Digital Commons Network^™

A Graduate-Level Field Course In Irrigation And Agricultural Water Management For An Immersive Learning Experience, Derek M. Heeren, László G. Hayde, Dean Eisenhauer, Peter G. Mccornick, Ali T. Mohammed, Aaron R. Mittelstet, Alan L. Boldt, Xin Qiao, David Mabie, Francisco Muñoz-Arriola

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Effective irrigation and agricultural water management (IAWM) is critical for food security and water security. A key requirement in designing, implementing and operation of IWM is the necessary knowledge and capacity on the farm, in the service industry and within the supply chain. Educational opportunities that not only teach the relevant principles of irrigated agriculture, but also the necessary applied skills are essential. An Irrigation Field Course was initiated by the IHE Delft Institute for Water Education (IHE Delft) and was later developed as a joint field course with IHE Delft, the University of Nebraska-Lincoln (UNL), and the Daugherty Water …

Complab V1.0: A Scalable Pore-Scale Model For Flow, Biogeochemistry, Microbial Metabolism, And Biofilm Dynamics, Heewon Jung, Hyun-Seob Song, Christof Meile

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Microbial activity and chemical reactions in porous media depend on the local conditions at the pore scale and can involve complex feedback with fluid flow and mass transport. We present a modeling framework that quantitatively accounts for the interactions between the bio(geo)chemical and physical processes and that can integrate genome-scale microbial metabolic information into a dynamically changing, spatially explicit representation of environmental conditions. The model couples a lattice Boltzmann implementation of Navier–Stokes (flow) and advection–diffusion-reaction (mass conservation) equations. Reaction formulations can include both kinetic rate expressions and flux balance analysis, thereby integrating reactive transport modeling and systems biology. We also …

Evaluating Management Zones And Crop-Sensing Relationships For Improved Irrigated Maize Nitrogen Management, Joel D. Crowther, John Parrish, Joe Luck, Richard Ferguson

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Active crop canopy sensors and management zones (MZ) are two methods of directing variable-rate, in-season nitrogen (N) fertilizer applications in maize (Zea mays L.). Researchers have suggested that integrating these two approaches may result in improved performance of sensor-based N application algorithms through increased N use efficiency and profitability. The objectives of this research study were to (1) identify soil and topographic variables that are related to in-season canopy reflectance and yield for soil-based MZ delineation and (2) determine if delineated MZ can identify areas with differential crop response to N fertilizer. N ramp blocks were placed end-to-end in field-length …

Agricultural Machinery Operator Monitoring System (Ag-Oms): A Machine Learning Approach For Real-Time Operator Safety Assessment, Terence Irumva, Herve Mwunguzi, Santosh Pitla, Bethany Lowndes, Aaron Yoder, Ka-Chun Siu

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The 2015 CS-CASH (Central States Center for Agricultural Safety and Health, 2015) Injury Surveillance Surveys showed that around 19% of injuries to agricultural producers are related to tractors or large agricultural machinery, yet only a limited number of studies are found that address tools and methods for monitoring safety behaviors of agricultural machinery operators in real-time. The current safety behavior monitoring approaches require an in-person presence, which can be both time- and cost-inefficient, and the other available methods lack a feedback element to alert operators in realtime. As a result, the research presented in this study aimed to develop an …

Crop Stress Sensing And Plant Phenotyping Systems: A Review, Geng Bai, Yufeng Ge

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Enhancing resource use efficiency in agricultural field management and breeding high-performance crop varieties are crucial approaches for securing crop yield and mitigating negative environmental impact of crop production. Crop stress sensing and plant phenotyping systems are integral to variable-rate (VR) field management and high-throughput plant phenotyping (HTPP), with both sharing similarities in hardware and data processing techniques. Crop stress sensing systems for VR field management have been studied for decades, aiming to establish more sustainable management practices. Concurrently, significant advancements in HTPP system development have provided a technological foundation for reducing conventional phenotyping costs. In this paper, we present a …

Goniometer In The Air: Enabling Brdf Measurement Of Crop Canopies Using A Cable-Suspended Plant Phenotyping Platform, Geng Bai, Yufeng Ge, Bryan Leavitt, John Gamon, David Scoby

