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Three Decades Of Rat Genomics: Approaching The Finish(Ed) Line, Theodore S Kalbfleisch, Melissa L Smith, Julia L Ciosek, Kai Li, Peter A Doris

The Brown Foundation: Institute of Molecular Medicine

The rat, Rattus norvegicus, has provided an important model for investigation of a range of characteristics of biomedical importance. Here we survey the origins of this species, its introduction into laboratory research, and the emergence of genetic and genomic methods that utilize this model organism. Genomic studies have yielded important progress and provided new insight into several biologically important traits. However, some studies have been impeded by the lack of a complete and accurate reference genome for this species. New sequencing and genome assembly methods applied to the rat have resulted in a new reference genome assembly, GRCr8, which …

Anxiety-Like Behaviors In Mice Unmasked: Revealing Sex Differences In Anxiety Using A Novel Light-Heat Conflict Test, Sydney E Lee, Sung-Hoon Park, John C Aldrich, Laura K Fonken, Andrew D Gaudet

The Brown Foundation: Institute of Molecular Medicine

Anxiety and chronic pain afflict hundreds of millions worldwide. Anxiety and pain are more prevalent in females compared to males. Unfortunately, robust sex differences in human anxiety are not recapitulated in rodent tests, and results from rodent pain studies frequently fail to translate clinically. Therefore, there is a need to develop tests that reflect the differential salience of anxiety or pain-related stimuli between the sexes. Accordingly, here we introduce the Thermal Increments Dark-Light (TIDAL) conflict test. The TIDAL test places an anxiety-relevant stimulus (dark vs. illuminated chamber) in conflict with a heat-related stimulus (incrementally heated vs. isothermic chamber); mice freely …

Three-Dimensional Environmentally Sustainable Neuromorphic Computing System Based On Natural Organic Memristor, Mohammed Rafeeq Khan

Graduate Theses and Dissertations (2019 - present)

A three-dimensional neuromorphic (3D) computing architecture based on environmentally sustainable natural organic honey memristors is proposed in this thesis. A set of comprehensive and experimental results indicate that the proposed systems exhibit remarkable inference accuracy, consistently surpassing the 90% threshold, even with different challenges such as device variations and nonlinearity. This study also considers four different conductance drift situations, the effects of analog-to-digital converter (ADC) quantization, and multiple algorithms, such as VGG8 and DenseNet-40. The deliverable of this thesis will test the stability of the proposed systems and explore their potential applications and scalability in real-world situations.

Covid-19 Risk Assessment Among Vulnerable Small Business Owners In El Paso County, Texas, Sadie H Conway, Denise Vasquez, Kristina D Mena, Louis D Brown, Soyoung Kwon, Janelle Rios

Faculty, Staff and Student Publications

Background: Our objective was to deliver actionable, worksite-specific COVID-19 risk assessments and mitigation strategies tailored to vulnerable workers in one of the highest-risk areas in the US.

Methods: Four trained, bilingual (English/Spanish) community health workers (CHWs) recruited small businesses (ie, ≤20 employees) across various industries and executed novel on-site infectious disease risk assessment surveys of at least one employer and one employee.

Results: Of 102 participating businesses (95% Hispanic-owned), 96% were characterized as "high risk" or "very high risk" for disease transmission. All businesses reported implementing at least one practice to reduce disease transmission; however, almost half of businesses lacked …

Bivariate Genome-Wide Association Study Of Circulating Fibrinogen And C-Reactive Protein Levels, Julie Hahn, Gerard Temprano-Sagrera, Natalie R Hasbani, Symen Ligthart, Abbas Dehghan, Alisa S Wolberg, Nicholas L Smith, Maria Sabater-Lleal, Alanna C Morrison, Paul S De Vries

Faculty, Staff and Student Publications

Background: Fibrinogen and C-reactive protein (CRP) play an important role in inflammatory pathways and share multiple genetic loci reported in previously published genome-wide association studies (GWAS), highlighting their common genetic background. Leveraging the shared biology may identify further loci pleiotropically associated with both fibrinogen and CRP.

