Digital Commons Network^™

Chronosort: Revealing Hidden Dynamics In Alphafold3 Structure Predictions, Matthew J. Argyle, William P. Heaps, Corbyn Kubalek, Spencer Gardiner, Bradley C. Bundy, Dennis Della Corte

Faculty Publications

Protein function emerges from dynamic conformational changes, yet structure prediction methods provide only static snapshots. While AlphaFold3 (AF3) predicts protein structures, the potential for extracting dynamic information from its ensemble predictions has remained underexplored. Here, we demonstrate that AF3 structural ensembles contain substantial dynamic information that correlates remarkably well with molecular dynamics simulations (MD). We developed ChronoSort, a novel algorithm that organizes static structure predictions into temporally coherent trajectories by minimizing structural differences between neighboring frames. Through systematic analysis of four diverse protein targets, we show that root-mean-square fluctuations derived from AF3 ensembles can correlate strongly with those from MD …

Rabies Virus-Vectored Lyme Disease Vaccine Provides Long-Term Protection Against Tick-Transmitted Borrelia Burgdorferi, Shantel Rios, Bibek Bhattachan, Christoph Wirblich, Anisha Chandwani, Kruthi Vavilikolanu, Jacob F. Myers, Chrysoula Kitsou, Utpal Pal, Matthias J. Schnell

Department of Microbiology and Immunology Faculty Papers

Lyme disease (LD) cases have doubled globally. LD is a tick-borne illness caused by the Borrelia burgdorferi sensu lato (Bb). If untreated, Bb can disseminate to distal organs, causing carditis, arthritis, and meningitis. Currently, no FDA-approved human LD vaccine exists on the market. This study used two approaches to incorporate OspA into the rabies virus (RABV) vaccine vector. We used the RABV-glycoprotein tail (RVG tail) and the Hendra virus (HeV) glycoprotein tail (HVG tail) to incorporate OspA, creating BNSP333-OspA-RVG and BNSP333-OspA-HVG, respectively. Both vaccines produced type-1 biased anti-OspA antibodies, but only BNSP333-OspA-HVG induced neutralizing antibodies and protected against Bb infection. …

Comparing Machine Learning, Deep Learning, And Reinforcement Learning Performance In Culex Pipiens Predictive Modeling, Wei Yin, Sanad H. Ragab, Michael G. Tyshenko, Teresa Patricia Feria-Arroyo, Tamer Oraby

School of Mathematical & Statistical Sciences Faculty Publications

Several machine learning (ML) and deep learning (DL) methods have been used to predict the presence of species in classification problems. Another set of methods, called reinforcement learning (RL), has been used in training agents to perform various tasks, but not in predicting species distribution. Culex pipiens (Diptera: Culicidae), commonly known as the common house mosquito, is a globally distributed species prevalent in temperate and subtropical regions. They serve as a primary vector for West Nile Virus (WNV), a mosquito-borne pathogen that affects humans and other animals. The study objective is to compare the performance of logistic regression, random forest …

Adsorptive Removal Of Arsenite And Cobalt By Commercial Sorbents, Sevda Joudiazar, Sushma Yadav, Zhiming Zhang, Anshuman Satpathy, Eustace Fernando, Roxana Rahmati, Junchul Kim, Rupali Datta, Dibyendu Sarkar

Michigan Tech Publications

Despite the prevalence and toxicity of heavy metals in the environment, arsenic and cobalt are of particular concern due to their high mobility and bioaccumulation potential, particularly in contaminated groundwater. Herein, we studied the adsorption behavior of commercially available sorbents, including Fluorosorb-100 (FS-100), Fluorosorb-200 (FS-200), and Filtrasorb-400 (F-400), for the removal of arsenite (As(III)) and cobalt (Co(II)), aiming at the selection of filter media in terms of future groundwater remediation. Kinetic analysis revealed that As(III) adsorption followed a pseudo-second-order model, while Co(II) showed mixed first- and second-order behavior, reflecting sorbent-dependent mechanisms. Equilibrium isotherm modeling revealed strong correlations with both Langmuir …

Cv: Philip Blankenship (Behavioral Neuroscience), Philip Blankenship

Psychology Department Faculty Curricula Vitae

No abstract provided.

