Digital Commons Network^™

Gut Dysbiosis Correlates With Covid-19 Severity, Ednita Escobar

CMC Senior Theses

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) impacts not only respiratory but also gut and oral microbiomes, influencing the manifestations of COVID-19. Each person’s unique microbiome consists of microorganisms such as bacteria, fungi, and viruses, some of which are symbiotic and others potentially harmful. Alterations in the gut microbiome, specifically, can affect the severity and symptoms of COVID-19. A review of studies indicate a pattern of gut dysbiosis in COVID-19 patients characterized by a decrease in beneficial microbiota and/or an increase in opportunistic pathogens. This gut imbalance correlates with disease severity, suggesting that the gut microbiome plays a significant role …

Comparative Study Of The Effects Of Dietary Supplements On Reproductive And Growth Performance In Sows And Nursery Pigs, Panumas Kongpanna

Chulalongkorn University Theses and Dissertations (Chula ETD)

This study evaluated the effects of dietary supplementation with a multi-strain probiotic containing Bacillus subtilis (5 × 107 CFU/g) and Lactobacillus plantarum (1 × 109 CFU/g) on reproductive performance in multiparous sows and growth performance in weaned piglets. In Experiment 1, 300 sows were assigned to control or probiotic diets across five parity groups (2, 3, 4, 5 and 6 to 9) using a 2 × 5 factorial design. Experiment 2 involved 120 weaned piglets randomly allocated to four dietary treatments: control, antibiotic, enzyme, or probiotic. Measurements included reproductive and litter performance, colostrum IgG, milk composition, and piglet growth, digestibility, …

The Differential Proteomic Response To Ischemic Stroke In Appalachian Subjects Treated With Mechanical Thrombectomy, Christopher J. Mclouth, Benton Maglinger, Jacqueline A. Frank, Kristin J. Hazelwood, Jordan P. Harp, Will Cranford, Shivani Pahwa, David Dornbos Iii, Amanda L. Trout, Ann M. Stowe, Justin F. Fraser, Keith R. Pennypacker

Neurology Faculty Publications

Introduction The Appalachia region of North America is known to have significant health disparities, specifically, worse risk factors and outcomes for stroke. Appalachians are more likely to have comorbidities related to stroke, such as diabetes, obesity, and tobacco use, and are often less likely to have stroke interventions, such as mechanical thrombectomy (MT), for emergent large vessel occlusion (ELVO). As our Comprehensive Stroke Center directly serves stroke subjects from both Appalachian and non-Appalachian areas, inflammatory proteomic biomarkers were identified associated with stroke outcomes specific to subjects residing in Appalachia. Methods There were 81 subjects that met inclusion criteria for this …

Rare Variant Analyses Validate Known Als Genes In A Multi-Ethnic Population And Identifies Antxr2 As A Candidate In Pls, Tess D. Pottinger, Joshua E. Motelow, Gundula Povysil, Cristiane A. Martins Moreno, Zhong Ren, Hemali Phatnani, The New York Genome Center Als Sequencing Consortium, Timothy J. Aitman, Javier Santoyo‑Lopez, Scottish Genomes Partnership, Hiroshi Mitsumoto, Als Cosmos Study Group, Pls Cosmos Study Group, Gtac Investigators, David B. Goldstein, Matthew B. Harms

Neurology Faculty Publications

Background Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease affecting over 300,000 people world‑ wide. It is characterized by the progressive decline of the nervous system that leads to the weakening of muscles which impacts physical function. Approximately, 15% of individuals diagnosed with ALS have a known genetic variant that contributes to their disease. As therapies that slow or prevent symptoms continue to develop, such as antisense oligonucleotides, it is important to discover novel genes that could be targets for treatment. Additionally, as cohorts continue to grow, performing analyses in ALS subtypes, such as primary lateral sclerosis (PLS), becomes possible …

Astrocytic Stress Response Is Induced By Exposure To Astrocyte-Binding Antibodies Expressed By Plasmablasts From Pediatric Patients With Acute Transverse Myelitis, Chad Smith, Kiel M. Telesford, Sara G. M. Piccirillo, Yamhilette Licon‑Munoz, Wei Zhang, Key M. Tse, Jacqueline R. Rivas, Chaitanya Joshi, Dilan S. Shah, Angela X. Wu, Ritu Trivedi, Scott Christley, Yu Qian, Lindsay G. Cowell, Richard H. Scheuermann, Ann M. Stowe, Linda Nguyen, Benjamin M. Greenberg, Nancy L. Monson