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The Bidirectional Reflectance Distribution Function (BRDF) quantifies the distribution of the spectral reflectance of a target surface at various viewing and illumination angles. In-field measurement of the BRDF of vegetation canopies improves the characterization of offnadir measurements and informs radiative transfer models of canopy reflectance, where the Lambertian assumption does not hold. However, current field goniometers are unable to measure BRDF efficiently, especially for tall vegetation across the growing season because of the limitations of clearance, field accessibility, and flexibility of the sensor field of view. In this study, we explored the potential of using a large-scale cable-suspended field phenotyping …

Osc-Co2: Coattention And Cosegmentation Framework For Plant State Change With Multiple Features, Rubi Quiñones, Ashok Samal, Sruti Das Choudhury, Francisco Muñoz-Arriola

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Cosegmentation and coattention are extensions of traditional segmentation methods aimed at detecting a common object (or objects) in a group of images. Current cosegmentation and coattention methods are ineffective for objects, such as plants, that change their morphological state while being captured in different modalities and views. The Object State Change using Coattention-Cosegmentation (OSC-CO²) is an end-to-end unsupervised deep-learning framework that enhances traditional segmentation techniques, processing, analyzing, selecting, and combining suitable segmentation results that may contain most of our target object’s pixels, and then displaying a final segmented image. The framework leverages coattention-based convolutional neural networks (CNNs) and …

Clim4omics: A Geospatially Comprehensive Climate And Multi-Omics Database For Maize Phenotype Predictability In The United States And Canada, Parisa Sarzaeim, Francisco Muñoz-Arriola, Diego Jarquin, Hasnat Aslam, Natalia De Leon Gatti

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The performance of numerical, statistical, and data-driven diagnostic and predictive crop production modeling relies heavily on data quality for input and calibration or validation processes. This study presents a comprehensive database and the analytics used to consolidate it as a homogeneous, consistent, multidimensional genotype, phenotypic, and environmental database for maize phenotype modeling, diagnostics, and prediction. The data used are obtained from the Genomes to Fields (G2F) initiative, which provides multiyear genomic (G), environmental (E), and phenotypic (P) datasets that can be used to train and test crop growth models to understand the genotype by environment (GxE) interaction phenomenon. A particular …

Estimating Battery Size Requirements For Tractor Electrification Of Row-Crop Planting Operations, Cheetown Liew, Andrew Donesky, Mark Freyhof, Ian Tempelmeyer, Santosh Kumar Pitla

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Power sources such as batteries, used for both on-road and off-road vehicles, are advancing at a rapid pace. Electric batteries are becoming more power dense, thus allowing them to be used as a power source to replace previous diesel or gasoline-powered systems. Efforts are underway to transition off-road agricultural vehicles from Internal Combustion Engine (ICE) vehicles to electric vehicles (EVs); however, the energy requirements of typical agricultural field operations need to be fully understood before such a transition can occur. Theoretical prediction equations available in the American Society of Agricultural and Biological Engineers (ASABE) standards or the use of engine …

Viral Chemotaxis Of Paramecium Bursaria Altered By Algal Endosymbionts, Huy V.N. Ho, David Dunigan, Miranda E. Salsbery, Irina Agarkova, Zeina Al-Ameeli, James L. Van Etten, John Delong

School of Biological Sciences: Faculty Publications

Chemotaxis is widespread across many taxa and often aids resource acquisition or predator avoidance. Species interactions can modify the degree of movement facilitated by chemotaxis. In this study, we investigated the influence of symbionts on Paramecium bursaria’s chemotactic behavior toward chloroviruses. To achieve this, we performed choice experiments using chlorovirus and control candidate attractors (virus stabilization buffer and pond water). We quantified the movement of Paramecia grown with or without algal and viral symbionts toward each attractor. All Paramecia showed some chemotaxis toward viruses, but cells without algae and viruses showed the most movement toward viruses. Thus, the endosymbiotic …

