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Optfill: A Tool For Infeasible Cycle-Free Gapfilling Of Stoichiometric Metabolic Models, Wheaton L. Schroeder, Rajib Saha

Mid-America Transportation Center: Final Reports and Technical Briefs

Stoichiometric metabolic modeling, particularly genome-scale models (GSMs), is now an indispens- able tool for systems biology. The model reconstruction process typically involves collecting informa- tion from public databases; however, incomplete systems knowledge leaves gaps in any reconstruc- tion. Current tools for addressing gaps use databases of biochemical functionalities to address gaps on a per-metabolite basis and can provide multiple solutions but cannot avoid thermodynami- cally infeasible cycles (TICs), invariably requiring lengthy manual curation. To address these limita- tions, this work introduces an optimization-based multi-step method named OptFill, which performs TIC-avoiding whole-model gapfilling. We applied OptFill to three fictional prokaryotic models …

An Unseen Synchrony Or Recurrent Resource Pulse Opportunity? Linking Fisheries With Aeroecology, Henry H. Hansen, Mark Pegg, Matthew Van Den Broeke, Doug Watkinson, Eva C. Enders

School of Natural Resources: Faculty Publications

Understanding insect and fish interactions from a spatial and temporal perspec-tive can have implications on large-scale phenology in freshwater systems, yet current information is limited. We employed a novel approach of combining information from acoustic telemetry for six freshwater fish species and weather radar to assess the phenology of mayfly emergence and foraging patterns of freshwater fish. We hypothesized that freshwater fish conduct synchronous movements with annual mayfly hatches as a pulse resource opportunity. Gener-alized additive models were developed to assess movement distance as a func-tion of species and time; before, during, and after annual mayfly hatch events. A cross-section …

Literature Review: Global Neonicotinoid Insecticide Occurrence In Aquatic Environments, Josephus F. Borsuah, Tiffany L. Messer, Daniel D. Snow, Steve D. Comfort, Aaron R. Mittelstet

School of Natural Resources: Faculty Publications

Neonicotinoids have been the most commonly used insecticides since the early 1990s. Despite their efficacy in improving crop protection and management, these agrochemicals have gained recent attention for their negative impacts on non-target species such as honeybees and aquatic invertebrates. In recent years, neonicotinoids have been detected in rivers and streams across the world. Determining and predicting the exposure potential of neonicotinoids in surface water requires a thorough understanding of their fate and transport mechanisms. Therefore, our objective was to provide a comprehensive review of neonicotinoids with a focus on their fate and transport mechanisms to and within surface waters …

Nutrient Cycling In Forage Production Systems, David A. Wedin, Michael P. Russelle

School of Natural Resources: Faculty Publications

In most forage production systems, the nutrients needed for plant growth are provided by the microbially-mediated breakdown and release of plant-available mineral nutrients from dead plant tissues, livestock excreta, soil organic matter, and geochemically-bound mineral forms. Even in fertilized forage systems, determining appropriate fertilizer or manure application rates requires a “systems” approach on the part of the manager (Rotz et al. 2005; Wood et al. 2012). Fertilizer additions are simply one input in the system of inputs, outputs, pools, and fluxes that characterize nutrient cycling in a particular ecosystem.

Treenuts And Groundnuts In The Eat-Lancet Reference Diet: Concerns Regarding Sustainable Water Use, Davy Vanhama, Mesfin Mekonnen, Arjen Y. Hoekstra

Daugherty Water for Food Global Institute: Faculty Publications

The EAT-Lancet universal healthy reference diet recommends an increase in the consumption of healthy foods, among which treenuts and groundnuts. Both are, however, water-intensive products, with a large water footprint (WF) per unit of mass and protein and already today contribute to blue water stress in different parts of the world. The envisaged massive required increase in nut production to feed a global population with this reference diet, needs to occur in a water-sustainable way. In this paper, we identify and quantify where current nut production contributes to local blue water stress and discuss options for water-sustainable nut production. We …

Potential Of Using Spectral Vegetation Indices For Corn Green Biomass Estimation Based On Their Relationship With The Photosynthetic Vegetation Sub-Pixel Fraction, Luan Peroni Venancio, Everardo Chartuni Mantovani, Cibele Hummel Do Amaral, Christopher M.U. Neale, Ivo Zution Gonçalves, Roberto Filgueiras, Fernando Coelho Eugenio

