Digital Commons Network^™

Conformation Of The U12-U6atac Snrna Complex Of The Minor Spliceosome And Binding By Ntc-Related Protein Rbm22, Joanna Ciavarella

Dissertations, Theses, and Capstone Projects

Splicing of precursor messenger (pre-m)RNA is a critical process in eukaryotes in which the non-coding regions, called introns, are removed and coding regions, or exons, are ligated to form a mature mRNA. This process is catalyzed by the spliceosome, a multi-mega Dalton ribonucleoprotein complex assembled from five small nuclear ribonucleoproteins (snRNP) in the form of small nuclear (sn)RNA-protein complexes (U1, U2, U4, U5 and U6) and >100 proteins. snRNA components catalyze the two transesterification reactions while proteins perform critical roles in assembly and rearrangement. U2 and U6 snRNAs are the only snRNAs directly implicated in catalyzing the splicing of pre-mRNA. …

Historical Ecology Of Norse Greenland: Zooarchaeology And Climate Change Responses, Konrad Smiarowski

Dissertations, Theses, and Capstone Projects

This thesis invokes Historical Ecology approach to better understand human impacts on marine and terrestrial ecosystems, and the creation of cultural landscapes and seascapes in Norse Greenland. It also investigates climate impacts on human economic strategies, as they vary substantially by island and region in the North Atlantic but were especially important in arctic Greenland.

The analysis centers on the animal bone data and uses both existing and newly generated zooarchaeological collections to contribute to the study of Norse Greenland and its place in human ecodynamics research. The newly analyzed archaeofauna shows that the culturally Nordic European settlers used to …

Linguistic Abstractions In Children’S Very Early Utterances, Qihui Xu

Dissertations, Theses, and Capstone Projects

How early do children produce multiword utterances? Do children's early utterances reflect abstract syntactic knowledge or are they the result of data-driven learning? We examine this issue through corpus analysis, computational modeling, and adult simulation experiments. Chapter 1 investigates when children start producing multiword utterances; we use corpora to establish the development of multiword utterances and a probabilistic computational model to account for the quantitative change of early multiword utterances. We find that multiword utterances of different lengths appear early in acquisition and increase together, and the length growth pattern can be viewed as a probabilistic and dynamic process.

Chapter …

High Water-Responsiveness Of Peptidoglycan And Its Water-Responsive Mechanism, Haozhen Wang

Dissertations, Theses, and Capstone Projects

Water-responsive materials that reversibly deform in response to humidity changes show great potential for developing muscle-like actuators for miniature and biomimetic robotics. This thesis demonstrates that peptidoglycan exhibits ultrahigh water-responsive actuation energy and power densities, which are orders of magnitude higher than those of frequently used actuators, such as piezoelectric actuators and dielectric elastomers. Surprisingly, peptidoglycan exhibits an energy conversion efficiency of ~66.8%, which could be attributed to its super-viscous nanoconfined water that efficiently translates water’s movement to peptidoglycan’s mechanical deformation. The systematic water-responsive characterizations of peptidoglycan from different microorganisms and peptide crystals indicate that enhanced H-bonding interactions in water-responsive …

Three Lenses Of Contrapower Sexual Harassment, Michael L. Ekema

Dissertations, Theses, and Capstone Projects

Contrapower sexual harassment refers to sexual harassment incidents where the perpetrator has less formal power within the organization than the person being victimized. Although the potential for inverse power dynamics were already identified in the early stages of sexual harassment research, the prevalence and antecedents of contrapower sexual harassment have rarely been examined. In addition, prior sexual harassment research has overwhelmingly prioritized gender as the focal variable of interest. This dissertation seeks to contribute to the literature on workplace incivility, organizational deviance, and counterproductive work behaviors by looking at contrapower harassment through three different lenses: The perspective of harassment targets, …

Primitivism, Performance Studies, And Modernist Time: Tracing An Alternative Genealogy Of Performance Studies Through Case Studies In Modernist Cultural Appropriation, Stephanie Vella

Dissertations, Theses, and Capstone Projects

This dissertation traces a genealogy of research methodologies for documenting, transmitting, and analyzing embodied, non-textual performance practices from the late-nineteenth through early-twentieth centuries. I uncover intersections between these methods and the conflations of race and temporality that are ubiquitously threaded through modernist cultural practices during this time in the form of primitivism. The researchers whose work I analyze all saw European modernity as fundamentally detached from physical culture, while viewing other cultures—especially those of the people most directly threatened by colonial and capitalist expansion during this time—as having access to a “lost” corporeal knowledge. I argue that primitivism is not …

