Environmental Engineering Commons^™

Minimal Interspecies Interaction Adjustment (Miia): Inference Of Neighbor-Dependent Interactions In Microbial Communities, Hyun-Seob Song, Joon-Yong Lee, Shin Haruta, William C. Nelson, Dong-Yup Lee, Stephen R. Lindemann, Jim K. Fredrickson, Hans C. Bernstein

Department of Agricultural and Biological Systems Engineering: Faculty Publications

An intriguing aspect in microbial communities is that pairwise interactions can be influenced by neighboring species. This creates context dependencies for microbial interactions that are based on the functional composition of the community. Context dependent interactions are ecologically important and clearly present in nature, yet firmly established theoretical methods are lacking from many modern computational investigations. Here, we propose a novel network inference method that enables predictions for interspecies interactions affected by shifts in community composition and species populations. Our approach first identifies interspecies interactions in binary communities, which is subsequently used as a basis to infer modulation in more …

Principal Variable Selection To Explain Grain Yield Variation In Winter Wheat From Features Extracted From Uav Imagery, Jiating Li, Arun-Narenthiran Veeranampalayam-Sivakumar, Madhav Bhatta, Nicholas D. Garst, Hannah Stoll, P. Stephen Baenziger, Vikas Belamkar, Reka Howard, Yufeng Ge, Jiating Li

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Background: Automated phenotyping technologies are continually advancing the breeding process. However, collecting various secondary traits throughout the growing season and processing massive amounts of data still take great efforts and time. Selecting a minimum number of secondary traits that have the maximum predictive power has the potential to reduce phenotyping efforts. The objective of this study was to select principal features extracted from UAV imagery and critical growth stages that contributed the most in explaining winter wheat grain yield. Five dates of multispectral images and seven dates of RGB images were collected by a UAV system during the spring growing …

Agenator: An Open Source Computer-Controlled Dry Aging System For Beef, Soon Kiat Lau, Felipe Azevedo Ribeiro, Jeyamkondan Subbiah, Chris R. Calkins

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Dry aging of beef is a process where beef is exposed to a controlled environment with the ultimate goal of drying the beef to improve its quality and value. Comprehensive investigations into the effects of various environmental conditions on dry aging are crucial for understanding and optimizing the process, but the lack of affordable equipment focused on data collection makes it difficult to do so. The Agenator was thus developed as an open source system with a suite of features for investigating dry aging such as: measuring and recording relative humidity, temperature, mass, air velocity, and fan rotational speed; precise …

A Machine Learning Approach For Improving Near-Real-Time Satellite-Based Rainfall Estimates By Integrating Soil Moisture, Ashish Kumar, Raaj Ramsankaran, Luca Brocca, Francisco Munoz-Arriola

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Near-real-time (NRT) satellite-based rainfall estimates (SREs) are a viable option for flood/drought monitoring. However, SREs have often been associated with complex and nonlinear errors. One way to enhance the quality of SREs is to use soil moisture information. Few studies have indicated that soil moisture information can be used to improve the quality of SREs. Nowadays, satellite-based soil moisture products are becoming available at desired spatial and temporal resolutions on an NRT basis. Hence, this study proposes an integrated approach to improve NRT SRE accuracy by combining it with NRT soil moisture through a nonlinear support vector machine-based regression (SVR) …

High-Speed, High-Frequency Ultrasound, In Utero Vector-Flow Imaging Of Mouse Embryos, Jeffrey A. Ketterling, Orlando Aristizabal, Billy Y. S. Yiu, Daniel H. Turnbull, Colin K. L. Phoon, Alfred C. H. Yu, Ronald H. Silverman

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Real-time imaging of the embryonic murine cardiovascular system is challenging due to the small size of the mouse embryo and rapid heart rate. High-frequency, linear-array ultrasound systems designed for small-animal imaging provide high-frame-rate and Doppler modes but are limited in regards to the field of view that can be imaged at fine-temporal and -spatial resolution. Here, a plane-wave imaging method was used to obtain high-speed image data from in utero mouse embryos and multi-angle, vector-flow algorithms were applied to the data to provide information on blood flow patterns in major organs. An 18-MHz linear array was used to acquire plane-wave …

Factors Related To Intra-Tendinous Morphology Of Achilles Tendon In Runners, Kai-Yu Ho, Ari Baquet, Yu-Jen Chang, Lung-Chang Chien, Michelle Harty, Gregory Bashford, Kornelia Kulig

