Digital Commons Network^™

In Memoriam: Holmes Rolston Iii, Editorial Board

The International Journal of Ecopsychology (IJE)

No abstract provided.

Life Goes On, But Better, Editorial Board

The International Journal of Ecopsychology (IJE)

" … During a solar flare* An exchange between two telegraph operators during the Carrington Event, the most intense solar flare recorded to date (September 2, 1859. Boston Evening Traveler)."

Structural Analysis Of Pseudomonas Phage Dev Virion-Associated Rna Polymerase (Gp71), James Scherer

All ETDs from UAB

DEV is a Pseudomonas aeruginosa bacteriophage part of a newly reclassified genus called Schitoviridae. This group of bacteriophages is also referred to as “N4-like” phages, after the prototypical Escherichia coli phage N4, originally isolated from sewage water in 19661. N4, and other phages in the group, contain a large, virion-associated RNA polymerase (vRNAP). This vRNAP is vital to the proliferation of the phage, as it performs the transcription of the early gene products and potentially acts as a motor that helps eject the viral genome into the host bacteria. In DEV, the vRNAP is also known as gene product 71 …

Resolution Of Physics And Deep Learning-Based Protein Engineering Filters: A Case Study With A Lipase For Industrial Substrate Hydrolysis, Spencer Gardiner, Peter Dollinger, Filip Kovacic, Jörge Pietruszka, Daniel Ess, Karl-Erich Jaeger, Gunnar F. Schröder, Dennis Della Corte

Faculty Publications

Computational enzyme design remains a powerful yet imperfect tool for optimizing biocatalysts, especially when targeting non-natural substrates. Using design tools we investigated Pseudomonas aeruginosa LipA, a lipase with a flexible lid domain crucial for substrate binding and turnover, aiming to enhance its hydrolysis of the industrially relevant substrate Roche ester. We generated an initial set of single-point mutations based on structural proximity to the active site and evaluated their effects using a computational pipeline integrating molecular dynamics (MD) simulations, density functional theory (DFT) calculations, and ensemble-based energy scoring. While we identified several active variants, attempts to rank them by activity …

The Benefits Of Combining Center-Based And Home-Based Care For Preschool Children, Savannah Christensen

Family Perspectives

Abstract: Research shows that the quality of care children receive in early childhood—whether from a parent, relative, or formal child care provider—significantly influences their cognitive, behavioral, and emotional development. This article analyzes several peer-reviewed sources to examine how different caregiving environments impact development and how these effects are moderated by the quality of care and the home environment. It also addresses how socioeconomic status can shape the quality of care children receive and the long-term outcomes associated with each caregiving type. While parents are typically seen as the ideal caregivers, children in nonparental care, such as with relatives or in …

Mechanistic Rationale For Toxic Aerosol Formation From Vaping And Dabbing With A Focus On Ketene Formation From Semi-Synthetic Cannabinoids, Kaelas Ryan Munger

Dissertations and Theses

Cannabis vaping is a relatively new route of administration that is increasingly common among youth and young adults. Cannabis vaping has been associated with cases of acute lung injury, especially among youth, and most often involves the heating and aerosolization of high-potency products having cannabinoid concentrations of ~ 50 % - 98 % w/w. Proponents argue that vaping is safer than smoking due to the characteristically lower temperatures and fewer plant materials. However, the extreme cannabinoid concentrations, along with non-natural formulations having undisclosed additives, require studies of the health effects of these products. Despite the popularity of cannabis concentrate vaping, …

Lineage-Associated Zinc Metalloprotease B And Its Impact On Cardiac Damage Elicited During Invasive Pneumococcal Disease, Jennifer Nichelle Luck

All ETDs from UAB

During invasive disease, certain strains of Streptococcus pneumoniae (Spn) can invade the myocardium, damaging cardiomyocytes and predisposing patients to life-threatening cardiac complications. To identify genetic loci involved in pneumococcal cardio-virulence, we performed a bacterial genome-wide association study using 825 genomes corresponding to 17 distinct Spn lineages associated with varying rates of cardiac complications during hospitalization for pneumonia. This led to the identification of an allele of zmpB, the gene encoding Zinc metalloprotease B (ZmpB). Infection of mice with a ZmpB deficient mutant, i.e., TIGR4ΔzmpB, found that ZmpB was required to form foci of infection in the heart, i.e., cardiac microlesions. …

Structural Basis For Promoter Recognition By Pseudomonas Phage Dev Virion Associated Rna Polymerase, Brittney Bird