Coercive Control And Trauma-Coerced Attachment In Commercial Sexual Exploitation: A Mixed-Method Examination, Kendra Doychak

Dissertations, Theses, and Capstone Projects

Commercial sexual exploitation (i.e., sex trafficking) can lead to myriad negative consequences for its victims, including exposure to coercive control and the development of trauma-coerced attachments. Scholars have offered theoretical conceptualizations of the relation between coercive environments and traumatic attachments, but this relationship is rarely empirically examined. The current study used data from 68 semi-structured interviews with former victims of sex trafficking to first, formally identify coercive control and second, empirically classify trauma-coerced attachment in this population. Mixed-method analysis were used to identify associations between coercive control and TCA in order to better explain how this abuse dynamic leads to …

A Pilot Feasibility Trial Of Mindfulness And Modification Therapy For Males Who Use Aggression, Jenny Mitchell

Dissertations, Theses, and Capstone Projects

Physical aggression incurs substantial harm to victims and witnesses, particularly when it occurs within close relationships such as family, friendships, or intimate partnerships. Men who use aggression against partners and other adults frequently experience high levels of psychopathology, including depression, posttraumatic stress symptoms, anxious/insecure attachment, paranoia, bipolar disorder, intermittent explosive disorder, personality disorders, and substance abuse, which contribute to use of aggressive behaviors. However, existing treatments for aggression often do not address these symptoms. It is important that treatments for aggression are grounded in theoretical literature and backed by empirical support in order to increase treatment engagement and effectiveness. Treatments …

Fathers Are Fathers Are Fathers: How Sociocultural Context And Sexual Orientation Influence The Gendering Of Children, Sarah M. Frantz

Dissertations, Theses, and Capstone Projects

Though the body of literature on gay father-headed families indicates there is no significant differences on measures of gender normativity and well-being between children raised with two dads and their peers raised by heterosexual parents, there is a proliferation of anti-LGBTQ+ policies throughout the United States aimed at limiting this community’s rights and silencing their lived experiences. Given that sociocultural and political environments vary greatly state-to-state, it is important to see how the specific context in which fathers live may impact their differential parenting of sons and daughters, their gender beliefs, and the way they feel they would navigate gender …

Biomarker, Treatment, And Socio-Demographic Factors Affecting Opioid Use Disorder Treatment Retention, Fernand A. De Los Reyes

Dissertations, Theses, and Capstone Projects

ABSTRACT

Biomarker, Treatment, and Socio-Demographic Factors

Affecting Opioid Use Disorder Treatment Retention

by

Fernand A. De Los Reyes

Advisor: Martha Velasco-Whetsell

Increasing mortality from opioid overdose and low treatment engagement are significant public health concerns. Along with increasing health care and criminal justice enforcement costs, there is an urgent need to study the factors associated with treatment retention in opioid use disorder. The study investigated the relative impact of the biomarker cholesterol on treatment retention in an opioid treatment program (OTP) clinic. Further, it examined the medical comorbidities, treatment, and socio-demographic variables that impact opioid use disorder treatment retention. This …

Function Of Atm And Msh2 During Dna Repair And Recombination, Emily Sible

Dissertations, Theses, and Capstone Projects

Class switch recombination (CSR) produces secondary immunoglobulin isotypes and requires AID-dependent DNA deamination of intronic switch (S) regions within the immunoglobulin heavy chain (Igh) gene locus. Non-canonical repair of deaminated DNA by mismatch repair (MMR) or base excision repair (BER) creates DNA breaks that permit recombination between distal S regions. ATM-dependent phosphorylation of AID at serine-38 (pS38-AID) promotes its interaction with APE1, a BER protein, suggesting that ATM regulates CSR through BER. However, pS38-AID may also function in MMR during CSR, although the mechanism remains unknown. To examine whether ATM modulates BER- and/or MMR-dependent CSR, Atm^-/- mice …

Antisocial Behavior And Callous Unemotional Traits In Youth: A Biosocial Approach, Yong Lin Huang

Dissertations, Theses, and Capstone Projects

Early life presence of antisocial behavior (e.g., aggression/delinquency) and psychopathic/callous-unemotional (CU) traits (lacking empathy/remorse, shallow affect) are precursors to juvenile crime and criminal offending in adulthood. Etiological research on antisocial/CU tendencies has implicated both neurobiological (e.g., alterations in brain function and structure) and environmental (social adversity, prenatal stress) underpinnings. It has been proposed that reward and punishment processing deficits may induce problematic traits and behavior, such that antisocial/CU tendencies may be linked to hypersensitivity to rewards and hyposensitivity to punishment. Studies in this area have generated inconsistent findings and focused primarily on adult and clinical samples, leaving youth and community …

