Digital Commons Network^™

Rna G-Quadruplexes Function As A Tunable Switch Of Fus Phase Separation, Jenny L. Carey, Miyuki Hayashi, Emily A. Welebob, Laura R. Ganser, Huan Wang, Kerry Buckhaults, Jacquelyn A. Depierro, Zheng Shi, James Shorter, Sua Myong, Aaron R. Haeusler, Lin Guo

Department of Biochemistry and Molecular Biology Faculty Papers

Fused in sarcoma (FUS) undergoes liquid-liquid phase separation (LLPS) to support essential cellular functions, but aberrant phase transitions promote toxic aggregation in neurodegenerative disease. Short RNA oligonucleotides can reverse this behavior, yet the structural determinants that govern RNA activity remain poorly defined. Here, we identify RNA G-quadruplexes (rG4s) as tunable structural motifs that potently modulate FUS LLPS. rG4 activity depends on its concentration and is modulated by rG4 length and stability: increasing repeat number switches rG4s from inhibitor to nucleator of FUS assembly, whereas chemical modifications that stabilize rG4 enhance inhibitory function and render these activities resilient to ionic perturbation. …

Butterfly Taxa Discovery Via Genomic Analysis, Jing Zhang, Qian Cong, Jinhui Shen, Leina Song, Nick V. Grishin

The Taxonomic Report of the International Lepidoptera Survey

Expanding a genomics-guided assessment of butterfly taxonomy, we integrate phylogenetic evidence from all protein-coding genes with morphological considerations to refine our understanding of butterfly systematics and discover new taxa. As a result, 2 subgenera, 39 species, and 5 subspecies are proposed as new (type species in original combinations or type localities are listed in parentheses): Erebia (Magda) magdalena uintana Grishin, ssp. n. (USA: Utah, Uintah Co.) in Nymphalidae Rafinesque, 1815; Myselasia rondea Grishin, sp. n. (Brazil: Rondônia), Myselasia pseudocrinon Grishin, sp. n. (Ecuador: Pastaza), Myselasia paramatuta Grishin, sp. n. (Ecuador: Morona-Santiago), Euselasia anapellos Grishin, sp. n. (Peru: Loreto), …

Assessing The Effectiveness Of Wetland Reserve Easements As Habitat For Birds In The Mississippi Alluvial Valley Of Eastern Arkansas, Colin K. Dobson

Student Theses and Dissertations

Globally, wetland habitats suffered major declines during the 20th century. In the 1990s, the United States government created the Wetland Reserve Program (later consolidated into the Agricultural Conservation Easement Program), to combat the loss of wetlands. Despite success in attracting landowners, minimal monitoring of properties enrolled into the program (easements) has occurred. In this study, we monitored avian communities at easements, compared avian diversity at easements to agriculture and bottomland forests, and quantified microhabitat, site-specific, and surrounding landscape features at easements. We also studied the demographic rates of an indicator species of bottomland forests, the Prothonotary Warbler (Protonotaria citrea) at …

Prediction Of Furniture Exports In Türkiye Using Machine Learning Methods, İlker Akyüz, Nadi̇r Ersen, Ti̇muçi̇n Bardak, Selahatti̇n Bardak

Turkish Journal of Agriculture and Forestry

In this study, it was aimed to predict Türkiye’s furniture exports for the period from January 2010 to May 2025 using machine learning methods based on macroeconomic indicators. The dataset consisted of 10 economic variables, including the furniture industry production index, capacity utilization rate, import volume, total exports, real effective exchange rate, producer price index, money supply, and oil prices, with 185 observations per variable and a total of 2035 data points. During the data preprocessing phase, no missing or outlier values were detected, and the data were divided into 70% training and 30% testing subsets. Decision tree, random forest, …

Ozonated Water Delays The Microbial Growth And Sensory Quality Loss Of Capia Pepper Fruit During Cold Storage, Yasi̇n Şi̇mşek, Mehmet Ali̇ Koyuncu, Derya Erbaş

