of time scales calculus, by exploring the mathematical foundations and applications of the Gompertz model, which is commonly used to describe growth phenomena in various fields such as biology and economics. This research seeks to analyze the Gompertz cumulative distribution functions (CDF) and probability density functions (PDF) across different time scales, including the real numbers R and integer multiples hN. Probability techniques will be used to derive the CDF and PDF associated with the Gompertz dynamic equations, and we will examine how varying the time scale impacts the characteristics …

Centrality Algorithms For Weighted Homogeneous Multilayer Networks, Ayomide Ayowole-Obi

Computer Science and Engineering Theses - Archive

Applications need to be modeled for analyses. With the availability of many alternate data Models, choosing one needs to be done carefully by considering the complexity of data to be modeled and its analyses requirements. Social networks and other newer applications are primarily relationship-oriented and also have multiple types of entities and relationships. Although simple and attributed graphs have been used historically for modeling these applications, recently, multilayer networks (or MLNs) have been shown to be more effective in preserving the semantics of the application better and further provide flexibility of analyses. However, choice of MLN as a data model …

Assembly And Testing Of A Closed Cycle Cryostat, Chris Maguire

Science University Research Symposium (SURS)

Closed cycle cryocoolers are commonly used in laboratories as they provide long-term, low-cost, low-maintenance operation. This project covers the assembly and testing of an Advanced Research Systems DE-202 closed cycle cryostat to provide a low temperature apparatus for undergraduate research and advanced laboratory projects. This system is useful for many applications including optics, condensed matter physics, spectroscopy, electrical characterization, microscopy, superconductivity, crystallography, and biological studies.

Cryostat assembly involved research and planning to build a custom frame for the cryocooler, assemble vacuum, water, gas and electrical systems, leak test, and fit components to laboratory utilities. Once setup is complete, the actual …

Using A Water Quality Index To Assess The Impacts Of Heavy Metals Contamination For Sustainable Water Management: A Case Study Of The Bang Pakong River, Thailand, Khin Yadana Soe, Pokchat Chutivisut, Wilailuk Niyommaneerat

Applied Environmental Research

Anthropogenic activities such as improper waste disposal, excessive fertilizer use, and industrial effluents cause heavy metal contamination in water, soil, and the atmosphere. Herein, the water quality index (WQI) was used to characterize heavy metal (i.e., cadmium (Cd), arsenic (As), and mercury (Hg)) contamination in the Bang Pakong River, Thailand. Specifically, water samples were collected during the dry season from four stations along the river from 2012–2022. The heavy metal concentrations in the samples were analyzed via atomic absorption spectrophotometry, and WQI values were calculated on the basis of standard water quality parameters. At the four sampling stations, high As …

Boden Lecture: Taxation Of Autonomous Artificial Intelligence, Reuven S. Avi-Yonah, Lucas Brasil Salama, Herbert Snitz, W. Robert Thomas

Articles

This Article proposes that tax can be a useful supplement to other measures to regulate Autonomous Artificial Intelligence (AAI) and limit its potential harmful effects. This proposal differs from command-and-control regulation of AAI along the lines of European Union legislation that may unduly limit the development of AAI. It also differs from existing proposals to tax AAI to generate revenue to help workers displaced by AAI programs, or to tax the data used by AAI The proposal is based on granting AAI programs like ChatGPT separate legal personhood, like corporate personhood, while incentivizing or requiring their corporate owner to place …

Development And Applications Of Capillary Vibrating Sharp-Edge Spray Ionization Coupled With Atmospheric Pressure Chemical Ionization (Cvssi-Apci), Madison Elizabeth Pursell

Graduate Theses, Dissertations, and Problem Reports (ETD)

Mass spectrometry (MS) is a technique that is used in fields in which both complex and non-complex mixtures are analyzed. The state-of-the-art ion sources that are utilized for MS are being demonstrated to be functional for direct infusion of samples as well as for use with online separations. However, ion sources, such as electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) can encounter problems such as ion suppression and an inability to ionize based on size and/or polarity, respectively. Further these sources are bulky and require gas flow, heat sources, and additional high voltage power supplies for optimal performance. …

