Life Sciences Commons^™

Data For Recreation Effects On Soil Carbon, Biocrust, Soil Stability, And Invasives In Indian Creek, Bears Ears National Monument, Elisabeth M. Currit, Tara B. Bishop, April Hulet, Nathan Allen Currit, Teresa Gomez, Nathan T. Thompson, Shannon Lambson, Heidi Jean Wilding Mann, Evan Miller, Erin Jones, Alexandra Olson, Katherine A. Anselmi, Meredith Murdock, Ella Reid, Kirsten Steele, Indy Lawrence, Neil Hansen

ScholarsArchive Data

This data is about how different types of recreation impact different soil and vegetation properties related to soil carbon in Indian Creek, Bears Ears National Monument. The data was collected from May 2023 to October 2023. It contains plant functional group cover, biocrust cover and type, soil stability, and compaction data for each individual site. There are 5-7 of each site type: camping, foot trails, and motorized offroading trails, and undisturbed sites, with a total of 30 sites. It also contains the code used to analyze the raw data and the figures created.

Effects Of Cryoprotective And Mitochondrial Stabilizing Agents On Vitrified Bovine Oocytes, Allison Hoang

LSU Master's Theses

Oocyte vitrification success is highly dependent on cryoprotectant agent (CPA) choice as well as possible additives that could help preserve mitochondrial membrane potential (mMP), reactive oxygen species (ROS) production, and calcium homeostasis within the cell. It is a delicate balance between levels needed for proper oocyte function and activation and levels needed to induce apoptotic pathways. The results of oocyte cryopreservation determine the eventual oocyte viability and subsequent fertilization and embryo development.

In this study potential permeating cryoprotectant combinations were explored such as ethylene glycol (EG) and propylene glycol (PG) or EG in combination with dimethyl sulfoxide (DMSO). Also, the …

Fabrication Of Antibacterial And Functional Films From Starch-Polyvinylpyrrolidone Composite Using Plasma Treatment And Silver Nanoparticles, Muhammad Nazrul Islam, Nikitha Modupalli, Md Mahfuzur Rahman

Food Science Faculty Publications and Presentations

Biopolymers and water-soluble nontoxic synthetic polymer composites using silver nanoparticles are astute approaches for antibacterial film fabrication. Moreover, surface treatment of the biopolymeric composite film by cold plasma can enhance the biocidal activity. Silver nanoparticles were synthesized by using the reduction method. Films were fabricated with different ratios of rice starch and polyvinylpyrrolidones (PVP) (1:0, 1:1, and 3:1), with and without silver (Ag) nanoparticles. A plasma jet was used to treat the film's surfaces by placing the Film 0.5 cm below the plasma discharge. Surface morphology was monitored by scanning electron microscopy (SEM), and the existence of Ag nanoparticles in …

Artificial Intelligence In Ocular Transcriptomics: Applications Of Unsupervised And Supervised Learning, Catherine Lalman, Yimin Yang, Janice L. Walker

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Transcriptomic profiling is a powerful tool for dissecting the cellular and molecular complexity of ocular tissues, providing insights into retinal development, corneal disease, macular degeneration, and glaucoma. With the expansion of microarray, bulk RNA sequencing (RNA-seq), and single-cell RNA-seq technologies, artificial intelligence (AI) has emerged as a key strategy for analyzing high-dimensional gene expression data. This review synthesizes AI-enabled transcriptomic studies in ophthalmology from 2019 to 2025, highlighting how supervised and unsupervised machine learning (ML) methods have advanced biomarker discovery, cell type classification, and eye development and ocular disease modeling. Here, we discuss unsupervised techniques, such as principal component analysis …

Suppression Of Cardiac Allograft Vasculopathy By A Macrophage Efferocytosis Receptor, Sahil Shah, Aparnaa Ananthakrishnan, Matthew Deberge, Kristofor Glinton, Rebecca T L Jones, Mallory Filipp, Ivana Shen, Joey Lockhart, Connor W Lantz, Edward B Thorp