Objectives: To identify novel genetic variants that are pleiotropic and associated with both fibrinogen and CRP, by integrating both phenotypes in a bivariate GWAS by using a multitrait GWAS.

Methods: We performed a bivariate GWAS to identify further pleiotropic genetic loci, using summary statistics of previously published GWAS on fibrinogen (n = 120 246) …

Identification Of Proteins Associated With Type 2 Diabetes Risk In Diverse Racial And Ethnic Populations, Shuai Liu, Jingjing Zhu, Hua Zhong, Chong Wu, Haoran Xue, Burcu F Darst, Xiuqing Guo, Peter Durda, Russell P Tracy, Yongmei Liu, W Craig Johnson, Kent D Taylor, Ani W Manichaikul, Mark O Goodarzi, Robert E Gerszten, Clary B Clish, Yii-Der Ida Chen, Heather Highland, Christopher A Haiman, Christopher R Gignoux, Leslie Lange, David V Conti, Laura M Raffield, Lynne Wilkens, Loïc Le Marchand, Kari E North, Kristin L Young, Ruth J Loos, Steve Buyske, Tara Matise, Ulrike Peters, Charles Kooperberg, Alexander P Reiner, Bing Yu, Eric Boerwinkle, Quan Sun, Mary R Rooney, Justin B Echouffo-Tcheugui, Martha L Daviglus, Qibin Qi, Nicholas Mancuso, Changwei Li, Youping Deng, Alisa Manning, James B Meigs, Stephen S Rich, Jerome I Rotter, Lang Wu

Faculty, Staff and Student Publications

Aims/hypothesis: Several studies have reported associations between specific proteins and type 2 diabetes risk in European populations. To better understand the role played by proteins in type 2 diabetes aetiology across diverse populations, we conducted a large proteome-wide association study using genetic instruments across four racial and ethnic groups: African; Asian; Hispanic/Latino; and European.

Methods: Genome and plasma proteome data from the Multi-Ethnic Study of Atherosclerosis (MESA) study involving 182 African, 69 Asian, 284 Hispanic/Latino and 409 European individuals residing in the USA were used to establish protein prediction models by using potentially associated cis- and trans-SNPs. The models were …

Perceived Stigma's Influence On The Association Between Suicide Risk Severity And Help-Seeking For Suicidal Crises, Donna Zastrow

Electronic Theses and Dissertations

Introduction: Unfortunately, research examining help-seeking for suicide is limited. This study examined age, race, gender, suicide risk severity, and perceived stigma as predictors of formal and informal help-seeking behaviors individuals engage in during suicidal crises, and explored perceived stigma as a moderator of the relationship between risk severity and help-seeking. Method: Data from 80 college students who had experienced a past suicidal crisis were analyzed using two moderation analyses. Results: Rates of formal (67.5%) and informal (86.2%) help-seeking were high in the study sample. Higher suicide risk severity was positively associated with formal help-seeking (b = …

Association Of Common And Rare Variants With Alzheimer’S Disease In More Than 13,000 Diverse Individuals With Whole-Genome Sequencing From The Alzheimer’S Disease Sequencing Project, Wan-Ping Lee, Seung Hoan Choi, Margaret G Shea, Po-Liang Cheng, Beth A Dombroski, Achilleas N Pitsillides, Nancy L Heard-Costa, Hui Wang, Katia Bulekova, Amanda B Kuzma, Yuk Yee Leung, John J Farrell, Honghuang Lin, Brian W Kunkle, Adam Naj, Elizabeth E Blue, Frederick Nusetor, Dongyu Wang, Eric Boerwinkle, William S Bush, Xiaoling Zhang, Philip L De Jager, Josée Dupuis, Lindsay A Farrer, Myriam Fornage, Eden Martin, Margaret Pericak-Vance, Sudha Seshadri, Ellen M Wijsman, Li-San Wang, Alzheimer's Disease Sequencing Project;, Gerard D Schellenberg, Anita L Destefano, Jonathan L Haines, Gina M Peloso

Faculty, Staff and Student Publications

INTRODUCTION: Alzheimer's disease (AD) is a common disorder of the elderly that is both highly heritable and genetically heterogeneous.