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The purpose of this study was to determine and explore factors (age, sex, anthropometry, running and injury/pain history, tendon gross morphology, neovascularization, ankle range of motion, and ankle plantarflexor muscle endurance) related to intra-tendinous morphological alterations of the Achilles tendon in runners. An intra-tendinous morphological change was defined as collagen fiber disorganization detected by a low peak spatial frequency radius (PSFR) obtained from spatial frequency analysis (SFA) techniques in sonography. Ninety-one runners (53 males and 38 females; 37.9 ± 11.6 years) with 8.8 ± 7.3 years of running experience participated. Height, weight, and waist and hip circumferences were recorded. Participants …

A Role For Nanoparticles In Treating Traumatic Brain Injury, Badrul Alam Bony, Forrest M. Kievit

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Traumatic brain injury (TBI) is one of the main causes of disability in children and young adults, as well as a significant concern for elderly individuals. Depending on the severity, TBI can have a long-term impact on the quality of life for survivors of all ages. The primary brain injury can result in severe disability or fatality, and secondary brain damage can increase the complexities in cellular, inflammatory, neurochemical, and metabolic changes in the brain, which can last decades post-injury. Thus, survival from a TBI is often accompanied by lifelong disabilities. Despite the significant morbidity, mortality, and economic loss, there …

Rapeseed Seedling Stand Counting And Seeding Performance Evaluation At Two Early Growth Stages Based On Unmanned Aerial Vehicle Imagery, Biquan Zhao, Jian Zhang, Chenghai Yang, Guangsheng Zhou, Youchun Ding, Yeyin Shi, Dongyan Zhang, Jing Xie, Qingxi Liao

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The development of unmanned aerial vehicles (UAVs) and image processing algorithms for field-based phenotyping offers a non-invasive and effective technology to obtain plant growth traits such as canopy cover and plant height in fields. Crop seedling stand count in early growth stages is important not only for determining plant emergence, but also for planning other related agronomic practices. The main objective of this research was to develop practical and rapid remote sensing methods for early growth stage stand counting to evaluate mechanically seeded rapeseed (Brassica napus L.) seedlings. Rapeseed was seeded in a field by three different seeding devices. A …

Early Prediction Of Soybean Traits Through Color And Texture Features Of Canopy Rgb Imagery, Wenan Yuan, Nuwan Kumara Wijewardane, Shawn Jenkins, Geng Bai, Yufeng Ge, George L. Graef

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Global crop production is facing the challenge of a high projected demand, while the yields of major crops are not increasing at sufficient speeds. Crop breeding is an important way to boost crop productivity, however its improvement rate is partially hindered by the long crop generation cycles. If end-season crop traits such as yield can be predicted through early-season phenotypic measurements, crop selection can potentially be made before a full crop generation cycle finishes. This study explored the possibility of predicting soybean end-season traits through the color and texture features of early-season canopy images. Six thousand three hundred and eighty-three …

Heterologous Expression And Functional Characterization Of A Gh10 Endoxylanase From Aspergillus Fumigatus Var. Niveus With Potential Biotechnological Application, Josman Velasco, Bianca Oliva, Evandro Jose Mulinari, Leidy Patricia Quintero, Awana Da Silva Lima, Aline Larissa Goncalves, Thiago Augusto Goncalves, Andre Damasio, Fabio Marcio Squina, Adriane Maria Ferreira Milagres, Asmaa Abdella, Mark R. Wilkins, Fernando Segato

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Xylanases decrease the xylan content in pretreated biomass releasing it from hemicellulose, thus improving the accessibility of cellulose for cellulases. In this work, an endo-β-1,4-xylanase from Aspergillus fumigatus var. niveus (AFUMN-GH10) was successfully expressed. The structural analysis and biochemical characterization showed this AFUMN-GH10 does not contain a carbohydrate-binding module. The enzyme retained its activity in a pH range from 4.5 to 7.0, with an optimal temperature at 60°C. AFUMN-GH10 showed the highest activity in beechwood xylan. The mode of action of AFUMNGH10 was investigated by hydrolysis of APTS-labeled xylohexaose, which resulted in xylotriose and xylobiose as the main products. AFUMN-GH10 …

Time-Domain And Frequency-Domain Reflectometry Type Soil Moisture Sensor Performance And Soil Temperature Effects In Fine- And Coarse-Textured Soils, Y. Zhu, S. Irmak, A. J. Jhala, M. C. Vuran, A. Diotto