Comparative Study Of Single Imputation Techniques For The Prediction Of Missing Dairy Data, Ahmed M. Gad Prof, Ahmed Abdelhakim Ahmed Mr, Eman Manaa Prof, Basant Shafik Dr, Sakr Mostafa Prof

Business Administration

Dairy farm records are a crucial component of effective livestock business management. Record analysis allows a farm’s owner to make informed decisions. Incomplete records are less useful for data analysis, so it's important to handle missing values correctly. This study compares different imputation methods for handling missing values in a dataset of dairy records comprising 997 records collected from 234 cows between 2012 and 2022. The dataset was screened against records with missing values and then deleted, resulting in 858 observations from 200 animals. There were missing values in two variables, with a missing percentage of 13.9%: days in milk …

Advancing Root Trait Measurements For A Deeper Understanding Of Soil Biogeochemistry, Brian Rinehart

Theses and Dissertations--Plant and Soil Sciences

Climate change is disrupting (agro)ecosystems, with the potential for significant losses in crop productivity and ecosystem resilience due to changes in water and biogeochemical cycling. These disruptions can also release more carbon dioxide into the atmosphere through the degradation of soil organic matter. Plant roots have emerged as a potential tool for mitigating these effects, given their roles in plant function and in driving soil biogeochemistry. While this interest is growing, our ability to implement root trait selection is limited due to constraints on characterizing roots and limited clarity on the effects of traits on plant and ecosystem function. My …

Establishing A Conventional Linac-Based Electron Flash Beam, Justin Defrancisco

Theses and Dissertations

Problems: A rediscovered radiotherapy technique, FLASH, involves increasing the dose rate to >40 Gy/s. For a given dose, FLASH is shown to decrease the normal tissue complication probability without affecting the tumor control probability. More preclinical studies are necessary to confirm and enable these desirable properties on humans. Current preclinical investigations have diverse constraints, requiring FLASH apparatuses with flexible parameters and accurate control. However, there are limited FLASH platforms available, the existing ones are costly. Our institution is not in possession of any such infrastructure. Even if available, dosimetry and beam control in FLASH are extremely lacking. There is …

Modelling The Impacts Of Recreational Catch-And-Release Variability On Fish Stock Dynamics, Brett Crisafulli

Theses: Doctorates and Masters

Recreational fisheries often lack sufficient data for robust stock assessments, and post-release mortality (PRM) of discarded fish, particularly demersal species, poses a significant threat to sustainability. Because demersal fish often experience higher PRM (often due to barotrauma and stress), the substantial global interest in their recreational fisheries (e.g., Australia, Gulf of Mexico, Western Baltic Sea) raises conservation concerns. This study employs three distinct modelling approaches, applied to four reef-dwelling demersal species, to support effective recreational fisheries management by addressing data uncertainty, unintended consequences of management changes, and PRM effects. Specifically, this thesis (1) evaluates variability in average weights of recreationally-caught …

Heterogeneous Clustering Of Multiomics Data For Breast Cancer Subgroup Classification And Detection, Joseph Pateras, Musaddiq Lodi, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

The rapid growth of diverse -omics datasets has made multiomics data integration crucial in cancer research. This study adapts the expectation–maximization routine for the joint latent variable modeling of multiomics patient profiles. By combining this approach with traditional biological feature selection methods, this study optimizes latent distribution, enabling efficient patient clustering from well-studied cancer types with reduced computational expense. The proposed optimization subroutines enhance survival analysis and improve runtime performance. This article presents a framework for distinguishing cancer subtypes and identifying potential biomarkers for breast cancer. Key insights into individual subtype expression and function were obtained through differentially expressed gene …

Quantifying Avian And Vegetation Communities On Agricultural Conservation Easement Wetlands In Eastern South Dakota, Katherine Millman

