Digital Commons Network^™

Uri Libraries' Ai Lab--Evolving To Meet The Needs Of Students And Research Communities, Harrison Dekker, Angel Ferria, Indrani Mandal

Technical Services Faculty Publications

No abstract provided.

Profiling The Plasmid Conjugation Potential Of Urinary Escherichia Coli, Cesar Montelongo Hernandez, Catherine Putonti, Alan J. Wolfe

Biology: Faculty Publications and Other Works

Escherichia coli is often associated with urinary tract infection (UTI). Antibiotic resistance in E. coli is an ongoing challenge in managing UTI. Extrachromosomal elements – plasmids – are vectors for clinically relevant traits, such as antibiotic resistance, with conjugation being one of the main methods for horizontal propagation of plasmids in bacterial populations. Targeting of conjugation components has been proposed as a strategy to curb the spread of plasmid-borne antibiotic resistance. Understanding the types of conjugative systems present in urinary E. coli isolates is fundamental to assessing the viability of this strategy. In this study, we profile two well-studied conjugation …

Improving Recombinant Zoster Vaccination Rates In Patients Receiving Biologic Therapy In The Rheumatology Clinics At The Orlando Va Healthcare System, Kathlyn Camargo Macias, Taylor Kann, Marilyn Mosquera, Ravi Shahu Khal, Ashwini Komarla

North Florida Division GME Research Day 2022

No abstract available.

Web-Based Platform For Analysis Of Rna Folding From High Throughput Chemical Probing Data, Christopher Jurich, Amir Brivanlou, Silvi Rouskin, Joseph D. Yesselman

Department of Chemistry: Faculty Publications

RNA structures play critical roles in regulating gene expression across all domains of life and viruses. Chemical probing methods coupled with massively parallel sequencing have revolutionized the RNA structure field by enabling the assessment of many structures in their native, physiological context. Previously, we developed Dimethyl-Sulfate-based Mutational Profiling and Sequencing (DMS-MaPseq), which uses DMS to label the Watson-Crick face of open and accessible adenine and cytosine bases in the RNA. We used this approach to determine the genome-wide structures of HIV-1 and SARS-CoV-2 in infected cells, which permitted uncovering new biology and identifying therapeutic targets. Due to the simplicity and …

Western Civilization: A Concise History, Sanford Robins, Christopher Brooks

SUBR Faculty Open Educational Resources

This class will discuss the history of Western Civilization (primarily Mesopotamia, the Near East, and Europe) from the earliest known civilizations to about the year 1500 CE. You will learn about major events, countries, ideas, and people and the impact that these had on their times and on how history developed. This knowledge is important for you to have because you are a person who lives in a society shaped by these events and ideas. The ultimate goal of this class is to help you understand how the flow of history has impacted the present and to help you understand …

Topological Hierarchies And Decomposition: From Clustering To Persistence, Kyle A. Brown

Browse all Theses and Dissertations

Hierarchical clustering is a class of algorithms commonly used in exploratory data analysis (EDA) and supervised learning. However, they suffer from some drawbacks, including the difficulty of interpreting the resulting dendrogram, arbitrariness in the choice of cut to obtain a flat clustering, and the lack of an obvious way of comparing individual clusters. In this dissertation, we develop the notion of a topological hierarchy on recursively-defined subsets of a metric space. We look to the field of topological data analysis (TDA) for the mathematical background to associate topological structures such as simplicial complexes and maps of covers to clusters in …

Stylosanthes Hamata - Environmental Weed Risk Assessment 2022, Department Of Primary Industries And Regional Development, Western Australia

Environmental Weed Risk Assessments

Introducing new plants to an area may have both positive and negative effects on the environment, economy and community. To minimise the negative environmental impact of introducing new agricultural species, DPIRD conducts a risk assessment procedure based on widely accepted scientific standards. This report assesses Caribbean stylo (Stylosanthes hamata). Caribbean stylo (Stylosanthes hamata) is an annual or short-lived perennial herbaceous legume. Individual plants behave as self-regenerating annuals or biennials. In the Northern Territory up to 40% of plants persist from one wet season to the next (Cameron 2010), but this varies depending on the length of the dry season. It …