Dietary Regulation Of Silent Synapses In The Dorsolateral Striatum, Allison M. Meyers

Dissertations, Theses, and Capstone Projects

Obesity and drugs of abuse share overlapping neural circuits and behaviors. Cravings for drugs of abuse increase during abstinence, a phenomenon known as incubation. In obesity, increased craving is observed in individuals during dieting. Diets often fail, with return to- or increase above- original weight. The extent to which this reflects an incubation phenomenon has not been carefully examined. One mechanism underlying incubation is the reemergence of a developmental mechanism called silent synapses. Silent synapses are 'temporary' synapses that are important for remodeling brain circuits. They are prevalent during early development but largely disappear by adulthood. Drugs of abuse increase …

A Polypharmacological Approach To Relapse Prevention In An Animal Model Of Heroin Addiction, Scott T. Ewing

Dissertations, Theses, and Capstone Projects

Chemical compounds that target dopamine (DA) D1 or D3 receptors have shown promise as potential interventions in animal models of cue-induced relapse. However, undesirable side effects or pharmacodynamic profiles have limited the advancement of new compounds in preclinical studies when administered as independent treatments. In this series of experiments, we explored the effects of co-administration of a D1-recepter partial agonist (SKF 77434) and a D3-receptor antagonist (NGB 2904) in heroin-seeking rats within a ‘conflict’ model of abstinence and cue-induced relapse. Rats were first trained to press a lever to self-administer heroin and drug delivery was paired contingently with cues (e.g., …

Elucidation Of Gene Essentiality And Genetic Determinants Of Intrinsic P-Aminosalicylic Acid Resistance In Mycobacterium Kansasii, Keith J. Levendosky

Dissertations, Theses, and Capstone Projects

Mycobacterium kansasii (Mk) is an opportunistic pathogen capable of causing tuberculosis-like pulmonary disease in immunocompromised individuals and those with other risk factors including chronic obstructive pulmonary disease or malignancy. Mk is frequently isolated from man-made water sources where it forms resilient biofilms, posing a health risk to these susceptible individuals. Despite its medical relevance as an environmental pathogen, and a close phylogenetic relationship with the obligate pathogen Mycobacterium tuberculosis (Mtb), few studies to date have probed the molecular biology and genetics of Mk. Here, we sought to apply a transposon (Tn) mutagenesis tool to dissect …

Transcriptional Mechanisms Of Neuroprotection In Excitotoxicity Driven Neurodegeneration In C. Elegans, Zelda Z. Mendelowitz

Dissertations, Theses, and Capstone Projects

Excitotoxicity is notorious for triggering neuronal cell death in both developmental and adult-onset neurodegenerative diseases. In excitotoxicity, excessive concentrations of Glutamate in the synapse overstimulate Glutamate Receptors (GluRs) on postsynaptic neurons. While GluR mediated degenerative mechanisms remain obscure, GluR activation was surprisingly found to also have a neuroprotective effect through activation of specific transcriptional programs. To identify evolutionarily conserved transcriptional programs in neuroprotection we use a C. elegans model of excitotoxic necrosis (glt-3;nuIs5). We have identified that non-canonical activation of the transcription factor CRH-1/CREB mediates neuroprotection in our excitotoxicity model. We found the Histone Acetyl Transferase, MYS-1/KAT6, and the neuronal …

The Social Construction Of Premenstrual Dysphoric Disorder (Pmdd), Raya Balabanova

Dissertations, Theses, and Capstone Projects

The creation of psychiatric diagnoses, otherwise known as psychiatric nosology, is a complex endeavor, one involving a great deal of social construction. One diagnosis in particular, premenstrual dysphoric disorder (PMDD), exemplifies the different factors that go into the creation of psychiatric labels. After decades of research, activism, and debates, PMDD was included in the diagnostic and statistical manual (DSM-5), which is widely used by clinicians in the U.S. This thesis aims to describe how the symptoms described by PMDD caught the attention of the medical profession and how PMDD was shaped into the diagnosis it is today. The introduction of …

Reproducing The Orient: A Critical Examination Of Western Media Representations Of China’S Uyghur Policies Between 2014 And 2021, R. Tiger Li

Dissertations, Theses, and Capstone Projects

This study examines the convergence of US state media and US-based mass media in news coverage of China’s policies in Xinjiang. Analysis of a sample of articles published by The New York Times, The Wall Street Journal, The Washington Post, and CNN between 2014 and 2021 found that stories citing US state media, Uyghur exile advocacy groups, or non-government organizations receiving US funding were significantly more negative in tone than articles using other sources. Articles citing state media and exile advocacy groups tended to frame China’s policies as an ideological challenge while other articles were more likely …