Daugherty Water for Food Global Institute: Faculty Publications

Crop biomass (Bio) is one of the most important parameters of a crop, and knowledge of it before harvest is essential to help farmers in their decision making. Both green and dry Bio can be estimated from vegetation spectral indices (VIs) because they have a close relationship with accumulated absorbed photosynthetically active radiation (APAR), which is proportional to total Bio. The aims of this study were to analyze the potential capacity of spectral vegetation indices in estimating corn green biomass based on their relationship with the photosynthetic vegetation sub-pixel fraction derived from spectral mixture analysis and to analyze the best …

Center For Grassland Studies, Volume 26, Issue 4, Winter 2020

Center for Grassland Studies: Newsletters

Workshop Focused on Improving Beef Production Systems

Director’s Column

Brad Goetsch Receives Omtvedt Innovation Award

Scholarships and Fellowship Applications Now Open

Spring Prescribed Burning Season

Beth Hildebrant to Intern at Pinehurst Resort

Center Develops Online Resource Page

Congratulations to December 2020 Graduates!

Evaluation of an Alternative Cow-Calf System

Looking for Continuing Education Units?

Parental Report Of Outcomes From A Randomized Trial Of In-Home Family Services, Kristin Duppong-Hurley, Matthew Lambert, Irina Patwardhan, Jay L. Ringle, Ronald W. Thompson, Jennifer Farley

University of Nebraska Public Policy Center: Publications

This study conducted a randomized trial to examine the efficacy of the Boys Town In-Home Family Services (IHFS) program for families of high-risk youth. Participants were recruited from a state helpline for families struggling with poor family functioning and child emotional or behavioral issues. Consent was obtained for 300 of which 152 were randomly assigned to participate in IHFS for 3–4 months and 148 were assigned to the services as usual comparison group. For the families in the treatment group, 18% did not participant in the intervention, and 66% of families received 20 or more service hours. Parent report data …

2nd-3rd Grade: English Level 3, Learning Packet #3 • Theme: Taking Care Of Myself, Samantha Monter, Tricia Gray, Kara Mitchell Viesca, Alexa Yunes

ICMEE Learning Packets: Level 3 of English Proficiency (K-12)

My Plan for the Week

Choose activities from the different content areas to complete each day. You can choose one or two activities from different areas to do during the day. Below is a list of the activities in each content area.

Reading - Food Groups - What we eat - Handwashing

Writing/ Grammar - How do you take care of yourself - How To Writing - Exercise Journal - Suffix Organizer - Suffix Matching

Vocabulary - Dictionary - Vocabulary Matching - Vocabulary Sentences

Physical Education - Yoga - Create a Workout - Walk around Your Neighborhood

Math - Crack …

4th-5th Grade: English Level 3, Learning Packet #4 • Theme: Nutrition, Claudia T. Yunes, Nicole M. Ponti, Tricia Gray, Alexa Yunes

ICMEE Learning Packets: Level 3 of English Proficiency (K-12)

These packets are self-contained. Everything a child will need to be successful with the activities is provided in the packet. Students will only need a writing utensil. Additional tools like crayons or scissors can be used, but do not have to be.

My Buddy, Choose a Buddy

Nutrition Glossary

Vocabulary Practice

Food from Many Cultures

Healthy Notes

How to Create 5 Days of Healthy Dinner

My 5-Day Dinner Menu Planner

My Physical Activity Planner

Cooking My Favorite Healthy Meal Sensory Poem

Family Cook Together

My Recipe

Math Unit Conversions

Kitchen Conversion Math

Food Components

My Informational Text in 3-2-1

Understanding …

Research And Creative Activity, July 1, 2019-June 30, 2020: Major Sponsored Programs And Faculty Accomplishments In Research And Creative Activity, University Of Nebraska-Lincoln, Office Of Research And Economic Development, University Of Nebraska–Lincoln

Office of Research and Economic Development: Publications

Foreword by Bob Wilhelm, Vice Chancellor for Research and Economic Development:

This booklet highlights successes in research, scholarship and creative activity by University of Nebraska–Lincoln faculty during the fiscal year running July 1, 2019, to June 30, 2020.