Sulfated Flavonoids In The Asteraceae, Alyssa Rice

Senior Honors Projects

Gypsum soils are a unique soil type with high levels of calcium and sulfur, which creates a harsh living environment for plants. To survive these conditions, plants have evolved a suite of mechanisms to survive these excess minerals, such as sulfur. In this study we aimed to determine if gypsum status was related to sulfated flavonoid production in plants of the Asteraceae. Flower and leaf tissues were collected from herbarium specimens representing gypsophiles, gypsovags, and gypsofuges. These tissues were analyzed for the presence of sulfated flavonoids using Thin Layer Chromatography (TLC). We observed sulfated flavonoid production in leaf and flower …

Cardiology And The Brain: How An Individual's Cardiovascular Health Relates To Their Mental Health, Megan Shea Kopicko

Senior Honors Theses and Projects

A scoping review was conducted to explore the relationship between the cardiovascular system and neurological system to determine if there is a connection between certain mental illnesses and heart health. This study was guided through implementation of Arksey and O’Malley’s (2005) framework for scoping reviews. A literature search was conducted using PubMed, CINAHL, Cochrane Library, and Google Scholar databases. Of the 934,251 sources found, only 21 studies met the study criteria and were ultimately selected for this study. Upon review, three themes were identified: (a) anxiety and cardiovascular disease; (b) schizophrenia and cardiovascular disease; and (c) depression and cardiovascular disease. …

"Only To Have A Say In The Way He Dies": Bodily Autonomy And Methods Of Execution, Alexandra L. Klein

Scholarly Articles

Capital punishment is one of the most significant intrusions into a person's bodily autonomy; the state takes a person's life. Even though the state has stripped a person on death row of much of their autonomy and intends to kill them, removing all autonomy, a person sentenced to death may, in some circumstances, choose how they will die. While most states rely on a single method of execution, some states permit a condemned person to choose among two or more methods of execution. Constitutional challenges to methods of execution requires the challenger to demonstrate a substantial risk of severe pain …

Catholic Seminarians On “Real Men”, Sexuality, And Essential Male Inclusivity., Medora W. Barnes

2022 Faculty Bibliography

This paper is based on an empirical study using in-depth qualitative interviews that examines how Roman Catholic undergraduate seminarians in the United States understand gender, sexuality and masculinity. The findings describe how seminarians reject interactionist and social constructionist models of gender, and rely on a strict biological based model where sex/gender are seen as a unified concept. This leads them to adopt an “essential male inclusivity”, where they argue that all people assigned male at birth have equal claim to “manhood”, which eases pressures on them to act in gender normative ways. The social-psychological and identity-based motivations of these beliefs …

Deoxybuzonamine Isomers From The Millipede Brachycybe Lecontii (Platydesmida: Andrognathidae), Tappy H. Jones, Daniel P. Harrison, Carla Menegatti, Emily Levers, Kenneth Knott, Paul Marek, Derek A. Hennen, Matt T. Kasson, Angie M. Macias, Brian Lovett, Ralph Saporito

2022 Faculty Bibliography

Millipedes (Diplopoda) are well known for their toxic or repellent defensive secretions. Here, we describe (6aR,10aS,10bR)-8,8-dimethyldodecahydropyrrolo[2,1-a]isoquinoline [trans-anti-trans-deoxybuzonamine (1a)] and (rel-6aR,10aR,10bR)-8,8-dimethyldodecahydropyrrolo[2,1-a]isoquinoline [trans-syn-cis-deoxybuzonamine (1b)], two isomers of deoxybuzonamine found in the chemical defense secretions of the millipede Brachycybe lecontii Wood (Colobognatha, Platydesmida, Andrognathidae). The carbon–nitrogen skeleton of these compounds was determined from their MS and GC-FTIR spectra obtained from the MeOH extract of whole millipedes, along with a subsequent selective synthesis. Their structures were established from their 1D (¹H, ¹³C) and 2D NMR (COSY, NOESY, multiplicity-edited HSQC, HSQC-TOCSY, HMBC) spectra. Additionally, computational chemistry (DFT and DP4) was used to identify the relative …

Gender Differences And The Influence Of Body Composition On Land And Pool-Based Assessments Of Anaerobic Power And Capacity, Jacquelyn N. Zera, Elizabeth F. Nagle, Emma Connell, Erin Curtin, Wilmina Marget, Anna P. Simonson, Takashi Nagai, John Abt, Scott Lephart

2022 Faculty Bibliography

No abstract provided.