Epigenetic Landscape In Lysosomal Storage Disorders: Mechanisms And Modulation, Andrés Felipe Leal, Harry Pachajoa, Shunji Tomatsu

Department of Pediatrics Faculty Papers

Lysosomal storage disorders (LSDs) are rare substrate-accumulating diseases primarily characterized by mutations in genes encoding proteins involved in lysosomal function, most of which have enzymatic activity. Resulting lysosomal dysfunction leads to the overaccumulation of non- or partially degraded substrates. While it is true that enzyme deficiency is the primary cause of LSDs, the epigenetic alterations in DNA methylation, miRNA expression, and histone modifications appear to be critical mechanisms involved in the pathogenesis of LSDs. As epigenetic marks are, in most cases, reversible, their study becomes vital to developing strategies aimed at reversing epigenome alterations. Although classical therapeutic alternatives aim to …

Reprogramming Tumor Microenvironment Via Systemic Delivery Of Tlr3 Agonist And Manganese Nanoparticle, Young Seok Cho, Xingwu Zhou, Xiaoqi Sun, Ziye Wan, Julia Crowther, Mariko Takahashi, Swetha Kodamasimham, Qi Wu, May Thazin Phoo, Youngseo Na, Kai Han, Zaiye Li, Anna Schwendeman, Steven P Schwendeman, Yu Leo Lei, James J Moon

Faculty, Staff and Student Publications

Toll-like receptor (TLR) agonists, as potent immunostimulatory adjuvants, play a critical role in linking the innate and adaptive immune responses. However, their antitumor effects as cancer immunotherapeutic agents have been limited. Here, we report our finding that manganese ion (Mn2+) potentiates various TLR agonists, leading to robust activation of the TLR pathway and the stimulator of interferon genes (STING) pathway among innate immune cells. In particular, we have observed robust antitumor efficacy after intratumoral administration of a TLR3 agonist and Mn2+. To achieve systemic codelivery of TLR3 agonist and Mn2+, we have developed a low-molecular-weight poly(inosinic:cytidylic acid)-Mn2+ coordination lipid nanoparticle …

Heritage-Based City Branding Case Study Of Fayoum City, Menna Mounir, Sameir Hammad

Mansoura Engineering Journal

Uniqueness and distinction have become fundamental requirements in promoting and branding cities. Influencing people's perceptions is best achieved by reinforcing the city's identity. This identity is the main component that can transform any ‘space’ into a ‘place’. Promoting a city should extend to highlighting the Heritage, landscape, religious sites, pathways, cuisine, inhabitants, activities, and personal experiences. These elements collectively express the city spirit and enrich visitors’ experience.

This study aims to enhance the image of heritage-based cities by exploring the potential for city branding and leveraging heritage to boost the national economy.

Fayoum was selected as a case study for …

Differences In Dieting Behavior In Athletic Trainers, Emily Madrak, Ki L. Cole, Bridget M. Miller, Jennifer L. Volberding

Journal of Sports Medicine and Allied Health Sciences: Official Journal of the Ohio Athletic Trainers Association

Introduction: Athletic trainers (ATs) have a foundational knowledge in many facets of health, including optimization of wellness. Though ATs may be actively trying to improve their own health, societal pressure can have a large impact on behavior. The purpose of this study was to identify differences between gender and years-certified in diet patterns in ATs. Methods: A cross-sectional survey was distributed to 2500 National Athletic Training Association members, It included a demographics section and five-item researcher-created questions regarding diet. Chi-square tests of independence were used to determine the relationship. Results: Significance was determined for gender and question 2, “Have …

Assessing The Role Of Social Media As A Complementary Source In Pharmacovigilance: Insights From Faers, X (Formerly Twitter), And Askapatient Data Across Multiple Drug Classes, Nwanneka Okere

Dissertations

Background: Adverse drug reactions (ADRs) pose significant public health challenges yet remain substantially underreported in traditional pharmacovigilance systems. Social media platforms and patient-reported outcome forums have emerged as potential complementary sources for capturing real-time patient experiences with medications, but their integration with established surveillance systems remains underexplored.

Purpose: This study examined ADR reporting patterns across FDA Adverse Event Reporting System (FAERS), X (formerly Twitter), and Askapatient to evaluate whether patient-generated digital data can complement traditional pharmacovigilance systems for enhanced drug safety monitoring.

