Digital Commons Network^™

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 …

Binding Of A [2fe-2s] Cluster Drives Dimerization Of Ferric Uptake Regulator (Fur) In Escherichia Coli, Fatemeh Najafi, Aidan G. Purcell, Finbar H. Homes, Huangen Ding

Faculty Publications

The ferric uptake regulator (Fur) is a global transcription factor that reversibly binds an iron-sulfur [2Fe-2S] cluster via the cysteine residues (site 3) in response to elevation of intracellular free Fe content in Escherichia coli. Here, we report that when E. coli Fur is expressed in E. coli cells grown in M9 medium supplemented with Fe or zinc (Zn), purified Fur binds a [2Fe-2S] cluster or Zn(II), respectively. While apo-form Fur is a monomer and has no DNA-binding activity, both the [2Fe-2S] cluster-bound Fur and the Zn(II)-bound Fur are homodimers and have a similar binding activity for the DNA sequence …

Magnetic Nanoparticles Tethered With Zn–Dpa For The Removal Of Bacteria From Red Blood Cell Suspension, Tochukwu P. Okonkwo, Rajendra P. Gautam, Jacob B. Limburg, Breckin L. Forstrom, Bowen J. Houser, Aaron Rappleyea, Tyler P. Green, Joseph P. Talley, Alexander D. Daum, Stacey J. Smith, Karine Chesnel, William G. Pitt, Roger G. Harrison

Faculty Publications

Bacterial infections continue to drive the need for more effective and rapid methods for bacterial analysis. To address this, magnetic nanoparticles (MNPs) have emerged as promising tools, especially when their surfaces are modified with bacteria binders. The bis-zinc–dipicolylamine (Zn–DPA) complex is known for its broad affinity to bacteria. We have synthesized MNPs via a thermal decomposition method, encapsulated them in silica, modified their surface with Zn–DPA, and tested their ability to remove bacteria. The MNPs retain their superparamagnetic properties and crystallite structure after being encapsulated. The MNPs coated with silica and Zn–DPA effectively bind and remove both Gram-positive and Gram-negative …

Time Series Changes Of Surficial Sediments On Eastern Ship Shoal, Louisiana Shelf, Adam Gartelman, Kehui Xu, Brian J. Roberts, David Samuel Johnson, Madison Liotta

Faculty Publications

Ship Shoal, a large transgressive sand body on the Louisiana continental shelf, is a critical sediment source for coastal restoration. This study evaluates spatial and temporal variability in sediment grain size, percents organic matter (%OM), and carbonate (%CO3) across the shoal crest (REF), Caminada Dredge Pit (CAM), and Terrebonne Dredge Pit (TER). Sediment samples were collected between 2020 and 2022 using box cores and analyzed for grain size, %OM, and %CO3, with temporal and spatial patterns assessed through statistical comparisons, correlation analyses, and random forest regression models. Results show that dredged areas act as sinks for fine-grained, organic-rich sediments, with …

A Comparison Of Characteristics Of Infilling Sediments In Three Mud-Capped Dredge Pits On The Louisiana Continental Shelf, Wenqiang Zhang, Kehui Xu, Chaochen Jia, Adam Gartelman, Omar Alawneh, Navid Jafari, Colin Herke, Madison Liotta, Samuel J. Bentley

Faculty Publications

Due to high sedimentation rate up to ~1 m/year, mud-capped dredge pits (MCDP) are often considered natural laboratories for studying sedimentary processes, slope stability and the impacts of dredging activities on marine environments. Although many studies have been performed on the Louisiana shelf, there is a lack of high spatial resolution research covering the eastern, central and western Louisiana shelf to comprehensively investigate sediment infilling. Eighteen vibracores were collected from the Peveto Channel dredge pit (PC), Raccoon Island dredge pit (RI) and Sandy Point dredge pit (SP), and more than 1300 samples were analyzed to study the spatial variation in …