The Impacts Of The Molecular Education And Research Consortium In Undergraduate Computational Chemistry On The Careers Of Women In Computational Chemistry, Kelly Anderson, Sarah Arradondo, K Aurelia Ball, Chrystal D. Bruce, Maria A. Gomez, Kedan He, Heidi Hendrickson, Lindsey Madison, Ashley Ringer Mcdonald, Maria C. Nagan, Carol Parish, Caitlin E. Scott, Patricia Soto, Aime'e Tomlinson, Mychel Varner

2022 Faculty Bibliography

The Molecular Education and Research Consortium in Undergraduate Computational Chemistry (MERCURY) has supported a diverse group of faculty and students for over 20 years by providing computational resources as well as networking opportunities and professional support. The consortium comprises 38 faculty (42% women) at 34 different institutions, who have trained nearly 900 undergraduate students, more than two-thirds of whom identify as women and one-quarter identify as students of color. MERCURY provides a model for the support necessary for faculty to achieve professional advancement and career satisfaction. The range of experiences and expertise of the consortium members provides excellent networking opportunities …

Om92, A Glp-1 Enhancer Mutation, Is An Allele Of Ekl-1, Samantha A. Stein, Olivia F. Zucaro, Harold E. Smith, Kevin F. O'Connell, Jill M. Spoerke, Eleanor M. Maine, James L. Lissemore

2022 Faculty Bibliography

Germline stem cell proliferation in C. elegans requires activation of the GLP-1/Notch receptor, which is located on the germline plasma membrane and encoded by the glp-1 gene. We previously identified several genes whose products directly or indirectly promote activity of the GLP-1 signaling pathway by finding mutations that enhance the germline phenotype of a glp-1(ts) allele, glp-1(bn18) . Here, we report phenotypic and molecular analysis of a new ekl-1 allele, ekl-1(om92) , that enhances the glp-1(bn18) phenotype. ekl-1(om92) is a 244 bp deletion predicted to generate a frameshift and premature termination codon, yielding a severely truncated protein, suggesting it is …

Roholtiella Volcanica Sp. Nov., A New Species Of Cyanobacteria From Kamchatkan Volcanic Soils, Lira A. Gaysina, Jeffrey R. Johansen, Aniket Saraf, Razeda Z. Allaguvatova, Sagarika Paul, Prashant Singh

2022 Faculty Bibliography

During a study of biodiversity of cyanobacteria in Gorely volcano soils (Kamchatka Peninsula), a strain of heterocytous, a false branching cyanobacterium with gradually tapered filaments, was isolated. Prominent features of the strain were purplish-grey trichomes and firm, distinct multilayered sheaths. Based on the results obtained from the morphological, ecological, and phylogenetic analysis using the 16S rRNA and 16S–23S ITS region, 16S–23S ITS secondary structure analysis, comparison of flanking regions of BoxB and V3 helices, and the p-distance between the 16S–23S ITS region, we describe our strain K7 as a novel species of the genus Roholtiella with the name Roholtiella volcanica …

Scale Development And Validation Of Transaction Cost Economics Typology For Contracts: A Systems Thinking Approach, Sedat Cevikparmak, Hasan Celik, Saban Adana, Hasan Uvet, Brian Sauser, David Nowiki

2022 Faculty Bibliography

A variety of contract typologies that exist in the literature are helpful in the exploration of different approaches in contractual relations, but only when measured with the right instruments. Although Transaction Cost Economics (TCE) has a distinct, high-level, and abstract typology for contracts, it still lacks a measurement scale. In this paper, a measurement scale for the TCE contract typology (classical, neo-classical, and relational contracts) was developed and validated, using systems thinking approach and experimental design to contribute to the empirical tests of TCE within the contracting realm. First, the antecedents of contract selection within the TCE literature were analyzed …

Intestinal Endothelial Cells Promote Hiv Latent Infection In Resting And Activated Cd4+ T-Cells, Nathan Dapprich, Jessica Eddy, Fisher Pham, Anding Shen

Summer Research

No abstract provided.