Methods: An explanatory sequential mixed-methods design analyzed 107,753 reports representing 289,740 individual ADR occurrences for …

Genome-Wide Crispr Screens Identify Critical Targets To Enhance Car-Nk Cell Antitumor Potency, Alexander Biederstädt, Rafet Basar, Jeong-Min Park, Nadima Uprety, Rejeena Shrestha, Francia Reyes Silva, Merve Dede, John Watts, Sunil Acharya, Donghai Xiong, Bin Liu, May Daher, Hind Rafei, Pinaki Banerjee, Ping Li, Sanjida Islam, Huihui Fan, Mayra Shanley, Jingling Jin, Bijender Kumar, Vernikka Woods, Paul Lin, Silvia Tiberti, Ana Karen Nunez Cortes, Xin Ru Jiang, Inci Biederstädt, Patrick Zhang, Ye Li, Seema Rawal, Enli Liu, Luis Muniz-Feliciano, Gary M Deyter, Elizabeth J Shpall, Natalie Wall Fowlkes, Ken Chen, Katayoun Rezvani

Faculty, Staff and Student Publications

Adoptive cell therapy using engineered natural killer (NK) cells is a promising approach for cancer treatment, with targeted gene editing offering the potential to further enhance their therapeutic efficacy. However, the spectrum of actionable genetic targets to overcome tumor and microenvironment-mediated immunosuppression remains largely unexplored. We performed multiple genome-wide CRISPR screens in primary human NK cells and identified critical checkpoints regulating resistance to immunosuppressive pressures. Ablation of MED12, ARIH2, and CCNC significantly improved NK cell antitumor activity against multiple treatment-refractory human cancers in vitro and in vivo. CRISPR editing augmented both innate and CAR-mediated NK cell function, associated with enhanced …

Tackling The Burden Of Envenomation In Africa: Advances, Challenges, And Strategic Priorities For Enhanced Diagnosis And Treatment, Khawla Ammouch, Nihal Mesmoudi, Noureddine Hammani, Jacob Galan, Abdellah Moustaghfir, Reto Stöcklin, Naoual Oukkache

Human Genetics Publications

Venomous animal envenomation remains a significant but neglected public health problem worldwide, with an estimated 5.4 million cases and up to 138,000 deaths annually. The burden is particularly acute in tropical and subtropical regions, especially sub-Saharan Africa, where rural and vulnerable populations face limited access to effective antivenoms and healthcare. Despite this, comprehensive data on envenomation incidence, clinical management, and outcomes remain scarce, hampering efforts to develop effective prevention and treatment strategies. This review synthesizes current knowledge on venomous animal diversity, epidemiology, and clinical manifestations globally, with a focus on Africa’s unique challenges. We examine critical gaps in antivenom production, …

Michigan Academician Volume 50, Issue 1

Michigan Academician

2025 Michigan Academy Conference abstracts.

Augmented Reality-Assisted E-Module On Temperature Andheat Content (Emarks), Tetri Sabrina, Ika Mustika Sari, Dedi Sasmita

Jurnal Pendidikan Sains

Temperature and heat content (calor) material in physics often involves concepts and phenomena that are difficult to observe directly or are abstract (such as energy transfer, particle movement, and changes in state). EMARKS (AR-based E-modules) are important because Augmented Reality (AR) allows the visualization of these abstract concepts in the form of interactive 3D models in the user's real environment. This helps students understand the concepts more concretely and easily. The development of E-modules is an innovation in learning media that is relevant to the demands of the digital era and the needs of modern students. The use of advanced …

Analysis Of An Effective Training Curriculum: Solutions Toincrease Participants' Interest In Training Teachingmaterials, Maulidya Husnul Khatimah, Yoto Yoto

Jurnal Pendidikan Sains

This research is important because it analyzes the curriculum as a primary tool for generating and maintaining participant interest. Curricula that are irrelevant, monotonous, or misaligned with participant needs are often the main causes of low motivation and participation. Furthermore, this research encourages the exploration and implementation of more innovative teaching methods and materials in training curricula. External pressure in the form of demands or instructions, rather than internal motivation, drives most training activities. This can reduce engagement and learning effectiveness. To overcome this, training institutions need to design programs that are relevant, flexible, and able to encourage participants' intrinsic …