Faculty, Staff and Student Publications

Cardiac allograft vasculopathy remains a major cause of late morbidity following heart transplantation. While accumulating evidence implicates innate macrophages in the inflammatory progression of CAV, the underlying mechanisms remain incompletely understood. In murine models of CAV, we identified proteolytic cleavage of MERTK, a key anti-inflammatory receptor on macrophages, as a contributing factor to CAV progression. In a model of CAV, MERTK deficiency accelerated allograft rejection and increased intimal leukocyte infiltration. In contrast, mice expressing a genetically cleavage-resistant form of MERTK (MertkCR/CR) exhibited prolonged graft survival, reduced intimal thickening, diminished immune cell infiltration, and decreased circulating effector T cells. …

Reproducibility Of Statistically Significant Phase Iii Oncology Trials: An In Silico Meta-Epidemiological Analysis, Alexander D Sherry, Pavlos Msaouel, Avital M Miller, Timothy A Lin, Joseph Abi Jaoude, Ramez Kouzy, Adina H Passy, Tomer Meirson, Nikolaos Ignatiadis, Zachary R Mccaw, Erik Van Zwet, Ethan B Ludmir

Faculty, Staff and Student Publications

Purpose: The conventional assumption that P values ≤ 0.05 imply reproducible effects has come under recent criticism. This concern is particularly relevant in oncology, as phase III oncology trials, which directly inform practice, are usually not repeated. Using advanced modeling techniques, we investigated the relationship between P values and reproducibility in oncology.

Methods: We obtained the signal-to-noise ratio distribution in phase III oncology using outcomes from 632 two-arm superiority trials enrolling 496,219 patients. With this distribution, we estimated successful replication probability as the probability that a replicate trial, having the same design, effect size, and standard error, would have a …

The Role Of Recruited Adipose Stromal Cells And Their Fibroblastic Differentiation In Cancer, Lingyi Cai, Mikhail G Kolonin, Dimitris Anastassiou

Faculty, Staff and Student Publications

Adipose stromal cells (ASCs) are perivascular mesenchymal progenitors of adipose tissue. In cancer patients, ASCs can mobilize and migrate to the tumor, where they subsequently play an important role in cancer progression. This biological process involves the conversion of recruited ASCs into cancer-associated fibroblasts (CAFs). ASC-derived CAFs influence the tumor microenvironment through extracellular matrix remodeling, vascularization, and immunomodulation. These and other processes mediated by secreted paracrine factors also affect gene expression in carcinoma cells to promote the epithelial-mesenchymal transition (EMT), metabolic adaptation, survival, and invasiveness of cancer cells. ASC-derived CAFs can enhance tumor aggressiveness, accounting in part for the link …

Montserrat Developments Impacting Local Coral Reefs, Emma I. Bartholomew

2025 Symposium

Montserrat is a small island in the Caribbean, and over half of the island is in the exclusion zone because of the active volcano, Soufrière Hills. In that half was the old capital, Plymouth, which has since been abandoned, and its old port. The old port was getting less reliable and accessible, so they decided to build a new port in Little Bay, closer to the seat of government in Brades. This study explored how the addition of the new port impacted the corals in that area. We explored several different bays and recorded the diversity and health of the …

Rear Leg-Derived Moment Contributes To Resistance Against Hip Extension In Bulgarian Split Squats, Hiroshi Arakawa, Hikaru Nakashima, Xuanrui Li, Michiya Tanimoto

International Journal of Exercise Science

International Journal of Exercise Science 18(7): 881-894, 2025. The Bulgarian split squat (BSS) is a unilateral exercise that emphasizes hip extension more than knee extension, compared to other squat variations. This study aimed to (1) empirically verify the existence of the rear leg-derived moment (M_RL)—a theoretically plausible but previously untested external resistive hip moment acting against the net hip extension moment (M_HE) of the front leg—and (2) examine how stance width and forward trunk-leaning angles affect M_RL during the BSS. Nine trained male participants performed bodyweight BSS under two stance conditions (wide and narrow) and …

16-Week Physical Transition From Professional Mma To Tactical Firefighting: A Case Study, Cole D. Smeester, Gabriel J. Sanders, Corey Peacock, Jose Antonio

