Digital Commons Network^™

Advancing Data Usability, Activity Modeling, And Stability Optimization In Computational Enzyme Design, Spencer Gardiner

Theses and Dissertations

A grand challenge of computational biology is to computationally design, in a single pass, a protein sequence that catalyzes an arbitrary chemical reaction at a high rate under specified conditions [1]. This work details advances in three essential areas on the path to that goal: data quality, activity prediction and modeling, and stability optimization. The structure and implementation of the Allotrope Simple Model (a FAIR data format for many scientific instruments) was examined in [2], setting the stage for training deep learning models on high-quality experimental datasets from diverse sources. In [3], the limits of physics-based and deep learning tools …

Biologists Study Ways To Increase Food Production For Growing World, Clara Turnage

University of Mississippi News

OXFORD, Miss. – With the world population expected to approach 10 billion by 2050, scientists are searching for ways to feed that many people with fewer resources. A new review outlines scientific advances that could help make food production more sustainable and resilient.

Parental Effects In Fall Webworm, Emma Sellers, Mykaela Tanino-Springsteen, Mayra Vidal, Dhaval Vyas, Gina Wimp, Mariana Abarca, Mattheau Comerford, Shannon Murphy

Data

The environment or experiences of a parent generation can impact the fitness of the next generation, a phenomenon known as parental effects. While a high-quality diet can directly benefit an individual and a low-quality diet can reduce fitness, a parental effect occurs only when there is a transgenerational response to these stimuli that manifests in the individual’s offspring. In dietary generalists, a parental effect could play an important role for offspring performance if the species experiences considerable variation in quality across host plants; positive parental effects may result from host matching between parents and offspring on high-quality host plants, whereas …

Microglial Swell1 Deficiency Drives Male-Specific Seizure Vulnerability But Paradoxical Neuroprotection Through Impaired Phagocytosis, Abhijeet S Barath, Aastha Dheer, Laura Montier, Mekenzie M Peshoff, Emily Dale, Flavia Goche, Thanh Thanh Le Nguyen, Mastura Akter, Fangfang Qi, Dimitrios Kleidonas, Lauren Harris, Sarah A Jewanee, Anthony D Umpierre, Dale B Bosco, Koichiro Haruwaka, Rajan Sah, Long-Jun Wu, Rongzhuo Hua, Tejaswani Datla

The Brown Foundation: Institute of Molecular Medicine

The discovery of genes encoding the volume-regulated anion channel (VRAC) has enabled detailed exploration of its cell type-specific roles in the brain. LRRC8A (SWELL1) is the essential VRAC subunit. We observed seizure-induced, subunit-specific changes in microglial VRAC expression and investigated its function using conditional KO (cKO) of LRRC8A in microglia. SWELL1 cKO mice exhibited a male-specific increase in kainate-induced seizure severity, yet showed paradoxical neuroprotection against seizure-associated neuronal loss. Mechanistically, SWELL1 deletion led to a cell-autonomous reduction in microglial density and decreased release of VRAC-permeable neuroactive metabolites, including taurine, GABA, and glutamate in culture. Additionally, impaired phagocytic kinetics and reduced …

Characterizing The Relationships Between Hydrology, Soil Biogeochemistry, And Green Ash Canopy Structure In Emerald Ash Borer-Affected Wetlands, Eva Switala

Theses

The invasion of the emerald ash borer (EAB; Agrilus planipennis) has caused mass mortality of native ash trees (Fraxinus spp.), devastating forested wetlands in the northeastern United States. Fifteen years post-introduction, the long-term ecological shifts and "new normals" of these ecosystems remain poorly understood. This project characterized patterns in EAB-affected forested wetlands by evaluating soil characteristics, biogeochemical cycling, hydrology, and green ash canopy across 12 sites with varying initial ash presence. Results revealed a clear separation between biogeochemically active and less active sites. Hydrologic differences emerged as a key driver of biogeochemical cycling, with higher soil moisture significantly increasing rates …

The Effect Of Aquatic Pollution On (Green) Microbial Communities In The Greater Rochester Area, Francesca Molee

Theses

Retention ponds are built in urban and suburban areas to catch the polluted runoff that would otherwise go into highly-valued freshwater ecosystems like the Great Lakes. They therefore make ideal model ecosystems to consider the effect of chemical, common pollution on aquatic communities. To understand the impact this aquatic pollution on both microbial community composition alongside green microbial physiological stress response, water column and sediment microbial communities were sampled from three retention ponds, and three non-retention, created ponds. The first part of this study focused on the microbial community composition. Using 16s amplicon sequencing on and subsequent analysis using Qiime2, …

Editorial: Plant Responses To Abiotic Stress: Unraveling Complex Mechanisms Through Genomics And Physiology, Mizanur Rahman, Takashi Asaeda, Md Harun Rashid

School of Earth, Environmental, & Marine Sciences Faculty Publications

No abstract provided.