Metamorphosis Imposes Variable Constraints On Genome Expansion Through Effects On Development, R. Lockridge Mueller, Clayton E. Cressler, R. S. Schwartz, R. A. Chong, M. A. Butler

School of Biological Sciences: Faculty Publications

Genome size varies ∼100,000-fold across eukaryotes and has long been hypothesized to be influenced by meta- morphosis in animals. Transposable element accumulation has been identified as a major driver of increase, but the nature of constraints limiting the size of genomes has remained unclear, even as traits such as cell size and rate of development co-vary strongly with genome size. Salamanders, which possess diverse metamorphic and non-metamorphic life histories, join the lung- fish in having the largest vertebrate genomes—3 to 40 times that of humans—as well as the largest range of variation in genome size. We tested 13 biologically-inspired hypotheses …

To What Extent Do Physiological Tolerances Determine Elevational Range Limits Of Mammals?, Jay F. Storz, Graham R. Scott

School of Biological Sciences: Faculty Publications

A key question in biology concerns the extent to which distributional range limits of species are determined by intrinsic limits of physiological tolerance. Here, we use common-garden data for wild rodents to assess whether species with higher elevational range limits typically have higher thermogenic capacities in comparison to closely related lowland species. Among South American leaf-eared mice (genus Phyllotis), mean thermogenic performance is higher in species with higher elevational range limits, but there is little among-species variation in the magnitude of plasticity in this trait. In the North American rodent genus Peromyscus, highland deermice (Peromyscus maniculatus) …

Stochasticity Directs Adaptive Evolution Toward Nonequilibrium Evolutionary Attractors, John Delong, Clayton E. Cressler

School of Biological Sciences: Faculty Publications

Stochastic processes such as genetic drift may hinder adaptation, but the effect of such stochasticity on evolution via its effect on ecological dynamics is poorly understood. Here we evaluate patterns of adaptation in a population subject to variation in demographic stochasticity. We show that stochasticity can alter population dynamics and lead to evolutionary outcomes that are not predicted by classic eco-evolutionary modeling approaches. We also show, however, that these outcomes are governed by nonequilibrium evolutionary attractors— these are maxima in lifetime reproductive success when stochasticity keeps the ecological system away from the deterministic equilibrium. These NEEAs alter the path of …

The Consumption Of Viruses Returns Energy To Food Chains, John Delong, James L. Van Etten, Zeina Al-Ameeli, Irina Agarkova, David Dunigan

School of Biological Sciences: Faculty Publications

Viruses impact host cells and have indirect effects on ecosystem processes. Plankton such as ciliates can reduce the abundance of virions in water, but whether virus consumption translates into demographic consequences for the grazers is unknown. Here, we show that small protists not only can consume viruses they also can grow and divide given only viruses to eat. Moreover, the ciliate Halteria sp. foraging on chloroviruses displays dynamics and interaction parameters that are similar to other microbial trophic interactions. These results suggest that the effect of viruses on ecosystems extends beyond (and in contrast to) the viral shunt by redirecting …

Ecological Boundaries And Constraints On Viable Eco-Evolutionary Pathways [Pre-Print], Kyle E. Coblentz, John Delong

School of Biological Sciences: Faculty Publications

Evolutionary dynamics are subject to constraints ranging from limitations on what is physically possible to limitations on the pathways that evolution can take. One set of evolutionary constraints, known as ‘demographic constraints’, constrain what can occur evolutionarily due to the population demographic or population dynamical consequences of evolution leading to conditions that make populations susceptible to extinction. These demographic constraints can limit the strength of selection or rates of environmental change populations can experience while remaining extant and the trait values a population can express. Here we further hypothesize that the population demographic and population dynamical consequences of evolution also …

Intraguild Predation Is Increased In Areas Of Low Prey Diversity In A Generalist Predator Community, Stella F Uiterwaal, Amber Squires, Bennett Grappone, Brian Dillard, Ariadne Castaneda, Sora L. Kim, John Delong

School of Biological Sciences: Faculty Publications

1. Niche differentiation and intraguild predation (IGP) can allow ecologically similar species to coexist, although it is unclear which coexistence mechanism predominates in consumer communities. Until now, a limited ability to quantify diets from metabarcoding data has precluded the use of sequencing data to determine the relative importance of these mechanisms.

