Digital Commons Network^™

Introducing "Identification Probability" For Automated And Transferable Assessment Of Metabolite Identification Confidence In Metabolomics And Related Studies., Thomas O Metz, Christine H Chang, Vasuk Gautam, Afia Anjum, Siyang Tian, Fei Wang, Sean M Colby, Jamie R Nunez, Madison R Blumer, Arthur S Edison, Oliver Fiehn, Dean P Jones, Shuzhao Li, Edward T Morgan, Gary J Patti, Dylan H Ross, Madelyn R Shapiro, Antony J Williams, David S Wishart

Faculty Research 2025

Methods for assessing compound identification confidence in metabolomics and related studies have been debated and actively researched for the past two decades. The earliest effort in 2007 focused primarily on mass spectrometry and nuclear magnetic resonance spectroscopy and resulted in four recommended levels of metabolite identification confidence─the Metabolite Standards Initiative (MSI) Levels. In 2014, the original MSI Levels were expanded to five levels (including two sublevels) to facilitate communication of compound identification confidence in high resolution mass spectrometry studies. Further refinement in identification levels have occurred, for example to accommodate use of ion mobility spectrometry in metabolomics workflows, and alternate …

Preparation And Characterization Using A New Schiff Base Ligand Derived From Benzoyl Isothiocyanate With Their Complexes And Study Of Their Biological Activity, Zaynab Faleh Ai-Janahi, Mohammed Hamid Said

Al-Mustaqbal Journal of Pharmaceutical and Medical Sciences

Complexes containing Nickel, Copper, and Zinc salts were prepared and studied in this study. Additionally, novel Schiff Base ligands were synthesized by reacting 6-aminopenicillinic acid with benzoyl isothiocyanate to produce L. The synthesized ligand was evaluated by physical measures and spectroscopic methods such as Fourier transform infrared spectroscopy, nuclear magnetic resonance, ultraviolet-visible light, mass spectroscopy, and micro elemental analysis. Metal salts of (Ni(II), Cu(II), and Zn(II)) were combined with novel ligands at a molar ratio of 1:2 [M:L] to prepare the complexes. Spectroscopic, magnetic susceptibility, molar conductivity, atomic absorption, and DTA methods were used to study the complexes that were …

Synthesis, Identification And Antibacterial Study Of New Ligand Derived From Benzothiazolemethanamine And Its Complexes With Some Metal Ions, Sahar Aqeel Hussain

Maaen Journal for Medical Sciences

A novel substituted 5-chloro-2-benzothiazolemethanamine ligand featuring an imine ‘(-N=CH-) category, 2-((((6-chlorobenzothiazol-2-yl) methyl)imino)methyl)-5-methoxyphenol (CBTMIM), was synthesized through the reaction of 2-benzothiazolemethanamine, 5-chloro, with 2-hydroxy-4-methoxybenzaldehyde in an absolute ethanolic solution. The azomethine ligand and its metal complexes have been identified by using mass spectrometry, ¹H and ¹³C NMR spectroscopy, C, H, N, and S elemental analysis, X-ray diffraction (XRD), (FESEM) microscopy, atomic absorbance spectroscopy. UV-visible spectroscopy, Fourier-transform infrared spectroscopy (FT-IR), magnetic susceptibility, and ionic conductance analysis. The chemical composition and additional measurement data of the metal complexes validate the stoichiometry of the metal: ligand ratio types that include; [M (L)], …

The Effects Of Active Substances Of Clinically Important Drugs On The Survival, Development, And Some Adult Traits Of Drosophila Melanogaster Meigen (Diptera: Drosophilidae), Gökçe Üstündağ, Kemal Büyükgüzel, Ender Büyükgüzel

Turkish Journal of Zoology

Drosophila melanogaster Meigen (Diptera: Drosophilidae) was used as a model organism and fed on an artificial diet with different clinically important drugs under laboratory conditions. The effects of fluconazole, acyclovir, and piperazine on the survivorship, development, adult longevity, fecundity, and hatching rate of the insect were investigated. The results showed that the highest concentration of fluconazole (1250 mg/L) significantly decreased both the rate of larvae reaching the 3rd instar and the rate of pupation from 93.00 ± 2.95% to 11.00 ± 2.59% (χ2 = 134.696; df = 1; p = 0.0001). The highest concentration of acyclovir (200 mg/L) significantly reduced …