Comparative Study Of Green Synthesis To Prepare Tio2 Nanoparticles From Plant Shard Leaves Extract By Using Microwave Irradiation And Microjet Plasma, Zainab Fakhri Merzah, Zainab J Shanan, Tayser Sumer Gaaz

Baghdad Science Journal

Plant extracts have been widely investigated as a safer alternative for the green synthesis of metal oxide nanoparticles. This study presents a green synthesis approach using shard leaf extract assisted by microwave irradiation and microjet plasma for the preparation of titanium dioxide nanoparticles (TiO₂ NPs). The synthesized nanoparticles were characterized using Field Emission Scanning Electron Microscopy (FESEM), X-ray diffraction (XRD), ultraviolet-visible spectroscopy (UV–Vis), Fourier Transform Infrared Spectroscopy (FTIR), and zeta potential (ZP) analysis. XRD results confirmed the formation of the anatase phase of TiO₂ without detectable brookite or rutile peaks, indicating high phase purity. The crystal structure was …

Synthesis And Characterization Of Zinc Oxide (Zno) Nanoparticles: From Chemical To Green Synthesis, Kawa S. Sulaiman, Ayoub S. Karim

Baghdad Science Journal

The present research focuses on the synthesis and comparative analysis of zinc oxide nanoparticles (ZnO NPs) produced through two distinct methodologies: a traditional sol-gel procedure and a sustainable green synthesis route. The green synthesis approach utilized Laurus Nobilis leaf extract as a natural reducing and stabilizing agent, offering an eco-friendly alternative to conventional chemical synthesis. To evaluate the structural, optical, and morphological properties of the resulting nanoparticles, both sets of samples were characterized using UV-Vis spectroscopy, XRD, energy-dispersive X-ray spectroscopy (EDX), FTIR, and Field Emission Scanning Electron Microscopy (FESEM). The XRD patterns confirmed the successful formation of a hexagonal wurtzite …

An Inf2-Dependent Actin-Mediated Step In Inositol 1,4,5-Trisphosphate Receptor Cluster Formation And Activity, Maite R. Zavala, Amrapali Ghosh, Suresh K. Joseph, Rajarshi Chakrabarti

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Intracellular calcium signaling plays a vital role in regulating various cellular processes including gene regulation, motility, metabolism, and cell death. Inositol 1,4,5-trisphosphate receptors (IP3Rs) on the endoplasmic reticulum (ER) are a major cation channel that regulates stimulus-induced calcium release from the ER. While several molecular players regulate the activity of IP3R, its regulation by actin filaments was uncharacterized. Here, we show that actin filaments polymerized by the specific actin nucleator INF2 facilitate agonist-induced IP3R activity. Our results demonstrate that INF2-mediated actin filaments regulate the formation and/or stability of IP3R clusters on the ER that have been previously shown to be …

Toolkit For Multistate Disease Progression Simulation And Treatment Decision-Making Aid, Can Xie, Ruosha Li, Wael Saber, Jorge E Cortes, Nicholas J Short, Xuelin Huang

Faculty, Staff and Student Publications

Background: The optimal timing of a treatment within therapy lines can maximize its benefit while minimizing risks and side effects. Because patients differ in clinical and biological characteristics, personalized treatment planning can support physicians' decision-making. However, multistate disease progression complicates the comparison of treatment strategies, motivating the development of a user-friendly web tool for multistate disease progression simulation and treatment decision support. Microsimulation is a natural approach for comparing prespecified treatment-timing strategies, where it generates disease trajectories for a large number of virtual patients matched to an individual patient's observed data. In our framework, microsimulation is performed using a multistate …

Enhancing Sleep Quality Through Sleep Hygiene Education Among Adults In A Faith-Based Community, Denielle Earle-Thompson

Doctor of Nursing Practice Projects

Background

Adults between 18 and 64 years of age require at least seven hours of sleep per night; however, many adults do not meet this recommendation, contributing to increased risks for chronic disease, impaired functioning, mood disturbances, and reduced quality of life. Poor sleep quality has been associated with weakened immunity, cardiovascular disease, diabetes, obesity, anxiety, depression, and decreased daytime performance. Obtaining adequate, good-quality sleep is essential for maintaining overall health and well-being. In faith-based communities, combining health education with spiritual support may provide a holistic approach that addresses both physical and emotional contributors to poor sleep.