The Effect Of Guided Inquiry Model With Deep Learningapproach On Student’S Hots In Elements, Compounds,And Mixtures At Junior High School, Friska Pakpahana, Retno Dwi Suyanti

Jurnal Pendidikan Sains

The current education curriculum places a strong emphasis on developing HOTS skills (such as analyzing, evaluating, and creating) to prepare students for the challenges of the 21st century. School learning often focuses on lower-level cognitive domains (memorizing and understanding). This research seeks to address this gap by offering a potentially effective learning model. The guided inquiry model positions students as active participants in learning, encouraging them to investigate, discover, and formulate concepts independently with teacher guidance. This strongly supports the development of critical thinking and problem-solving skills. Therefore, this study aims to analyze the effect of the guided inquiry model …

Development Of Problem-Based Learning Worksheet Toenhance Ecoliteracy: Human Impact On Ecosystem, Ulina M.S. Simangunsong, B. Manurung, Martina Asiati Napitupulu

Jurnal Pendidikan Sains

Ecoliteracy (ecological literacy) is an individual's ability to understand basic ecological principles and make environmentally responsible decisions. Improving ecoliteracy is a crucial foundation for realizing Education for Sustainable Development (ESD), which prepares students to become proactive citizens in protecting the environment. The problem-based learning model helps students learn on their own by using real-world environmental cases to get them to think critically and solve problems. Therefore, this research aims to determine the effectiveness of using problem-based learning worksheets to enhance the ecoliteracy of seventh-grade students. The development model used is 4-D. The research instruments include expert validation forms for subject, …

Development Of E-Lkpd Assisted By Phet Colorado Basedon Discovery Learning: Critical Thinking Skills On Lightmaterial At Junior High School, Flora Yani Saragih, Pintor Simamora

Jurnal Pendidikan Sains

Critical thinking is necessary for 21st-century pupils, but PISA data suggest that Indonesian students, especially junior high school students, lack it. The junior high science/physics light material is abstract and involves in-depth reasoning (reflection, refraction, and shadow generation). Without critical thinking, kids memorize formulas or notions without analyzing real phenomena. Discovery learning involves pupils discovering concepts via observation and experimentation. Critical thinking requires initiative, exploration, and reasoning, which these foster. Therefore, this study aims to develop E-LKPD based on Discovery Learning assisted by an interactive simulation of PhET Colorado to strengthen the critical thinking skills of grade VIII students on …

Guided Inquiry Learning Assisted By Crossword Puzzlemedia: Student Scientific Literacy And Critical Thinkingability For Middle School, Agis Putri Niswa, Mariati Purnama Simanjuntak, Ramlan Silaban, Fauziyah Harahap, Ridwan Abdullah Sani

Jurnal Pendidikan Sains

Scientific literacy and critical thinking skills are two fundamental competencies that students need in the 21st century. Scientific literacy is essential for students to understand and use scientific knowledge to make informed decisions, while critical thinking trains students to analyze information, evaluate arguments, and solve problems logically. Therefore, the intent of this study was to determine the effect of the guided inquiry learning model assisted by crossword puzzle media on students’ scientific literacy and critical thinking skills. The type of research used was quasi-experimental with a two-group pretest-posttest design. The sample consisted of two classes: class VII-8 as the control …

Program Transition Success: A Practical Guide For Educators Moving Sbae Programs, Evey Choat

Department of Agricultural Leadership, Education, and Communication: Dissertations, Theses, and Student Research

What tools, strategies, and support systems can help agriculture educators navigate leadership transitions and sustain program success when moving between schools or communities? Teacher mobility and leadership transitions within School-Based Agricultural Education (SBAE) present unique challenges to program continuity, community relations, and professional sustainability. Unlike other subject areas, SBAE teachers often manage multifaceted responsibilities—as classroom instructors, FFA advisors, and community liaisons—making transitions between programs especially complex. This project addresses the lack of structured support for educators navigating these transitions by developing a Program Transition Guide specifically tailored to the needs of agricultural educators in Nebraska.