2. Here, we pair a recent metabarcoding quantification approach with stable isotope analysis to examine diet composition in a wolf spider community.

3. We compare the prevalence of resource partitioning and IGP in these spiders and test whether factors that influence foraging performance, including individual identity, morphology, prey community …

Pathways Of Density Dependence And Natural Selection In Modern Humans, John Delong

School of Biological Sciences: Faculty Publications

Living things depend on a flow of energy and materials to grow, reproduce, and maintain their bodies. Populations are aggregations of individuals, so they too depend on resources. Humans use many fuels derived from the Earth’s photosynthetic energy, which in turn support a population that often occurs at unusually high densities for a mammal. Like most populations, growing human populations may experience negative feedbacks from population size unless the socio-economic system in which the population lives grows fast enough to maintain resource flows to individuals and to limit the downsides of high density. I map out a simple view of …

Functionally Redundant Multimodal Predator Cues Elicit Changes In Prey Foraging Behavior, Fiona G. Shogren, Eileen Hebets, John Delong

School of Biological Sciences: Faculty Publications

Many prey species can assess the risk of predation from information acquired through different sensory systems. For many animals, this information is detected with sensory organs specialized for visual (sight) or chemical (smell or taste) stimuli. It is unclear; however, whether information acquired through multiple sensory systems is functionally redundant or interchangeable, especially if the message is the same. Here, we assess prey response to unimodal visual and chemical cues as well as multimodal (visual + chemical) cues. We specifically test if a foraging individual shows a stronger behavioral response to risk when they can perceive that risk through multimodal …

Longitudinal Variations In Antibody Responses Against Sars-Cov-2 Spike Epitopes Upon Serial Vaccinations, Dicle Yalcin, Sydney J. Bennett, Jared Sheehan, Amber J. Trauth, For Yue Tso, John T. West, Michael E. Hagensee, Alistair J. Ramsay, Charles Wood

School of Biological Sciences: Faculty Publications

The COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) impacted healthcare, the workforce, and worldwide socioeconomics. Multi-dose mono- or bivalent mRNA vaccine regimens have shown high efficacy in protection against SARSCoV- 2 and its emerging variants with varying degrees of efficacy. Amino acid changes, primarily in the receptor-binding domain (RBD), result in selection for viral infectivity, disease severity, and immune evasion. Therefore, many studies have centered around neutralizing antibodies that target the RBD and their generation achieved through infection or vaccination. Here, we conducted a unique longitudinal study, analyzing the effects of a three-dose mRNA vaccine …

Gene Regulatory Changes Underlie Developmental Plasticity In Respiration And Aerobic Performance In Highland Deer Mice, Rena M. Schweizer, Catherine M. Ivy, Chandrasekhar Natarajan, Graham R. Scott, Jay F. Storz, Zachary A. Cheviron

School of Biological Sciences: Faculty Publications

Phenotypic plasticity can play an important role in the ability of animals to tolerate environmental stress, but the nature and magnitude of plastic responses are often specific to the developmental timing of exposure. Here, we examine changes in gene expression in the diaphragm of highland deer mice (Peromyscus maniculatus) in response to hypoxia exposure at different stages of development. In highland deer mice, developmental plasticity in diaphragm function may mediate changes in several respiratory traits that influence aerobic metabolism and performance under hypoxia. We generated RNAseq data from diaphragm tissue of adult deer mice exposed to (1) life-long …

Higher Concentrations Of Microplastics In Runoff From Biosolid-Amended Croplands Than Manure-Amended Croplands, Nasrin Naderi Beni, Shahab Karimifard, John Gilley, Tiffany Messer, Amy Schmidt, Shannon L. Bartelt-Hunt