Turkish Journal of Agriculture and Forestry

The aim of the present research was to evaluate, for the first time, the effect of ozonated water treatments on the postharvest quality of capia pepper (Capsicum annuum L. ‘Kaptan’). The peppers were harvested at the optimum time and transported to the laboratory immediately. Uniform and quality fruit was selected and precooled. After precooling, the fruit was divided into four groups. The first three groups were immersed in ozonated water at three different concentrations (1.0, 2.0 and 3.0 ppm) for 15 min. The last group (control) was immersed in distilled water for 15 min. The peppers were kept at room …

Interview With Orca Winner John Hibbing, Political Science; How Political Attitudes Correlate With Physiological Traits, Mark A. Griep, John Hibbing

UNL ORCA Interview Series

Dr. John Hibbing was awarded the ORCA in 1993. John was born in 1953 in Paullina, Iowa. He earned a bachelor's in secondary education from Dana College in Blair, Nebraska, but then realized that teaching high school wasn't for him. Instead, he attended the University of Iowa, where he earned a master's and doctorate in political science. In 1981, he joined the University of Nebraska-Lincoln as an assistant professor of political science and rose quickly through the ranks. Initially, he studied the reasons that members of the U.S. Congress retire. This led to a longer-term collaboration with Kevin Smith and …

The Change Of Yield, Growth, And Fruit Quality In Rubygem Strawberry Using Arbuscular Mycorrhizal Species, Selma Kuru Berk

Turkish Journal of Agriculture and Forestry

Arbuscular mycorrhizal fungi (AMF), which exist symbiotically with plant roots, affect plant growth, yield, and fruit quality. The effects of AMF vary depending on the cultivar and mycorrhizal type. In this study, the effects of different AMF types on the Rubygem strawberry cultivar, widely grown in Türkiye, were examined. Gigaspora margarita and Funneliformis mosseae AMF species were applied to plant roots at seedling planting. Fruit quality criteria, including yield, acidity, soluble solid content, phenolic compounds, organic acids, crown and root development, and the number of daughter plants and stolons, were examined. The highest yield was 431.02 g in G. margarita. …

Multidimensional Scaling (Mds) Analysis Of Fire Blight Resistance In Apple Genotypes Selected From The Eastern Black Sea Region Of Türkiye, Kubi̇lay Kurtuluş Baştaş, Hati̇ce Dumanoğlu, Veli̇ Erdoğan, Ahmet Aygün, Rabi̇a Albayrak Deli̇ali̇oğlu, Sai̇d Efe Dost, Ümi̇t Serdar, Özgün Kalkişim, Sali̇h Maden, Zahi̇de Kocabaş

Turkish Journal of Agriculture and Forestry

Erwinia amylovora is the causal agent of fire blight, which is known as one of the most destructive diseases of apple. The use of fire blight-resistant cultivars/rootstocks is one of the most effective methods available to manage this disease. We previously selected 199 local apple cultivars that showed no clearly visible symptoms of fire blight on the plants from the coastline of the eastern Black Sea Region in Türkiye. The region is characterized by the highest rainfall and humidity levels in the country. In this research, young plants of these genotypes grafted onto MM.106 rootstock were screened for fire blight …

Intrathecal (G4c2)149 Delivery In C9orf72-Deficient Mice Yields Mild Motor Dysfunction And Als/Ftd Pathological Hallmarks, Katelyn Russell, Amelia Shahrabi, Suleyman Akerman, Matthew D. Byrne, Jeffrey Rothstein, Davide Trotti, Brigid Jensen, Aaron Haeusler

Farber Institute for Neuroscience Faculty Papers

A repeat expansion in C9ORF72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), yet existing mouse models incompletely engage spinal regions implicated in disease. Here, an adeno-associated virus encoding (G4C2)149 repeats was delivered via neonatal intrathecal injection, achieving widespread CNS expression with robust spinal cord targeting. This approach was applied to mice with graded loss of endogenous C9orf72 to interrogate both gain- and loss-of-function mechanisms. Longitudinal motor, behavioral, and pathological analyses revealed that repeat expression primarily drives mild, progressive muscle weakness, whereas coordination deficits were largely genotype dependent. Subtle gait abnormalities and hyperactivity …

Main-Chain Ion-Pair Polybenzimidazole Membranes Enabling Reduced-Temperature Ht-Pemfc Operation (Down To 120°C), Brian C. Benicewicz, Huina Lin