Guided by Transformational Leadership Theory …

Mechanisms Of Antibody-Mediated Protection In Severe Acute Respiratory Syndrome Coronavirus 2 Infection, Samantha Mackin

Arts & Sciences Graduate Student Theses and Dissertations

ABSTRACT OF THE DISSERTATION Mechanisms of Antibody-Mediated Protection in Severe Acute Respiratory Syndrome Coronavirus 2 Infection by Samantha Rae Mackin Doctor of Philosophy in Biology and Biomedical Sciences Immunology Washington University in St. Louis, 2025 Professor Michael S. Diamond, Chair Coronaviruses (CoVs) are enveloped, non-segmented, positive-sense RNA viruses belonging to the Coronaviridae family. The subfamily Coronavirinae includes four genera: alpha-, beta-, gamma-, and deltacoronaviruses. While gamma- and deltacoronaviruses primarily circulate in wild or domestic birds and have shown the potential for cross-species transmission, alpha- and betacoronaviruses mainly infect mammals, resulting in respiratory illnesses that can be mild or severe. Over …

A Multi-Faceted Study Of Antibiotic-Resistant, Opportunistic Pathogens In Wastewater And Environmental Water, Jeanette Calarco

USF Tampa Graduate Theses and Dissertations

More than 2.8 million infections due to antibiotic-resistant bacteria occur annually in the United States, and more than 35,000 people die as a result. Domestic wastewater (sewage), which contains antibiotic-resistant bacteria and antibiotic resistance genes, is collected at treatment plants for removal of contaminants, e.g. pathogenic microorganisms and nutrients. While wastewater treatment is designed to remove antibiotic-resistant bacteria and other microorganisms through treatment and disinfection, some bacteria may escape treatment. Treated wastewater effluent is generally discharged into surface waters; however, some fraction of the effluent may be used as recycled water. Compromised wastewater collection infrastructure and sewage spills can disseminate …

Cofilin Inhibition Ameliorates Piezo2 And Ampa Dysfunction In A Mouse Model Of Angelman Syndrome, Luis O Romero, Manisha Bade, Elisa Carrillo, Sonia Paz-López, Syed A M Hasan, William James Antonisamy, Vasanthi Jayaraman, Zahoor A Shah, Valeria Vásquez, Julio F Cordero-Morales

Faculty, Staff and Student Publications

Angelman syndrome (AS) is a neurogenetic disorder characterized by motor coordination and cognitive deficits. In AS, hippocampal neurons show reduced filamentous (F-)actin, a decrease we also reported in dorsal root ganglia (DRG) neurons, along with impaired mechanosensitive ion channel activity. Currently, there are no pharmacological targets to prevent the decrease of F-actin in AS. Here, we utilize a first-in-class selective cofilin inhibitor (SZ-3) to restore PIEZO2 function in DRG neurons and glutamate-evoked currents in hippocampal neurons from AS mice. Using atomic force microscopy, we demonstrate that inhibiting cofilin, an actin-severing protein, with SZ-3 increases cellular stiffness by stabilizing the actin …

A Study Of Nonlinear Duffing Equations Using The Haar Wavelet Method, Kumbinarasaiah S., Yeshwanth R., Nandeesh K C.

Mansoura Engineering Journal

The main goal of this study is to solve Duffing equations, which are nonlinear differential equations (DEs), using the Haar wavelet technique. The solutions to this equation for an externally pushed and damped oscillator show intriguing dynamic behavior. Mathematicians have recently become more interested in wavelet analysis because of its real-world applications. A few real-world problems have been considered to assess the current methodology. Here, the (OMI) Operational Matrix of Integration and collocation points transform the non-linear ODEs into a system of nonlinear algebraic equations. The resulting system of algebraic equations is then solved using the Newton-Raphson technique to retrieve …

Serum Response Factor Is Essential For Endometrial Function And Prevention Of Inflammatory Fibrosis, Ryan M Marquardt, Sara A Grimm, San-Pin Wu, Peter F Lais, Shu-Yun Li, Xin Xu, Erin Smithberger, David Cunefare, Charan Ganta, David Olson, Eunhee M Jeong, Jae-Wook Jeong, Bruce A Lessey, John P Lydon, Francesco J Demayo