Recovery Of Benthic Macroinfauna Six Years After Dredging, David Samuel Johnson, Manisha Pant, Andrew Nemeth, Emelie Foster, Adam Gartelman, Stacy Calhoun-Grosch, Kehui Xu, Brian J. Roberts, James Nelson

Faculty Publications

In soft-sediment communities, benthic macroinfauna can recover quickly (sometimes < 1 year) from dredging. However, it’s unclear how recovery is influenced if dredging dramatically changes abiotic factors. We determined recovery of benthic macroinfauna from dredging on a sandy shoal (Ship Shoal, Louisiana, USA), six years after dredging. Because the dredged area infilled with mud instead of sand and changed local abiotic conditions, we hypothesized that the benthic community had not recovered. Our results support this hypothesis. Although the dredged community had, on average, 160% greater density and 170% greater macroinfaunal biomass than the reference community, these increases were driven by the opportunistic and seasonally variable dwarf clam, Mulinia lateralis. Community structure differed starkly between the regions. Haustoriid amphipods and amphioxus (Branchiostoma floridae) dominated the reference community. However, these taxa were largely absent from the dredged community, which was dominated by opportunistic species such as M. lateralis and the fringe-gilled mudworm Paraprionospio pinnata. Community differences were largely driven by bottom-water dissolved oxygen and sediment grain size. Our results suggest that the dredged areas are still in a transitional phase of recovery after six years – dominated by opportunistic, hypoxia-tolerant species. Our results suggest that abiotic factors such as grain size and hypoxia are important in structuring benthic communities and their recovery rates. Thus, to achieve faster recovery of the biological community, dredging should be conducted in a way that minimizes long-term impacts on abiotic conditions.

A Test Of The Abundant-Center Hypothesis For Stream Fishes, Matthew L.W. Zink, Brandon K. Peoples, Julian D. Olden, Lily M. Thompson, William K. Annis, Stephen R. Midway

Faculty Publications

The abundant-center hypothesis (ACH) provides a conceptual model for predicting range-wide distributions of species abundance, suggesting that abundance peaks in the center of the geographic range and declines towards range edges. Empirical studies testing the ACH and its subsequent derivations predominantly occurred in terrestrial systems and reported mixed support. Moreover, none of these models consider the possibility of multiple geographic areas of elevated abundance (which we refer to as ‘abundant cores'). Naturally dispersal limited species may exhibit multiple abundant cores, requiring refinement of the ACH. We used fish species abundances from 29 206 community monitoring surveys and weighted geospatial kernel …

Dsm-5 Based Algorithms For The Autism Diagnostic Interview-Revised For Children Ages 4–17 Years, Linnea A. Lampinen, Shuting Zheng, Lindsay Olson, Vanessa H. Bal, Audrey E. Thurm, Amy N. Esler, Stephen M. Kanne, So Hyun Kim, Catherine Lord, China Pareneau, Kerri P. Nowell, Jane E. Roberts, Nicole Takahashi, Somer L. Bishop

Faculty Publications

Background: The Autism Diagnostic Interview, Revised (ADI-R) is a caregiver interview that is widely used as part ofthe diagnostic assessment for Autism Spectrum Disorder (ASD). Few large-scale studies have reported the sensitivityand specificity of the ADI-R algorithms, which are based on DSM-IV Autistic Disorder criteria. Kim and Lord (Journalof Autism and Developmental Disorders, 2012, 42, 82) developed revised DSM-5-based toddler algorithms, which areonly applicable to children under 4 years. The current study developed DSM-5-based algorithms for children ages4–17 years and examined their performance compared to clinical diagnosis and to the original DSM-IV-basedalgorithms. Methods: Participants included 2,905 cases (2,144 ASD, 761 …

Artificial Intelligence In Head And Neck Cancer: Towards Precision Medicine, Jacob Hagen, Logan Hornung, William Barham, Supratik Mukhopadhyay, Adam Bess, Kevin Contrera, Devraj Basu, Vlad Sandulache, Guillaume Spielmann, Sagar Kansara

