Digital Commons Network^™

Psychometric Properties Of The Standardized Assessment Of Concussion In Youth Football: Validity, Reliability, And Demographic Factors, Arthur C. Maerlender, Eric Smith, P. Gunnar Brolinson, Jillian Urban, Steven Rowson, Amaris Ajamil, Eamon T. Campolettano, Ryan A. Gellner, Srinidhi Bellamkonda, Mireille E. Kelley, Derek Jones, Alex Powers, Jonathan Beckwith, Joseph J. Crisco, Joel Stitzel, Stefan Duma, Richard M. Greenwald

Center for Brain, Biology, and Behavior: Faculty Publications

The objective of this study was to determine the psychometrics (reliability, validity) of the original Standardized Assessment of Concussion (SAC) in a youth sample (ages 11 to 13). Demographic factors of race, level of vocabulary knowledge, mother’s level of education were also considered. Over 150 youth football athletes completed the SAC and a brief battery of NIH Toolbox cognitive tests as part of a larger study on biomechanical factors in youth sport concussion. This was a within-subjects design (pre-season, post-season assessments), and correlational analysis of convergent and discriminant validity. Between groups analysis based on demographic differences was also employed. The …

Modeling Interactions Between Brain Function, Diet Adherence Behaviors, And Weight Loss Success, Amanda N. Szabo-Reed, Laura E. Martin, Jinxiang Hu, Hung-Wen Yeh, Joshua Powell, Rebecca J. Lepping, Trisha M. Patrician, Florance J. Breslin, Joseph E. Donnelly, Cary R. Savage

Center for Brain, Biology, and Behavior: Faculty Publications

Summary

Introduction: Obesity is linked to altered activation in reward and control brain cir-cuitry; however, the associated brain activity related to successful or unsuccessful weight loss (WL) is unclear.

Methods: Adults with obesity (N = 75) completed a baseline functional magnetic res-onance imaging (fMRI) scan before entering a WL intervention (ie,3-month diet and physical activity [PA] program). We conducted an exploratory analysis to identify the contributions of baseline brain activation, adherence behavior patterns, and the asso-ciated connections to WL at the conclusion of a 3-month WL intervention. Food cue-reactivity brain regions were functionally identified using fMRI to index brain activation …

Males With Chronic Ankle Instability Demonstrate Deficits In Neurocognitive Function Compared To Control And Copers, Adam B. Rosen, Melanie L. Mcgrath, Arthur C. Maerlender

Center for Brain, Biology, and Behavior: Faculty Publications

The purpose of this study was to determine if there were neurocognitive deficits among controls, copers and those with chronic ankle instability (CAI). Participants included those without history of ankle injury (n = 14), ankle sprain copers (n = 13) and patients with self-reported CAI (n = 14). They completed a battery of valid and reliable computer-based neurocognitive tests. The differences between neurocognitive domain scores were compared across the Control, Coper and CAI groups. Patients with CAI had lower composite memory, visual memory and simple attention compared to controls. In males with CAI, large differences in memory and attention were …

Neural Bases Of Phonological And Semantic Processing In Early Childhood, Avantika Mathur, Douglas H. Schultz, Yingying Wang Dr.

Center for Brain, Biology, and Behavior: Faculty Publications

During the early period of reading development, children gain phonological (letter-to-sound mapping) and semantic knowledge (storage and retrieval of word meaning). Their reading ability changes rapidly, accompanied by learning-induced brain plasticity as they learn to read. This study aims at identifying the neural bases of phonological and semantic processing in early childhood by using a combination of univariate and multivariate pattern analysis. Nineteen typically developing children between the age of five and seven performed visual word-level phonological (rhyming) and semantic (related meaning) judgment tasks during functional magnetic resonance imaging scans. Our multivariate analysis showed that young children with good reading …

Semantic Segmentation Of Sorghum Using Hyperspectral Data Identifies Genetic Associations, Chenyong Miao, Alejandro Pages, Zheng Xu, Eric Rodene, Jinliang Yang, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