Faculty, Staff and Students Publications

Pregnancy requires a supportive uterine environment facilitated by steroid hormone–regulated differentiation of endometrial stromal fibroblasts into decidual cells and tight control of inflammation. Serum response factor (SRF) is a widely expressed transcription factor essential for mesenchymal cell growth and differentiation with noted roles in hormonal regulation of muscle tissues but little characterization in reproductive organs. Here, we reveal that endometrial SRF is dysregulated in human endometriosis and is critical for female reproductive success in mice through regulation of endometrial stromal and epithelial cells. Immunohistochemical analysis identified decreased endometrial SRF expression in infertile endometriosis patient tissues. RNAi-based SRF knockdown in human …

Deforestation Affecting Developing Nations, Nicole Villa

Sustainability Conference

Deforestation continues to be a growing problem around the globe, while it is affecting wildlife what can be overlooked is the challenges it’s creating for the livelihood of nations. This goes beyond losing the biodiversity of our ecosystems but social consequences with the scarcity of water in Malawi, rise in health risks in Democratic Republic of Congo and negative effects of agricultural expansion in Belize. Overall social conflict in these areas that are suffering to grow. Furthermore, I aim to cover the major challenges previously mentioned followed by counteracts of deforestation including action plan in Brazil, efforts of other countries …

Assessing Antimicrobial Properties Of Plant-Derived Ellagic Acid Supplements, Noah S. Schuhmann, Andrew Mclaughlin, Julian Barrera

Humboldt Journal of Microbiology

Bacteria present in the human gut microbiota are affected by compounds with antimicrobial properties. Phenolic compounds extracted from plants have been shown to exhibit significant antimicrobial capacity at certain concentrations, which makes them an area of interest to researchers. Ellagic acid is one such phenolic compound, present in nuts and berries that many people consume on a regular basis. Supplements containing concentrated ellagic acid provide an additional source for the compound. It is known that, in the body, ellagic acid is metabolized into urolithins, which contribute to health through their anticancer and anti-inflammatory qualities. In this study, we investigated the …

Comparative Analysis Of Probiotic Viability In Alcoholic And Non-Alcoholic Kombucha, Isabella N. Cerrone, Brooke Pirkle, Danielle Williamson, Gianna Vendrell, Chloe Kraft

Humboldt Journal of Microbiology

Kombucha is a fermented tea beverage valued for its probiotic and antimicrobial properties that arise from complex molecular interactions between yeast, acetic acid bacteria (AAB), lactic acid bacteria (LAB), and metabolic byproducts of fermentation. With the rising demand for non-alcoholic versions of traditionally alcoholic kombucha beverages, ethanol reduction methods have become common, though their impact on probiotic viability and antimicrobial properties remains poorly understood. This study investigates the effects of ethanol removal on kombucha’s functional properties, including probiotic survival, antimicrobial activity, and organic acid composition (pH). We compared alcoholic and non-alcoholic versions of JuneShine kombucha across five flavors. Probiotic viability …

Elucidating The Relationship Between Water Quality And Antibiotic Resistance Of Rainwater Microbes Across Western Humboldt County, Theo P. Murphy, Eve Wendley, Justice Laskowski, Tyler Paredes

Humboldt Journal of Microbiology

Limited studies have been conducted regarding the fecal contamination and microbial dispersal through rainwater, with no known studies investigating the potential connection between antibiotic resistant microbes and water quality in rainwater. This study seeks to identify the presence of a correlation between water quality and incidence of antibiotic resistance in rainwater microbes. We hypothesize that there will be a correlation between these two variables. We additionally anticipate a high incidence of fecal contamination across rural and urban collection sites alike, with fecal contamination being more prevalent in rural areas than urban locals. To determine water quality, we measured the concentration …

Selecting Irrigated Alfalfa Varieties, Mckenna S. Barney, Earl Creech, Matt Yost

All Current Publications

Selecting an alfalfa variety is one of the most important decisions an alfalfa producer can make and is the cornerstone of successful alfalfa production. Variety selection directly impacts yield potential, forage quality, stand persistence, pest and disease resistance, and environmental adaptation—all factors that can have a major economic impact. Informed decisions can be made by carefully considering the goals of your operation and adhering to the criteria outlined in this fact sheet.