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 …

Gpcr To Channel Communication In A Membrane Signaling Pathway, Yuxi Zhang

Student Theses and Dissertations

G-protein-coupled receptors (GPCRs) regulate a variety of downstream effector proteins, making them essential for many physiological processes. For example, in the heart, the activation of beta-adrenergic receptors (βARs) and the stimulatory G protein (Gαs) leads to the opening of downstream hyperpolarization-activated cyclic nucleotide–gated (HCN) channels, resulting in an accelerated heart rate. In contrast, activation of M2 muscarinic receptors (M2Rs) and the inhibitory G protein (Gαi) opens G protein-gated inward rectifier K⁺ (GIRK) channels, slowing the heart rate. In addition to the Gαs and Gαi pathways, there is also the Gαq signaling pathway. In this pathway, activation of Gq-coupled GPCRs can …

A Scent Of Direction: Exploring Adaptive Olfactory Navigation In Drosophila, Chad Morton

Student Theses and Dissertations

Animals rely on environmental cues, such as odors, to navigate through complex and often dynamic landscapes. While olfactory navigation has traditionally been modeled as a reflexive behavior driven by immediate sensory cues, whether flies can leverage more sophisticated strategies, integrating sensory input with spatial memory and internal representations of their surroundings, remains unclear. A key challenge in studying olfactory navigation lies in the invisible and unpredictable nature of odor plumes, which has made it challenging to accurately assess the ongoing sensory experiences of an animal. To address this challenge, we developed a novel virtual reality (VR) system that head-fixed Drosophila …

Precipitation, Perceptions, And Participation: An Analysis Of Individual Perceptions Of Santa Ana Watershed Project Authority's Cloud Seeding Pilot Program And Suggestions For Public Outreach And Communications, Rachel A. Rowlee

Pitzer Senior Theses

Cloud seeding is a form of weather modification intended to increase the amount of precipitation by introducing a seeding agent. The Santa Ana Watershed Project Authority (SAWPA) has implemented a four-year cloud seeding pilot program utilizing silver iodide as a seeding agent during rain storm events. Over the last year, SAWPA received various feedback, much of which exists in the social media realm. This research consists of open-ended interviews with water resource managers, SAWPA employees, and individuals expressing disapproval of the program on social media and Instagram comment analyses. Interview and comment analyses are put into conversation with the theory …

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

Marquette Law Review

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 …

Asymmetric Synthesis Of Bioactive Scaffolds Via Organocatalysis, Melody Guo

Yale Graduate School of Arts and Sciences Dissertations

Chiral catalysts allow chemists to access enantioenriched materials without the use of proportionate amounts of chiral reagents, while lowering the energy barrier of the original reaction. One way to form bioactive, heteroatom-containing scaffolds asymmetrically is through the use of chiral organocatalysts. This dissertation covers the development of stereoselective reaction methodology to access bioactive scaffolds and mechanistic investigations into intriguing features therein. Chapter 1 describes the development of the asymmetric synthesis of axially chiral quinazolinones. In this project, complementary applications for two different scaffold classes of chiral phosphoric acid (CPA) catalysts are found. We observe that while a C2-symmetric CPA catalyst …

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 …

Biodiversity Conservation And The Ever-Expanding Web Of Federal Laws Regulating Nonfederal Lands: Time For Something Completely Differenct?, J.B. Ruhl

University of Colorado Law Review

No abstract provided.

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 …

Space Agriculture, Biotechnology, And Terraforming: Rethinking The Paradigm Of Harmful Contamination, Francesca Giannoni-Crystal

Journal of Air Law and Commerce

As humanity transitions from sporadic exploratory space missions to permanent settlements on celestial bodies (like the Moon or Mars), agriculture biotechnology, and, potentially, terraforming projects will be essential for establishing self-sustaining settlements.

These activities raise critical issues concerning the interpretation of the principle of harmful contamination under Article IX of the Outer Space Treaty (OST) and its implementation through the Committee on Space Research’s Policy on Planetary Protection (COSPAR Policy) referred together in this article as the “Planetary Protection Framework,” which is primarily oriented toward exploration with scientific integrity rather than permanent habitation.

The challenge lies in the fact that …

Overconfidence Bias Amongst Student Investors, William Winship

Economics Honors Papers

No abstract provided.

Womb To Waste: Climate Change’S Silent Attack On Reproductive Rights, Jenna Caron

Research Days Posters 2025

Women experience disproportionate impact on the effects of climate change—they’ve proven more likely to die in a climate disaster, rely on the resources that the climate crisis devastates, and to experience gender-based violence. This study examines the reproductive health within gender-based violence, positing that women residing in economically disadvantaged countries, identifying with historically marginalized communities, and/or possessing harmful medical predispositions, experience more severe maternal and fetal health outcomes. By examining data and academic literature through biomedical and biological studies of sexual violence, birth rates, climate-related stressors, and harmful pollutants, this study concludes a strong connection between climate-related weather conditions and …

Interpretable And Data-Driven Machine Learning Models For Analyzing High-Dimensional Biological Data, Junchen Yang