Faculty Publications

Over the past 20 years, the capabilities of artificial intelligence (AI) have gained significant interest. While AI has been implemented to various degrees in several disciplines, its unique applications in head and neck cancer (HNC) remain underdeveloped. This narrative review examines the existing body of literature regarding the use of AI in HNC. Studies to date have demonstrated AI’s utility across multiple phases of the HNC treatment continuum. Despite its promise, integrating AI into clinical practice faces several challenges, including concerns about system integrity, generalizability, privacy, and bias. In this review, we address these challenges and offer insights into future …

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 …

Effect Of Short-Chain Polymer Binders On The Mechanical And Electrochemical Performance Of Silicon Anodes, Fei Sun, L. Zurita-Garcia, Dean R. Wheeler

Faculty Publications

Polymer binders are crucial components in providing both mechanical support and chemical stability to the structure of porous Li-ion electrodes. Particularly in silicon anodes, the active material undergoes substantial volume expansion of up to 275%. Due to the mechanical constraint of the current collector, these silicon materials tend to expand in the normal direction while exhibiting substantial particle rearrangement and plastic deformation. Conventional rigid binders such as polyacrylic acid (PAA) and polyimide (PI), while providing satisfactory initial capacity, do not eliminate diminished long-term performance. Our research attempts to develop binder formulations that can accommodate sufficient flexibility for the substantial volume …

Development Of Respiratory Sinus Arrhythmia In Young Infants With Autism Spectrum Disorder, Preterm Birth, And Typical Development, Jessica Bradshaw, John E. Richards, Julia Yurkovic-Harding, Eilis Mclaughlin

Faculty Publications

Respiratory sinus arrhythmia (RSA) is a key index of parasympathetic function and environmental adaptability. Lower resting RSA has been linked to preterm (PT) birth in infancy and autism spectrum disorder (ASD) in childhood, yet RSA across the first 2 years in young infants born PT or later diagnosed with ASD remains unknown. This study examined resting RSA and mean interbeat interval (IBI) development from 1 to 24 months in infants at varying ASD likelihoods, including infant siblings of children with ASD and those born PT. A longitudinal design tracked resting RSA and mean IBI in 137 infants from 1 to …

Ruth Gatrell, Myrna J. Layton

Faculty Publications

Ruth Josephine Barton was born on December 23, 1921, in Farmington, Utah. Her parents were Lloyd and Edna (Cottrell) Barton. When the Bartons married, Edna already had a five-year-old daughter, Helen, from a previous marriage. Ruth was the first of two children born to Edna’s second marriage. The family was living in Mount Pleasant, Utah, but returned to the home of Edna’s father, Edward Cottrell, for the birth of the baby. She was named Ruth for the biblical heroine, and Josephine because she shared a birthday with the prophet Joseph Smith. A younger sister, Laura Jean, joined the family in …

Decreasing Foraminiferal Flux In Response To Ongoing Climate Change In The Santa Barbara Basin, California, Emily Harvard, Katherine Cherry, Claudia R. Benitez-Nelson, Eric Tappa, Catherine V. Davis

Faculty Publications

The rapid response of foraminiferal assemblages to changing climate makes their shells an invaluable geological record of the past. However, the time frame over which foraminifera respond to climatic signals and the specific drivers influencing assemblage composition and abundance remain obscure. We focus on the impact of ongoing, anthropogenic climate change on planktic foraminifera in the California Current ecosystem, which would appear as a nearly instantaneous event in the sediment record. The Santa Barbara Basin sediment trap, located off the coast of California, USA since 1993, provides a record of more than 30 years of particulate and foraminiferal flux in …

Menopause-Related Changes In Sleep And The Associations With Cardiometabolic Health: A Narrative Review, Joshua R. Sparks, Xuewen Wang Ph.D., Faha