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The performances of six time-domain reflectometry (TDR) and frequency-domain reflectometry (FDR) type soil moisture sensors were investigated for measuring volumetric soil-water content (θ_v) in two different soil types. Soil-specific calibration equations were developed for each sensor using calibrated neutron probe-measured θ_v. Sensors were also investigated for their performance response in measuring θ_v to changes in soil temperature. The performance of all sensors was significantly different (P<0.05) than the neutron probe-measured θ_v, with the same sensor also exhibiting variation between soils. In the silt loam soil, the 5TE sensor had the lowest root mean squared error (RMSE) of 0.041 …

Optimization Of Process Parameters And Fermentation Strategy For Xylanase Production In A Stirred Tank Reactor Using A Mutant Aspergillus Nidulans Strain, Asmaa Abdella, Fernando Segato, Mark R. Wilkins

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The present work studied the optimization of aeration rate, agitation rate and oxygen transfer and the use of various batch fermentation strategies for xylanase production from a recombinant Aspergillus nidulans strain in a 3 L stirred tank reactor. Maximum xylanase production of 1250 U/mL with productivity of 313 U/mL/day was obtained under an aeration rate of 2 vvm and an agitation rate of 400 rpm using batch fermentation. The optimum volumetric oxygen transfer coefficient (kLa) for efficient xylanase production was found to be 38.6 h1. Fed batch mode and repeated batch fermentation was also performed with kLa was 38.6 h1. …

Antibiotic Resistance Gene Profile Changes In Cropland Soil After Manure Application And Rainfall, Morgan Meyers, Lisa Durso, John E. Gilley, Heidi Waldrip, Lana Castleberry, Amy Millmier Schmidt

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Land application of manure introduces gastrointestinal microbes into the environment, including bacteria carrying antibiotic resistance genes (ARGs). Measuring soil ARGs is important for active stewardship efforts to minimize gene flow from agricultural production systems; however, the variety of sampling protocols and target genes makes it difficult to compare ARG results between studies. We used polymerase chain reaction (PCR) methods to characterize and/or quantify 27 ARG targets in soils from 20 replicate, long-term no-till plots, before and after swine manure application and simulated rainfall and runoff. All samples were negative for the 10 b-lactamase genes assayed. For tetracycline resistance, only source …

Optimization Of Process Parameters And Fermentation Strategy For Xylanase Production In A Stirred Tank Reactor Using A Mutant Aspergillus Nidulans Strain, Asmaa Abdella, Fernando Segato, Mark R. Wilkins

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The present work studied the optimization of aeration rate, agitation rate and oxygen transfer and the use of various batch fermentation strategies for xylanase production from a recombinant Aspergillus nidulans strain in a 3 L stirred tank reactor. Maximum xylanase production of 1250 U/mL with productivity of 313 U/mL/day was obtained under an aeration rate of 2 vvm and an agitation rate of 400 rpm using batch fermentation. The optimum volumetric oxygen transfer coefficient (kLa) for efficient xylanase production was found to be 38.6 h-1. Fed batch mode and repeated batch fermentation was also performed with kLa was 38.6 h …

System For Optimizing Fed-Batch Hydrolysis Of Biomass, Chao Tai, Deepak R. Keshwani

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Provided herein is a system for optimizing the fed-batch hydrolysis of biomass.

System And Method For Monitoring Pleural Fluid, Dimitrios Miserlis, Kim Cluff, Abby M. Kelly, Suzanne J. Higgins, Max H. Twedt

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The disclosure is directed to intrapleural air leak detection and monitoring. According to various embodiments of the disclosure, an air leak may be detected utilizing at least one sensor to determine whether fluid extracted from a pleural cavity of a patient includes carbon dioxide and/or a second substance. The second substance may be a foreign substance inhaled by the patient to confirm presence of the air leak. The air leak may be further monitored over a period of time by collecting temporally successive measurements associated with detected concentrations of carbon dioxide. Therefore, tissue damage and recovery may be assessed according …

Hydrogen Peroxide Sensors For Biomedical Applications, Jakob Meier, Eric M. Hofferber, Joseph A. Stapleton, Nicole M. Iverson

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Hydrogen peroxide (H2O2) is an important molecule within the human body, but many of its roles in physiology and pathophysiology are not well understood. To better understand the importance of H2O2 in biological systems, it is essential that researchers are able to quantify this reactive species in various settings, including in vitro, ex vivo and in vivo systems. This review covers a broad range of H2O2 sensors that have been used in biological systems, highlighting advancements that have taken place since 2015.