Yale Graduate School of Arts and Sciences Dissertations

High-dimensional biological data, including single-cell omics, are prevalent in modern biology for characterizing a wide range of biological processes and phenomena. Although our capacity to generate such data has expanded at an unprecedented pace, significant challenges remain in extracting the informative features and the underlying biological signals. In particular, these datasets not only exhibit high dimensionality but also suffer from issues including inherent noise, low signal-to-noise ratio, and intrinsic heterogeneity. While machine learning models hold great promise for analyzing such data, their complexity and sensitivity to data characteristics often impede biological interpretability. To address these interconnected challenges, this thesis develops …

Studies On The Structural Basis Of Oxygenic Photosynthesis, David Flesher

Yale Graduate School of Arts and Sciences Dissertations

Oxygenic photosynthesis — performed on all seven continents by green plants, algae, and cyanobacteria — supports the global biome through its ability to capture and store light energy. This is achieved through a series of protein complexes collectively known as the photosynthetic apparatus. During my PhD research, I’ve investigated the structural basis for how these protein complexes capture this light energy and transduce it to redox energy. My thesis work, summarized in this dissertation, can be grouped in two broad research themes: (i) structural studies on Nature’s water oxidation reaction, explored in Part I of this dissertation; and (ii) the …

Light Sheet Microscopy For 3d Nanoscale Imaging, Hannahmariam Mekbib

Yale Graduate School of Arts and Sciences Dissertations

Advances in expansion microscopy, a super resolution microscopy technique in which samplesare expanded up to ~8,000 times their original volume, require new microscope modalities to image the large sample sizes. These new techniques should be suitable for imaging large sample volumes, yet need to maintain the high 3D resolution of 250-500 nm of high-end confocal microscopy to provide the maximum level of detail and thereby reveal nanoscale cellular ultrastructure. Axially Swept Light Sheet Microscopy (ASLM) has emerged as a promising technique for generating high-resolution images at high-throughput. However, current designs struggle with the trade-off between limited resolution and field-of-view (FOV) …

Euphorbia Tirucalli Leaf Extract Induces Apoptosis And Inhibits Cell Migration In Hsc-3 Tongue Cancer Cells, Imelda Ongkiwijaya, Rahmi Amtha, Ferry Sandra, Muhammad I. Rizal, Armelia S. Widyarman, Widya Lestari

Journal of Dentomaxillofacial Science

No abstract provided.

Brain On Drugs: The Rewarding And Punishing Effects Of Addiction And Relapse, Abby Ferrell

Undergraduate Honors Theses

Addiction is a multidimensional disorder that is heavily influenced by behavior, biology, and social interaction. These factors work together to make addiction persist and make relapse easier. Three major models of addiction are explored--behaviorism, biology, and social learning theory, which all contribute to the understanding of addiction, and their respective treatments can be individual, and when integrated. Behavior models highlight how conditioning and reinforcement contribute to addiction, while biological studies focus on dopamine changes in the brain that alter other areas of brain chemistry. Social learning theories add to the environmental cue associations that behaviorism mentions briefly. The implications that …

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 …

An Examination Of Adverse Childhood Experiences (Aces) And Post-Traumatic Growth (Ptg): A Quantitative Analysis Of The Variability Of Growth In Adulthood, Tasanya Rowe

Master's Theses or Doctor of Nursing Practice

ABSTRACT

This study examined the relationship between childhood and adolescent trauma, specifically Adverse Childhood Experiences (ACEs), and posttraumatic growth (PTG) in adulthood. Particular attention was given to the role of demographic variables, including race, gender, and socioeconomic status, in shaping trauma responses and recovery outcomes. A quantitative, cross-sectional, correlational, quasi-experimental design was employed. Participants (N = 132; aged 18–65 years) were recruited from general education classes at Fort Hays State University and the surrounding community. Participants completed a survey comprising the Juvenile Victimization Questionnaire–Reduced Item Version and the Posttraumatic Growth Inventory. Data were analyzed using bivariate correlations, ANOVAs, and multiple …

Molecular And Cellular Mechanisms Of Lim Protein Mechanotransduction, Donovan Yong Zhi Phua

Student Theses and Dissertations

For tissues to develop and maintain mechanical homeostasis, cells must be able to perceive and respond to mechanical cues in their local environments (mechanosense). While there has been significant progress in understanding the physiological significance of mechanosensation, the mechanisms by which proteins convert mechanical stimuli into biochemical signals (mechanotransduction) are poorly understood. The actin cytoskeleton serves as a nexus for cellular mechanotransduction, generating and transducing forces into intracellular signals that coordinate cell migration, cellular contractility, organelle dynamics, and gene expression. However, our understanding of the molecular mechanisms by which cytoskeletal mechanotransduction is achieved is limited. LIM domain proteins are a …