Faculty Publications

Proton exchange membrane (PEM) fuel cells are promising for clean and efficient energy conversion across diverse applications. High-temperature PEM fuel cells (HT-PEMFCs) using phosphoric acid (PA)-doped polybenzimidazole (PBI) can operate up to 200°C, but at lower temperatures, water-induced PA loss often leads to performance degradation and reduced durability. In this work, we present a new class of main-chain ion-pair PBI membranes by integrating the imidazolium-biphosphate ion-pair units directly into the PBI backbone. This design results in membranes with high acid content, stronger acid-polymer interactions and stabilized acid retention. In single-cell tests, the Im+-PBI15-3 wt.% exhibits peak power densities of 0.79 …

Synthetic-Chicken-Fillets, Chirantan Sen Mukherjee, Seung-Chul Yoon, William J. Beksi

Agriculture

This Synthetic-Chicken-Fillets dataset contains 1,000 synthetic 3D meshes designed to capture the natural variance and size diversity of real broiler fillets. The collection was developed to test automated woody breast detection algorithms within a physics-based simulation environment. We utilized a seed dataset of 2D depth maps derived from 40 real-world RGBD point cloud scans. These real depth maps were fed into a few-shot transfer learning pipeline using a generative adversarial network architecture. The resulting generated depth maps were reconstructed back into 3D meshes. The length and thickness of each mesh were randomly scaled based on physical measurements of real broiler …

Hiv-1 Tat-Driven Glutamate Dysregulation: Implications For Cognitive Impairment In Hand, Brenna Duffy, Michael Nonnemacher, Sandhya Kortagere

Kimmel Cancer Center Faculty Papers

PURPOSE OF REVIEW: HIV-1-associated neurocognitive disorders (HAND) manifest in 15% to 50% of people with HIV, impairing learning and memory and executive function. The chronic generation of HIV-1 Transactivator of transcription (Tat) likely contributes to HAND via direct neuronal toxicity and glial-mediated toxicity. This review summarizes our current understanding of how chronic Tat generation from microglia and astrocytes promote glutamate excitotoxicity.

RECENT FINDINGS: In recent years, the indirect effects of Tat through the activation of glial cells have gained significant interest. This review highlights microglia and astrocytes as HIV-1 reservoirs that release Tat protein in the central nervous system. Specific …

(Re)Claiming Homeplace: Dance As Embodied Resistance & Healing For Health & Spatial Justice, Preeya G. Kannan

University Honors Theses

This thesis argues that dance functions as both an upstream public health intervention and a form of radical spatial resistance; creating healing, agency, and belonging among historically marginalized communities. Drawing on bell hooks' concept of homeplace, Jasbir Puar's assemblage theory, Nancy Krieger's eco-social theory, and Katherine McKittrick's Black geographies, I position the body as both an ecological and political landscape shaped by histories of colonialism, racial capitalism, displacement, and resilience.

Through this community-based participatory research study, Homeplace, I explore dance as a form of social prescription that centers liberation rather than pathology. Movement is often reduced in public health discourse …

Elucidating The Function Of Yedk In Response To Dna Damage, Hank Munro

University Honors Theses

Apurinic/Apyrimidinic (AP) sites are one of the most prevalent forms of DNA damage. These lesions arise spontaneously or during base excision repair of modified DNA bases and are potentially mutagenic in both mammalian and bacterial cells. 5-hydroxymethylcytosine binding, ES cell specific (HMCES), a protein found in eukaryotic cells, has been shown to form a stable DNA-protein crosslink with AP sites in single stranded DNA and to reduce the number of AP sites occurring either spontaneously or after alkylative DNA damage, resulting in increased genome stability. YedK, the Escherichia coli ortholog of HMCES exhibits some of the same biochemical properties as …

Evaluating The Impact Of Early Contractor Involvement On Enhancing The Performance Of Construction Projects In Egypt, Samah Saleh Abdelraof, Ayman Ahmed Ezzat Othman, Lamees Mostafa Ahmed