Journal for Sports Neuroscience

Firefighters, whose occupation involves intense physical, mental, and environmental demands, must be physically and mentally prepared to perform job-specific tasks effectively and safely. Nearly half of all injuries sustained on and off the fireground are musculoskeletal, highlighting issues in the preparation and maintenance strategies for work preparedness among firefighters. This case study examines the effectiveness of a 16-week conventional, conjugate strength and conditioning model on a fire recruit transitioning from a career as a professional MMA fighter. Specific data metrics were used to assess increases in firefighter-specific performance (i.e., EPAT time and body composition). After the 16-week program, the participant …

Idmatch Bike Fitting Enhances Power Output In Recreational Cyclists: A Pilot Study, Evan T. Hoyt, Gregory N. Ruegsegger

International Journal of Exercise Science

International Journal of Exercise Science 18(2): 864-880, 2025. Optimizing bike position is essential for enhancing cycling performance, improving comfort, and reducing injury risk. This study examined the acute effects of a bike fit using the idmatch^® system on power output, rate of perceived exertion (RPE), and discomfort in recreational cyclists. Twelve participants (10 males, 2 females; 37.0 ± 9.4 years) underwent an idmatch system bike fit, which employs three-dimensional motion capture to optimize rider position. Cyclists completed a six-second peak power test (PPT6) and a 20-minute functional threshold power (FTP) test before and after the fit. Performance metrics (power, …

The Complexity Of Promoting Physical Activity In English State Primary Schools: An In-Depth Qualitative Analysis Of The Role Of Social Context, Robert Walker, Danielle House, Alice Porter, Ruth Salway, Simona Kent-Saisch, Michael Beets Ph.D., David Revalds Lubans, Frank De Vocht, Russell Jago

Faculty Publications

Background

Primary schools present an opportunity to equitably promote physical activity. To date, school-based interventions have had limited success. Contextual differences between schools could be a key factor that contributes to this lack of impact. However, the elements that constitute a school’s social context (i.e. the organisational, political, cultural, and sociodemographic characteristics) and how they might impact on primary school physical activity are unclear. The aims of this study were to conduct an in-depth qualitative analysis of state primary school social context related to physical activity and, using this analysis, provide recommendations for policy and practice.

Methods

We conducted one-to-one …

08.25.2025 Ored Connect, Liz Williamson

ORED Newsletter

• Research Security Required Training
• ORED Research Reception

Identification, Abundance, And Behavior Of North American Bobcat (Lynx Rufus) Along Road Mitigation Structures Designed For Endangered Species In South Texas, Victoria Hanley, Kevin W. Ryer, Md. Saydur Rahman, John H. Young Jr., Richard J. Kline

School of Integrative Biological & Chemical Sciences Faculty Publications

Endangered species are increasingly used as the target species in implementing and constructing new wildlife crossing structures (WCS). Highways in South Texas fragment the landscape and result in high road mortality for endangered species such as ocelots (Leopardus pardalis, a medium-sized spotted wild cat). In response, the Texas Department of Transportation constructed nine WCS on Farm-to-Market 106 (FM 106), a road which bisects Laguna Atascosa National Wildlife Refuge in Cameron County, Texas. With ocelots being rare and elusive, bobcats (Lynx rufus) are often used as a surrogate species to study felid behavior at road mitigation structures …

A Comparison Of Diving Behavior Of Goose-Beaked And Dense-Beaked Whales From Tagging Studies In Multiple Ocean Basins, Jay Barlow, Robin W. Baird, Janelle Badger, Gregory S. Schorr, Erin A. Falcone, Shannon N. Coates, Peter L. Tyack, Andrew J. Read, Leigh S. Hickmott, John W. Durban, Diane Claridge, Natacha Aguilar De Soto, Daniel Miranda Gonzalez, Fleur Visser, Machiel G. Oudejans, Stacy L. De Ruiter, David A. Sweeney, Brenda K. Rone, Stephanie L. Watwood