Grain Yield, Crop And Basal Evapotranspiration, Production Functions And Water Productivity Response Of Drought-Tolerant And Non-Drought-Tolerant Maize Hybrids Under Different Irrigation Levels, And Population Densities: Part I. In Western Nebraska's Semi-Arid Environments, Ali T. Mohammed, Suat Irmak, William Kranz, Simon Van Donk, C. Dean Yonts

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Grain yield, crop evapotranspiration (ETc), basal evapotranspiration (ETb), ETc-yield production functions (ETYPF), and crop water use efficiency (CWUE) response of three drought-tolerant (DT) and one non-drought-tolerant (NDT) maize (Zea mays L.) hybrids to two plant population densities (PPDs) [84,000 plants ha-1 (high PPD) and 59,300 plants ha-1 (low PPD)] and three irrigation levels were researched at two semi-arid locations: North Platte (WCREC) and Scottsbluff (MAL), Nebraska, in 2010, 2011, and 2012. The irrigation levels were fully irrigated (FIT), early cutoff (ECOT), and rainfed (RFT). Precipitation in 2010 was above average, 2011 was a normal year, and 2012 was one of …

Microcontroller Based Granular Urea Application Attachment For Rice Transplanter, Md Towfiqur Rahman, Md Monjurul Alam, Md Mosharraf Hossain, Muhammad Rashed Al Mamun

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Transplanting and fertilizer application for rice production in Bangladesh are tedious, time consuming and laborious task, and mostly done manually. Mechanical transplanting of rice becoming popular in the country in recent years and few machines have been developed for granular urea deep placement, however, having some limitations. Placing granular urea precisely along with rice transplanting, an attempt was under taken to design and fabricate an electronic control granular urea applicator to be attach with a 4-row walk behind type rice transplanter. Fabrication of the electronic granular urea applicator was done in the workshop of the Department of Farm Power and …

Improving Retrievals Of Crop Vegetation Parameters From Remote Sensing Data, Nathaniel Levitan

Dissertations and Theses

Agricultural systems are difficult to model because crop growth is driven by the strongly nonlinear interaction of Genotype x Environment x Management (G x E x M) factors. Due to the nonlinearity in the interaction of these factors, the amount of data necessary to develop and utilize models to accurately predict the performance of agricultural systems at an operational scale is large. Satellite remote sensing provides the potential to vastly increase the amount of data available for modelling agricultural systems as a result of its high revisit time and spatial coverage. Unfortunately, there have been significant difficulties in deploying remote …

Variability Of E. Coli In Streambed Sediments And Its Implication For Water Quality, Sadia Salam

Electronic Theses and Dissertations

Fecal indicator bacteria (FIB), including E. coli, are the number one cause of water quality impairments in the United States according to the USEPA. FIB are used as a predictor to identify the possible presence of pathogens in waterbodies. E. coli is a useful indicator of gastrointestinal (GI) related illnesses from contact with fresh water. While surface water is routinely monitored for water quality, streambed sediments are rarely considered as a source of FIB to the overlying water column. This study focuses on understanding the variation of E. coli concentrations in streambed sediments and the potential impact of sediment sources …

Comparative Analysis Of Mosquito Trap Counts In The Peruvian Amazon: Effect Of Trap Type And Other Covariates On Counts And Diversity, George W. Peck, Fanny Castro-Llanos, Victor Lopez-Sifuentes, Erica Lindroth

Civil and Environmental Engineering Faculty Publications and Presentations

Efficient detection of multiple species of adult mosquitoes in various habitats using effective traps is a crucial 1st step in any disease prevention program. Novel trap types that target tropical vectors of human diseases require field testing in the habitat of the vector–disease system in question. This paper analyzes a series of mosquito trapping studies conducted at Mapacocha, San Juan Bautista District, Loreto, Peru, during August–September 2013 and April–May 2014. Six trap configurations were evaluated in forest and rural locations. Adult mosquito counts were analyzed using full Bayesian inference of multilevel generalized linear models and posterior probability point estimates of …

Invasion Of The P Elements: Tolerance Is Not Futile, Colin D. Meiklejohn, Justin P. Blumenstiel

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Organisms are locked in an eternal struggle with parasitic DNA sequences that live inside their genomes and wreak havoc on their host’s chromosomes as they spread through populations. To combat these parasites, host species have evolved elaborate mechanisms of resistance that suppress their activity. A new study in Drosophila indicates that, prior to the acquisition of resistance, individuals can vary in their ability to tolerate the activity of these genomic parasites, ignoring or repairing the damage they induce. This tolerance results from variation at genes involved in germline development and DNA damage checkpoints and suggests that these highly conserved cellular …

Causal Loop Development Activity, Ali Mirchi

All ECSTATIC Materials

Students will work in groups to develop a causal loop diagram (CLD) to illustrate the structure and expected behavior of the fictional water short state of Nevizonato facilitate qualitative discussion of expected outcomes of a proposed water management strategy. This activity requires familiarity with systems thinking and system dynamics modeling. CLDs are introduced as a fundamental systems thinking tool for conceptual modeling.