Alkaloid-Based Chemical Defenses In 11 Species Of Bufonid Poison Frogs From Brazil (Bufonidae: Melanophryniscus), Emily Staufer

Masters Theses

The term ‘poison frog’ describes members of five anuran families that are capable of sequestering lipophilic, alkaloid-based chemical defenses from their prey. Alkaloid defenses can vary widely within and among poison frog species, mostly linked to differences in availability of arthropod prey at different scales. While research has mainly focused on alkaloid variation within the dendrobatid and mantellid poison frogs, bufonid poison frogs in the genus Melanophryniscus demonstrate high inter- and intra-species alkaloid variation, and some members are capable of both sequestering dietary alkaloids and synthesizing alkaloids metabolically. However, of the 31 species of Melanophryniscus, only eight have ever had …

“Albertania” And “Egbenema”, Panding Biodiversity In The Oculatellaceae (Cyanobacteria)., Mildred Akagha

Masters Theses

To conduct molecular studies of cyanobacteria of Lagos, Nigeria, a total of eight soil/subaerial samples were collected in Lagos State, Nigeria, and used to isolate cyanobacterial cultures that were characterized microscopically, sequenced, and phylogenetically analyzed. Within the resulting set of cultures, a number of Synechococcales were observed, particularly belonging to Oculatellaceae. “Egbenema” and two new putative species of the recently described genus Albertania were found. Both genera belong to a supported clade within the Oculatellaceae that includes Trichotorquatus and Komarkovaea. The two new putative species of Albertania, “A. egbensis” and “A. latericola”, were from …

Faculty Notes, John Carroll University

Faculty Notes - John Carroll University

Spring 2022, Volume 15, Issue 1

Head Impact Exposure In Youth And Collegiate American Football, Grace B. Choi, Eric P. Smith, Stefan M. Duma, Steven Rowson, Eamon Campolettano, Mireille E. Kelley, Derek A. Jones, Joel D. Stitzel, Jillian E. Urban, Amaris Genemaras, Jonathan G. Beckwith, Richard M. Greenwald, Arthur C. Maerlender, Joseph J. Crisco

Center for Brain, Biology, and Behavior: Faculty Publications

The relationship between head impact and subsequent brain injury for American football players is not well defined, especially for youth. The objective of this study is to quantify and assess Head Impact Exposure (HIE) metrics among youth and collegiate football players. This multiseason study enrolled 639 unique athletes (354 collegiate; 285 youth, ages 9–14), recording 476,209 head impacts (367,337 collegiate; 108,872 youth) over 971 sessions (480 collegiate; 491 youth). Youth players experienced 43 and 65% fewer impacts per competition and practice, respectively, and lower impact magnitudes compared to collegiate players (95th percentile peak linear acceleration (PLA, g) competition: 45.6 vs …

Constructing Neural Network Models From Brain Data Reveals Representational Transformations Linked To Adaptive Behavior, Takuya Ito, Guangyu Robert Yang, Patryk Laurent, Douglas H. Schultz, Michael W. Cole

Center for Brain, Biology, and Behavior: Faculty Publications

The human ability to adaptively implement a wide variety of tasks is thought to emerge from the dynamic transformation of cognitive information. We hypothesized that these transformations are implemented via conjunctive activations in “conjunction hubs”—brain regions that selectively integrate sensory, cognitive, and motor activations. We used recent advances in using functional connectivity to map the flow of activity between brain regions to construct a task-performing neural network model from fMRI data during a cognitive control task. We verified the importance of conjunction hubs in cognitive computations by simulating neural activity flow over this empirically-estimated functional connectivity model. These empiricallyspecified simulations …

Affective Flexibility As A Developmental Building Block Of Cognitive Reappraisal: An Fmri Study, Jordan E. Pierce, Eisha Haque, Maital Neta

Center for Brain, Biology, and Behavior: Faculty Publications

Cognitive reappraisal is a form of emotion regulation that involves reinterpreting the meaning of a stimulus, often to downregulate one’s negative affect. Reappraisal typically recruits distributed regions of prefrontal and parietal cortex to generate new appraisals and downregulate the emotional response in the amygdala. In the current study, we compared reappraisal ability in an fMRI task with affective flexibility in a sample of children and adolescents (ages 6–17, N = 76). Affective flexibility was defined as variability in valence interpretations of ambiguous (surprised) facial expressions from a second behavioral task. Results demonstrated that age and affective flexibility predicted reappraisal ability, …

Differential Impact Of Biological And Behavioral Traits On Postexercise Energy Intake In Men Andwomen, Christoph Höchsmann, Safiya E. Beckford, Jeffery A. French, Julie B. Boron, Jared Stevens, Karsten Koehler

Department of Psychology: Faculty Publications

The energy intake response to exercise is highly variable and energy (over-) compensation via increased post-exercise energy intake occurs in some individuals but not others. In explorative analyses, we aimed to identify biological and behavioral predictors of post-exercise ad libitum energy intake and whether these predictors differ from ad libitum energy intake after rest.