Faculty Publications

This narrative review examines the complex relationship between sleep changes during the menopausal transition and cardiometabolic risks. The most common complaint about sleep is increased awakenings during sleep. Other complaints include having trouble falling asleep, waking up too early, insufficient and non-restorative sleep, and overall poor quality. Sleep determined using objective methods also indicates that greater awakenings after sleep onset are associated with the period of menopausal transition. Polysomnography recordings suggest physiological hyperarousal during sleep. Changes in other sleep metrics, such as sleep latency and sleep duration, are less consistent, and some studies suggest they may not worsen during the …

Working Group Report: Developing A Playbook Of Equitable Grading Practices, Stephen H. Edwards, David L. Largent, Ben Schafer, Debarati Basu, Amy Csizmar Dalal, Dan Garcia, Brian Harrington, Kevin Lin, Dan S. Myers, Christian Roberson, Giulia Toti, Brett Wortzman

Faculty Publications

Traditional points-based grading can have negative impacts. As a result, many educators are experimenting with alternative grading practices that are more equitable for students. However, educators often face challenges in implementing equitable grading practices due to a lack of clear, practical descriptions of techniques and the fact that not all techniques are universally applicable. This working group addresses this problem using a three-pronged strategy: conducting a systematic literature review to gather documented techniques, compiling ''recipes'' or concrete descriptions of these techniques, and publishing them in an open-source, online ''playbook'' of equitable grading practices as a community resource for educators. This …

“I Feel Like A Lot Of Times Women Are The Ones Who Are Problem-Solving For All The People That They Know”: The Gendered Impacts Of The Pandemic On Women In Alaska, Marya Rozanova-Smith, Andrey N. Petrov

Faculty Publications

The impacts of the COVID-19 pandemic and post-pandemic recovery in urban communities in the Arctic have been substantial, but their gendered aspects remain largely unknown. The goal of this study was to enhance the understanding of the gender-based impact on women in the urban areas of Alaska by exploring strengths and constraints to resilience in the social and economic domains of gender equality during and in the aftermath of the COVID-19 pandemic. Drawing on grounded theory methodology, this study is based on 29 in-depth, semi-structured interviews. The study methodology utilized a conceptual framework that integrated deficit-based and strength-based analytical perspectives. …

Two Decapod Crustaceans, Panopeus Herbstii And Petrolisthes Armatus, Stabilize Their Gaze Using Achromatic Visual Cues, But Not The Angle Of Linearly Polarized Light, M. Janakis, S. Guirges, A. C. Grant, I. Paris, E. F. Lopresti, Daniel Isaac Speiser

Faculty Publications

No abstract provided.

Bovine Neutrophil Migration, Cd11a/Cd18 Expression, And Cytokine Response To Co-Culture With Mammary Gland Endothelial Cells And Epithelial Cells, David J. Mcclenahan

Faculty Publications

Movement of leukocytes from the circulatory system into a site of inflammation is a highly complex process. The migration of neutrophils into the lumen of the mammary gland during mastitis is no exception. There is information about the involvement of bacterial-produced products during this process, but less is known regarding the role of host products. Two bovine cell lines, a primary mammary gland endothelial cell line and an immortalized bovine mammary gland epithelial cell line (Mac-T), along with freshly isolated bovine neutrophils, were used to study this further. The cell lines were grown on inserts and in wells of tissue-culture …

Nitrogen Fertilizer Equivalence Of Red Clover When Inter-Seeded Into Corn, Hannah R. Francis, Ting Fung Ma, Rodrigo Werle, Chelsea H. Zegler, Daniel H. Smith, Douglas J. Soldat, Erika Marin-Spiotta, Matthew D. Ruark

Faculty Publications

Inter-seeding red clover (Trifolium pratense L.) provides an alternative method toincorporate cover crops into continuous corn (Zea mays L.) in the Upper US Midwest. Red clover is a leguminous cover crop that can grow in low-radiation environments and is winter hardy. Systems with red clover have demonstrated improved corn yield and a fertilizer N equivalence but understanding these effects with inter-seeding war-rants further investigation. The objectives of this study were to determine the effect of inter-seeding red clover on (i) plant-available N during and after red clover decomposition, (ii) optimum N rates for corn, and (iii) corn yields. The …