This study describes the evaluation of a range of approaches to semantic segmentation of hyperspectral images of sorghum plants, classifying each pixel as either nonplant or belonging to one of the three organ types (leaf, stalk, panicle). While many current methods for segmentation focus on separating plant pixels from background, organ-specific segmentation makes it feasible to measure a wider range of plant properties. Manually scored training data for a set of hyperspectral images collected from a sorghum association population was used to train and evaluate a set of supervised classification models. Many algorithms show acceptable accuracy for this classification task. …

Isoseq Transcriptome Assembly Of C3 Panicoid Grasses Provides Tools To Study Evolutionary Change In The Panicoideae, Daniel S. Carvalho, Aime V. Nishimwe, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

The number of plant species with genomic and transcriptomic data has been increasing rapidly. The grasses—Poaceae—have been well represented among species with published reference genomes. However, as a result the genomes of wild grasses are less frequently targeted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses can aid the study of domestication, gene discovery for breeding and crop improvement, and improve our understanding of the evolution of C₄ photosynthesis. Here, we used long-read sequencing technology to characterize the transcriptomes of three C₃ panicoid grass species: Dichanthelium oligosanthes, Chasmanthium laxum, and …

Oxidosqualene Cyclases Involved In The Biosynthesis Of Triterpenoids In Quercus Suber Cork, Lucas Busta, Olga Serra, Ok Tae Kim, Marisa Molinas, Irene Peré-Fossoul, Mercè Figueras, Reinhard Jetter

Center for Plant Science Innovation: Faculty Publications

Cork is a water-impermeable, suberin-based material harboring lignin, (hemi)cellulose, and extractable small molecules (primarily triterpenoids). Extractables strongly influence the properties of suberin-based materials. Though these previous findings suggest a key role for triterpenoids in cork material quality, directly testing this idea is hindered in part because it is not known which genes control cork triterpenoid biosynthesis. Here, we used gas chromatography and mass spectrometry to determine that the majority (>85%) of non-polar extractables from cork were pentacyclic triterpenoids, primarily betulinic acid, friedelin, and hydroxy-friedelin. In other plants, triterpenoids are generated by oxidosqualene cyclases (OSCs). Accordingly, we mined Quercus suber …

Plant Segmentation By Supervised Machine Learning Methods, Jason Adams, Yumou Qiu, Yuhang Xu, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

High-throughput phenotyping systems provide abundant data for statistical analysis through plant imaging. Before usable data can be obtained, image processing must take place. In this study, we used supervised learning methods to segment plants from the background in such images and compared them with commonly used thresholding methods. Because obtaining accurate training data is a major obstacle to using supervised learning methods for segmentation, a novel approach to producing accurate labels was developed. We demonstrated that, with careful selection of training data through such an approach, supervised learning methods, and neural networks in particular, can outperform thresholding methods at segmentation.

Advances In Plant Phenomics: From Data And Algorithms To Biological Insights, Sunil Kumar Kenchanmane Raju, Addie M. Thompson, James Schnable

Center for Plant Science Innovation: Faculty Publications

The measurement of the characteristics of living organisms is referred to as phenotyping (Singh et al., 2016). While the use of phenotyping in plant biology and genetics can be traced back at least to Gregor Mendel sorting and counting peas by shape and pod color 160 years ago, addressing current questions in plant biology, genetics, and breeding often requires increasingly precise phenotyping of a wide range of traits. Accurate phenotyping has played a role in both novel discoveries about the fundamental biology of plants and the development of improved crop varieties around the world. With the advent of inexpensive genotyping …

Leaf Angle Extractor: A High-Throughput Image Processing Framework For Leaf Angle Measurements In Maize And Sorghum, Sunil Kumar Kenchanmane Raju, Miles Adkins, Alex Enersen, Daniel Santana De Carvalho, Anthony J. Studer, Baskar Ganapathysubramanian, Patrick S. Schnable, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

PREMISE: Maize yields have significantly increased over the past half-century owing to advances in breeding and agronomic practices. Plants have been grown in increasingly higher densities due to changes in plant architecture resulting in plants with more upright leaves, which allows more efficient light interception for photosynthesis. Natural variation for leaf angle has been identified in maize and sorghum using multiple mapping populations. However, conventional phenotyping techniques for leaf angle are low throughput and labor intensive, and therefore hinder a mechanistic understanding of how the leaf angle of individual leaves changes over time in response to the environment.