METHODS: We investigated the association of AD with both common variants and aggregates of rare coding and non-coding variants in 13,371 individuals of diverse ancestry with whole genome sequencing (WGS) data.

RESULTS: Pooled-population analyses of all individuals identified genetic variants at apolipoprotein E (APOE) and BIN1 associated with AD (p < 5 × 10

DISCUSSION: We observed that complementary pooled-population and subgroup-specific analyses offered unique insights into the genetic architecture of AD.

HIGHLIGHTS: We determine the association of genetic variants with Alzheimer's disease (AD) using …

Evaluation Of The Etiology Of Recurrent Pregnancy Loss (Rpl): An Explanatory Mixed Methods Study Exploring Obstetrician Gynecologist Clinical Provider Behaviors And Factors Contributing To Incomplete Evaluations, Emelia Grant

Doctor of Philosophy in Translational Health Sciences Dissertations

Background: More than 50% of patients with recurrent pregnancy loss (RPL) are left without explanations for their losses. However, current research suggests that up to 90% of these individuals could receive explanations through evidence-based laboratory testing. Professional guidelines vary in their recommendations for laboratory testing and RPL evaluation, which can contribute to delayed or fragmented care and untreated maternal disease. Inequities in access to genetic testing further complicate the diagnostic landscape of RPL since payor policies often determine which tests are covered, leaving many patients without access due to financial constraints.

Objective: This study aimed to evaluate current practices of …

Mechanical Stability Of Body-Centered Cubic Iron At Earth's Core Pressure And Temperature Conditions Using A Molecular Graph Kernel Regression And Gaussian Process., Blaise Awola Ayirizia

Open Access Theses & Dissertations

We used machine learning to study nonmagnetic BCC iron in conditions similar to thosefound in the Earthâ??s core. Our model predicts the stability of BCC iron at high temperatures and pressures by analyzing a dataset from ab initio molecular dynamics simulations. The framework uses Gaussian process regression to make predictions by comparing the similarity between molecules. This comparison is made using the marginalized graph kernel. To use the marginalized graph kernel, the framework applies a spatial adjacency rule to convert molecules into graphs, where the vertices and edges are labeled by elements and interatomic distances, respectively. We can use this …

The Journey And Lived Experience Of Dropout, Hispanic, Teen Fathers, Patricia Ann Cuevas

Open Access Theses & Dissertations

The dropout phenomenon in the United States is an ongoing concern, especially regarding teen fathers. The purpose of this qualitative phenological study was to examine how Hispanic men who fathered a child as adolescent understood and made sense of their lived experiences of dropping out of high school and later returning to their studies. Semi-structured interviews were utilized to gather the data. An analysis of the findings was conducted, revealing the themes of emotional distress, expectations, hard lessons, and the impact of fatherhood. The themes were then applied to the theorical framework of Sensemaking. The results revealed that the participants …

Geotechnical Aspects Of Extraterrestrial Regolith Simulants, Jesus Baca

Open Access Theses & Dissertations

Geotechnical engineering has been crucial to the success of construction projects on Earth, and now it is time to extend this expertise to other celestial bodies. As NASA planned the Apollo missions, geotechnical engineers conducted extensive studies to understand the properties of lunar soil, using analogs like volcanic ash and other terrestrial materials to simulate the moon's surface. Nevertheless, it was not until the inception of the year 1968 that the Surveyor landers were able to give the first actual estimates of the moon soil geotechnical characteristics such as bearing capacity, void ratio, etc. With the development of more refined …

Integrating Responsible And Ethical Conduct Of Research Into Cures: A Longitudinal Study Observing Professional Development Of Fellows Within The Ethics Network For Course-Based Opportunities In Undergraduate Research, Aimee Angelica Hernandez-Gaytan

Open Access Theses & Dissertations

No abstract provided.