Neurology Faculty Publications

Background Pediatric acute transverse myelitis (ATM) accounts for 20–30% of children presenting with a first acquired demyelinating syndrome (ADS) and may be the first clinical presentation of a relapsing ADS such as multiple sclerosis (MS). B cells have been strongly implicated in the pathogenesis of adult MS. However, little is known about B cells in pediatric MS, and even less so in pediatric ATM. Our lab previously showed that plasmablasts (PB), the earliest B cell subtype producing antibody, are expanded in adult ATM, and that these PBs produce self‑reactive antibodies that target neurons. The goal of this study was to …

The Impacts Of Gut-Supporting Feed Additives On The Growth Performance, Gut Health, Blood Chemistry, And Immune Status Of Broiler Chickens Exposed To Different Stressors, Richard A. Adefioye

Theses and Dissertations--Animal and Food Sciences

Three experiments were conducted to examine the effects of different feed additives in mitigating stress in broiler chickens. Experiment 1 used 504-day-old male by-product Cobb breeder chicks with 8 treatments replicated 9 times with 7 birds per replicate cage, structured as a 2x4 factorial arrangement of treatments. All birds were on the experimental diets for 20 days. There were 2 levels of lipopolysaccharide (LPS) challenge [no challenge vs. LPS challenge at 1 mg/kg BW) and 4 types of feed additives [no additive, 0.05% PostB, 0.1% PostB, and 0.1% Tynagen^TM]. In experiment 2, 672-day-old male by-product Cobb breeder chicks …

Investigating Antimicrobial Producing Bacteria Within The Soil, Adam Zwawi

A with Honors Projects

Genetic sequencing techniques used to identify soil antibiotic bacteria

Rna Therapeutics For Fibrolamellar Hepatocellular Carcinoma, Christoph Neumayer

Student Theses and Dissertations

Fibrolamellar hepatocellular carcinoma (FLC) is a rare liver cancer characterized by a recurrent fusion of the heat shock protein DNAJB1 and the catalytic subunit of protein kinase A (PRKACA). Due to limited efficacy of conventional treatments such as chemotherapy and radiation my work explored new therapeutic options. As DNAJB1::PRKACA is known to initiate tumorigenesis, I reasoned that it would be an ideal target for a therapeutic. However, it was not known if FLC tumors are still dependent on DNAJB1::PRKACA or if cells achieved independence of the initial oncogene. To test if FLC is dependent on the oncokinase I screened short …

Language Models For Rare Disease Information Extraction: Empirical Insights And Model Comparisons, Shashank Gupta

Theses and Dissertations--Computer Science

End-to-end relation extraction (E2ERE) is a crucial task in natural language processing (NLP) that involves identifying and classifying semantic relationships between entities in text. This thesis compares three paradigms for end-to-end relation extraction (E2ERE) in biomedicine, focusing on rare diseases with discontinuous and nested entities. We evaluate Named Entity Recognition (NER) to Relation Extraction (RE) pipelines, sequence-to-sequence models, and generative pre-trained transformer (GPT) models using the RareDis information extraction dataset. Our findings indicate that pipeline models are the most effective, followed closely by sequence-to-sequence models. GPT models, despite having eight times as many parameters, perform worse than sequence-to-sequence models and …

Effects Of Pancreatic Amylin On The Peripheral And Cns Immune Response In A Model Of Type-2 Diabetic Brain Injury, Edric Da'shon Winford

Theses and Dissertations--Neuroscience

Type-2 diabetes (T2D) is a metabolic disorder that increases the risk for cerebrovascular disease and dementia and is associated with the progression of Alzheimer's Disease; however, the mechanisms responsible for T2D-associated dementia are still poorly understood. T2D leads to alterations of the innate and adaptive immune response that contribute to its progression, but how these cells contribute to cognitive decline during T2D is unknown. As there are no approved therapeutics for T2D that modulate the immune response, it is important that we investigate how peripheral immune cells contribute to cognitive decline during T2D. Amylin is an amyloidogenic hormone synthesized and …

Contributions Of The Replication Initiator Protein Dnaa To Physiology And Virulence Of The Lyme Disease Spirochete, Andrew Krusenstjerna

Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics

Borrelia burgdorferi, the etiological agent of Lyme disease, is the most prevalent vector-borne disease in the United States. The spirochetal population is naturally maintained by consistently cycling between Ixodid ticks and small vertebrates. To survive within these diverse niches, B. burgdorferi has evolved a unique physiology and regulatory network to sense and respond to environmental fluxes. Replication is a hallmark of the Lyme spirochete’s enzootic life cycle, specifically at the nymphal tick-to-vertebrate interface. The mechanisms and regulatory schema for the basic cellular processes in B. burgdorferi, or indeed any member of the phylum spirochaetota, are largely unknown. The central hypothesis …