All ETDs from UAB

Bacteriophage DEV, a member of the Schitoviridae family, encodes a large virion-associated RNA polymerase (vRNAP) and shows significant potential for use in phage therapy. However, many aspects of DEV’s biology remain poorly understood, especially how it regulates transcription once inside the host. Recent work in our lab suggests that gene product 71 (gp71) functions as a DNA-dependent vRNAP. Analogous to the vRNAP of coliphage N4, gp71 likely initiates transcription by recognizing single-stranded DNA templates that contain early gene hairpin promoters. Based on this, my working hypothesis is that specific interactions between gp71 and the DEV early promoters PE1 and PE5 …

Effect Of Fiber Structure Heterogeneity On The Estimation Of Material Parameters For Cardiac Scar Tissue Mechanics, Desmond Maximilian Flanagan

All ETDs from UAB

Over one million Americans suffer from myocardial infarction (MI) per year. After MI, the heart muscle is replaced by scar, whose mechanical properties play a critical role in outcomes for surviving patients. Previously, Caggiano et al. induced MI in rats, and ex-tracted the scar tissue samples for microscopy and mechanical testing. Building on this, we investigate the effect of incorporating microscopy-derived fiber heterogeneity on the estimation of stress and material parameters. We studied the effect of fiber orientation heterogeneity on the mechanical characteriza-tion of scar tissues using finite element models (FEM) that replicated biaxial tests. We used three constitutive models—Mooney-Rivlin, …

Optimizing Plant Nutrient Uptake: Cost Function Sensitivity Analysis Of The Fun Model, Gabriel Alpay, Joshua B. Fisher, Renato K. Braghiere, Edward R. Brzostek, Gabriella R. Dauber, Kara Allen, Rosemary A. Fisher

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

This study explores the cost functions of the Fixation & Uptake of Nutrients (FUN) model, which aims to optimize the amount of carbon used when plants acquire their necessary nutrients from the soil to maximize nitrogen (N) and phosphorus (P) uptake while minimizing the carbon cost. Specifically, we aimed to quantify the sensitivity of FUN outputs to the parameters belonging to the cost of nitrogen and phosphorus uptake functions by arbuscular mycorrhizal and ectomycorrhizal fungi. We present three dimensions of sensitivity analysis: (1) adjusting all parameters at the same time; (2) keeping one parameter constant while varying the other; and, …

Creating Sustainable School And Home Gardens: Using Citizen Science, Kaitlin U. Campbell, Rita Hagevik, Kathy Cabe Trundle

All Current Publications

Citizen science, also called community-based science or participatory science, provides a way for anyone to gather data, along with scientists, around a scientific question or phenomenon. Citizen science offers immense value to both the general public and scientists. This fact sheet provides resources to connect readers to citizen science projects.

The Impact Of Public Relations Strategies On The Effectiveness Of Epidemic Management In Jordan: A Case Study Of Covid-19, Hazem Jamil Al-Rahahleh

Middle East Journal of Communication Studies

This study aimed to explore the impact of public relations strategies on the effectiveness of epidemic management in Jordan, using the COVID-19 pandemic as a case study. The study employed the descriptive-analytical method, which is based on the systematic description and interpretation of social and media phenomena. The findings revealed that public relations play a pivotal strategic role in managing health crises by building public trust, preparing communication plans, and formulating awareness messages in coordination with relevant authorities. The study recommended the need to enhance the training of public relations personnel in managing communication during health crises, to continue diversifying …

Analyzing The Role Of A Dual-Function Diguanylate Cyclase / Phosphodiesterase For Attachment And Motility In Agrobacterium Tumefaciens, Priya Aryal

Theses and Dissertations

Cyclic diguanylate monophosphate (c-di-GMP) is a second messenger that is responsible for attachment and motility in many prokaryotic systems and controls the signaling pathway for the motile to sessile transition in many bacteria. Many c-di-GMP-metabolizing proteins are diguanylate cyclases (DGCs), responsible for the synthesis of c-di-GMP and characterized by a c-di-GMP synthesizing domain, e.g., GGDEF domain. Other c-di-GMP-metabolizing proteins contain c-di-GMP degradative domains, e.g., EAL, characterized by phosphodiesterase activity (PDE). In Agrobacterium tumefaciens, out of 31 predicted proteins regulating the c-di-GMP level, this project focuses on the predicted dual-function DGC/PDE, DcpB. We hypothesized that DcpB plays a role in the …

09.08.2025 Ored Connect, Liz Williamson

ORED Newsletter

• Researcher training opportunities
• Project to increase PhD student success
• ORED online training opportunities

Data From: Nek4 Suppresses Cell Proliferation In Bt20 Triple-Negative Breast Cancer Cells By Diminishing Expression Of Cell Cycle Genes, While Its Depletion Mitigates Proliferation In Other Cell Lines, Amanda Ashley

Chemistry & Biochemistry: Datasets

No abstract provided.