Nitrogen Fertilizer Equivalence Of Red Clover When Inter-Seeded Into Corn, Hannah R. Francis, Ting Fung Ma, Rodrigo Werle, Chelsea H. Zegler, Daniel H. Smith, Douglas J. Soldat, Erika Marin-Spiotta, Matthew D. Ruark

Faculty Publications

Inter-seeding red clover (Trifolium pratense L.) provides an alternative method to incorporate cover crops into continuous corn (Zea mays L.) in the Upper US Midwest. Red clover is a leguminous cover crop that can grow in low-radiation environments and is winter hardy. Systems with red clover have demonstrated improved corn yield and a fertilizer N equivalence but understanding these effects with inter-seeding warrants further investigation. The objectives of this study were to determine the effect of inter-seeding red clover on (i) plant-available N during and after red clover decomposition, (ii) optimum N rates for corn, and (iii) corn …

Ocean And Coastal Acidification Monitoring Priorities For The Northeast Us And Eastern Canada, Christopher Hunt, Austin Pugh, Jake Kritzer, Samantha Siedlecki, Kumiko Azetsu-Scott, Parker Gassett, Diane Lavoie, Adam Pimenta, Amy Trice, Elizabeth Turner

Faculty Publications

The Interagency Working Group on Ocean Acidification Monitoring Prioritization Plan 2024 calls for Coastal Acidification Networks to identify the ocean and coastal acidification (OCA) monitoring needs most important for their regions. The Northeast Coastal Acidification Network (NECAN) organized a webinar series to study regional needs, which culminated with a workshop in November 2023. This workshop led to the identification of six priority new Monitoring Needs in addition to the maintenance of current monitoring efforts:

• Improve spatial and temporal scale of monitoring co-located OCA variables and biological measurements to better resolve variability of acidification dynamics in concert with biological processes …

A Meta-Analysis Of Historic Drinking Water Emergency Events Reported In News Articles, Victor Yu, Haiying Wang, Weiwei Mo

Faculty Publications

This study seeks to investigate historical drinking water contamination events that reported by news media to find the key determinants of their outcomes, including the duration and economic cost, and to quantitatively describe the characteristics of past contamination events. ProQuest Global Newsstream and Regional Business News were used to identify an initial list of events and supplemented by additional search on specific information including the response actions, economic cost, and more. These events were analyzed using descriptive statistics, correlation analysis, and regression modeling. Smaller community water systems were found to be more frequently impacted by contamination events. Use restrictions, except …

Expanding Functionalities Of Immune Receptors Through Simultaneous Transfer Of Sensor And Helper Nlrs, Dongjiao Wang, Qibin Wu, Daowen Wang, Youxiong Que, Zheng Qing Fu

Faculty Publications

No abstract provided.

Expanding Functionalities Of Immune Receptors Through Simultaneous Transfer Of Sensor And Helper Nlrs, Dongjiao Wang, Qibin Wu, Daowen Wang, Youxiong Que, Zheng Qing Fu

Faculty Publications

No abstract provided.

Growth Of Cylindrical Micelles And Their Use To Prepare Porous Materials With Tailored Dimensions And Alignment, Mengxue Zhang, Xiaomeng Li, Chuanbing Tang, Morgan Stefik

Faculty Publications

Materials with cylindrical pores are optimal for electrochemical devices and filtration due to their straight paths with minimal tortuosity when aligned. Polymer templates have led to many individual cylindrical architectures however the independent tailoring of pore and wall dimensions has remained elusive. Here short cylindrical micelle templates (PEO-b-PS) with glassy cores enabled the fabrication of sample series with constant cylindrical pore diameter (∼63 nm) and tailored wall thickness (TiO₂, ∼45–100 nm). This ShortCyl series (aspect ratio 4.25) had modest alignment that was attributed to the low free-energy cost for misalignment. Though the plasticized micelles (DCM present) …