Conclusions:Post-exercise energy intake is associatedwithdifferent factors than energy intake after rest and behavioral and biological traits differentially affect post-exercise energy intake in men and women. In women, habitual exercise behavior seems to predict postexercise energy intake, protecting against compensatory eating. Inmen, appetite-regulating hormones play a role …

Fddm1 And Fddm2, Two Sgs3-Like Proteins, Function As A Complex To Affect Dna Methylation In Arabidopsis, Shengjun Li, Weilong Yang, Yunfeng Liu, Guangyong Li, Xiang Liu, Yaling Liu, James R. Alfano, Chi Zhang, Bin Yu

Center for Plant Science Innovation: Faculty Publications

DNA methylation is an important epigenetic modification required for the specific regulation of gene expression and the maintenance of genome stability in plants and animals. However, the mechanism of DNA demethylation remains largely unknown. Here, we show that two SGS3-like proteins, FACTOR OF DNA DEMETHYLATION 1 (FDDM1) and FDDM2, negatively affect the DNA methylation levels at ROS1-dependend DNA loci in Arabidopsis. FDDM1 binds dsRNAs with 50 overhangs through its XS (rice gene X and SGS3) domain and forms a heterodimer with FDDM2 through its XH (rice gene X Homology) domain. A lack of FDDM1 or FDDM2 increased DNA methylation levels …

Qteller: A Tool For Comparative Multi-Genomic Gene Expression Analysis, Margaret R. Woodhouse, Shatabdi Sen, David Schott, John L. Portwood Ii, Michael Freeling, Justin W. Walley, Carson M. Andorf, James Schnable

Center for Plant Science Innovation: Faculty Publications

Motivation: Over the last decade, RNA-Seq whole-genome sequencing has become a widely used method for measuring and understanding transcriptome-level changes in gene expression. Since RNA-Seq is relatively inexpensive, it can be used on multiple genomes to evaluate gene expression across many different conditions, tissues and cell types. Although many tools exist to map and compare RNA-Seq at the genomics level, few web-based tools are dedicated to making data generated for individual genomic analysis accessible and reusable at a gene-level scale for comparative analysis between genes, across different genomes and meta-analyses. Results: To address this challenge, we revamped the comparative gene …

S-Glutathionylation Of Chicken Breast Extract, Isabella Fransisco

Senior Honors Projects

The purpose of this experiment was to analyze chicken breast fractions through affinity chromatography for protein modifications by glutathione disulfide (GSSG). The fractions were incubated with different concentrations of GSSG to determine potential modified proteins. There were proteins modified with GSSG at 33 kDa in fraction I, at 16 kDa, 36 kDa, and 44kDa in fraction II, and at 36 kDa in fraction III for the concentration dependent reactions. In the time dependent reaction for fraction II, there were two major proteins at 65 kDa and 176 kDa that were modified by GSSG. Lastly, we suggest that the major modified …

What Is Transpersonal Psychology? A Concise Definition Based On 20 Years Of Research, Glenn Hartelius

International Journal of Transpersonal Studies

Research on definitions of the field of psychology and themes in the literature of the field over a period of 20 years inform this description: Transpersonal psychology is a transformative psychology of the whole person embedded within a diverse, interconnected, and evolving world that pays particular attention to states of consciousness and developmental models reflecting expansion beyond conventional notions of self. Each element of this definition is examined, as well as the four phases of definitional development within the field from its founding in 1968 up to the present.

Improved Database Filtering Technology Enables More Efficient Ab Initio Design Of Potent Peptides Against Ebola Viruses, Thomas Ripperda, Yangsheng Yu, Atul Verma, Elizabeth Klug, Michellie Thurman, St. Patrick Reid, Guangshun Wang

Journal Articles: Pathology and Microbiology

The rapid mutations of viruses such as SARS-CoV-2 require vaccine updates and the development of novel antiviral drugs. This article presents an improved database filtering technology for a more effective design of novel antiviral agents. Different from the previous approach, where the most probable parameters were obtained stepwise from the antimicrobial peptide database, we found it possible to accelerate the design process by deriving multiple parameters in a single step during the peptide amino acid analysis. The resulting peptide DFTavP1 displays the ability to inhibit Ebola virus. A deviation from the most probable peptide parameters reduces antiviral activity. The designed …