Purpose

The purpose …

Quantitative Genetic Analysis Of Baboon Facial Variation Challenges A Classic Papionin Trait, A. Thiebaut, C. C. Roseman, Michael Mahaney, Leslea J. Hlusko

Human Genetics Publications

The Linnaean family of monkeys that includes baboons, macaques, and mandrills (among others) is notably characterized by large, extended muzzles that vary in lateral nasal dorsum profile. In paleontological studies, this variation is referred to as the anteorbital drop (AOD). Here, we first devise a method to quantify this phylogenetic character. We then employ quantitative genetic analyses using a MCMCglmm model of facial variation in a captive, pedigreed baboon colony (n = 934), including admixed individuals derived from at least two Papio species, from the Southwest National Primate Research Center to assess the quantitative variation of the AOD, its …

Bayesian Subgroup Learning Of Spatially Resolved Transcriptomics Data, Hou-Cheng Yang, Huimin Li, Guanyu Hu, Qiwei Li

School of Mathematical & Statistical Sciences Faculty Publications

Recent advancements in spatially resolved transcriptomics (SRT) technologies have enabled the comprehensive molecular and spatial characterization of single cells, providing valuable insights into the cellular organization of tissues. SRT techniques, such as single-molecule fluorescence in situ hybridization (FISH)-based methods (e.g., seqFISH, STARmap) and next-generation sequencing (NGS)-based methods (e.g., spatial transcriptomics, 10x Visium), allow for the measurement of gene expression across large populations of cells or tissue spots. These approaches generate high-dimensional data that integrate both molecular profiles and spatial context, which is crucial for understanding tissue structure and function in areas like development, neuroscience, and cancer biology. Identifying spatially variable …

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), …

A Guide To Change Management Using The Sarah Model, Sara Kern, Sarah Barbrow, Sarah Jane Dooley, Sarah E. Lester, Sarah Over

Library Scholarship

Academic libraries are the heart of colleges and universities and, as such, are often centrally involved in and impacted by changes in the greater higher education landscape. For those working in these spaces, familiarity with strategies for managing change is essential to support yourself and others during especially turbulent times. The SARAH model, described below in bullet points with our modifications in brackets, offers a memorable way to understand responses to change, be they our own or others.

S - Shock or Surprise
A – Anger [Anxiety, Alert, or Anticipation]
R – Resistance or Rejection [Re-engagement, or Rationalization]
A - …

Colostrum Management For Dairy Calves: Key Practices For Calf Health And Performance, Drew Swartz, Jacob Hadfield, Kalen Taylor, Maggi Mathews

All Current Publications

This fact sheet provides practical recommendations for dairy producers to improve colostrum management and support calf health and performance.

Program (Pdf), Department Of Orthopaedics

Dept. of Orthopaedics: Robert D. D’Ambrosia Lectureship & Research Day

Program with abstracts for the 22nd Annual Dept of Orthopaedics Annual Robert D. D’Ambrosia Lectureship & Research Day held June 20, 2026.

Vector-Borne Viral Diseases In Horses, Sunutcha Suntrarachun

The Thai Journal of Veterinary Medicine

Vector-borne viral diseases are major threats to equine health worldwide. These infections are transmitted by arthropod vectors such as mosquitoes, biting midges, and horseflies, resulting in clinical manifestations ranging from mild febrile illness to severe neurological, respiratory, circulatory, or hematologic disorders with high mortality rates. Major equine vector-borne viral diseases include African horse sickness (AHS), equine infectious anemia (EIA), equine encephalomyelitis (Eastern: EEE, Western: WEE, and Venezuelan: VEE), West Nile virus (WNV), and Japanese encephalitis (JE). Each disease is caused by a distinct viral pathogen and transmitted by specific vectors that influence their epidemiology and geographic distribution. Transmission occurs through …