University Faculty Publications and Creative Works

Studies of cetacean diving behavior in multiple locations in different ocean basins allow for an assessment of variability within and among populations. We examine foraging dive behaviors of goose-beaked whales (Ziphius cavirostris) and dense-beaked whales (Mesoplodon densirostris) using data from 132 tagged whales in seven locations in the Pacific and Atlantic Oceans and the Mediterranean Sea. Acoustic recording tags are used to identify foraging dives by the presence of echolocation. For other tag types, foraging dives are identified based on maximum dive depth. Five parameters are used to characterize foraging dives: maximum dive depth, foraging dive duration, dive cycle duration, …

Heterogeneity Of Molecular Subtypes In Multifocal And Multicentric Breast Cancer, Anna M. Schmitz

Research from the Berry Summer Thesis Institute, 2025

Multifocal and multicentric breast cancers (MMBC), commonly referred to as multiple synchronous ipsilateral breast cancers, are heterogeneous diseases. There is a high degree of diversity between and within the tumors of a MMBC-bearing patient. Tumor heterogeneity can describe multiple features, such as morphological and molecular profiles. Knowledge about a patient's tumor heterogeneity can be used to determine a prognosis and treatment plan. However, transferring our growing knowledge of heterogeneity in MMBC into a clinical setting remains a challenge due to the large degree of diversity between tumor microenvironments and the cancer cells that tumors are composed of. This review article …

Crossroads Of Covid-19 And Alzheimer’S: Investigating Sars-Cov-2 Nsp6 And Orf7a In Amyloid-Β42 Toxicity, Jeffrey William Huettemann, Amit Singh

Research from the Berry Summer Thesis Institute, 2025

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in several hundred million contracted cases of coronavirus disease 2019 (COVID-19) and a global pandemic. In some of these cases, previous neurological diseases, such as Alzheimer’s disease (AD), seemed to progress much more rapidly after the COVID-19 infection. Thus, we became interested in studying the effects of SARS-CoV-2 infection on prior neurological disease progressions.

To modulate this condition, we used Drosophila melanogaster as a genetic model system. We had previously developed the Alzheimer’s Disease Fly Model with expression of human amyloid beta 42 (Aβ42) peptide, which is responsible for extracellular Aβ-42 …

A Mini Review On Rodent Models Of Autism Spectrum Disorder (Asd), Rachel Zeller

Research from the Berry Summer Thesis Institute, 2025

Autism spectrum disorder (ASD) is a neurodevelopmental disorder typically diagnosed at a young age. ASD symptoms include deficits in social behavior, repetitive and restrictive behaviors, anxiety, as well as alterations in sensory gating and sensitivity, learning, memory, and attention performance. Since ASD emerges from a combination of genetic and environmental factors, clinical treatment of these conditions presents with challenges. Being able to model behavioral and neurobiological aspects of this disorder at the preclinical level using rodents allows for further investigation of the pathophysiological basis of this disorder. This mini review will focus on selected genetic and pharmacological rodent models of …

Co-Culture 3d Model For Breast Cancer, Anh Duc Nguyen

Research from the Berry Summer Thesis Institute, 2025

The ability to replicate the tumor microenvironment using 3D models have allowed researchers to study the tumors in vitro closer to their in vivo counterparts without the drawbacks of those models. The 3D co-culture model is an improved version of the 3D monoculture model, capable of replicating the tumor microenvironment, letting researchers study cancer response mechanism, tumor metastases, drug resistance, simulate cell-cell interactions, etc., in breast cancer. The models can be classified into four classes based on their formation method and content, all of which have different advantages and disadvantages.

Evaluating The Environmental Determinants Of Tadpole Mouthpart Deformities, Nicholas J. Canfield

Research from the Berry Summer Thesis Institute, 2025

Amphibians are among the most threatened group of animals on the planet, with over 40% of living species facing an extinction risk. These organisms are highly sensitive to environmental change due to their highly permeable skin and complex life cycle that exposes them to stressors in both aquatic and terrestrial ecosystems. Amphibian populations that are closely monitored can serve as valuable bioindicators of environmental health because they typically respond rapidly to habitat degradation, decreased water quality, and changes in climate. Tadpoles in particular may act as a “canary in a coal mine” for aquatic ecosystems because they easily develop anatomical …