Émigrés As Aneks: Polish Intellectuals Between East And West, 1968–1989, Lukasz Chelminski

Dissertations, Theses, and Capstone Projects

This work focuses on Aneks (1973-1989), a publication that a small group of post-1968 émigrés, mostly Polish Jews, created in exile. Conceptualized as an “annex” to intellectual life in Poland, the publication was founded to help Polish intellectuals look beyond the country to better understand national problems. At the core of the enterprise were the Smolar brothers, who were in a unique position to offer such help: soon after their forced emigration due to rising antisemitism in communist Poland, Aleksander began to study with the great French liberal, Raymond Aron, and Eugeniusz began a career at the Polish section of …

The Making Of A Bilingual University In The 21st Century, Michael Mena

Dissertations, Theses, and Capstone Projects

At the southernmost tip of Texas, the University of Texas Rio Grande Valley (UTRGV) opened its doors on August 31, 2015 as a ‘bilingual, bicultural, and biliterate’ campus—the only one of its kind and at a scale never before attempted in the United States. This is a categorical achievement in the near 200 year-long quest for the educational advancement of Latinxs in Texas—a state historically structured by white supremacist ideologies, violent economic and political disenfranchisement, as well as a racially segregated education system designed to maintain exploitative labor practices (Montejano 1987; González 1990, 2013, 1999; Blanton 2004). This constitutes the …

Novel Therapeutic Strategies For Alzheimer’S Disease: Targeting Toll-Like Receptor Signaling And A Multi-Target Approach, Giovanni Oliveros

Dissertations, Theses, and Capstone Projects

Alzheimer’s disease (AD) is multifactorial, and its hallmarks include the formation of amyloid-beta (Ab) plaques and neurofibrillary tau tangles, accompanied by an increase in glial cell activation, culminating in neurodegeneration, chronic neuroinflammation, and cognitive decline in human patients. AD will cost the United States over $300 million this year alone and is projected to cost over $1 trillion by 2050, AD is a serious concern for the aging population, and efforts need to be redirected towards more effective therapeutic intervention strategies. Drugs aimed at halting AD progression have so far proven unsuccessful due to the development of pharmaceuticals that target …

A Survey Study Of Speech-Language Therapists’ Experiences With Teletherapy At The Onset Of The Covid-19 Crisis, Jason A. Rosas

Dissertations, Theses, and Capstone Projects

The present study aimed to understand how delivering pediatric treatment services via ‘teletherapy’ affected speech-language therapists (SLTs) during the initial outbreak of the COVID-19 pandemic crisis in 2020. SLTs reported on their experiences with the change from in-person to remote service delivery via two national surveys distributed at the start of the pandemic between April 2020 and July 2020. To explain SLTs’ survey responses, this dissertation introduced the Professional Adaptation Model (PA Model). The PA Model facilitated evaluation of the SLTs’ professional environment and the psychological constructs of their professional identity believed to influence the transition to speech-language teletherapy. Specifically, …

The Behavioral And Gene Expression Effects Of Loss Or Exhaustion Of Sonic Hedgehog From Dopamine Neurons, Dustin R. Zuelke

Dissertations, Theses, and Capstone Projects

Mesencephalic dopamine neurons (DAN) signal motivation and reward prediction errors. Their collective functions are considered critical for the translation of thought into context appropriate actions. Dopaminergic dysfunction has severe consequences: (1) DAN degeneration is a major determinate of Parkinson’s Disease (PD), (2) disturbed dopaminergic signaling in schizophrenia leads to unorganized learning, and (3) chemically induced dopaminergic signaling results in impulse control disorders (ICDs) and life-threatening addictions. The use of the dopamine (DA) precursor L-Dopa for DA replacement therapy in PD patients produces motor and behavioral side-effects such as L-Dopa induced dyskinesias (LID), ICDs, and a propensity for opioid addiction. Despite …

Free Improvisation Pedagogy: An Arts Based Research Approach To Promoting Student Agency And Embracing Difference, Nicholas Catino

Dissertations, Theses, and Capstone Projects

Free Improvisation Pedagogy explores the changing perspectives of students as they co-create musical improvisations. Free improvisation is understood as a site for transformative pedagogy, with the possibility for people to break free of structures, think and perform independently, broaden their perspective of proper tonality, engage in musical democracy and equality of voice, and participate in music making that is active, participatory, and continually evolving.