The Next Frontier In The Study Of Noncovalent Bonding: Transition Metals, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

As work continues unabated in the study of noncovalent bonding, particularly σ-hole bonds, new challenges have emerged as the participation of transition metals in interactions of this sort is fast becoming appreciated. While there are certain similarities with the halogen, chalcogen, etc, bonds, in which the main group elements participate, there are certain unique properties of these metal atoms that must be analyzed before a complete understanding can be attained. As one example, these atoms tend to act simultaneously as both electron donors and acceptors, a synergistic action that amplifies the overall bond strength. Ideas are expressed in this paper …

Lewy Body Dementia Promotion By Air Pollutants, Xiaodi Zhang, Haiqing Liu, Xiao Wu, Longgang Jia, Kundlik Gadhave, Lena Wang, Kevin Zhang, Hanyu Li, Rong Chen, Ramhari Kumbhar, Ning Wang, Chantelle E Terrillion, Bong Gu Kang, Bin Bai, Minhan Park, Ma Cristine Faye Denna, Shu Zhang, Wenqiang Zheng, Denghui Ye, Xiaoli Rong, Liu Yang, Lili Niu, Han Seok Ko, Weiyi Peng, Lingtao Jin, Mingyao Ying, Liana S Rosenthal, David W Nauen, Alex Pantelyat, Mahima Kaur, Kezia Irene, Liuhua Shi, Rahel Feleke, Sonia García-Ruiz, Mina Ryten, Valina L Dawson, Francesca Dominici, Rodney J Weber, Xuan Zhang, Pengfei Liu, Ted M Dawson, Shizhong Han, Xiaobo Mao

Faculty, Staff and Student Publications

Evidence links air pollution to dementia, yet its role in Lewy body dementia (LBD) remains unclear. Here we showed in a cohort of 56.5 million individuals across the U.S. that PM2.5 exposure raises LBD risk. Mechanistically, we found PM2.5 exposure led to brain atrophy in wild-type mice, an effect not seen in α-synuclein (αSyn)-deficient mice. PM2.5 exposure generated a highly pathogenic αSyn strain, PM-PFF, with enhanced proteinase K-resistance and neurotoxicity, resembling αSyn LBD strains. PM2.5 samples from China, the U.S., and Europe consistently induced proteinase-resistant αSyn strains and in vivo pathology. Transcriptomic analyses revealed shared responses between PM2.5-exposed mice and …

Leslie Combs And His Life In Chaos, Stanley C. Krippner

Journal of Conscious Evolution

The purpose of this contribution is to review what Leslie Combs described as his “Life in Chaos” and our interaction over the years. Beginning with our meeting at the founding of the Society for Chaos Theory in Psychology in 1991, this tribute traces his journey from early educational challenges to his emergence as a pioneering theorist in consciousness studies. It highlights our decades-long collaboration in the study of dreams, creativity, and the evolution of consciousness, celebrating his enduring legacy as both a brilliant psychologist and a cherished friend.

Keywords: Allan Leslie Combs, Stanley Krippner, chaos theory, systems theory, consciousness …

Effect Of Ipomoeassin F On The Synthesis Of Membrane And Secretory Proteins In Triple-Negative Breast Cancer Cells, Brihget Sicairos, Jianhong Zhou, Zhijian Hu, Qingyang Zhang, Wei Q. Shi, Yuchun Du

Biological Sciences Faculty Publications and Presentations

Ipomoeassin F (Ipom-F) is a natural compound that exhibits a potent cytotoxic effect on triple-negative breast cancer (TNBC) cells. The mechanism underlying this selective potency remains unclear. To elucidate this mechanism, we analyzed the proteome profiles of the TNBC MDA-MB-231 cells after exposure to Ipom-F at different time points and increasing doses using a quantitative proteomic method. Our proteomic data demonstrate that the major effect of Ipom-F on MDA-MB-231 cells is the inhibition of membrane and secreted protein expression. These findings align with the recently uncovered molecular mechanism of action of Ipom-F, which binds to Sec61-alpha and inhibits the cotranslational …