An Investigation Of Hydro-Morphological Changes At The Estuarine Outlet Of Kitchener Drain, Northern Coast Of Egypt, Nada Mansour, Karim Nassar, Mahmoud El-Gamal, Tharwat Sarhan

Mansoura Engineering Journal

In recent years, sedimentation and coastline erosion have occurred in the Kitchener Drain, where its outflow meets the Mediterranean Sea. Several measures have been taken to mitigate the impact of these problems. Excavation continues toward the drain's outlet, and there have been multiple stages of hard protection work, such as groins along the drain's eastern and western banks. What would happen if the working near the drain was kept, where accretion and erosion are most severe. The Coastal Modelling System (CMS) was used to find it out. The two-dimensional hydrodynamic circulation model known as the CMS is outfitted with modules …

Novel Nano-Composite Materials (Nncms) With The Designations J1, J2, And J3 For Removal Several Harmful Ions, Mohammed K. Al-Doseri, Safaa. R. Fouda, Mohamed Mossad, Mahmoud H. Mahmoud

Mansoura Engineering Journal

The most toxic material to the environment is heavy metals. remove heavy metals from wastewater is done by adsorption. Many papers have been done using different materials to take off toxic dangerous ions from wastewater. Noval Nano-composites material (NNCM)as designated as J1, J2, and J3 the most used adsorbents in this study. To conduct the experiments, synthetic wastewater was generated in the lab. Batch experiments were conducted to create the best conditions for removing these ions from the wastewater. The optimum conditions obtained were 90 min optimum contact time, and pH equal seven, optimal NNCM dose was 0.5 g/L achieving …

Performance Analysis Of Computational Methods For Predicting Protein Function In Rare Diseases, Aichetou Mohamed Sidiya, Hanin Alzaher, Razan Almahdi, Tayeb Brahimi

Effat Undergraduate Research Journal

Protein function prediction is crucial for understanding the underlying mechanisms of rare diseases. With the increasing availability of computational methods including machine learning-based approaches, network-based methods, and sequence-based methods, predicting protein functions has become more accessible. However, it is not clear which of these methods performs better or how they compare to each other in terms of accuracy, efficiency, and scalability. In this study, we evaluate several computational methods for predicting protein functions in rare diseases using key performance indicators (KPIs). We analyze the strengths and weaknesses of each method and provide recommendations for researchers and clinicians interested in using …

The Effects Of Exercise Training In A Novel Full-Body Compression Garment On Anaerobic Performance In Healthy Men, Benjamin W. Cunningham, Mikayla M. Reese, Jesse M. Jansen, Benjamin S. Minier, Curtis A. Cornell, Faith C. Benedict, Joshua T. Mayne, Justin A. O'Dell, Gabriel M. Lysak, James R. Sackett

International Journal of Exercise Science

International Journal of Exercise Science 18(8): 836-851, 2025. Although acutely donning compression garments improves several markers of athletic performance, the effects of training in compression garments remains largely unexplored. Thus, this study aimed to determine the effects of exercise training while donning a novel full-body compression garment on multiple measures of anaerobic performance. Sixteen sedentary males (age: 21±3 y; BMI: 25±3 kg/m²) completed 4 weeks of training with (CG; n=8) or without (CON; n=8) a novel full-body compression garment. Subjects performed a 40m sprint (time and velocity), a 5-repetition maximum barbell back squat (barbell weight and serratus anterior …

Change In Free-Living Daily Steps Does Not Affect Vo2max Adaptation In Response To A Supervised Aerobic Walking Program In Females Ages 18-45, Catherine L. Jarrett, Brandon J. Sawyer, Wesley Tucker, Dharini M. Bhammar, Justin R. Ryder, Siddhartha Angadi, Glenn A. Gaesser

International Journal of Exercise Science

International Journal of Exercise Science 18(5): 852-863, 2025. We hypothesized that an increase in nonexercise physical activity (NEPA), assessed by daily steps outside of steps accrued during supervised exercise training sessions, would be positively correlated with the change in VO_2max. Females ages 18-45 yr (n = 44; 30 ± 7 yr; 67.7 ± 18.3 kg; 24.9 ± 6.4 kg/m²) completed 36 supervised training sessions on a motorized treadmill (3 sessions/week, 30 min/session) over 12 weeks, at 70% VO_2max (80% max heart rate). VO_2max was assessed at baseline, 4, 8, and 12 weeks, and …

Advancing Rfid Systems: From Head Orientation To Robotic Localization Using Passive Tags, Guilherme Ricardo Mendes Da Silva Barreto De Figueiredo

Doctoral Dissertations

No abstract provided.

