Digital Commons Network^™

Longitudinal Multi-Omics In Alpha-Synuclein Drosophila Model Discriminates Disease- From Age-Associated Pathologies In Parkinson’S Disease, Justin Moore, Timothy Wu, Justin Dhindsa, Omar El Fadel, Anh Le, Alma Perez, Bismark Amoh, Akash Tarkunde, Katy F Zhu, Matthew Avalos, Eric B Dammer, Duc M Duong, Nicholas T Seyfried, Joshua M Shulman, Ismael Al-Ramahi, Juan Botas

Duncan NRI Faculty and Staff Publications

Parkinson's disease (PD) starts decades before symptoms appear, usually in the later decades of life, when age-related changes are occurring. To identify molecular changes early in the disease course and distinguish PD pathologies from aging, we generated Drosophila expressing alpha-synuclein (αSyn) in neurons and performed longitudinal bulk transcriptomics and proteomics on brains at six time points across the lifespan and compared the data to healthy control flies as well as human post-mortem brain datasets. We found that translational and energy metabolism pathways were downregulated in αSyn flies at the earliest timepoints; comparison with the aged control flies suggests that elevated …

Molecular Identification Of The Italian Soldiers Found In The Second World War Mass Grave Of Ossero, Barbara Di Stefano, Barbara Bertoglio, Filomena Melchionda, Monica Concato, Solange Sorçaburu Ciglieri, Alessandro Bosetti, Pierangela Grignani, Eros Azzalini, Yasmine Addoum, Raffaella Vetrini, Fabiano Gentile, Francesco Introna, Serena Bonin, Chiara Turchi, Carlo Previderè, Paolo Fattorini

Faculty, Staff and Students Publications

Background/objectives: DNA analysis is the most reliable method for the identification of human skeletal remains, especially the ones found in mass disasters or recovered from mass graves. To this aim, DNA was extracted from bones and teeth allegedly belonging to 27 Italian soldiers executed during the Second World War and exhumed from a mass grave in Ossero (Croatia).

Methods: A selection of 131 different bone samples (petrous bones, femurs, metacarpal, and metatarsal bones) and 16 molar teeth were used for DNA extraction. Autosomal and Y-chromosome STR profiles were determined using a conventional CE approach, while a panel of 76 microhaplotypes …

Hematopoietic Cell Transplant Compared With Standard Care In Adolescents And Young Adults With Sickle Cell Disease, Mark C Walters, Mary Eapen, Yiwen Liu, Fuad El Rassi, Edmund K Waller, John E Levine, John J Strouse, Joseph H Antin, Suhag H Parikh, Nitya Bakshi, Carlton Dampier, Jennifer J Jaroscak, Shayla Bergmann, Trisha Wong, Vamsi Kota, Betty Pace, Lazaros J Lekakis, Premal Lulla, Robert S Nickel, Kimberly A Kasow, Uday Popat, Wally Smith, Lolie Yu, Nancy Difronzo, Nancy Geller, Naynesh Kamani, Elizabeth S Klings, Kathryn Hassell, Adam Mendizabal, Keith Sullivan, Donna Neuberg, Lakshmanan Krishnamurti

Faculty, Staff and Students Publications

Disease-modifying therapies are standard of care (SOC) for sickle cell disease (SCD), but hematopoietic cell transplantation (HCT) has curative potential. We compared outcomes prospectively through 2 years after biologic assignment to a donor or no donor (SOC) arm based on the availability of an HLA-matched sibling or unrelated donor (BMT CTN 1503). A donor search was commenced after eligibility confirmation. The primary end point was a comparison of survival between the treatment arms 2 years after biologic assignment. Power calculations required 60 participants in the donor arm and 140 in the no donor arm to determine if early transplant-related mortality …

Conformational Free Energy Landscape Of A Glutamate Transporter And Microscopic Details Of Its Transport Mechanism, Sundar Thangapandian, Ashkan Fakharzadeh, Mahmoud Moradi, Emad Tajkhorshid