Enhancement Of Zika Virus Infection By West Nile And Dengue Virus Antibody Positive Cord-Blood Samples From Mothers In El Paso-Texas, Jeanette Orbegozo

Open Access Theses & Dissertations

The recent Zika virus (ZIKV) outbreak and its association with microcephaly cases and other neurological syndromes are important public health concerns. A phenomenon known as antibody-dependent enhancement (ADE) involves preexisting flavivirus antibodies to a specific flavivirus that enhances the severity of a second infection with a different flavivirus. Since ZIKV is related to flaviviruses like West Nile virus (WNV) and dengue virus (DENV), prior exposure to these viruses could elicit cross-reactive antibodies that may enhance a subsequent ZIKV infection. Therefore, this study aimed to determine if WNV and DENV antibodies from cord blood enhanced ZIKV infection in vitro. Initially, a …

Functional Analysis Of The Zebrafish Orthologs Of Host Cell Factor 1 Gene, David Paz

Open Access Theses & Dissertations

Host Cell Factor C1 (HCFC1) is a transcriptional co-activator factor that regulates the expression of over 5000 different downstream target genes in human cells. Missense mutations in the HCFC1 gene cause methylmalonic acidemia homocysteinemia cblX type (cblX). cblX, a multiple congenital anomaly syndrome (MCA) characterized by abnormal brain development, craniofacial abnormalities, metabolic deficits, and intractable epilepsy. Published studies suggest that HCFC1 regulates neural precursor proliferation, number, and differentiation. However, these results were derived from studies that were performed with nonsense alleles or transient knockdown approaches. Although these results demonstrate the importance of HCFC1 in brain development, they do not replicate …

Water Fluoridation: The Evidence Behind The Risk Of Fluoride Use, Margherita Fontana D.D.S., Ph.D., Carlos González-Cabezas D.D.S., M.S.D., Ph.D., Livia Tenuta D.D.S., M.Sc., Ph.D.

The Journal of the Michigan Dental Association

The debate surrounding fluoride use for caries control has intensified due to recent events, including a National Toxicology Program (NTP) report and a court ruling mandating EPA action on fluoride levels in tap water.

Despite concerns about fluoride's potential neurodevelopmental impact at high concentrations, current evidence shows no adverse effects at the recommended levels of 0.7 ppm in U.S. community water fluoridation programs. While studies in regions with endemic fluorosis suggest an association between high fluoride exposure and lower IQ, methodological limitations undermine causal conclusions.

Global and U.S. health authorities, including the WHO and ADA, reaffirm the safety and efficacy …

Enhancing The Utility Of Unmanned Autonomous Vehicles (Uavs) With Model-Based Systems Engineering (Mbse) And Modular Open Systems Approach (Mosa), Aimee Barraza

Open Access Theses & Dissertations

Unmanned Autonomous Vehicles (UAVs) have emerged as versatile tools with significant implications across various industries, particularly in defense. The technological advancements in UAVs have revolutionized military operations, surveillance, and reconnaissance capabilities. However, there exist challenges such as environmental factors affecting sensor and flight performance, limited battery life restricting flight durations, and payload capacity constraints impeding task efficiency.This paper delves into the importance of UAVs in different industries, specifically focusing on their pivotal role in the Department of Defense. It emphasizes the necessity of technological upgrades to overcome current challenges and proposes the adoption of a Modular and Open System Approach …

Functionalized Carbon Quantum Dots: A Promising Nanomaterial For Investigating Their Potential In Neurodegenerative Disease Treatment, Sherin M. El Morsy

Open Access Theses & Dissertations

Neurodegenerative diseases such as Parkinson's Disease (PD), Alzheimer's Disease (AD), and Huntington's Disease (HD) remain incurable, despite extensive research into therapeutic development. In the United States of America, the annual cost of PD and AD in terms of patient care and lost productivity is approximately $200 billion. Consequently, there is a critical and unaddressed need for the development of innovative drugs and drug delivery systems that can decelerate, stop, or ideally reverse neurodegenerative diseases. The dissertation presented here focuses on devising strategies to target PD through multiple mechanisms, including the inhibition of protein aggregation and the reduction of oxidative stress. …

Redefining Approaches For Measuring Landscape Subsidence And Permafrost Degradation In Arctic Tundra Environments, Tabatha Lynn Fuson