Centrosomal And Non-Centrosomal Microtubule Networks Coordinate To Drive Nuclear Dynamics In Developing Epithelium, Rashmi Budhathoki

Electronic Theses and Dissertations

The morphogenesis of developing tissues relies on extensive cellular rearrangements in shape, position, and identity. A key process in reshaping tissues is cell intercalation-driven elongation, where epithelial cells align and intercalate along a common axis. Typically, analyses focus on how peripheral cortical forces influence cell shape changes. Less attention is given to how inhomogeneities in internal structures, particularly the nucleus, impact cell shaping. Here, we examine how pulsed contractile and extension dynamics interact with the nucleus in elongating Drosophila embryos. Our data show that tightly packed nuclei in apical layers hinder tissue remodeling/oscillatory behaviors. We identify two mechanisms for resolving …

Role Of Nucleic Acids As Chaperones In Protein Folding, Zijue Huang

Electronic Theses and Dissertations

Many proteins have slow folding times in vitro that are physiologically untenable. To combat this challenge, ATP-dependent chaperonins are thought to possess the unique ability to catalyze protein folding. Performing quantitative model selection using protein folding and unfolding data, we here show that short nucleic acids containing Gquadruplex (G4) structure can also catalyze protein folding. Performing the experiments as a function of temperature demonstrates that the G4 reshapes the underlying driving forces of protein folding. To understand the structural basis of this catalytic activity, we introduce NMR method to solve the structures, at base-level resolution, of a multiconformer G4 with …

Predicting Regional Cerebral Blood Flow Using Voxel-Wise Resting-State Functional Mri, Hongjie Ke, Bhim M Adhikari, Yezhi Pan, David B Keator, Daniel Amen, Si Gao, Yizhou Ma, Paul M Thompson, Neda Jahanshad, Jessica A Turner, Theo G M Van Erp, Mohammed R Milad, Jair C Soares, Vince D Calhoun, Juergen Dukart, L Elliot Hong, Tianzhou Ma, Peter Kochunov

Faculty, Staff and Student Publications

Background: Regional cerebral blood flow (rCBF) is a putative biomarker for neuropsychiatric disorders, including major depressive disorder (MDD).

Methods: Here, we show that rCBF can be predicted from resting-state functional MRI (rsfMRI) at the voxel level while correcting for partial volume averaging (PVA) artifacts. Cortical patterns of MDD-related CBF differences decoded from rsfMRI using a PVA-corrected approach showed excellent agreement with CBF measured using single-photon emission computed tomography (SPECT) and arterial spin labeling (ASL). A support vector machine algorithm was trained to decode cortical voxel-wise CBF from temporal and power-spectral features of voxel-level rsfMRI time series while accounting for PVA. …

Does Green Stem Photosynthesis Affect Plant Drought Tolerance And Recovery In Avocado?, Nadia A. Valverdi, Paula Guzmán-Delgado, Gregory R. Goldsmith, Eleinis Ávila-Lovera

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Woody plants with green stems may have advantages over non-green-stemmed plants in that extra photosynthetic carbon gain has the potential to improve plant drought tolerance and aid drought recovery. However, most studies relating to green stem photosynthesis and drought tolerance have been conducted on non-horticultural plants under natural growing conditions. We investigated whether avocado green stem photosynthesis enhances drought tolerance and recovery. We applied light exclusion and drought treatments to 3-year-old potted trees of cultivars ‘Hass’ and ‘Fuerte’. Measurements of soil moisture, midday stem water potential, stem photosynthesis, bark chlorophyll concentration, concentration of sugars + starch and stem hydraulic conductivity …