Physical Sciences and Mathematics Commons^™

Pathogenicity In Chickens And Turkeys Of A 2021 United States H5n1 Highly Pathogenic Avian Influenza Clade 2.3.4.4b Wild Bird Virus Compared To Two Previous H5n8 Clade 2.3.4.4 Viruses, Mary J. Pantin-Jackwood, Erica Spackman, Christina Leyson, Sungsu Youk, Scott A. Lee, Linda M. Moon, Mia K. Torchetti, Mary L. Killian, Julianna B. Lenoch, Darrell R. Kapczynski, David E. Swayne, David L. Suarez

USDA Wildlife Services: Staff Publications

Highly pathogenic avian influenza viruses (HPAIVs) of subtype H5 of the Gs/GD/96 lineage remain a major threat to poultry due to endemicity in wild birds. H5N1 HPAIVs from this lineage were detected in 2021 in the United States (US) and since then have infected many wild and domestic birds. We evaluated the pathobiology of an early US H5N1 HPAIV (clade 2.3.4.4b, 2021) and two H5N8 HPAIVs from previous outbreaks in the US (clade 2.3.4.4c, 2014) and Europe (clade 2.3.4.4b, 2016) in chickens and turkeys. Differences in clinical signs, mean death times (MDTs), and virus transmissibility were found between chickens and …

Relation Between Halogen Bond Strength And Ir And Nmr Spectroscopic Markers, Akhtam Amonov, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The relationship between the strength of a halogen bond (XB) and various IR and NMR spectroscopic quantities is assessed through DFT calculations. Three different Lewis acids place a Br or I atom on a phenyl ring; each is paired with a collection of N and O bases of varying electron donor power. The weakest of the XBs display a C–X bond contraction coupled with a blue shift in the associated frequency, whereas the reverse trends occur for the stronger bonds. The best correlations with the XB interaction energy are observed with the NMR shielding of the C atom directly bonded …

An Overview Of Elements And Relations: Aspects Of A Scientific Metaphysics, Martin Zwick

Systems Science Faculty Publications and Presentations

A talk on my book, Elements and Relations: Aspects of a Scientific Metaphysics. Book description:

This book develops the core proposition that systems theory is an attempt to construct an “exact and scientific metaphysics,” a system of general ideas central to science that can be expressed mathematically. Collectively, these ideas would constitute a non-reductionist “theory of everything” unlike what is being sought in physics. Inherently transdisciplinary, systems theory offers ideas and methods that are relevant to all of the sciences and also to professional fields such as systems engineering, public policy, business, and social work. To demonstrate the generality …

Raccoon Spatial Ecology In The Rural Southeastern United States, Jacob E. Hill, Madison L. Miller, James L. Helton, Richard B. Chipman, Amy Gilbert, University Of Georgia, Guha Dharmarajan, Olin E. Rhodes Jr.

USDA Wildlife Services: Staff Publications

The movement ecology of raccoons varies widely across habitats with important implications for the management of zoonotic diseases such as rabies. However, the spatial ecology of raccoons remains poorly understood in many regions of the United States, particularly in the southeast. To better understand the spatial ecology of raccoons in the southeastern United States, we investigated the role of sex, season, and habitat on monthly raccoon home range and core area sizes in three common rural habitats (bottomland hardwood, upland pine, and riparian forest) in South Carolina, USA. From 2018–2022, we obtained 264 monthly home ranges from 46 raccoons. Mean …

Volcanic Diffuse Volatile Emissions Tracked By Plant Responses Detectable From Space, Robert R. Bogue, Peter M. J. Douglas, Joshua B. Fisher, John Stix

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Volcanic volatile emissions provide information about volcanic unrest but are difficult to detect with satellites. Volcanic degassing affects plants by elevating local CO2 and H2O concentrations, which may increase photosynthesis. Satellites can detect plant health, or a reaction to photosynthesis, through a Normalized Difference Vegetation Index (NDVI). This can act as a potential proxy for detecting changes in volcanic volatile emissions from space. We tested this method by analyzing 185 Landsat 5 and 8 images of the Tern Lake thermal area (TLTA) in northeast Yellowstone caldera from 1984 to 2022. We compared the NDVI values of the thermal area with …

University Of Arkansas, Chemistry And Biochemistry Department Graduate Student Publications, 2018- November 2023. 39p., Jeremy Smith, Lutishoor Salisbury

University Libraries Faculty Publications and Presentations

This report provides a compilation of the research publications by the Chemistry and Biochemistry (CHBC) Graduate students for the period: 2018-November 2023. It includes publications by the CHBC graduates and those where a CHBC faculty was the main advisor. It includes a summary of the research. The listing is organized according to type of publications within specific years.