METHODS …

Methods And Compositions For Obtaining Useful Plant Traits, Sally Mackenzie, Michael Fromm, Kamaldeep Viridi, Yashitola Wamboldt

Center for Plant Science Innovation: Faculty Publications

The present invention provides methods for obtaining plants that exhibit useful traits by perturbation of plastid function in plant rootstocks and grafting the rootstocks to scions. Methods for identifying genetic loci that provide for useful traits in plants and plants produced with those loci are also provided. In addition, plants that exhibit the useful traits, parts of the plants including seeds, and products of the plants are provided as well as methods of using the plants. Recombinant DNA vectors and transgenic plants comprising those vectors that provide for plastid perturbation are also provided.

Interspecific Analysis Of Diurnal Gene Regulation In Panicoid Grasses Identifies Known And Novel Regulatory Motifs, Xianjun Lai, Claire Bendix, Lang Yan, Yang Zhang, James C. Schnable, Frank G. Harmon

Center for Plant Science Innovation: Faculty Publications

Background: The circadian clock drives endogenous 24-h rhythms that allow organisms to adapt and prepare for predictable and repeated changes in their environment throughout the day-night (diurnal) cycle. Many components of the circadian clock in Arabidopsis thaliana have been functionally characterized, but comparatively little is known about circadian clocks in grass species including major crops like maize and sorghum.

Results: Comparative research based on protein homology and diurnal gene expression patterns suggests the function of some predicted clock components in grasses is conserved with their Arabidopsis counterparts, while others have diverged in function. Our analysis of diurnal gene expression in …

Voxel Carving-Based 3d Reconstruction Of Sorghum Identifies Genetic Determinants Of Light Interception Efficiency, Mathieu Gaillard, Chenyong Miao, James C. Schnable, Bedrich Benes

Center for Plant Science Innovation: Faculty Publications

Changes in canopy architecture traits have been shown to contribute to yield in- creases. Optimizing both light interception and light interception efficiency of agri- cultural crop canopies will be essential to meeting the growing food needs. Canopy architecture is inherently three-dimensional (3D), but many approaches to measuring canopy architecture component traits treat the canopy as a two-dimensional (2D) structure to make large scale measurement, selective breeding, and gene identifi- cation logistically feasible. We develop a high throughput voxel carving strategy to reconstruct 3D representations of sorghum from a small number of RGB photos. Our approach builds on the voxel carving …

Compounds For Increasing Lipid Synthesis And Storage, Concetta Dirusso, Nishikant Wase

Center for Plant Science Innovation: Faculty Publications

This invention relates to methods for increasing lipid accumulation and lipid production in cells. Methods of producing biofuel from cells and preparing nutraceuticals comprising lipids produced according to a method provided herein are also provided.

Non-Homology-Based Prediction Of Gene Functions In Maize (Zea Mays Ssp. Mays), Xiuru Dai, Zheng Xu, Zhikai Liang, Xiaoyu Tu, Silin Zhong, James C. Schnable, Pinghua Li

Center for Plant Science Innovation: Faculty Publications

Advances in genome sequencing and annotation have eased the difficulty of identifying new gene sequences. Predicting the functions of these newly identified genes remains challenging. Genes descended from a common ancestral sequence are likely to have common functions. As a result, homology is widely used for gene function pre- diction. This means functional annotation errors also propagate from one species to another. Several approaches based on machine learning classification algorithms were evaluated for their ability to accurately predict gene function from non-homology gene features. Among the eight supervised classification algorithms evaluated, random- forest-based prediction consistently provided the most accurate gene …