Reference Values For Intraocular Pressure In Collared Scops Owls (Otus Lettia) Measured Using Rebound Tonometry, Yun-Shan Chiu, Chau-Hwa Chie, Pin-Huan Yu, Chung-Tien Lin

The Thai Journal of Veterinary Medicine

In this study, we aimed to establish species-specific reference values for intraocular pressure (IOP) in clinically healthy collared scops owls (Otus lettia) using rebound tonometry. Twelve free-living owls were included, and twentyfour eyes were examined. All owls were physically restrained in an upright position without sedation. Intraocular pressure was measured in both eyes using rebound tonometry (TONOVET; iCare Finland Oy, Vantaa, Finland) in d mode. No significant difference in IOP was observed between the right and left eyes. The mean IOP values were 10.42 ± 1.24 mmHg (median, 11 mmHg; range, 8–12 mmHg) in the right eye and 10.75 ± …

Patients Willingness To Seek Help From Pharmacists In The Management Of Rheumatoid Arthritis: A Qualitative Study, Omkar Ghodke, Erin Holmes, Meagen Rosenthal, Yinan Huang, Marie Barnard

Podiums

Background: This study explored the willingness of rheumatoid arthritis (RA) patients to seek help from pharmacists for their disease management. While pharmacist interventions are known to enhance medication adherence and health outcomes, patient engagement with pharmacists remains low. Understanding the factors that influence RA patients' willingness to use pharmacy services is essential for improving patient outcomes and optimizing the role of pharmacists in RA management. Using the Integrative Model of Behavioral Prediction (IMBP), this study identified the factors influencing willingness to use pharmacists and pharmacy services among patients with RA. Methods: This study utilized semi-structured interviews targeting individuals 26 years …

Cost-Effectiveness Of Donanemab And Lecanemab Over A Lifetime Horizon For Patients With Early Alzheimers Disease, Xiangxiang Jiang, Gang Lv, Amber Burroughs, Jun Wu, Jing Yuan, Kevin Lu

Podiums

Background: Donanemab was recently approved following the 2023 approval of lecanemab for early Alzheimers disease (AD). While both therapies represent important advances in disease-modifying treatments, substantial concerns remain regarding their clinical value and affordability. Existing cost-effectiveness analyses have only compared each drug to placebo. A direct economic comparison between the two therapies is needed to better inform healthcare decision-making. Methods: We developed a five-state Markov model to evaluate the lifetime cost-effectiveness of donanemab versus lecanemab from the US healthcare system perspective. Clinical inputs were derived from an indirect treatment comparison using published trial data. Costs, utilities, and transition probabilities were …

Maternal Perspectives On Support Needs: Insights From The Fonofale Model, Sara Lani Ditto

Theses and Dissertations

This interpretative phenomenological analysis (IPA) explored the lived experiences of parents raising children with disabilities in American Samoa. Five participants across two focus groups shared their perspectives on navigating educational, healthcare, and community systems while supporting their children with disabilities. Using the fonofale model as a cultural framework, the study incorporated culturally responsive methodology including card sort activities to facilitate dialogue on potentially sensitive topics. Analysis followed the Nizza et al. (2021) IPA approach, progressing from exploratory notes to experiential statements, clustered themes, and finally overarching themes. Findings revealed four major themes: systemic burden on parents, structural and service gaps, …

Hierarchical Parcel Swapping: A Novel Model In Turbulence, Masoomeh Behrang

Theses and Dissertations

Turbulent mixing plays a central role in a wide range of engineering and natural systems, particularly in reactive flows where turbulence--chemistry interactions strongly influence reaction rates, flame structure, and emissions. Accurately modeling these interactions remains a major challenge due to the multiscale and stochastic nature of turbulence, as well as the nonlinear coupling between transport and chemical kinetics. This dissertation develops and evaluates the Hierarchical Parcel Swapping (HiPS) model, a fully stochastic framework designed to represent turbulence-driven transport and scalar mixing without relying on traditional gradient-based closures. HiPS is investigated both as a standalone turbulence model and as a subgrid …