Open Access Theses & Dissertations

As climate change accelerates in the Arctic, the degradation of permafrost is leading to significant landscape transformation in tundra landscapes. This dissertation investigates the multifaceted responses of permafrost systems to warming, focusing on the dynamics of surface elevation changes and active layer thickness (ALT) across the North Slope of Alaska. In this study, I explore the capacity of repeat Terrestrial Laser Scanning (TLS) technology for modeling tundra features and detecting surface subsidence, specifically how different climate and landscape conditions during scanning impact TLS model precision. We also compare TLS model precision estimates to TLS model accuracy by comparing elevation values …

General Purpose Gpu Benchmarks For Neural Networks, Jose Maria Granados

Open Access Theses & Dissertations

Neural networks are a field of computing experiencing a rise in popularity in recent years due to the utilization of graphics processing units as their computational centerpiece. The lack of neural network benchmarks for the open-source Nyuzi architecture, a developing general-purpose processor with graphical processing capabilities, is the focus of this thesis. This work aims to determine whether Nyuziâ??s performance counters and traceable events suffice for performance tuning of neural network implementations. Given the mathematical intensity of neural networks, a strong emphasis is placed on events related to arithmetic instructions. Experimenting with neural network implementations in C and C++, existent …

Chipless 3d Microfluidic Rf Sensing, Sheikh Dobir Hossain

Open Access Theses & Dissertations

Effective management of the cold chain is essential to uphold the quality and safety of products vulnerability to physical factors like temperature, humidity, pressure, etc., including perishable foods, pharmaceuticals, and vaccines. Chipless Radio Frequency Identification (RFID) sensors have become increasingly favored as a viable technology for tracking, inventory, and sensing industries due to their wireless and non-line of sight (NLOS) situations, straightforward fabrication, cost efficiency, and adaptability to challenging environmental conditions. However, there is still a need for advancements in RFID sensors to make them promise for cold chain applications. Integration of flexibility and non-volatile memory into the existing RFID …

Environmental Change As A Driver Of The Evolution Of Migratory Behavior In Suboscine Birds, Emily Johns

Open Access Theses & Dissertations

Avian migration, particularly long-distance seasonal migratory movement, has long captured the attention of researchers and the public alike. However, the evolutionary origins of migratory behavior are poorly understood, in part due to limited understanding of the full range of migratory strategies including short-distance and intra-tropical movements. We examine the climatic drivers of migration across suboscine birds, a group of roughly 1,300 primarily Neotropical species with a complex array of migratory strategies. Our reconstructions of the evolutionary history of suboscine migration reveal that migratory behavior is labile and is lost approximately twice as often as it is gained. We find that …

Ultra-High Temperature Ceramics: Materials, Manufacturing, And Machine Development, Joseph Matthew Munoz

Open Access Theses & Dissertations

This research aimed to advance the 3D printing of ultra-high-temperature ceramic matrix composites (UHTCMCs) and develop a custom Direct Ink Writing (DIW) system with multimaterial and in-line mixing capabilities. The study first focused on creating ZrB₂–SiC composites reinforced with aligned silicon carbide fibers (SiCf) using paste extrusion. By formulating suspensions with a preceramic polymer (SMP-10), ZrB₂, and SiCf, the study assessed how fiber alignment influenced key properties such as thermal and electrical conductivity and mechanical strength. Green curing and pyrolysis transformed the printed parts into UHTCMCs, with results showing substantial improvements in thermal conductivity—nearly double that of non-aligned parts—and a …

Development Of A Novel Autoantibody Panel For Prostate Cancer Detection Based On Immunoproteomic Profiling And Cancer Driver Genes, Cuipeng Qiu

Open Access Theses & Dissertations

Prostate cancer (PCa) is the second most frequent cancer in males with 1.47 million new cases and 396,700 deaths worldwide in 2022. It is the second leading cause of cancer-related deaths among males in the United States with over 35,000 estimated deaths in 2024. PCa is a type of indolent cancer that can progress to an advanced metastatic castration-resistant (mCRPC) stage if not detected and treated early. Screening precancerous lesions or early tumor detection is an effective strategy to reduce the mortality of cancer. Despite the development of effective screening methods, such as the prostate-specific antigen (PSA) test, the specificity …