Examining The Role Of The M1 Motif Of Abcr1 Srna In Agrobacterium Tumefaciens, Daniel Arango-Cardona

Theses and Dissertations

Agrobacterium tumefaciens is a gram-negative alphaproteobacterium that is one of the causative agents of crown gall tumors on plants. Its ability to transform plants using its T-DNA has been studied to improve plant-mediated transformation. sRNAs are small regulatory RNAs that play a role in gene expression in a variety of organisms and bind to target proteins or mRNAs. A. tumefaciens contains two sibling sRNAs, called AbcR1 and AbcR2, which are conserved among alphaproteobacteria. A. tumefaciens AbcR1 and AbcR2 are closely related, exhibiting 69% sequence identity, similar secondary and tertiary structure, and a conserved motif, M2, believed to direct target interactions. …

09.02.2025 Ored Connect, Liz Williamson

ORED Newsletter

• NIH Specific Aims Statement RED Talk
• NSF Research Security Training 

Resource Assessment Report No. 5: West Coast Deep Sea Crustacean Resource 2024 Assessment, Emma-Jade Tuffley, Simon De Lestang

Resource Assessment Reports

The West Coast Deep Sea Crustacean resource consists of crystal crab (snow) (Chaceon albus), champagne crab (spiny) (Hypothalassia acerba) and giant crab (Pseudocarcinus gigas). The resource is mainly accessed by the commercial West Coast Deep Sea Crustacean Managed Fishery (WCDSCMF), which primarily targets crystal crabs. The West Coast Rock Lobster Managed Fishery (WCRLMF) also retains a small amount of champagne crabs as byproduct of deep-water rock lobster fishing. The WCDSCMF is a pot-based fishery using baited pots operated in a long-line formation in shelf edge waters ( > 150 m in depth) off the West …

Resource Assessment Report No. 3: Gascoyne Demersal Scalefish Resource 2024 Assessment, Emily A. Fisher, Rachel Marks, Sybrand A. Hesp, Ainslie Denham, Gary Jackson, David V. Fairclough

Resource Assessment Reports

The Gascoyne Demersal Scalefish Resource (GDSR) comprises over 80 species inhabiting inshore (20-250 m deep) and offshore ( > 250 m deep) waters in the Gascoyne Coast Bioregion (GCB; south of Onslow to north of Kalbarri). The GDSR is primarily targeted by commercial, charter and recreational boat-based line fishers. Snapper and Goldband Snapper are the indicator species selected for monitoring and assessing the status of the inshore suite of the GDSR, while Ruby Snapper and Greybanded Grouper are the indicators for the offshore suite.

Periodic assessments of GDSR indicator species demonstrated that historical fishing of Snapper led to stocks being below …

Resource Assessment Report No. 2: West Coast Demersal Scalefish Resource 2025 Assessment, Emily A. Fisher, David V. Fairclough, Elaine Lek, Jeremy Briggs, Sybrand Alex Hesp, Ainslie Denham

Resource Assessment Reports

The West Coast Demersal Scalefish Resource (WCDSR) comprises over 100 species inhabiting inshore (20-250 m deep) and offshore ( > 250 m deep) waters of the West Coast Bioregion (WCB; north of Kalbarri to east of Augusta). The WCDSR is primarily targeted by commercial, charter and recreational boat-based line fishers, including the commercial West Coast Demersal Scalefish (Interim) Managed Fishery (WCDSIMF). Indicator species selected for monitoring and assessing the status of the inshore suite of the WCDSR include Snapper, WA Dhufish and Baldchin Groper, while indicators for the offshore suite include Hapuku, Bass Groper and Blue-eye Trevalla.

The WCDSR is more …

Gene Expression Of Anthocyanin Pigments In The California Native Plant Leptosiphon Parviflorus: Interactions Between Flower Color Morphology And Abiotic Stressors, Weston Gonor

Master's Theses

For plants to survive in harsh conditions imposed by abiotic stressors, they must develop mechanisms of adaptation. One of the common types of adaptation seen in plants is the production of anthocyanin pigments, which have been shown to protect plants from UV radiation, metabolic stress, and drought. In this study, we used the flower color polymorphic species Leptosiphon parviflorus to investigate the role of anthocyanin pigments in protecting plants from abiotic stress. To accomplish this, RNA samples were taken from flower, leaf and root tissue of different flower color morphs of Leptosiphon parviflorus (Polemoniaceae) grown in high magnesium and water …