University Of Arkansas, Chemistry And Biochemistry Department Research Publications, 2014- November 2023. 107p., Jeremy Smith, Lutishoor Salisbury

University Libraries Faculty Publications and Presentations

This report provides a compilation of the research publications by the Chemistry and Biochemistry faculty for the period: 2014 - November 2023. The information was gathered from major databases in science and technology including Web of Science, SciFinder, Reaxys, PubMed, IEEE Explore and Engineering Index. At least one author in each of the publications has the CHBC department as its affiliation. It includes a table summarizing the research. The listing is organized according to type of publications within specific years.

Precipitation And Greenness In Pastoral Lands Of East Turkana, Kenya, Paul Akpejeluh

School of Natural Resources: Dissertations, Theses, and Student Research

Pastoralism has long supported livelihoods and provided essential ecosystem services in landscapes of East Africa. Vegetation productivity is central to the functioning of pastoral systems but may be affected by changes in climate and landuse. Vegetation monitoring is important for understanding the effects of global change in pastoral lands; however, it can be time and resource intensive. Remote sensing provides opportunities for efficient multi-scale monitoring of vegetation and climatic drivers. In this thesis, I explore the utility of satellite and UAV remote sensing for monitoring vegetation and precipitation trends and relationships in the East of Lake Turkana Region of northern …

Connecting The Nebraska Water Quality Index To The Aquatic Microbial Community Of The North Platte River Basin, Nebraska, Paula R. Guastello

School of Natural Resources: Dissertations, Theses, and Student Research

The Nebraska Water Quality Index, under development by the Nebraska Department of Environment and Energy, summarizes in a single value eight environmental parameters that have been monitored in Nebraska for nearly 20 years. Water quality parameters including those used in the Nebraska Water Quality Index have been shown in previous studies to impact bacterial growth. As such, this index has the potential to correlate with the freshwater microbial community. Here, I relate the Nebraska Water Quality Index to microbial community composition and structure using 16S rRNA gene amplicon sequence data collected from the North Platte River Basin, Nebraska. This index …

Experimental Studies On The Operation Of Agricultural Crops Mowing Unit With Simultaneous Chopping And Incorporation Of Stubble Into The Soil, Volodymyr Nadykto, Sergey Kiurchev, Tatiana Chorna, Taras Hutsol, Szymon Głowacki, Anatoliy Rud, Alona Shevtsova, Igor Ryabov, Katarzyna Szwedziak

Sociology Faculty Publications and Presentations

For harvesting crops, one-phase and two-phase methods are most often used. When implementing the second one, mounted and trailed units are used. The latter is becoming less and less used due to the problems with movement stability in the horizontal plane because of the asymmetric layout. A stubble background, which is susceptible to solar and wind influences, is formed as a consequence of application of the mounted harvesting unit, As a result, the field’s soil in the inter-swath space intensively loses moisture. A harvesting unit based on a tractor with rear steerable wheels has been designed to eliminate this shortcoming. …

Convolutional Neural Network-Based Gene Prediction Using Buffalograss As A Model System, Michael Morikone

Complex Biosystems PhD Program: Dissertations

The task of gene prediction has been largely stagnant in algorithmic improvements compared to when algorithms were first developed for predicting genes thirty years ago. Rather than iteratively improving the underlying algorithms in gene prediction tools by utilizing better performing models, most current approaches update existing tools through incorporating increasing amounts of extrinsic data to improve gene prediction performance. The traditional method of predicting genes is done using Hidden Markov Models (HMMs). These HMMs are constrained by having strict assumptions made about the independence of genes that do not always hold true. To address this, a Convolutional Neural Network (CNN) …

Motif-Cluster: A Spatial Clustering Package For Repetitive Motif Binding Patterns, Mengyuan Zhou