Electronic Theses and Dissertations

The Prairie Pothole Region of eastern South Dakota contains numerous small depressional wetlands, colloquially known as potholes, that provide important ecosystem services, including water storage, water quality improvement, and wildlife habitat. The Agricultural Conservation Easement Program (ACEP) was established by the U.S. Department of Agriculture to protect and restore wetlands and grasslands on private land through easements such as Wetland Reserve Easements. Although ACEP requires management practices intended to maintain or improve habitat quality, few studies have evaluated their effectiveness at supporting wildlife communities and vegetation integrity. To address this gap, we evaluated wetlands at 30 ACEP sites and 20 …

An Integrated Wetland Condition Index And Environmental Metric Framework For The Prairie Pothole Region, Mercedes L. Batalla

Electronic Theses and Dissertations

The USDA-NRCS Agricultural Conservation Easement Program (ACEP) assists landowners with protecting, restoring, and enhancing wetlands. Evaluating wetland conservation efforts is crucial for informing future management decisions. However, assessment frameworks vary across regions and among stakeholders. The Prairie Pothole Region is an ecologically unique landscape characterized by its abundance of wetlands that provide important ecosystem services. To evaluate wetlands enrolled in ACEP, I sampled forty-five semi-permanent wetlands in the Prairie Pothole Region from July – August 2023 and 2024. I selected and sampled twenty-six wetlands enrolled in ACEP. Nineteen additional wetlands not enrolled in ACEP were also sampled; these included nine …

The Utilization Of Alcohol Dehydrogenase (Adh) Enzymes In Stereocontrolled Synthesis, Gaurav Pramod Kudalkar

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Clostridium acetobutylicum alcohol dehydrogenase (CaADH) has been shown to catalyze the stereoselective reduction of a broad array of carbonyl compounds. This study uses a Hammett linear free-energy relationship (LFER) analysis to gain insight into CaADH enzyme mechanism across three substrate classes: aryl aldehydes, aryl β-keto esters, and aryl trifluoromethyl ketones. Kinetic data were collected by monitoring NADPH fluorescence, and Michaelis-Menten kinetics were applied. Hammett plots reveal that hydride transfer is rate-limiting for aldehydes and β-keto esters (ρ > 0), while it is proposed that dehydration is rate-limiting for trifluoromethyl ketones (ρ < 0). ¹³C NMR confirmed significant hydration in trifluoromethyl ketones. The …

Increased Thermal Stability And Retained Antibacterial Properties In A Sulbactam And Amantadine Salt: Towards Effective Antibacterial-Antiviral Combination Therapies, Josephine Bicknell, Ivan Bondarenko, Alice Colatrella, Elani J. Cabrera-Vega, Jesus Daniel Loya, Delbert S. Botes, Jay L. Mellies, Gonzalo Campillo-Alvarado

Chemistry Faculty Publications and Presentations

A clinically relevant multidrug solid comprising sulbactam (β-lactamase inhibitor) and amantadine (antiviral) displays enhanced thermal stability and sustained antibacterial activity compared to starting materials.

We describe the formation of a multidrug salt comprising sulbactam (SUL, β-lactamase inhibitor) and amantadine (AMNH, antiviral). Physicochemical investigation of the SUL·AMNH salt revealed enhanced thermal stability compared to pristine starting materials. In vitro studies found that salt formation in SUL·AMNH does not disrupt antibacterial activity against model organisms Escherichia coli and Staphylococcus epidermidis. To our knowledge, we show the first β-lactamase inhibitor-antiviral salt where both components have been approved by the U.S. Food and Drug …

Current Status And The Significance Of Local Wisdom Biofertilizer In Enhancing Soil Health And Crop Productivity For Sustainable Agriculture: A Systematic Literature Review, Irwandhi, Fiqriah Hanum Khumairah, Emma Trinurani Sofyan, Nadia Nuraniya Kamaluddin, Anne Nurbaity, Diyan Herdiyantoro, Tualar Simarmata