Department of Civil and Environmental Engineering: Faculty Publications

Land-applied municipal biosolids, produced from municipal wastewater treatment sludge, contributes to microplastics contamination in agroecosystems. The impacts of biosolids on microplastic concentrations in agricultural soil have been previously investigated, however, the potential for microplastics transport from biosolid-amended croplands has not been previously quantified. In this study, manure and biosolids were applied to field plots, runoff was collected following natural precipitation events and the potential of bacterial biofilm to grow on different microplastic morphologies was investigated. Higher concentrations of microplastics were detected in runoff from plots with land-applied biosolid in comparison with manure-amended and control plots. Fibers and fragments were the …

Histidine Enhances The Anticancer Effect Of Gemcitabine Against Pancreatic Cancer Via Disruption Of Amino Acid Homeostasis And Oxidant—Antioxidant Balance, Narendra Kumar, Satyanarayana Rachagani, Gopalakrishnan Natarajan, Alexandra Crook, Thiyagarajan Gopal, Vinothkumar Rajamanickam, Jyoti B. Kaushal, Sirpu N. Nagabhishek, Robert Powers, Surinder K. Batra, Viswanathan Saraswathi

Robert Powers Publications

Simple Summary: Amino acid metabolism is aberrantly altered in pancreatic cancer (PC). Evidence suggests that circulating histidine (His) levels are low in PC. However, the role of His in modulating the progression of PC remains unknown. We determined the role of His in altering the therapeutic effectiveness of gemcitabine (Gem) against PC. We provide evidence that the expression of histidine ammonia lyase (HAL), an enzyme involved in His catabolism, is greatly increased in mouse and human pancreatic tumors. We show that combining His with Gem led to enhanced cytotoxic effects against aggressive PC cell lines. Our metabolomics analysis revealed that …

Multiplatform Untargeted Metabolomics, Micah J. Jeppesen, Robert Powers

Robert Powers Publications

Metabolomics samples like human urine or serum contain upwards of a few thousand metabolites, but individual analytical techniques can only characterize a few hundred metabolites at best. The uncertainty in metabolite identification commonly encountered in untargeted metabolomics adds to this low coverage problem. A multiplatform (multiple analytical techniques) approach can improve upon the number of metabolites reliably detected and correctly assigned. This can be further improved by applying synergistic sample preparation along with the use of combinatorial or sequential non-destructive and destructive techniques. Similarly, peak detection and metabolite identification strategies that employ multiple probabilistic approaches have led to better annotation …

Germination And Simulated Gastrointestinal Digestion Of Chickpea (Cicer Arietinum L.) In Exhibiting In Vitro Antioxidant Activity In Gastrointestinal Epithelial Cells, Ashley Newton, Kaustav Majumder

Department of Food Science and Technology: Faculty Publications

Plant-based proteins, in particular pulse proteins, have grown in popularity worldwide. Germination, or sprouting, is an effective method to release peptides and other dietary compounds. However, the combination of germination and gastrointestinal digestion in enhancing the release of dietary compounds with potential health-beneficial biological activity has yet to be entirely elucidated. The present study illustrates the impact of germination and gastrointestinal digestion on the release of dietary compounds with antioxidant activity from chickpeas (Cicer arietinum L.). Germination up to 3 days (D0 to D3) increased the peptide content by denaturing chickpea storage proteins and increased the degree of hydrolysis …

Warm Land Surface Temperatures And Eastern Asian Homo, Robert Patalano, Hong Yang

Biological and Biomedical Sciences Department Faculty Journal Articles

Climate change and hominin evolution are inextricably linked. Pleistocene climate variability, for example, is thought to have had major influences on hominin morphology, brain size, and diversity. However, clear cause-and-effect relationships between specific climatic events and major evolutionary occurrences are difficult to establish due to temporal and spatial gaps in paleoclimatic, paleoenvironmental, and archaeological records. A new branched GDGT paleotemperature record from the Lantian Basin of Central China (Lu et al., 2022), a location known for the earliest hominin presence in East Asia, illustrates warm land surface temperatures over a two-million-year period between 2.6 and 0.6 Ma, a critical time …

The Expression And Significance Of Long Non-Coding Rna Itgb2-As1 In Renal Clear Cell Carcinoma, Wei Zhou, Zhi-Gang Liu, Lian-Qu Wang