Impact Of Short-Distance Road Transportation On Horse Health, Erica Jacquay

Theses and Dissertations--Veterinary Science

Horses are regularly transported across the United States; however, the reasons for travel, trip lengths, and management practices are not well characterized. While long distance transportation has been associated with increased incidences of health-related problems, the impact of short distance transportation on horse health is less understood. Notably, aged horses ( > 15 years) have an altered immune response following short-distance transportation, but this has yet to be compared to young horses. It is also unknown whether transportation stress would alter endocrine responses of horses with metabolic disorders, such as insulin dysregulation (ID) or pituitary pars intermedia dysfunction (PPID).

The objectives …

Genomic Studies Of The Equine Bloodworm, Strongylus Vulgaris, Nichol Ripley

Theses and Dissertations--Veterinary Science

Strongylus vulgaris is the most pathogenic nematode parasite of grazing horses worldwide. This gastrointestinal parasitic nematode is in the family Strongylidae under the subfamily Strongylinae, or Strongylins. While the epidemiology, complete life cycle, and high pathogenicity of the fourth and fifth larval stages of S. vulgaris are well established, we understand very little about its biology. This parasite is renowned for its unique life cycle and capacity to cause arterial damage, leading to significant health and economic impacts for the equine industry. It also is the most intensively documented Strongylin; however, S. vulgaris has yet to gain drug resistance as …

Development Of Functional Plasmonic Nanoceria For The Ultrasensitive Detection Of Ebola Glycoprotein, Carissa A. Sutton

Graduate Theses/Dissertations

Infectious diseases have been increasing in both severity and prevalence, leading to increasing economic burdens and health concerns. Ebola hemorrhagic fever is an infectious disease that is both highly communicable and highly fatal. Current detection methods for the virus have high specificity and sensitivity but have long and/or complicated procedures that do not allow for early virus detection in highly affected areas. Compared to the lengthy procedure of reverse transcription-polymerase chain reaction (RT-PCR), real-time RT-PCR is more time-efficient; however, specificity and sensitivity are reduced. Since early detection of the virus is the only way to increase survival rates, sensitive detection …

Unsung Heroes In Conservation: Evaluating The Limitations Faced By New England Wildlife Rehabilitation Centers And Proposing Solutions For Their Support And Recognition, Shaylee M. Sarmiento

Honors Theses and Capstones

Wildlife rehabilitation is an often-unacknowledged practice within the overarching field of wildlife protection and conservation. This practice involves the treatment and hopeful release of wild animals affected by various ailments. With the continued expansion of and interest in the field, it could be assumed that wildlife rehabilitation is supported and funded by government bodies, but this is not the case. Because of the lack of funding and resources, many wildlife rehabilitation centers cannot achieve their full rehabilitative potential and expand their reach in the conservation world. Additionally, an absence of support leads critics to question the ethical standards of wildlife …

Introducing Comprehensive Sexuality Education And Hiv Prevention And Treatment Methods Through Pop-Up Clinics To Secondary School Girls In Kwazulu-Natal, South Africa, Eliza I. Tobin, Joaquin Carlos Pinga, Caitlyn Stanya

Capstone Showcase

Human immunodeficiency virus (HIV) is a retrovirus that attacks the immune system leading to people living with HIV (PLHIV) immunodeficient and more susceptible to other infections or diseases (UNAIDS, 2023b). This can lead to acquired immunodeficiency syndrome (AIDS) within 8-10 years of infection (UNAIDS, 2023b). HIV does not always present symptoms, making it hard for people to identify their HIV status without proper screening. The lack of awareness around a person’s status has led HIV to spread worldwide. In addition to the worldwide spread of HIV, there is no cure for the disease, however, antiretroviral therapy (ART) is mainly used …

Copper Resistance In Staphylococcus Epidermidis: Role Of The Multicopper Oxidase Gene, Caroline Sundal

Scripps Senior Theses

The ongoing struggle against antibiotic resistance and the lack of new antibiotic discoveries being made is a threat to global health. Alternate forms of antibacterial treatment are an important area of research to increase the treatment efficacy of clinical antimicrobial applications. In this research paper, we examine the model organism Staphylcoccus epidermidis, one of the leading causes of nosocomial infection. S. epidermidis normally resides on skin and mucus, however, can become an opportunistic pathogen if it invades the body, entering the bloodstream via the insertion of medical and prosthetic devices. Copper was a traditional therapy in ancient Egypt used for …