I Will Defend My Self, Emily Ward Hawkins

Theses and Dissertations

This thesis examines caregiving and motherhood as forms of load-bearing infrastructure. Cultural narratives often portray motherhood through sentimental images of joy, tenderness, and devotion, obscuring the structural labor that sustains family life. This project examines maternal labor as a largely unseen system of support that organizes family life while often remaining backgrounded. Caregiving reorganizes time, space, ambition, embodiment, and future orientation within maternal life. Through sculptural works using architectural materials and construction systems, such as oriented strand board, blueprint racks, metal armatures, and graph paper, the project visualizes caregiving as a structural condition. These materials reference the language of architecture …

Practical Implementation Of Ethnomathematics To Increase The Engagement, Math Self-Efficacy, And Hawaiian Cultural Identity Of HawaiʻI Algebra 2 Students, Kamalani George Mamatuki Kaluhiokalani

Theses and Dissertations

The underrepresentation of Hawaiian cultural practices in mathematics education has contributed to a disconnect between students' cultural identities and their academic experiences, resulting in diminished engagement among Native Hawaiian learners. This design-based research examines the integration of ethnomathematics into high school mathematics curricula, with a focus on Hawaiian cultural practices as frameworks for teaching mathematical concepts. Participants include approximately 100 students in Hawaiʻi from a public school and a private school, as well as two mathematics teachers with varying degrees of experience in culturally responsive pedagogy and ethnomathematics. Employing a mixed-methods approach, the study collects data through classroom observations, teacher …

Calibration And Validation Of An Ogden Material Model For Thermoplastic Polyurethane In 3d-Printed Tensegrity Structures, Caleb C. Swain

Theses and Dissertations

This work is motivated by ongoing efforts within the Smart Materials, Adaptronics, and Shock Laboratory (SMASH Lab) at Brigham Young University (BYU) to develop variable-stiffness, external fixators using 3D-printed tensegrity structures. In the process of designing and evaluating these systems, the need arose to accurately model the nonlinear mechanical behavior of thermoplastic polyurethane (TPU), the primary material used in prototype fabrication. This thesis investigates how accurately a calibrated Ogden material model can predict the nonlinear mechanical response of TPU in 3D-printed tensegrity structures. Experimental data were used to calibrate the parameters of the hyperelastic constitutive model through nonlinear optimization. An …

Institutional Influences And The Governance And Administration Of The Programa Produtor De Água Payment For Ecosystem Services Program In Brazil, Thomas G. Safford

Faculty Publications

Payment-for-Ecosystem-Services (PES) has been promoted as an innovative approach to environmental governance capable of simultaneously advancing conservation and sustainable development objectives. While studies commonly assess the ecological and economic performance of PES schemes, less attention has been given to their organizational and administrative effectiveness. This study examines these governance dimensions of one of Latin America’s most prominent PES initiatives—the Water Producer Program (WPP) in Brazil. Drawing on a meta-synthesis of 125 publications, the analysis investigates how regulative, normative, and cultural-cognitive institutional forces shaped WPP implementation. Guided by neo-institutional theory and institutional bricolage, findings show that WPP governance operated through hybrid …

Artificial Intelligence–Driven Paradigm Transformation In Biopharmaceutical R&D: Applications And Emerging Scenarios, Lili Liu, Mingyue Zheng, Ye Yuan, Xutong Li, Rong Fan, Wei Wei, Jinxin Zhao, Guobin Qi, Hua Yue, Likun Gong, Songping Zhang, Jiachen Li, Yuchen Sun, Xiaoyan Chen, Yao Chen, Xin Liu, Xiao Zhang, Yuehong Gao, Jianfeng Li, Kaixian Chen, Guanghui Ma, Jianmin Yue

Bulletin of Chinese Academy of Sciences (Chinese Version)

The biopharmaceutical industry is a critical domain underpinning national scientific and technological innovation development and public health. With the rapid advancement of artificial intelligence (AI) and its deep integration with the life sciences, biomedicine research is undergoing a paradigm shift from traditional experience-driven trial-and-error approaches to data-driven and predictive validation-based models. This study systematically examines the pathways for reshaping research in biomedicine paradigms under the convergence of data-driven, mechanism-driven, and intelligence-driven approaches. It focuses on recent advances in the application of AI across key stages, including drug discovery and design, druggability evaluation, delivery system design and optimization, nonclinical and clinical …

2026issue6content

Bulletin of Chinese Academy of Sciences (Chinese Version)

No abstract provided.