Chemistry & Biochemistry Faculty Publications and Presentations

Removing glutamate from the synaptic cleft is vital for proper function of the brain. Excitatory amino acid transporters mediate this process by uptaking the neurotransmitter from the synaptic cleft back to the cell after its release. The archaeal homolog, GltPh, an aspartate transporter from Pyrococcus horikoshii, presents the best structurally characterized model for this family of transporters. In order to transport, GltPh undergoes elevator-like conformational changes between inward-facing (IF) and outward-facing (OF) states. Here, we characterize, at an atomic level, the OF=+/- IF transition of GltPh in different apo/bound states using a combination of ensemble-based enhanced sampling techniques, employing more …

Driving Renewable Energy Continuance In Malaysia Through Reinforcement Sensitivity, Technology Infrastructure And Psychological Factors, Rajat Subhra Chatterjee, Siti Norida Wahab, Md. Uzir Hossain Uzir

Plymouth Business School

Purpose: Based on the reinforcement sensitivity theory (RST), this study aims to examine the key factors that influence users’ renewable energy (RE) continuance intention. More importantly, the mediating role of excitement and the moderating role of technology infrastructure (TEC) and anxiety in the renewable energy continuance intention (RECI) is explored. Design/methodology/approach: A survey was conducted among RE users in Malaysia and the results of a questionnaire survey of 397 were analysed using partial least square structural equation modelling. Findings: The study’s findings highlight the significant roles of excitement and anxiety in RE intentions, emphasizing the impact of psychological factors and …

Towards An Inclusive Conference Experience: Evaluation Of The Education And Outreach Symposium At The Microbiology Society Annual Conference 2024, Melissa Lacey, Michael Dillon, Sean Goodman, Victoria Easton, Alison Graham

Peninsula Medical School

The Microbiology Society Education and Outreach Symposium serves as a platform for microbiology educators to share contemporary practices with an international audience. The Symposium is held yearly during the Microbiology Society’s Annual Conference and has become increasingly popular among conference attendees. In an effort to create an inclusive and engaging environment, the 2024 Symposium included contributions from participants at all career stages and from diverse global regions through a variety of presentation formats, including invited talks, offered presentations, flash talks and posters. Cabaret-style seating was used to encourage discussion amongst participants, and digital tools were used for anonymous feedback and …

Flipping Out: Role Of Arginine In Hydrophobic Interactions And Biological Formulation Design, Jonathan W.P. Zajac, Praveen Muralikrishnan, Idris Tohidian, Xianci Zeng, Caryn L. Heldt, Sarah L. Perry, Et. Al.

Michigan Tech Publications

Arginine has been a mainstay in biological formulation development for decades. To date, the way arginine modulates protein stability has been widely studied and debated. Here, we employed a hydrophobic polymer to decouple hydrophobic effects from other interactions relevant to protein folding. While existing hypotheses for the effects of arginine can generally be categorized as either direct or indirect, our results indicate that direct and indirect mechanisms of arginine co-exist and oppose each other. At low concentrations, arginine was observed to stabilize hydrophobic polymer folding via a sidechain-dominated direct mechanism, while at high concentrations, arginine stabilized polymer folding via a …

Why Can’T We Keep Making Antibiotics?, Kien Bui

Osmosis Magazine

Globally, the annual number of deaths due to antibiotic resistance infections is estimated to be 700,000, which can climb significantly with new viral diseases. The acquisition of antibiotic resistance in bacteria is a process related to the use of antibiotics to cure bacterial diseases. As bacteria replicate, mutations occur randomly, and there is a certain probability that this mutation introduces an antibiotic resistant gene. Upon exposure to antibiotics, all bacteria are cleared out, except for the ones that are antibiotic resistant. In other words, antibiotics significantly increase the gene frequency of the antibiotic resistant gene, allowing these bacteria to grow …

Exercise As A Drug: The Pharmacological Benefits Of Muscular Endurance Training For Type Ii Diabetes, Zack Ruighaver

Osmosis Magazine

In the United States, between 34 and 36 million people suffer from type II diabetes. That’s a little more than 1 in 10 Americans. Although type II diabetes typically develops in people 45 or older, cases are appearing more frequently in younger populations. But what if I told you that there was a drug that could help reverse this trend? No, I’m not talking about metformin or Ozempic. I’m talking about exercise – more specifically, muscular endurance training.