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Previous efforts in using genome-wide analysis of transcription factor binding sites (TFBSs) have overlooked the importance of ranking potential significant regulatory regions, especially those with repetitive binding within a local region. Identifying these homogenous binding sites is critical because they have the potential to amplify the binding affinity and regulation activity of transcription factors, impacting gene expression and cellular functions. To address this issue, we developed an open-source tool Motif-Cluster that prioritizes and visualizes transcription factor regulatory regions by incorporating the idea of local motif clusters. Motif-Cluster can rank the significant transcription factor regulatory regions without the need for experimental …

Building The Soil Carbon Sponge At Murray Wells Farm, Tambellup, Western Australia, Wendy Bradshaw

Natural resources published reports

Peter and Wendy Bradshaw farmed at Murray Wells Farm about 25 km west of Tambellup for around 46 years until they sold and retired in 2022. They produced barley, oats, merino and prime lambs on an annual rainfall of 450 mm over 1,000 arable hectares. The farm was on a moderately undulating landscape with a mix of soils including sandy duplex, well-drained sand over gravel over clay, shallow sandy or loamy gravel over cemented laterite and red to brown loamy soils.Their farming philosophy was to view agriculture as an ecological enterprise that included them as part of the ecosystem, and …

Agricultural Groundcover Update October 2023, Justin Laycock

Natural resources published reports

Summary

• About 98% of the grainbelt had adequate vegetative groundcover (more than 50%) to prevent wind erosion in October 2023. This amount of groundcover is normal at the end of spring and pre-harvest in most areas.
• There was a larger than average area with 51–60% groundcover, and groundcover in these areas is expected to reduce over summer to below 50%.
• About 2% of the grainbelt (293,000 ha) had less than 50% groundcover, which is inadequate to prevent wind erosion. Mullewa to Morawa Ag Soil Zone had the highest risk of wind erosion and 8% of this farmland had inadequate groundcover. …

Groundwater System Characterisation: Fortescue Alluvial Fan, Michael J. Donn, Olga V. Barron, Axel Suckow, Chris Turnadge, John A. Simons, Robert J. Paul, Christopher Schelfhout Dr

Natural resources commissioned reports

This report focuses on groundwater system characterisation in the region north of Newman, based on analysis of pre-existing data and data newly acquired during project activities. Groundwater system characterisation was an important research component supporting the assessment of managed aquifer recharge opportunities, using mine dewatering surplus generated (due to mining below the watertable) at large BHP Billiton Iron Ore operations in the eastern Pilbara mining zone, and aiming to support irrigated agriculture. The assessment area is located north of Ethel Gorge and covers the Upper Fortescue River floodplain and surroundings. The project added much knowledge to this largely ‘data-poor’ region, …

Transforming Agriculture In The Pilbara: Newman Managed Aquifer Recharge (Mar) Feasibility Assessment, Michael J. Donn, Joanne L. Vanderzalm, Olga V. Barron

Natural resources commissioned reports

In the Newman region, DPIRD commissioned an assessment of the potential for managed aquifer recharge (MAR) near Newman using surplus water resulting from mine dewatering as the water supply for irrigated agriculture. The objectives of the MAR assessment were to:

• identify focus area for MAR feasibility assessment within the initial larger area of interest for MAR
• assess the viability of MAR with mine dewater near Newman to support development of irrigated agriculture, in keeping with national and state MAR guidelines
• identify key risks associated with MAR with mine dewater for irrigation supply, and identify knowledge/investigation required to adequately assess risks …

Skin Lipids Alone Enable Conspecific Tracking In An Invasive Reptile, The Argentine Black And White Tegu Lizard (Salvator Merianae), M. Rockwell Parker, Eric A. Tillman, Lauren A. Nazarian, Megan L. Barlowe, Julianna M. Lincoln, Bryan M. Kluever

USDA Wildlife Services: Staff Publications

Locating potential mates in non-native habitats is one of the most important challenges faced by invasive vertebrate species. The Argentine black and white tegu lizard (Salvator merianae) is a major invasive reptile species in the contiguous United States and is rapidly expanding its range across Florida and the Southeast, in part due to inadequate management strategies and tools. Because a wide array of reptiles, especially squamates (snakes and lizards), have been well-studied for their reliance on chemical cues to locate conspecifics, our project aimed to isolate chemical cues from tegus and assess the ability of adult males and …

Are Plant–Soil Feedbacks Caused By Many Weak Microbial Interactions?, Julia K. Aaronson, Andrew Kulmatiski, Leslie E. Forero, Josephine Grenzer, Jeanette M. Norton