Neighborhood Socioeconomic Status And Overall Survival Among Children With Acute Lymphoblastic Leukemia, Anna Hoppmann, Debroah M. Hurley, Stuart Cramer, Monique J. Brown Ph.D., Mph

Faculty Publications

A disadvantaged neighborhood, as represented by area-level socioeconomic status (SES) has been associated with adverse outcomes among children with acute lymphoblastic leukemia (ALL) in the US, but the duration of impact after ALL diagnosis is not well understood. This retrospective cohort study utilized the National Cancer Database (NCDB) to examine the impact of area-level SES on overall survival among children with ALL. Median income and education quartiles based on residential zip code were used to create a composite area-level SES variable. Individual-level variables included age, sex, race, year of diagnosis, primary payer, distance to care, rurality, time to treatment, and …

Assessing The Costs Of Constructed Floating Wetlands For The Treatment Of Surface Waters And Wastewater, John Awad, Christopher Walker, Declan Page, Muhammad Arslan, Sarah A. White, Terry Lucke, Simon Beecham, Ryan J. Winston, William H.J. Stonsnider, Phil Nicodemus, Chris Streb, John Van Leeuwen

Faculty Publications

The development of constructed floating wetlands (CFWs) as a nature-based solution for water treatment has progressed over the last 25 years. However, full-scale CFW adoption remains relatively limited due in part to the uncertainty regarding the costs of CFWs in terms of capital and operational expenditure (CAPEX and OPEX) and treatment capacity. This study reports on the costs of 11 international CFW schemes including the factors affecting CAPEX and OPEX and levelized costs of nitrogen and phosphorus removal. The estimated levelized CAPEX and OPEX ranged from US$15/m² to $2537/m² and from $0.5/m² y⁻¹ to $181/m² y⁻¹, respectively, for CFW schemes …

Application And Comparison Of Satellite-Derived Sea Surface Temperature Gradients To Identify Seasonal And Interannual Variability Off The California Coast: Preliminary Results And Future Perspectives, Jorge Vazquez-Cuervo, Marisol García-Reyes, David S. Wethey, Daniele Ciani, Jose Gomez-Valdes

Faculty Publications

The application of satellite-derived sea surface temperature in coastal regions is critical for resolving the dynamics of frontal features and coastal upwelling. Here, we examine and compare sea surface temperature (SST) gradients derived from two satellite products, the Multi-Scale Ultra-High Resolution SST Product (MUR, 0.01° grid scale) and the Operational SST and Ice Analysis (OSTIA, 0.05° grid scale), available through the Group for High Resolution SST (GHRSST). Both products show similar seasonal variability, with maxima occurring in the summer time frame. Additionally, both products show an increasing trend of SST gradients near the coast. However, differences exist between the two …

Radioactive Contamination And Climate Warming Affect Physiological Performance Of Chornobyl Barn Swallows, Zbyszek Boratyríski, Timothy Mousseau, Anders Pape Møller

Faculty Publications

Global warming and degradation of natural habitats are the two main factors causing ecophysiological stress on individuals and risk for biodiversity. Hyperthermia is a common response to stress in homeothermic animals, in particular to heat, pathogens and environmental contamination. Resilience of biological systems to global warming may be deteriorated in polluted habitats. Here we investigated how body temperature of a wild bird, the barn swallow (Hirundo rustica), responded to global warming while simultaneously exposed to radioactive contamination from the Chernobyl accident. Our results showed that both high air temperatures (t = 15.55, df = 335, p <  0.0001) and elevated environmental radioactive contamination (t = 5.18, df = 8.09, p = 0.0008) increased internal body temperature of individuals. The additive effect suggests that birds might suffer hyperthermia in locally contaminated habitat (1.47% body temperature increase) while simultaneously exposed to globally rising temperatures (1.95% body temperature increase), potentially reducing the fitness of individual and the maintenance of breeding colonies. The cumulative and interactive negative effects of multiple stressors, such as those emerging from increasing habitat degradation and climate change, will likely contribute to biodiversity losses globally.