Letter From The Editor, Andrew Watts

Osmosis Magazine

Dear Reader,

Thank you for opening Osmosis Magazine. We are excited to bring you more accessible, intriguing stories in science and technology spanning the disciplines of biology, chemistry, psychology, and mathematics as well as faculty interviews.

Our goal as a magazine is to share the joy of science with the UR community in an accessible and entertaining fashion. We hope that you enjoy reading this Fall edition of Osmosis Magazine.

Finally, this is the last edition where I will serve as Editor in Chief. It has been a pleasure to work on this project with so many talented writers and …

Osmosis Magazine - Fall 2024

Osmosis Magazine

Osmosis is a student read, led, and written publication from the University of Richmond, focusing on all aspects of healthcare and science.

Fostering Belief And Belonging: Catalysts For Success In Stem, Andrew Watts

Osmosis Magazine

As an aspiring scientist, have you ever found yourself consumed by the suffocating pressure to be perfect? Does the weight of failure loom ominously over your endeavors, threatening to derail your aspirations? And in the quiet moments of introspection, do whispers of self-doubt emerge, casting shadows of uncertainty over your path forward in STEM? I know I certainly have.

An Investigation Of Idaho Phragmites, Paxton Mills

Osmosis Magazine

In fall 2022, the Idaho State Department of Agriculture reached out to the lab of Dr. Carrie Wu, Associate Professor of Biology at the University of Richmond, for assistance in determining the genetic lineage of a suspected invasive stand of Phragmites australis, a wetland reed which has proved to be particularly troublesome throughout its introduced range. Like most invasive species, Phragmites wreaks havoc by outcompeting native plants, which disrupts normal ecosystem operations.

Meet The Pollock Lab: Understanding Breast Cancer And Disease Development, Jeff Tsai

Osmosis Magazine

In October 2023, I was eagerly looking for my lab home, as most Gottwald students would refer to the process. I had the pleasure of talking with Dr. Julie Pollock about her significant research in breast cancer. A great part of the reason why I enjoy learning about proteins and their functions is because of my mother’s history of battling stage II breast cancer. During my time taking care of her and eventually taking a class at the University of Richmond studying gene regulation and protein functions, I gained a greater appreciation for the work that biochemists do in breaking …

Osmosis Magazine - Spring 2024

Osmosis Magazine

Osmosis is a student read, led, and written publication from the University of Richmond, focusing on all aspects of healthcare and science.

Breaking Up With The Anti-Hero: How 303(B)(3) Can Help Law Schools Mitigate Their Perennial Devices, Prices, Vices, And Crises, Kelly M. Gamble

Maine Law Review

The American Bar Association’s issuance of Standard 303(b)(3) represents a pivotal shift compelling law schools to adapt their approach to the evolving needs of law students, lawyers, and the profession. The Standard serves as an invitation to re-evaluate the relationship between the primary curriculum and student support frameworks. This Article proposes a comprehensive approach to infuse professional identity development throughout the first year of law school. While professional identity development requires ongoing efforts, sometimes tailored to particular practice interests, this Article contends that all students benefit from early explicit instruction on foundational professional identity competencies. This Article first outlines the …

Seafood Mislabeling: Molecular Strategies To Identify Fish Species And Rethinking Public Outreach In Taiwan And The U.S., Ping Yen (Jeff) Tsai

Osmosis Magazine

Swapping identical fish with substitutes has been a widespread issue across the globe. Despite the valiant efforts of policymakers, seafood misidentification continues to be pervasive among large and small vendors, from sushi venues to grocery stores in the United States.

The Origins Of Mathematics: Invented Or Discovered?, Andrew Watts

Osmosis Magazine

A divisive subject amongst students of all ages, Mathematics remains an integral part of each student’s educational journey. Why is that? you may wonder. The answer is that Mathematics lies at the center of the natural world.