Wildland Resources Student Research

We used high-throughput sequencing and multivariate analyses to describe soil microbial community composition in two four-year field plant–soil feedback (PSF) experiments in Minnesota, USA and Jena, Germany. In descending order of variation explained, microbial community composition differed between the two study sites, among years, between bulk and rhizosphere soils, and among rhizosphere soils cultivated by different plant species. To try to identify soil organisms or communities that may cause PSF, we correlated plant growth responses with the microbial community composition associated with different plants. We found that plant biomass was correlated with values on two multivariate axes. These multivariate axes …

Statistical And Machine Learning Approaches To Describe Factors Affecting Preweaning Mortality Of Piglets, Md Towfiqur Rahman, Tami M. Brown-Brandl, Gary A. Rohrer, Sudhendu R. Sharma, Vamsi Manthena, Yeyin Shi

Department of Biological Systems Engineering: Papers and Publications

High preweaning mortality (PWM) rates for piglets are a significant concern for the worldwide pork industries, causing economic loss and well-being issues. This study focused on identifying the factors affecting PWM, overlays, and predicting PWM using historical production data with statistical and machine learning models. Data were collected from 1,982 litters from the United States Meat Animal Research Center, Nebraska, over the years 2016 to 2021. Sows were housed in a farrowing building with three rooms, each with 20 farrowing crates, and taken care of by well-trained animal caretakers. A generalized linear model was used to analyze the various sow, …

Wics Conference 2023: Moving Beyond The Ordinary, Daren Redfearn, Daran Rudnick

WICS Conferences

The theme of this year’s WICS Conference is Moving Beyond the Ordinary with the goal of addressing Team Science. Our vision is to provide opportunities and connection points among IANR faculty to leverage their individual knowledge, skills, abilities, and passions. A tendency for land grant institutions is often to deliver information biased from a single, primary discipline and perspective. This is known as comfort zone mega bias and has been defined as “the tendency to drag a problem into our comfort zone and solve the problem that we know how to solve, rather than solving the problem that needs to …

Substrate Specificity In Abc Transporters Using The E. Coli Methionine Import System, John H. Guardado

Featured Student Work

ATP-binding cassette (ABC) transporters use the energy of ATP to move substrates across membranes against a concentration gradient. The role of ABC transporters is crucial in several essential cellular functions and mutations in ABC transporters in humans have been linked to several conditions, including cystic fibrosis, liver disease, and diabetes. Despite their central roles in homeostasis, the mechanism of ABC transporters remains poorly understood. Our research is focused on studying an ABC importer in E. coli, as a model system, to examine the mechanism of substrate specificity and transport. The bacterial methionine import system consists of a membrane-embedded transporter, MetNI, …

Nutritional Challenges Of Substituting Farmed Animals For Wild Fish In Human Diets, Sebastian A. Heilpern, Rafael M. Almeida, Kathryn J. Fiorella, Alexander S. Flecker, Demetra Williams, Peter B. Mcintyre

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

Wild fisheries provide billions of people with a key source of multiple essential nutrients. As fisheries plateau or decline, nourishing more people will partially rely on shifting consumption to farmed animals. The environmental implications of transitions among animal-sourced foods have been scrutinized, but their nutritional substitutability remains unclear. We compared concentrations of six essential dietary nutrients across >5000 species of wild fishes, aquaculture, poultry and livestock species, representing >65% of animals consumed globally. Wild fishes are both more nutrient-dense and variable than farmed animals; achieving recommended intake of all nutrients with farmed species could require consuming almost four times more …

Deep Learning For Plant Bioinformatics: An Explainable Gradient-Based Approach For Disease Detection, Muhammad Shoaib, Babar Shah, Nasir Sayed, Farman Ali, Rafi Ullah, Irfan Hussain

All Works

Emerging in the realm of bioinformatics, plant bioinformatics integrates computational and statistical methods to study plant genomes, transcriptomes, and proteomes. With the introduction of high-throughput sequencing technologies and other omics data, the demand for automated methods to analyze and interpret these data has increased. We propose a novel explainable gradient-based approach EG-CNN model for both omics data and hyperspectral images to predict the type of attack on plants in this study. We gathered gene expression, metabolite, and hyperspectral image data from plants afflicted with four prevalent diseases: powdery mildew, rust, leaf spot, and blight. Our proposed EG-CNN model employs a …