Chromosome Segregation Dynamics During Meiosis I, Meiosis Ii, And Mitosis Cell Divisions In Acheta Domesticus (House Crickets), Sweta Aryal

Master’s Theses

Chromosomes exhibit diverse types of organization and movement during the cell division process. Meiosis is essential for sexual reproduction, producing haploid cells from diploid precursors. In meiosis I, homologous chromosomes pair up, and separate in anaphase I, with two chromatids moving toward each pole. In meiosis II, the sister chromatids move to opposite poles during anaphase II and produce haploid cells. In contrast, in mitosis, the chromosomes are copied and distributed to produce genetically identical diploid somatic cells. Understanding the behavior of chromosomes during mitosis and meiosis is significant for accurate chromosome segregation to prevent birth defects and diseases like …

Mechanochemical Synthesis Of Ni(Ii)-Tptz Complexes With Co-Ligands: Spectroscopy, Dft, And Biological Studies, Deepak Senapati, Anulipsa Priyadarshini, Debadutta Samal, P. Ramesh Babu, Satyanarayan Sahoo, Narayan Chandra Bera, Raghabendra Samantaray, Jagannath Panda, Rojalin Sahu

Journal of Metals, Materials and Minerals

New mixed-ligand Ni(II) complexes [Ni(tptz)(1,10-phen)] (1), [Ni(tptz)(2-Mimd)2] (2), and [Ni(tptz)Imd)2] (3) were synthesized via a green, solvent-free mechanochemical approach using ball milling. The primary ligand used was 2,4,6-tris(2-pyridyl)-1,3,5-triazine (tptz), with secondary ligands being 1,10-phenanthroline, 2-methyl imidazole, and imidazole, respectively. Structural characterization by IR, UV-Visible, photoluminescence spectroscopy, and powder X-ray diffraction, supported by DFT calculations, revealed a distorted square planar geometry for complex 1 and distorted tetrahedral geometries for complex-2 and complex-3. Notably, bathochromic shifts in the UV-Vis spectra confirm metal-ligand charge transfer transitions and extended π-delocalization. Powder XRD analysis determined average crystallite sizes of 17.86 nm (1), 25 nm (2), …

Tryptophan Kynurenine Pathway-Based Imaging Agents For Brain Disorders And Oncology-From Bench To Bedside, Erik Stauff, Wenqi Xu, Heidi H. Kecskemethy, Sigrid A. Langhans, Vinay V. R. Kandula, Lauren W. Averill, Xuyi Yue

Jefferson Hospital Staff Papers and Presentations

Tryptophan (Trp)-based radiotracers have excellent potential for imaging many different types of brain pathology because of their involvement with both the serotonergic and kynurenine (KYN) pathways. However, radiotracers specific to the kynurenine metabolism pathway are limited. In addition, historically Trp-based radiopharmaceuticals were synthesized with the short-lived isotope carbon-11. A newer generation of Trp-based imaging agents using the longer half-lived and commercially available isotopes, such as fluorine-18 and iodine-124, are being developed. The newly developed amino acid-based tracers have been demonstrated to have favorable radiochemical and imaging characteristics in pre-clinical studies. However, many barriers still exist in the clinical translation of …

Investigating The Role Of Prostasin In Angiogenesis: A Chorioallantoic Membrane Model Approach, Zaima Aline

Honors Undergraduate Theses

Prostasin, also known as PRSS8 or CAP1, is a glycosylphosphatidylinositol (GPI)-anchored extracellular serine protease involved in various physiological and pathophysiological processes. Prostasin expression is observed during key phases of trophoblast invasion and placental development, critical steps in embryo implantation in Rhesus monkeys. This suggests a role for prostasin in extracellular matrix remodeling and tissue invasion, both essential for a healthy pregnancy. Moreover, prostasin appears vital for development as studies in mice show that a germline knockout of the gene leads to significant placental defects and eventual embryonic death, highlighting its importance in vascular and structural development within the placenta.

Building …

Mapping The Functional Network Of Human Cancer Through Machine Learning And Pan-Cancer Proteogenomics, Zhiao Shi, Jonathan T Lei, John M Elizarraras, Bing Zhang

Faculty, Staff and Students Publications

Large-scale omics profiling has uncovered a vast array of somatic mutations and cancer-associated proteins, posing substantial challenges for their functional interpretation. Here we present a network-based approach centered on FunMap, a pan-cancer functional network constructed using supervised machine learning on extensive proteomics and RNA sequencing data from 1,194 individuals spanning 11 cancer types. Comprising 10,525 protein-coding genes, FunMap connects functionally associated genes with unprecedented precision, surpassing traditional protein-protein interaction maps. Network analysis identifies functional protein modules, reveals a hierarchical structure linked to cancer hallmarks and clinical phenotypes, provides deeper insights into established cancer drivers and predicts functions for understudied cancer-associated …