Migration-Associated Variation In Blood Parasitism, Body Condition, And Stress In Gambel’S White-Crowned Sparrows (Zonotrichia Leucophrys Gambelii), Julianna Deibel

Scripps Senior Theses

Migration is a widespread behavior in animals which both causes and is motivated by fluctuations in nutrient availability. Migration is ecologically important, as it connects areas of differing primary productivities and carries pathogens over distance. The relationship between migration and disease is complex, sensitive to anthropogenic disturbance, and influenced by ecological cycles as well as host, vector and parasite life cycles. Four central migration-infection mechanisms have been proposed: migratory susceptibility, migratory exposure, migratory escape, and migratory culling. These mechanisms may yield increased or decreased infection post-migration, based on migration’s physiological tax and the concentration of pathogens along migratory pathways.

To …

Concepts In Animal Parasitology, Chapter 07: Biostatistics For Parasitologists: A Painless Introduction [Parascript Approaches], Jenő Reiczigel, Marco Marozzi, Fábián Ibolya, Lajos Rózsa

Concepts in Animal Parasitology

Covers biostatistics for parasitologists and includes discussion of taking samples, frequency distribution of host individuals across infection classes, sample size, prevalence, mean intesity, median intensity, stochasic equality of intensities, abundance, crowding, levels of aggregation, parasite sex ratio, parasite species richness, interactions between parasite species, and the tool Quantitative Parasitology on the Web (QPweb).

Chapter 7 in Concepts in Animal Parasitology on biostatistics for parasitologists by Jenő Reiczigel, Marco Marozzi, Fábián Ibolya, and Lajos Rózsa. 2024. S. L. Gardner and S. A. Gardner, editors. Zea Books, Lincoln, Nebraska, United States. doi: 10.32873/unl.dc.ciap007

Concepts In Animal Parasitology, Chapter 58: Acanthocephala Rudolphi, 1808 (Phylum), Scott Monks

Concepts in Animal Parasitology

An overview of the phylum Acanthocephala Rudolphi, 1808, also called the thorny-headed or spiny-headed worms, including discussion of their general morphology, life cycles, classification, and phylogenetic relationships.

Chapter 58 in Concepts in Animal Parasitology, by Scott Monks. 2024. S. L. Gardner and S. A. Gardner, editors. Zea Books, Lincoln, Nebraska, United States. doi: 10.32873/unl.dc.ciap058

Nano-Pulse Treatment Overcomes The Immunosuppressive Tumor Microenvironment To Elicit In Situ Vaccination Protection Against Breast Cancer, Anthony Nanajian, Megan Scott, Niculina I. Burcus, Brittney L. Ruedlinger, Edwin A. Oshin, Stephen J. Beebe, Siqi Guo

Bioelectrics Publications

We previously reported that nano-pulse treatment (NPT), a pulsed power technology, resulted in 4T1-luc mammary tumor elimination and a strong in situ vaccination, thereby completely protecting tumor-free animals against a second live tumor challenge. The mechanism whereby NPT mounts effective antitumor immune responses in the 4T1 breast cancer predominantly immunosuppressive tumor microenvironment (TME) remains unanswered. In this study, orthotopic 4T1 mouse breast tumors were treated with NPT (100 ns, 50 kV/cm, 1000 pulses, 3 Hz). Blood, spleen, draining lymph nodes, and tumors were harvested at 4-h, 8-h, 1-day, 3-day, 7-day, and 3-month post-treatment intervals for the analysis of frequencies, death, …

Prevalence Of Resistant Escherichia Coli Isolated From Local Meats Sold In Tema Metropolis, Ghana, Frederick Adzitey, Innocent Allan Anachinaba, Charles Addo-Quaye Brown, Nurul Huda, Masmuniri Rambli

ASEAN Journal on Science and Technology for Development

Contamination of meat by Escherichia coli (E. coli) can take its source from the live animal or by cross contamination. The study determined the prevalence of resistance of E. coli isolated from locally produced meats in the Tema Metropolis. Beef (n=200), chicken (n=200) and pork (n=200) were randomly selected and evaluated for the presence of E. coli using the procedure in the Bacteriological Analytical Manual of USA-FDA. The disc diffusion method was used for antibiotic susceptibility test of E. coli (n=55) isolates. Locally produced beef (67%), chicken (41%) and pork (23%) were contaminated by E. coli. Escherichia coli isolates were …

Biology News 2024, University Of Northern Iowa. Department Of Biology.