Osmosis Magazine - Spring 2023

Osmosis Magazine

Osmosis is a student read, led, and written publication from the University of Richmond, focusing on all aspects of healthcare and science.

Disentangled Graph Learning

Defensive Publications Series

Graph Neural Networks (GNNs) have shown significant success in learning from graph-structured data. However, their performance often degrades on heterophilous graphs, where connected nodes tend to have dissimilar features. This paper introduces the Disentangled Graph Learning Network (DGLN), a novel GNN model designed specifically to learn on heterophilous networks by disentangling node features into structural and content components. DGLN uses an adaptive aggregation module and a graph reconstruction module to learn node representations and model network structure. We provide a detailed description of DGLN, including its algorithm, and implementation with PyTorch. Experimental results on several benchmark heterophilous datasets show that …

Dual-Channel Graph Neural Network

Defensive Publications Series

Graph Neural Networks (GNNs) have achieved significant success in modeling graph-structured data. However, their performance degrades on heterophilous graphs, where connected nodes tend to have dissimilar features. In this paper, we introduce the Dual-Channel Graph Neural Network (DCGNN), a novel GNN architecture designed to handle both homophily and heterophily by processing information through dual channels. DCGNN employs a homophily channel to capture information from similar nodes and a heterophily channel to learn from dissimilar nodes. We describe the detailed algorithm and provide a Python implementation using PyTorch. Extensive experimental results on benchmark heterophilous graph datasets demonstrate that DCGNN significantly outperforms …

Structure-Aware Graph Neural Network For Node Classification

Defensive Publications Series

Graph Neural Networks (GNNs) have shown impressive results in analyzing graph-structured data. However, their performance is often compromised when applied to heterophilous graphs, where connected nodes tend to have dissimilar features. This paper introduces the Structure-Aware Graph Neural Network (SAGNN), a novel GNN architecture designed to handle heterophilous graphs by explicitly encoding and leveraging structural information. SAGNN uses a structure encoding module to generate structural node features, followed by an adaptive message aggregation mechanism based on structural similarity, and finally a structure-aware combination module to generate final embeddings. We provide the algorithm of SAGNN and also a Python implementation with …

Graph Transformer With Adaptive Subgraph Sampling

Defensive Publications Series

Graph Neural Networks (GNNs) have shown great promise in various graph-based tasks. However, their performance often suffers when applied to heterophilous graphs, where connected nodes exhibit dissimilar features. In this paper, we introduce the Heterophily-Aware Graph Transformer (HAGT), a novel GNN architecture that leverages an adaptive subgraph sampling technique with graph Transformer layers to effectively learn from heterophilous graphs. HAGT employs relational attention to capture complex node interactions and to effectively aggregate information. We present a detailed algorithm and implementation of HAGT using PyTorch. Experimental results on several benchmark heterophilous datasets show that HAGT outperforms standard GNNs and state-of-the-art heterophilyfocused …

Conservation Status Of Virginia Populations Of The Rare And Jeopardized Bridle Shiner, Notropis Bifrenatus, Wayne C. Starnes, Gabriela M. Hogue, Morgan E. Raley

Southeastern Fishes Council Proceedings

The Bridle Shiner, Notropis bifrenatus (Cope, 1867), Family Leuciscidae, is a small minnow species that ranges in Atlantic coastal river drainages of eastern North America from the St. Lawrence in Canada southward to the Santee River basin of South Carolina. Over several decades notable declines throughout its range have been observed and multiple natural resource agencies note it to be jeopardized with probable extirpations evident in a number of drainages. The Virginia Department of Game and Inland Fisheries recognized the need to assess the status of the Bridle Shiner within its historical range in Virginia. Here we report the results …

Hiv And Bacterial Lps Synergistically Activate Aim2 Inflammasome In Primary Human Oral Keratinocytes, Md Shafayat Jamil, Deepa Roy, Upal Roy, Hansapani Rodrigo, Nirakar Sahoo, Chun Xu