Saudi Medical Journal

Objectives: To explore the expression and significance of long non-coding RNA ITGB2-AS1 in kidney renal clear cell carcinoma (KIRC). Methods: The expression of ITGB2-AS1 in KIRC tissues of 45 KIRC patients in the first affiliated hospital of Henan University, Henan, China, from September 2018 to December 2020, KIRC cells were detected and the relationship of ITGB2-AS1 and overall survival of KIRC patients were analyzed. The expression of ITGB2-AS1 in KIRC cells Caki-1 and ACHN was interfered, and the changes of cell proliferation, invasion, migration, and apoptosis were detected. Dual luciferase reporter gene assay and RNA pull-down assay were carried out …

Morbidity Profile Among Older People At Primary Health Care Centers In Saudi Arabia During The Period 2012-2020, Maysoon M. Al-Amoud, Doaa I. Omar, Eman N. Almashjary, Shaker A. Alomary

Saudi Medical Journal

Objectives: To evaluate the morbidity profile and explore the geriatric giants, health problems, and their risk factors among old people in the older people health clinics at primary health care centers (PHCCs) in Saudi Arabia. Methods: This is a record-based descriptive cross-sectional study. Data was collected between 2012-2020 using the health data of older people to whom comprehensive geriatric assessment (CGA) was carried out at 1,481 PHCCs in Saudi Arabia. Data included sociodemographic and health related characteristics, medications, results of CGA, complete clinical examination, and laboratory results. Assessment was carried out for diabetes, hypertension, obesity, underweight, vision and hearing impairments, …

Post-Traumatic Stress Disorders Among Syrian Refugees Residing In Non-Camp Settings In Jordan, Iman A. Basheti, Shahnaz Mohammed Ayasrah, Rajaa Ali Al-Qudah

Saudi Medical Journal

Objectives: To measure the prevalence and severity of post-traumatic stress disorders (PTSD) among Syrian refugees and explore its association with various factors. Methods: A cross-sectional study was carried out among a convenience snowball sample of Syrian refugees residing in non-camp settings in Jordan in 2019. A 4-part self-administered structured questionnaire was used to collect data. Part one included socio-demographic data, part 2 included an Arabic version of Harvard Trauma Questionnaire (HTQ) (part I: trauma event and part IV: trauma symptoms), part 3 was related to participants’ physical symptoms, and part 4 to participants’ satisfaction with the healthcare they received. Results: …

Short-Term Risk Estimation And Treatment Planning For Cardiovascular Disease Patients After First Diagnostic Catheterizations With Machine Learning Models, Guochang Ye, Peshala Thibbotuwawa Gamage, Vignesh Balasubramanian, John K.-J. Li, Ersoy Subasi, Munevver Mine Subasi, Mehmet Kaya

Mathematics and System Engineering Faculty Publications

Cardiovascular disease (CVD) is the leading cause of death. CVD symptoms may develop within a short-term after diagnostic catheterizations and lead to life-threatening situations. This study is the first to apply machine learning (ML) methods to predict subsequent adverse cardiovascular events/treatments for patients within 90 days after their first diagnostic catheterizations. Patients (6539) without previously diagnosed CVD were selected from the DukeCath dataset. Ten ML methods were used. Three medical outcomes, varied cardiovascular-related scenarios, percutaneous coronary intervention (PCI) treatments, and coronary artery bypass graft (CABG) treatments, were targeted individually. With patient medical history, vital measurements, laboratory results, and the number …

An Investigation Of The Effect Of Cyclic Loading Of Bone On Osteocyte Processes Spanning Micro-Cracks As A Driver Of Targeted Remodelling Of Bone, Morgana Pires Afonso Shirsath

Doctoral

Bone remodelling is essential to maintain and improve the quality of bones. This occurs with the action of specialised cells - osteoclasts and osteoblasts - which replace the old bone tissue with new in regions where damage has occurred. Osteocytes are responsible for signalling the presence of damage and trigger the bone remodelling response. According to the Scissors Model, the presence of micro-cracks causes rupture of the osteocyte processes by fatigue because of the repeated stretching resulting from the relative movement of micro-crack faces, when bone is subjected to cyclic loads.