Novel Therapuetic Approaches For Chagas Disease, Juan Carlos Silva

Open Access Theses & Dissertations

Chagas disease (CD) is caused by the hemoflagellate protozoan Trypanosoma cruzi. This disease is considered one of the 20 neglected tropical diseases (NTD), and it is estimated that 6 to 8 million people worldwide are diagnosed with CD. In the United States, Chagas infection is not reported in all states; however, most reported CD cases are chronic infections. Chagas infection is characterized by two phases: an acute and a chronic phase. Until this present moment, no prophylactic or therapeutic human vaccine is available. However, in a recent study in a murine model, our group showed that the synthetic 20-merpeptide (DAENPGGEVFNDNKKGLSRV) …

Analysis Of Microbiome In Various Human Medical Conditions Using Next-Generation Sequencing Of The 16s Rrna Gene, Pallavi Sharma

Electronic Theses and Dissertations

Studies of human microbiomics, spanning diverse anatomical sites, offer a unique perspective into the complex microbial communities within the body. Influenced by age, gender, and disease, it mirrors broader microbial ecosystems. This study specifically delves into the ocular and gastrointestinal tract microbiome, comparing its composition in 43 healthy and diseased patients using 16S rRNA gene sequencing. We identified a rich microbial landscape, identifying over 338 bacterial taxa. Notably, Acinetobacter, Cutibacterium, Acidovorax and Herbaspirillum were prevalent in the ocular samples and Akkermansia, Faecalibacterium, and Anaerostipes were mostly prevalent in gut samples. Moreover, dry eye disease conditions were characterized by …

Neural Network Architecture Search Enabled Wide-Deep Learning (Nas-Wd) Integrated Hyperspectral Imaging Understanding For Woody Breast In Poultry Processing, Chaitanya Kumar Reddy Pallerla

Graduate Theses and Dissertations

The development and implementation of a Wide & Deep (WD) learning model tailored for classification and regression tasks utilizing spectral data provides a robust solution to evaluate woody breast (WB) conditions in poultry fillets. This process begins with thorough data preprocessing, which includes loading spectral and classification datasets, imputing missing values with medians, and splitting the data into training and testing sets to ensure rigorous model evaluation. The WD model architecture integrates wide linear models and deep neural networks to harness the strengths of both approaches. The wide component excels at memorizing sparse feature interactions, while the deep component captures …

Enhancing Selection Intensity With High-Throughput Phenotyping Data In Plant Breeding, Ashmita Upadhyay

Graduate Theses and Dissertations

Genomic prediction (GP) has proven to be an essential tool to accelerate the cultivar development pipeline by predicting the performance of un-phenotyped lines in the field of plant breeding. However, the prediction accuracy is bounded by the heritability of the target trait, limiting the efficiency of the single-trait GP model. To overcome the limitation, a multi-trait genomic prediction model using high-throughput phenotyping (HTP) data can be used to leverage secondary traits to boost the predictive ability of the target trait. This study aimed to assess the efficiency of the multi-trait (MT)- GP model powered by HTP derived secondary traits in …

Roger Williams University 2024 President's Report: A Message From President Miaoulis, Roger Williams University

Life of the Law School (1993- )

No abstract provided.

Assessing The Influence Of Native And Invasive Grasses On The Behavior Of Aedes Aegypti In South Texas, Emily Medelez

Theses and Dissertations

Invasive grasses in South Texas can have widespread negative effects, displacing native species, reducing biodiversity, and posing risks to public health. These grasses may flourish in moist, shaded environments, which not only support their growth but also creates habitats favorable for mosquito activity. This can increase the population and alter the behavior of mosquitoes, potentially raising the risk of disease transmission. In this thesis, I look at the behavior of mosquito species Aedes aegypti, primary vector of the yellow fever virus. I analyzed the influence of oviposition, flight and resting behaviors. I tested the relative attraction of Aedes mosquitoes …