Alpine Plants And Climate Change: Tracking Community Shifts In Yosemite National, Brooke L. Wallasch

Master's Theses

As climate change progresses, alpine plant communities are predicted to shift upslope as they track temperature over time. Relative to lowland environments, alpine areas are experiencing a faster rate of temperature change due to a phenomenon referred to as elevation-dependent warming. A common approach for tracking plant communities shifts over time, is to conduct resurveys of the same area at several time points, as the Global Observational Research Initiative in Alpine Environments (GLORIA) has done on mountain summits around the world since 2001. In 2011-2013, GLORIA developed a supplemental survey method whereby belt transects were established downslope of summits in …

Adaptive Water Body Detection: Integrating Deep Learning, Normalised Difference Water Index, And Vector Data For Farm Dam Water Monitoring With Omniwatermask, Nicholas J. Wright, John M A Duncan, Nik Callow, Sally E. Thompson, Richard J. George

Natural Resources Research Articles

Farm dams are important water security features supporting both agricultural production and the natural environment. In Australia alone, over two million farm dams provide the water resources underpinning rural and regional primary industries with an annual export value of $80 billion. However, monitoring these water bodies to understand water security and vulnerability is challenging, primarily because of their large quantity, size and highly variable spectral signatures. These characteristics result in difficulty determining thresholds for index-based water detection methods and add to the difficulty of creating adequate training datasets for deep learning methods. We present an adaptive approach named OmniWaterMask (OWM) …

Root Exudates: The Rhizospheric Frontier For Advancing Sustainable Plant Protection, Muhammad Rahil Afzal, Misbah Naz, Youbo Yu, Lisha Yan, Peiyi Wang, Janaki Mohotti, Gefei Hao, Jing-Jiang Zhou, Zhou Chen, Libo Zhang, Qian Wang

Faculty Publications

Root exudates (REs), a diverse array of bioactive metabolites secreted by plant roots in response to environmental stimuli, serve as key mediators of rhizosphere ecology and plant defense responses, offering a promising avenue for sustainable pest management and eco-friendly plant protection. While earlier reviews primarily focus on root exudates in the context of general rhizosphere dynamics and plant-microbial interactions, critical knowledge gaps persist in REs-plant-pest tripartite interactions, the mechanistic basis of REs-mediated plant defense, and their practical integration with integrated pest management (IPM) frameworks. This review provides a synthesis of the latest literature on the biochemical diversity and functions of …

Ibi-Dt: A Novel Approach Combining Individualized Bayesian Inference And Decision Tree For Identifying Cancer Drivers And Their Interactions, Md Asad Rahman, Gregory F. Cooper, Jinying Zhao, Xinghua Lu, Jinling Liu

Engineering Management and Systems Engineering Faculty Research & Creative Works

Cancer is mainly caused by a relatively small portion of somatic genome alterations (SGAs), called cancer drivers. Despite success in identifying a good number of cancer drivers, many more remain to be discovered to explain various cancers. Moreover, limited tools are available to identify potential interactions among cancer drivers for a better understanding of oncogenesis. To tackle these challenges, we have developed a novel approach called individualized Bayesian inference using a decision tree (IBI-DT). IBI-DT recognizes the genetic heterogeneity among cancer patients, where different individuals or patient subgroups of distinct genomic makeup may have different drivers. IBI-DT works by constructing …

Resource Assessment Report No. 4: North Coast Demersal Scalefish Resource - Kimberley 2025 Assessment, Fabian Trinnie, Rubie Evans-Powell, Ainslie Denham, Sybrand A. Hesp, Corey Wakefield, Craig L. Skepper, Brett Crisafulli, Stephen J. Newman

Resource Assessment Reports

The North Coast Demersal Scalefish Resource (NCDSR) comprises ecological suites of tropical demersal fish species that occur predominantly in inshore waters (20–250 m deep) and offshore waters ( > 250 m deep) of the North Coast Bioregion (NCB). More than 60 demersal species are landed by fisheries operating in the Kimberley and Pilbara regions of the NCB each year, including high-value snappers (Lutjanidae), groupers (Epinephelidae), and emperors (Lethrinidae). As outlined in the NCDSR Harvest Strategy (DPIRD, 2017), the Kimberley resource is currently monitored through annual reviews of total removals and catch rate trends of indicator species, as well as periodic (every …