A High-Throughput Phenotyping Pipeline For Image Processing And Functional Growth Curve Analysis, Ronghao Wang, Yumuo Qiu, Yuzhen Zhou, Zhikai Liang, James Schnable

Center for Plant Science Innovation: Faculty Publications

High-throughput phenotyping system has become more and more popular in plant science research. The data analysis for such a system typically involves two steps: plant feature extraction through image processing and statistical analysis for the extracted features. The current approach is to perform those two steps on different platforms. We develop the package “implant” in R for both robust feature extraction and functional data analysis. For image processing, the “implant” package provides methods including thresholding, hidden Markov random field model, and morphological operations. For statistical analysis, this package can produce nonparametric curve fitting with its confidence region for plant growth. …

Leaf Angle Extractor: A High-Throughput Image Processing Framework For Leaf Angle Measurements In Maize And Sorghum, Sunil Kumar Kenchanmane Raju, Miles Adkins, Alex Enersen, Daniel Santana De Carvalho, Anthony J. Studer, Baskar Ganapathysubramanian, Patrick Schnable, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

PREMISE: Maize yields have significantly increased over the past half-century owing to advances in breeding and agronomic practices. Plants have been grown in increasingly higher densities due to changes in plant architecture resulting in plants with more upright leaves, which allows more efficient light interception for photosynthesis. Natural variation for leaf angle has been identified in maize and sorghum using multiple mapping populations. However, conventional phenotyping techniques for leaf angle are low throughput and labor intensive, and therefore hinder a mechanistic understanding of how the leaf angle of individual leaves changes over time in response to the environment.

METHODS: High-throughput …

Advances In Plant Phenomics: From Data And Algorithms To Biological Insights, Sunil K. Kenchanmane Raju, Addie M. Thompson, James Schnable

Center for Plant Science Innovation: Faculty Publications

The measurement of the characteristics of living organisms is re- ferred to as phenotyping (Singh et al., 2016). While the use of phe- notyping in plant biology and genetics can be traced back at least to Gregor Mendel sorting and counting peas by shape and pod color 160 years ago, addressing current questions in plant biology, genet- ics, and breeding often requires increasingly precise phenotyping of a wide range of traits. Accurate phenotyping has played a role in both novel discoveries about the fundamental biology of plants and the development of improved crop varieties around the world. With the advent …

Metabolic Profiles Of Six African Cultivars Of Cassava (Manihot Esculenta Crantz) Highlight Bottlenecks Of Root Yield, Toshihiro Obata, Patrick A.W. Klemens, Laise Rosado-Souza, Armin Schlereth, Andreas Gisel, Livia Stavolone, Wolfgang Zierer, Nicolas Morales, Lukas A. Mueller, Samuel C. Zeeman, Frank Ludewig, Mark State, Uwe Sonnewald, H. Ekkehard Neuhaus, Alisdair R. Femie

Center for Plant Science Innovation: Faculty Publications

Cassava is an important staple crop in sub-Saharan Africa, due to its high productivity even on nutrient poor soils. The metabolic characteristics underlying this high productivity are poorly understood including the mode of photosynthesis, reasons for the high rate of photosynthesis, the extent of source/sink limitation, the impact of environment, and the extent of variation between cultivars. Six commercial African cassava cultivars were grown in a greenhouse in Erlangen, Germany, and in the field in Ibadan, Nigeria. Source leaves, sink leaves, stems and storage roots were harvested during storage root bulking and analyzed for sugars, organic acids, amino acids, phosphorylated …

Increased Power And Accuracy Of Causal Locus Identification In Time Series Genome-Wide Association In Sorghum1[Open], Chenyong Miao, Yuhang Xu, Sanzhen Liu, Patrick S. Schnable, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