Research Symposium

Background: HIV infection profoundly disrupts the oral microbiome, increasing the presence of Gram-negative bacteria such as Porphyromonas gingivalis (P. gingivalis), which is detected in over 80% of cases. P. gingivalis secretes lipopolysaccharide (LPS), a potent immune stimulant that can damage primary human oral keratinocytes (HOK) even in antiretroviral therapy (cART) treated people with HIV (PWH). HOK cells respond to bacterial and viral stimuli by activating inflammasome complexes, including AIM2, a DNA-sensing inflammasome protein. While LPS alone is known to trigger canonical and non-canonical pathways, leading to inflammasome activation, our study investigates how HIV exposure synergizes with LPS to induce the …

Elevated Familism As A Protective Factor Against Type 2 Diabetes And Alzheimer’S Disease In The Rgv Hispanic Communities, Juan F. Lopez, Luis Aguillon, Chun Xu, Daniela Ollervides Charles, Gladys Maestre

Research Symposium

Background: Alzheimer’s Disease (AD) and Type 2 Diabetes Mellitus (T2DM) are significant contributors to cognitive decline, disproportionately affecting Hispanic/Latino populations. T2DM increases the risk of AD and dementia through mechanisms such as insulin resistance, chronic inflammation, and neurodegeneration (Umegaki, 2014; González et al., 2020). Social determinants such as socioeconomic status, healthcare access, and cultural factors, including familism, exacerbating disease progression (Vega et al., 2017). Familism—a cultural value emphasizing strong family ties, loyalty, and caregiving—may play a dual role, both as a factor shaping disease management and as a potential protective element.

Elevated familism can foster supportive family networks that …

Leveraging Large Language Models For Knowledge-Free Weak Supervision In Clinical Natural Language Processing, Enshuo Hsu, Kirk Roberts

Faculty, Staff and Student Publications

The performance of deep learning-based natural language processing systems is based on large amounts of labeled training data which, in the clinical domain, are not easily available or affordable. Weak supervision and in-context learning offer partial solutions to this issue, particularly using large language models (LLMs), but their performance still trails traditional supervised methods with moderate amounts of gold-standard data. In particular, inferencing with LLMs is computationally heavy. We propose an approach leveraging fine-tuning LLMs and weak supervision with virtually no domain knowledge that still achieves consistently dominant performance. Using a prompt-based approach, the LLM is used to generate weakly-labeled …

Solid Wastes From Geothermal Energy Production And Implications For Direct Lithium Extraction, William T. Stringfellow, Mary K. Camarillo

Pacific Faculty Work

Direct lithium extraction (DLE) of brines after geothermal power production offers opportunities to produce environmentally benign “green” lithium; however, some environmental impact is inevitable. We examined solid waste production at geothermal power plants in southern California that are also locations for planned DLE facilities. Currently, the geothermal plants in this region produce approximately 79,800 metric tons (wet weight) per year of solid waste, which represents about 28 metric tons per GWh of net electricity production or approximately 500 mg solids per kg geothermal brine. Approximately 15% of this waste requires management as hazardous waste. Solids produced during power production represent …

Ec2vec: A Machine Learning Method To Embed Enzyme Commission (Ec) Numbers Into Vector Representations, Mengmeng Liu, Xialong Ni, J. Ramanujam, Michal Brylinski

Faculty Publications

Enzyme commission (EC) numbers play a vital role in classifying enzymes and understanding their functions in enzyme-related research. Although accurate and informative encoding of EC numbers is essential for enhancing the effectiveness of machine learning applications, simple EC encoding approaches suffer from limitations such as false numerical order and high sparsity. To address these issues, we developed EC2Vec, a multimodal autoencoder that preserves the categorical nature of EC numbers and leverages their hierarchical relationships, resulting in more meaningful and informative representations. EC2Vec encodes each digit of the EC number as a categorical token and then processes these embeddings through a …

University Of New Hampshire 2024-2025 Faculty Senate Xxix - March 10, 2025 Minutes Summary, Faculty Senate

Faculty Senate Agendas & Minutes

No abstract provided.