Mansoura Engineering Journal

The construction industry constitutes a critical pillar of Egypt’s national economic growth and sustainable development. Despite its strategic importance, the sector continues to face persistent challenges, including chronic cost overruns, schedule delays, and inadequate coordination among stakeholders. These inefficiencies are largely attributed to the dominance of the traditional Design–Bid–Build (DBB) system, which enforces a rigid separation between design and construction, fostering adversarial relationships and project disputes, which highlights the need for alternative procurement approaches. This research investigates the impact of Early Contractor Involvement (ECI) as a collaborative procurement alternative to enhance project performance. Case studies show that ECI improves early-stage …

The Neuroprotective Effect Of Cdc42 Inhibition In The G93a Mutant Hsod1 Mouse Model Of Als, Andrea Koly

Undergraduate Theses, Capstones, and Recitals

Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disease characterized by the selective loss of upper and lower motor neurons, leading to muscle weakness, neuromuscular junction (NMJ) degeneration, paralysis, and eventual death due to respiratory failure. Despite extensive research, effective disease-modifying therapies remain limited, underscoring the need to identify novel molecular targets involved in ALS pathogenesis. Dysregulation of Rho family GTPases has been implicated in neurodegeneration, with Rac and Rho exerting opposing effects on neuronal survival; however, the role of the closely related GTPase Cdc42 remains poorly understood in ALS. In this study, the therapeutic potential of inhibiting …

Differential Roles Of Moesin And Vasp In Β-Catenin-Associated Networks During Zebrafish Heart Regeneration, Allen Rutman

Undergraduate Theses, Capstones, and Recitals

With cardiovascular disease remaining as the leading cause of mortality worldwide, it is largely due to the limited regenerative capacity of the human heart. However, zebrafish (Danio rerio) can fully regenerate cardiac tissue following injury, providing a valuable model for studying the mechanisms of heart repair. To investigate these mechanisms, we used proteomics methods in the past. Proximity labeling is a technique that identifies proteins based on their physical proximity to a protein of interest. It can be applied in organisms and in living cells (Roux et al., 2012; Cho et al., 2020). We used proximity labeling to characterize protein …

The Palm Farm Next-Door: Land Concessions, Livelihoods, And Nutrition In Plantation-Adjacent Communities, Julia Entwistle

Electronic Theses and Dissertations

Large-scale land concessions have reshaped agrarian landscapes globally, yet their implications for community land tenure, livelihoods, and nutrition remain unevenly understood. This dissertation examines how plantation agriculture and foreign investment have transformed land access, labor relations, and food systems in Liberia, a country with one of the highest proportions of land under concession globally. Guided by a political ecology framework, the study employs a mixed-methods design integrating policy analysis, in-depth interviews, and household surveys across two palm oil concession sites. The findings show that ambiguous land policies historically facilitated dispossession, while recent legal reforms have enabled communities to strategically mobilize …

Food System Science Lesson-1 For First Graders. Makhá Waókiyapi: Soil Helpers, Feeding The Land That Feeds Us (Lesson About Regenerative Agriculture), Arlene A. Abao, Madhav P. Nepal

iLEARN Teaching Resources

In this engaging Grade 1 Science adventure, students become "Earth Doctors" as they discover that the soil beneath their feet is a living, breathing community! Guided by the Lakota value of Mitákuye Oyás’iŋ (all are related), children will learn that Makhá (the Earth) is not just "dirt," but a relative that provides us with everything we need to live. Students will get their hands dirty investigating the "Soil Helpers"—the worms, roots, and tiny bugs that work like a team to keep the land healthy. They will explore the three golden rules of being a good neighbor to the Earth: Compost …

Food System Science Lesson-2 For First Graders. Makhózula Etáŋhaŋ Wiyútapi Ke: From Planting To Eating, Arlene A. Abao, Madhav P. Nepal

iLEARN Teaching Resources

Feeding the Land That Feeds Us In this delicious adventure, kids will trace the journey of their food from the deep, dark soil all the way to their lunch forks! They will discover that the land is like a giant, magical kitchen called Makhózula, where plants cook up energy using sunlight and "vitamins" from the soil. Students will learn that when we eat a crunchy carrot or a sweet berry, we are actually tasting the strength of the Earth and the warmth of the sun. Through stories of Wopila (gratitude), they’ll see that the food system is a big, …