Jurnal Kultivasi

Soil fertility is recognized as a crucial factor in supporting plant growth and productivity. The utilization of biofertilizers as environmentally friendly fertilizers is aimed at enhancing soil fertility and plant productivity. This study aims to explore the potential of local material for developing local wisdom biofertilizers (LWB) for achieving sustainable agriculture. A systematic literature review was conducted using bibliometric analysis, Preferred Reporting Items for Systematic Reviews, and Meta-Analyses (PRISMA) method, employing the Scopus search engine with the keywords "local AND wisdom AND biofertilizer" OR "biofertilizer" OR "local AND microorganism" OR "soil AND health OR crop AND productivity OR sustainable agriculture". …

(Featured Artist) The Aromatic Herb Garden, Sophia Samra

The Synapse: Intercollegiate science magazine

No abstract provided.

The Application Of High-Resolution Mass Spectrometry For The Analysis Of Biopolymers, Metabolites, And Biologically Relevant Small Molecules, Christ Duc Tran

Graduate Doctoral Dissertations

High-resolution mass spectrometry (HRMS), as its name suggests, possesses high resolving power that enables the separation of ions with very close mass values. This is particularly beneficial for analyzing complex samples where numerous compounds may have similar masses, as it helps prevent signal overlaps and ensures an accurate spectral analysis. The current work explores the diverse applications of high-resolution mass spectrometry in oligonucleotide research, organic synthesis and medicinal chemistry. Oligonucleotide research: Chapters 2-5 present the research results from studies that employed ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC-HRMS) to understand the pharmacokinetics of RNA interference (RNAi) therapeutics. The …

Holistic Correlation Measure For Enhanced Encapsulation Of Trait Heterogeneity And Discovery Of Co-Expression, Zachary Valleroy

Theses

Large-scale, high-dimensional data analyses can be computationally prohibitive due to combinatorial explosion of the search space for finding complex patterns; a viable alternative is network modeling for abstraction and quantifying intrinsic data associations. Prominent network analysis methods furnish frameworks for model synthesis and validation but rely on standard correlation measures impaired by semi-supervised biases, latent heterogeneity, and uneven discretization techniques. Here we investigate a holistic measure for encapsulating data heterogeneity for enhanced efficacy of revealing complex patterns through network analysis. Our unique correlation metric, K-medoids Utility for Duo Original Similarities (Kudos), exhaustively factors real-valued analyte data to compute …

Gmc-4190 Cellnucleirag - Smart Search Tool For Cell Nuclei Research, Sai Chandana Koganti

C-Day Computing Showcase

CellNucleiRAG is a specialized tool developed to address a significant challenge in medical research: the rapid retrieval and synthesis of detailed information on cell nuclei. Understanding cell nuclei characteristics is crucial in fields like pathology, oncology, and diagnostics, where detailed cell analysis can guide disease identification and treatment planning. However, accessing relevant, organized information on specific cell nuclei types, datasets, models, and methods is often time-consuming, requiring manual searches through multiple, disparate sources. CellNucleiRAG solves this problem by acting as a smart search engine, designed specifically for cell nuclei research, combining traditional retrieval methods with advanced AI capabilities. Built with …

A Revision Of Hong Kong Harvestmen : Biodiversity, Ecological Preferences And Geographical Distribution, Kai Teck Desmond Tan

Lingnan Theses (MPhil & PhD)

Opiliones, or harvestmen, is a common animal found throughout the world, there are currently over 6,650 species worldwide but the actual number is estimated to exceed 10,000, making it the third largest order in the class Arachnida. Despite its diversity, it is a rather understudied group. In Hong Kong, there are four described species, but the most recent relevant literature dates back to the at least the early 20th century. This thesis focuses on two common species found in Hong Kong: one previously described species (Heterobiantes geniculatus) and one new species (Pseudoleiobunum lutulentum sp. nov.). I …