Widespread Dominance Of Methane Ebullition Over Diffusion In Freshwater Aquaculture Ponds, Renske J. E. Vroom, Sarian Kosten, Rafael M. Almeida, Raquel Mendonça, Ive S. Muzitano, Icaro Barbosa, Jonas Nasário, Ernandes S. Oliveira Junior, Alexander S. Flecker, Nathan Barros

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

An ever-increasing demand for protein-rich food sources combined with dwindling wild fish stocks has caused the aquaculture sector to boom in the last two decades. Although fishponds are potentially strong emitters of the greenhouse gas methane (CH₄), little is known about the magnitude, pathways, and drivers of these emissions. We measured diffusive CH₄ emissions at the margin and in the center of 52 freshwater fishponds in Brazil. In a subset of ponds (n = 31) we additionally quantified ebullitive CH₄ fluxes and sampled water and sediment for biogeochemical analyses. Sediments (n = 20) were …

The Accumulation And Growth Of Pseudomonas Aeruginosa On Surfaces Is Modulated By Surface Mechanics Via Cyclic-Di-Gmp Signaling, Liyun Wang, Yu-Chern Wong, Joshua M. Correira, Megan Wancura, Chris J. Geiger, Shanice S. Webster, Ahmed Touhami, Benjamin J. Butler, George A. O’Toole, Richard M. Langford

Physics and Astronomy Faculty Publications and Presentations

Attachment of bacteria onto a surface, consequent signaling, and accumulation and growth of the surface-bound bacterial population are key initial steps in the formation of pathogenic biofilms. While recent reports have hinted that surface mechanics may affect the accumulation of bacteria on that surface, the processes that underlie bacterial perception of surface mechanics and modulation of accumulation in response to surface mechanics remain largely unknown. We use thin and thick hydrogels coated on glass to create composite materials with different mechanics (higher elasticity for thin composites; lower elasticity for thick composites) but with the same surface adhesivity and chemistry. The …

A Classical Fall Statistics Problem, Timothy L. Meyer

Cornhusker Economics

An evaluation of traditional baseball measures and suggestions for alternatives, centering on statistics related to the offensive quality of a player.

Belowground Growth Strategies Of Native And Invasive Rhizomatous Perennial Grasses In Response To Precipitation Variability, Clipping, And Competition, Surendra Bam, Jacqueline P. Ott, Jack Butler, Lan Xu

Natural Resource Management Faculty Publications

Invasive clonal species may exhibit different growth strategies than their native clonal competitors. In this study, we examined the spatial distribution of tiller outgrowth and the bud bank by comparing the investment in phalanx versus guerilla growth of a native and invasive perennial grass in North America. We also examined the efect of altered precipitation frequency, clipping, and competition on their clonal growth strategies. Investment in phalanx and guerilla growth was assessed by examining live propagule and tiller production from the plant crown versus its rhizomes. Although invasive Bromus inermis and native Pascopyrum smithii exhibited similar clonal growth strategies as …

The Coastal Monitor: Vol. 10 No. 2, John Tanacredi Ph.D.

The Coastal Monitor

Stephen J. Gould’s prophetic piece, “The Golden Rule: A Proper Scale for Our Environmental Crisis”, noted that, “Patience enjoys a long pedigree of favor”, which he elaborated, “usually involves a deep understanding of the fundamental principle… rarely grasped in daily life – the effects of scale.” Scientists observe changes incessantly, in dimensions and time, from microscopic conditions of cellular biology to the inconceivable distances of galaxies and their influences on Earth.

Bioplastics In The Ci, Brenna Kusleika, Isabella Cabral, Marie Cadene

Hungry for Sustainability - Anna Bowen, Biology and Environmental Science

No abstract provided.

Analyzing The Ramifications Of Climate Change On Mental Health, Salvatore A. Medori

Student Publications

When thinking about the vast array of impacts that the climate crisis has on humanity, there are many things that come to mind, but mental health impacts are likely not one of them. Even though research demonstrates that mental effects from any form of disaster far exceed the physical health implications mental health impacts of the largest disaster facing humanity since the Second World War are rarely considered at all, let alone when solutions are being created. This has led to a hidden crisis emerging underneath an even larger crisis, with serious consequences for most individuals across the globe. The …