Biology News

Contents:

Letter from the Department Head --- 2
Bolton Award Winner --- 3
Goldwater Scholarship Winner --- 3
Purple and Old Gold Award Winner --- 3
Faculty News Roundup --- 4
New Hires --- 6
UNI Botanical Center --- 7
Alumni Information Request --- 7
Support Our Programs --- 8
Floyd Fellowship Award Winner --- 8

Driving Cars Down Memory Lane: Uncovering Car Memory T Cell And Antigenspecific Endogenous T Cells Importance In Durable Responses Against Melanoma, Asmaa Mohamed

Dartmouth College Ph.D Dissertations

Responsiveness to chimeric antigen receptor (CAR) T cell therapy correlates with CAR T cell expansion and persistence in vivo. Multiple working strategies improve CAR T cell persistence by increasing stem-like properties or by sustaining CAR T cell activity with combination therapies. Herein, we describe the intrinsic ability of CAR T cells to differentiate into memory T cells, the effect of cytokine armoring, and neoadjuvant CD4 depletion therapy on CAR and tumor-specific endogenous memory T cells. TRP1-specific CAR T cells alone or in combination with Super2 + IL-33 (S233) armoring and/or CD4 depletion therapy were evaluated in the immunocompetent B16F10 melanoma …

Inflammation And Tumor Progression: The Differential Impact Of Saa In Breast Cancer Models, Daniel Wilhelm Olivier, Carla Eksteen, Manisha Du Plessis, Louis De Jager, Lize Engelbrecht, Nathaniel Wade Mcgregor, Preetha Shridas, Frederick C. De Beer, Willem J. S. De Villiers, Etheresia Pretorius, Anna-Mart Engelbrecht

Saha Cardiovascular Research Center Faculty Publications

Background: Previous research has shown that the Serum Amyloid A (SAA) protein family is intricately involved in inflammatory signaling and various disease pathologies. We have previously demonstrated that SAA is associated with increased colitis disease severity and the promotion of tumorigenesis. However, the specific role of SAA proteins in breast cancer pathology remains unclear. Therefore, we investigated the role of systemic SAA1 and SAA2 (SAA1/2) in a triple-negative breast cancer mouse model.

Methods: Syngeneic breast tumors were established in wild-type mice, and mice lacking the SAA1/2 (SAADKO). Subsequently, tumor volume was monitored, species survival determined, the inflammatory profiles of mice …

Novel Engineering Approaches For Orthopedic Injury Treatment And Infection Diagnosis, Cynthia Co

Bioengineering Dissertations - Archive

Bioengineering has made significant contributions to the treatment of orthopedic injury through interdisciplinary approaches. Central to these advancements are many orthopedic implants, including anchors and joint replacements, which have been designed to restore mobility. Despite their functional efficacy, these products have limited lifespan and are associated with many complications, such as implant-associated infection. The success of implant design and function, both in the short and long term, is paramount for enhancing patient outcomes and overall well-being. Therefore, my thesis work is dedicated to addressing these critical challenges, aiming to maximize their treatment effect while minimizing the implant-associated complications.

Long-term patient …

2024 American Society For Microbiology Awards And Prize Program: Clinical Microbiology Honorees, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.

Asymptomatic Rectal Bacterial Pathogens Show Large Prospective Relationships With Hiv Incidence In A Cohort Of Young Sexual And Gender Minorities: Implications For Sti Screening And Hiv Prevention, Ross A. Baiers, Daniel T. Ryan, Antonia Clifford, Erik Munson, Richard D'Aquila, Michael E. Newcomb, Brian Mustanski

Clinical Lab Sciences Faculty Research and Publications

Background

We estimated the predictive value of rectal (bacterial sexually transmitted infection [bSTI]) pathogen detection for future HIV seroconversion among young adult sexual and gender minorities (YSGMs) assigned male at birth (AMAB).

Methods

Data were collected between March 2018 and August 2022 from RADAR, a longitudinal cohort study of YSGMs AMAB living in the Chicago metropolitan area (n = 1022). Rates of rectal bSTIs and the proportion of self-reported rectal bSTI symptoms are reported. We examined whether the presence of rectal bSTIs predicted HIV seroconversion using generalized estimating equations (GEEs).

Results

Participants tested reactive for rectal Mycoplasma genitalium (MGen), Neisseria …

Serologic Correlation Of A Research-Use-Only Treponema Pallidum Transcription-Mediated Amplification Assay Performed On Rectal Swabs From A Longitudinal Cohort Of Young Men Who Have Sex With Men, Amanda Zapp, Hannah Hudson, Erik Munson, Elizabeth Thelen, Daniel Ryan, Richard D'Aquila, Brian Mustanski

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.

Ai Is A Viable Alternative To High Throughput Screening: A 318-Target Study, Martin St. Maurice

Biological Sciences Faculty Research and Publications

High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, …