Cover Crops Have Negligible Impact On Soil Water In Nebraska Maize–Soybean Rotation, J. Burdette Barker, Derek M. Heeren, Katja Koehler-Cole, Charles Shapiro, Humberto Blanco-Canqui, Roger W. Elmore, Christopher A. Proctor, Suat Irmak, Charles A. Francis, Tim M. Shaver, Ali T. Mohammed

Department of Agricultural and Biological Systems Engineering: Faculty Publications

One perceived cost of integrating winter cover cropping in maize (Zea mays L.) and soybean [Glycine max (L.) Merr.] rotation systems is the potential negative impact on soil water storage available for primary crop production. The objective of this 3-year study was to evaluate the effects of winter cover crops on soil water storage and cover crop biomass production following no-till maize and soybean rotations. Locations were near Brule (west-central), Clay Center (south-central), Concord (northeast), and Mead (east-central), Nebraska, United States. Treatments included crop residue only (no cover crop) and a multi-species cover crop mix, both broadcast-seeded before …

Plant Community Composition, Floristic Quality, And Establishment Of Roadside Revegetation In Nebraska, Usa, Jonathan M. Soper

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Roadside revegetation poses a challenge and opportunity for biodiversity conservation, as the land area occupied by roadsides is not expected to decline in the future. In the context of roadside revegetation activities in rural regions dominated by agricultural land uses, revegetation efforts can establish plant communities that offer unique species that would otherwise be absent on the landscape. To determine the efficacy of roadside revegetation efforts in 1) providing plant communities of high biodiversity value and 2) meeting the expectations of roadside revegetation managers for establishment, we quantified botanical composition, floristic quality, and success in seeding efforts to meet manager …

Tradeoffs In Model Performance And Effort For Long-Term Phosphorus Leaching Based On In Situ Field Data, Ryan P. Freiberger, Derek M. Heeren, Dean E. Eisenhauer, Aaron R. Mittelstet, Guillermo Baigorria

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Phosphorus and N are critical nutrients for agriculture but are also responsible for surface water enrichment that leads to toxic algal growth. Although P loading to surface waters has traditionally been thought to occur primarily in surface runoff, contributions from subsurface transport can also be significant. The primary objectives of this research were to evaluate several methods of representing macropore flow and transport in a finite element model using plot-scale infiltration and leaching data and to compare several models of various levels of complexity to simulate long-term P leaching. To determine flow and transport parameters, single- and dual-porosity models in …

Portable Flux Tower Deployments Field Campaign Report, M. S. Torn, L Kuepper, S. C. Biraud, D. P. Billesbach

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Contents

Acronyms and Abbreviations...................................................................... iii

1.0 Summary ....................................................... 1

2.0 Results ........................................... 1

3.0 Publications and References ................................................. 2

4.0 Lessons Learned .................................................................... 2

U.S. Agro-Climate In 20th Century: Growing Degree Days, First And Last Frost, Growing Season Length, And Impacts On Crop Yields, Meetpal Singh Kukal, Suat Irmak

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Significant air temperature changes have occurred globally during the 20th century, which are spatially variable to a considerable degree and these changes can have substantial implications in agroecosystem productivity. The agroclimate indicators that are responsible in these contexts are first fall frost (FFF), last spring frost (LSF), climatological growing season (CGS) length, and heat accumulation (growing degree days, GDD). We explore spatial and temporal trends associated with these indices across the continental U.S. (CONUS) during 1900–2014 using datasets collected at 1218 sites. On average, FFF has been occurring later (by 5.4 days century⁻¹), and LSF has been occurring …

Development Of A Digital Rain-Sensing Irrigation Pump Controller And An Android Enabled Bluetooth Paddlewheel Flowmeter, Jayendra Mishra

Graduate Theses and Dissertations

For better irrigation efficiency, it is recommended that farmers track their water consumption to avoid over-irrigating. However, it is difficult to implement this as it is labor intensive to supervise pumps manually and available technologies require high investment. Therefore, a rain sensing pump controller for 3-phase electric irrigation pumps and a stand-alone portable Android enabled paddlewheel flowmeter has been developed to test their feasibility.

The pump timer is a retrofit device for irrigation pump panels. The controller allows an irrigator to start and stop the pump with less supervision. An infrared rain sensor is integrated with the controller to measure …