Food System Science Lesson-3 For First Graders. Mitakuye Oyasin: The Invisible Web (We Are All Related, An Ecological Knowledge Lesson), Arlene A. Abao, Madhav P. Nepal

iLEARN Teaching Resources

 In this heart-centered science lesson, students will discover the beautiful Lakota concept of Mitakuye Oyasin, which teaches us that "we are all related." Rather than seeing nature as a collection of separate things, children will learn to see the Invisible Web, the magical connections between the sun, soil, water, plants (flora), and animals (fauna). Through a hands-on "Yarn Web" activity and outdoor exploration, students will move beyond being just observers and start seeing themselves as stewards (caretakers) of their environment. They will learn that when we help a bee or protect a stream, we are helping our own Earth family. …

A Computational Micropatterning Approach To Study Caveolae And Protein Localization In Vascular Biology, Andrew B. Grespin

Electronic Theses and Dissertations

Caveolae are specialized, flask-shaped membrane invaginations highly expressed in endothelium and dysregulated in atherosclerosis. Caveolae play a central role in buffering membrane tension, yet the principles governing their spatial organization remain elusive. Thus, we sought to generate the most comprehensive and systematic analysis of blood vessel caveolar spatial organization. However, cell culturing, the backbone of human-focused biological research, does not standardly do well to model physiologically relevant cell behaviors such as migration or polarity-based tissue formation, particularly for punctate proteins and structures like caveolae. Micropatterns are cell-adhesive shapes that biophysically confine cell(s) to a user defined geometry which stereotype organelle …

Determination Of Hematobiochemical Parameters And Egg Quality Traits Of Turkish Sultan Chickens, Mehmet Naci̇ Oktay, Ruhi̇ Kabakçi, Ali̇ Karapinar, Gökhan Şen, Taha Altuğ, Yasi̇n Şenel

Turkish Journal of Veterinary & Animal Sciences

The present study aimed to investigate the hematological and biochemical blood parameters, along with selected egg quality traits, of Turkish Sultan chickens. A total of 90 blood samples collected from 60-week-old hens and roosters and 129 eggs collected from 50 hens were analyzed. The findings showed that hematological parameters such as red blood cells (RBC), hemoglobin (HGB), packed cell volume (PCV), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), and heterophil-to-lymphocyte (H/L) ratio, as well as biochemical markers such as aspartate aminotransferase (AST), lactate dehydrogenase (LDH), and uric acid levels, were significantly higher in roosters. The average egg weight, shape …

The In Vitro Feeding Of Hyalomma Marginatum (Koch, 1844), Nesli̇han Ölmez, Bariş Sari, Zati̇ Vatansever

Turkish Journal of Veterinary & Animal Sciences

Ticks are obligate hematophagous ectoparasites that play a major role in the transmission of pathogens affecting both animals and humans. Investigations into tick biology, pathogen transmission, and the development of effective control strategies have traditionally depended on the extensive use of laboratory animals. Consequently, the development of reliable in vitro feeding systems is a valuable alternative approach with the potential to reduce animal use in tick research. In the present study, a previously described silicone membrane artificial feeding system was modified and applied for the in vitro feeding of Hyalomma marginatum (Koch, 1844). Feeding units were prepared using bovine blood …

Defining Replication-Driven Vulnerabilities In High Grade Serous Ovarian Cancers, Natasha Maya Ramakrishnan

Arts & Sciences Graduate Student Theses and Dissertations

High grade serous ovarian carcinoma (HGSOC) is an aggressive, highly lethal subtype of ovarian cancer. These cancers are typically diagnosed in later stages and are associated with poor patient prognosis. Additionally, HGSOC is characterized by numerous markers of genomic instability and defects in DNA repair pathways, vulnerabilities which have been exploited by the advancement of chemotherapy. Despite these clinical advancements, HGSOC remains a significant therapeutic challenge due to emergence of chemoresistance and limited targeted treatment options. Taken together, these factors highlight an ongoing need to study the development of HGSOC and its progression to identify more effective treatment opportunities. We …