The phenotypes of plants develop over time and change in response to the environment. New engineering and computer vision technologies track these phenotypic changes. Identifying the genetic loci regulating differences in the pattern of phenotypic change remains challenging. This study used functional principal component analysis (FPCA) to achieve this aim. Time series phenotype data were collected from a sorghum (Sorghum bicolor) diversity panel using a number of technologies including conventional color photography and hyperspectral imaging. This imaging lasted for 37 d and centered on reproductive transition. A new higher density marker set was generated for the same population. Several genes …

Using Climate To Explain And Predict West Nile Virus Risk In Nebraska, Kelly Smith, Andrew Tyre, Jeff Hamik, Michael Hayes, Yuzhen Zhou, Li Dai

National Drought Mitigation Center: Faculty Publications

We used monthly precipitation and temperature data to give early warning of years with higher West Nile Virus (WNV) risk in Nebraska. We used generalized additive models with a negative binomial distribution and smoothing curves to identify combinations of extremes and timing that had the most influence, experimenting with all combinations of temperature and drought data, lagged by 12, 18, 24, 30, and 36 months. We fit models on data from 2002 through 2011, used Akaike's Information Criterion (AIC) to select the best‐fitting model, and used 2012 as out‐of‐sample data for prediction, and repeated this process for each successive year, …

Recommendations On Alaskan Arctic Coast Port Access Route Study

United States Marine Mammal Commission

No abstract provided.

Maker Fridays: Engaging Rural And Underrepresented High School Students In Pre-Engineering Design And Creativity, Michelle Howell-Smith, Kirstie Bash

Nebraska Center for Research on Children, Youth, Families, and Schools: Faculty Publications

The engineering field struggles to develop sufficient interest and sustained participation across underrepresented demographic groups including women and individuals from rural, Hispanic, or Native American origin. It is critical to foster interest in engineering during formative years when students are deciding career paths. Northeast Community College (Northeast) addressed the shortage of diverse students entering into engineering fields by developing a course to engage rural and underrepresented high school students in maker design and creativity and to determine best practices that attract and retain these students. The Maker Fridays pre-engineering course was part of the Fridays@Northeast program that targets high school …

Quantitative Nmr-Based Biomedical Metabolomics: Current Status And Applications, Alexandra A. Crook, Robert Powers

Department of Chemistry: Faculty Publications

Nuclear Magnetic Resonance (NMR) spectroscopy is a quantitative analytical tool commonly utilized for metabolomics analysis. Quantitative NMR (qNMR) is a field of NMR spectroscopy dedicated to the measurement of analytes through signal intensity and its linear relationship with analyte concentration. Metabolomics-based NMR exploits this quantitative relationship to identify and measure biomarkers within complex biological samples such as serum, plasma, and urine. In this review of quantitative NMR-based metabolomics, the advancements and limitations of current techniques for metabolite quantification will be evaluated as well as the applications of qNMR in biomedical metabolomics. While qNMR is limited by sensitivity and dynamic range, …

Methods Ofmaking And Using Lignin Derivatives, Mark Alan Helle, Chin Li Cheung

Department of Chemistry: Faculty Publications

Materials and methods for preparing reactive lignin and for preparing a bio-based adhesive are described herein.

Timber Talk, Vol. 58, No. 1, March 2020

Timber Talk: Nebraska Forest Industry Newsletter

Timber Talk, Vol. 58, No. 1, March 2020

Timber Talk, Vol. 58, No. 2, July 2020

Timber Talk: Nebraska Forest Industry Newsletter

Timber Talk, Vol. 58, No. 2, Junly2020

Timber Talk, Vol. 58, No. 3, September 2020

Timber Talk: Nebraska Forest Industry Newsletter

Timber Talk, Vol. 58, No. 3, September 2020

Geographic Distribution Of Chronic Wasting Disease Resistant Alleles In Nebraska, With Comments On The Evolution Of Resistance, H. Vazquez-Miranda, R. M. Zink

School of Natural Resources: Faculty Publications

No abstract provided.

Fire Support And Field Artillery Operations, United States Army

United States Army: Field Manuals

Fire Support and Field Artillery Operations, United States Army Field Manual FM 3-09