Working with a small group of High School students in suburban New York, this research explores these topics and documents, through audio, video, visual art, and conversation, how students experience this type of music making and …

Understanding Parental Engagement At The Nexus Of Race, Class, Gender, And Sexual Orientation: An Examination Through Anti-Black White Settler Colonialism, Alyssa P. Lyons

Dissertations, Theses, and Capstone Projects

In the great scramble to remedy the inequalities of American education, the term “parental engagement” has remained a stubborn fixture in political, educational, and public discourse since the 1960s. Parental engagement has been offered as a possible mitigation tool in the fight for educational justice. This has led to ample social science research exploring the significance and impact of parental engagement on a host of educational outcomes. With much of the sociological theorizing of education stuck in the 1960s, scholars need new ways of theorizing to better understand the role of parental engagement in not alleviating educational inequalities—but in maintaining …

A New Approach For Congestive Heart Failure And Arrhythmia Classification Using Downsampling Local Binary Patterns With Lstm, Süleyman Akdağ, Fatma Kuncan, Yilmaz Kaya

Turkish Journal of Electrical Engineering and Computer Sciences

Electrocardiogram (ECG) is a vital diagnosis approach for the rapid explication and detection of various heart diseases, especially cardiac arrest, sinus rhythms, and heart failure. For this purpose, in this study, a different perspective based on downsampling one-dimensional-local binary pattern (1D-DS-LBP) and long short-term memory (LSTM) is presented for the categorization of Electrocardiogram (ECG) signals. A transformation method named 1DDS-LBP has been presented for Electrocardiogram signals. The 1D-DS-LBP method processes the bigness smallness relationship between neighbors. According to the proposed method, by downsampling the signal, the histograms of 1D local binary patterns (1D-LBP) calculated from the obtained signal groups are …

A New Network-Based Community Detection Algorithm For Disjoint Communities, Peli̇n Çeti̇n, Şahi̇n Emrah Amrahov

Turkish Journal of Electrical Engineering and Computer Sciences

A community is a group of people that shares something in common. The definition of the community can be generalized as things that have common properties. By using this definition, community detection can be used to solve different problems in various areas. In this study, we propose a new network-based community detection algorithm that can work on different types of datasets. The proposed algorithm works on unweighted graphs and determines the weight by using cosine similarity. We apply a bottom-up approach and find the disjoint communities. First, we accept each node as an independent community. Then, the merging process is …

Chemical Disease Relation Extraction Through The Combination Of Multiple Mention Levels: Relscan+, Stanley Chika Onye, Nazi̇fe Di̇mi̇li̇ler, Ari̇f Akkeleş

Turkish Journal of Electrical Engineering and Computer Sciences

Chemical-induced disease (CID) relation extraction has been pivotal in the understanding of biological processes. A CID relation between a chemical and disease entity may be extracted either from a single sentence or from two or more adjacent sentences. We use `intrasentence level' to refer to the mention of the desired entities in the same sentence and `intersentence level? to refer to the mention of these entities in two or more adjacent sentences. This study proposes a three-phase architecture for extracting CID relations from biomedical literature by considering both sentence levels and additionally the combination of these two sentence levels which …

Design And Implementation Of A Low Cost And Portable Tactile Stimulator, Coşkun Kazma, Vecdi̇ Emre Levent, Merve Çardak, Ni̇zametti̇n Aydin

Turkish Journal of Electrical Engineering and Computer Sciences

When central nervous system has a problem, somatic area I and II respond to stimulation differently. Therefore, it is possible to identify some of the central nervous diseases when somatosensory on the fingertip is stimulated and responses are recorded and analyzed. We designed a system to stimulate the mechanoreceptors on fingertips. It is composed of a mechanical system for fingertip stimulation, an embedded controller, a control computer, and a software to control overall operation. During test, mechanoreceptors are stimulated according to the test protocols. Individuals' answers are recorded to be evaluated by the developed software. In this study, several design …

Rates Of Future Climate Change In The Gulf Of Mexico And The Caribbean Sea: Implications For Coral Reef Ecosystems, A. E. Lawman, S. G. Dee, K. L. Delong, A. M.S. Correa

Faculty Publications

Rising temperatures and ocean acidification due to anthropogenic climate change pose ominous threats to coral reef ecosystems in the Gulf of Mexico (GoM) and the western Caribbean Sea. Unfortunately, the once structurally complex coral reefs in the GoM and Caribbean have dramatically declined since the 1970s; relatively few coral reefs still exhibit a mean live coral cover of >10%. Additional work is needed to characterize future climate stressors on coral reefs in the GoM and the Caribbean Sea. Here, we use climate model simulations spanning the period of 2015–2100 to partition and assess the individual impacts of climate stressors on …