Bap1 Loss Links Myc Activation, Stress Response Vulnerability, And Disease Progression In Kidney Cancer, Ilya Strunilin

Arts & Sciences Graduate Student Theses and Dissertations

BAP1, a chromatin modifier, is a frequently mutated tumor suppressor in clear cell renal cell carcinoma (ccRCC). Mutations in BAP1 are associated with a more aggressive and lethal disease. However, the downstream mediators of BAP1 loss in ccRCC oncogenesis are not well understood. To better understand mechanisms of BAP1-mediated tumor suppression, I have extensively characterized the very early transcriptional mediators of BAP1 loss in a postnatal kidney-specific genetic knockout model. Because VHL loss is the initiating event in ccRCC, we modeled Bap1 loss in a Vhl-deficient background. I have found that Vhl/Bap1 double-knockout cells of PT segment S2 strongly activate …

Structure-Based Discovery Of Malate Dehydrogenase Inhibitors With Efficacy Against C. Parvum Oocysts, Ankita Bharatbhai Kheni

Biochemistry and Molecular Biology

Cryptosporidium parvum, the etiological agent of Cryptosporidiosis (diarrheal illness) represents a significant global health burden, particularly affecting immunodeficient and pediatric populations. Since the parasite has a highly reduced mitochondrion and relies on glycolysis, enzymes such as C. parvum malate dehydrogenase (CpMDH), which are believed to be indispensable for parasite viability due to their pivotal roles in NAD⁺ regeneration and redox balance, remain largely unexplored as therapeutic targets. The present study employed a multifaceted experimental and computational strategy to evaluate the inhibitory activity of two lead-like and drug-like small molecules, referred to as compound 1.8 and compound 1.5, against the cofactor …

Mapping The Neuroexposome: Integrative Analysis Of Dementia Risk Factors Through Multi-Omics And Environmental Profiling In The Egyptian Population., Mai Ahmed Saadzaghloul Othman

Theses and Dissertations

Background: Dementia represents one of the most pressing public health challenges of the twenty-first century, with the global burden projected to reach 153 million cases by 2050. Egypt, as the most populous Arab nation, faces a corresponding rise in age-related diseases, yet comprehensive data from low- and middle-income countries remain severely limited. The neuroexposome framework, integrating genetic susceptibility, environmental exposures, and metabolic alterations, offers a powerful strategy to characterize the complex interplay between internal and external risk factors for Alzheimer's disease (AD) and Alzheimer's disease Related Dementias (ADRD).

Objectives: This thesis aimed to: (1) examine the distribution of APOE alleles …

The Gut Microbiome, The Gut-Brain Axis, And College Student Well-Being, Idi Mckay

University Honors Theses

This literature review examines how diet, stress, environmental exposure, and food accessibility may influence college students' mental health and academic performance through the gut microbiome and the Gut-Brain Axis (GBA). Current microbiome research often focuses on early childhood development, clinical disease populations, or older adults, while overlooking college-age students who experience significant social, environmental, and biological transitions. College students frequently face food insecurity, irregular eating patterns, chronic stress, inconsistent sleep schedules, and reduced access to nutrient-dense foods, all of which may influence microbial diversity and overall gut health.

This thesis explores how modern campus environments and lifestyle factors may contribute …

High Mobility Group Motif Proteins’ Role In Fibrosis, Inflammation, And Vascular Injury In Systemic Sclerosis, Fabian A. Mendoza, Sonsoles Piera-Velazquez, Sergio A. Jimenez

Jefferson Institute of Molecular Medicine Papers and Presentations

Systemic Sclerosis (SSc) is an idiopathic systemic autoimmune disease characterized by progressive cutaneous and systemic fibrosis, severe vasculopathy, and multiple humoral and cellular immunological alterations. The pathogenesis of SSc is highly complex and remains incompletely elucidated. The fibrotic process is a crucial component of SSc and is responsible for organ failure and high mortality. Although an increasing understanding of the fibrotic process has enabled the clinical development of antifibrotic therapeutic agents, these agents have limited clinical efficacy. Recently, the potential role of a group of transcription factors containing a High Mobility Group (HMG) motif, in the development and pathological manifestations …