It lists investigators, project titles and funding sources on major grants and sponsored awards received during the year; fellowships and other recognitions and honors bestowed on our faculty; books published by faculty; performances, exhibitions and other creative activity; and patents and licensing agreements issued. Based on your feedback, the Office of Research and Economic Development expanded this publication to include peer-reviewed journal …

Survival Of A Serotype 4b Strain And A Serotype 1/2a Strain Of Listeria T Monocytogenes, Isolated From A Stone Fruit Outbreak Investigation, On Whole Stone Fruit At 4 °C, Antonio J. De Jesus, Ishani Sheth, Hee Jin Kwon, Zhujun Gao, Jessica Palmer, Minji Hur, Thomas S. Hammack, Dumitru Macarisin, Yi Chen

United States Food and Drug Administration: Publications

In the summer of 2014, a multistate outbreak of listeriosis associated with contaminated stone fruit (peach and nectarine) was reported. A serotype 4b variant Listeria monocytogenes (Lm) strain of singleton Sequence Type (ST) 382 was isolated from clinical samples and stone fruit associated with the outbreak. A serotype 1/2b Lm strain of ST5, Clonal Complex 5 was isolated only from outbreak-associated stone fruit, not from clinical samples. Here we investigated the fate of the serotype 4b and 1/2b strains, at two inoculation levels (high level at 3.7 logCFU/fruit and low level at 2.7 logCFU/fruit), on the surfaces of white peach, …

Adult Perceptions Of The Relative Harm Of Tobacco Products And Subsequent T Tobacco Product Use: Longitudinal Findings From Waves 1 And 2 Of The Population Assessment Of Tobacco And Health (Path) Study, Tara Elton-Marshall, Pete Driezen, Geoffrey T. Fong, K. Michael Cummings, Alexander Persoskie, Olivia Wackowski, Kelvin Choi, Annette Kaufman, David Strong, Shannon Gravely, Kristie Kristie, Jonathan Kwan, Maansi Bansal-Travers, Mark Travers, Andrew Hyland

United States Food and Drug Administration: Publications

Objectives: To examine: (1) How perceptions of harm for seven non-cigarette tobacco products predict sub- sequent use; (2) How change in use is associated with changes in perceptions of product harm; (3) Whether sociodemographic variables moderate the association between perceptions and use.

Methods: Data are from the adult sample (18+) of the Population Assessment of Tobacco and Health (PATH) Study, a nationally representative longitudinal cohort survey conducted September 2013-December 2014 (Wave 1 (W1) n = 32,320) and October 2014-October 2015 (Wave 2 (W2) n = 28,362).

Results: Wave 1 users and non-users of e-cigarettes, filtered cigars, cigarillos, and pipes, who …

An Evaluation Of The Usda's Policy To Reduce Listeria Illnesses In Ready‐To‐Eat Meat And Poultry Products, Travis Minor, Matt Parrett

United States Food and Drug Administration: Publications

Using 1998–2008 data collected by the Centers for Disease Control and Prevention on foodborne illnesses and outbreaks, we examine the economic impact of the United States Department of Agriculture's proposed and final rules to reduce the incidence of Listeria monocytogenes (Lm) in ready‐to‐ eat meat and poultry products. Using a difference‐in‐ differences approach, we find that these rules together reduced meat‐related Lm illnesses by about 60 per year, which we attribute to reductions in both the number and average size of meat‐related Lm outbreaks. We then monetize this illness reduction using an underreporting and underdiagnosis multiplier of 2.3 and an …

Genomics-Based Re-Examination Of The Taxonomy And Phylogeny Of Human And Simian Mastadenoviruses: An Evolving Whole Genomes Approach, Revealing Putative Zoonosis, Anthroponosis, And Amphizoonosis, June Kang, Ashrafali Mohamed Ismail, Shoaleh Dehghan, Jaya Rajaiya, Marc W. Allard, Haw Chuan Lim, David W. Dyer, James Chodosh, Donald Seto

United States Food and Drug Administration: Publications

With the advent of high-resolution and cost-effective genomics and bioinformatics tools and methods contributing to a large database of both human (HAdV) and simian (SAdV) adenoviruses, a genomics-based re-evaluation of their taxonomy is warranted. Interest in these particular adenoviruses is growing in part due to the applications of both in gene transfer protocols, including gene therapy and vaccines, as well in oncolytic protocols. In particular, the re-evaluation of SAdVs as appropriate vectors in humans is important as zoonosis precludes the assumption that human immune system may be na€ıve to these vectors. Additionally, as impor- tant pathogens, adenoviruses are a model …

The Impact Of The Abuse-Deterrent Reformulation Of Extended-Release T Oxycontin On Prescription Pain Reliever Misuse And Heroin Initiation, Carolyn Wolff, William N. Dowd, Mir M. Ali, Chandler Mcclellan, Angelica Meinhofer, Lukas Glos, Ryan Mutter, Matthew Rosenberg, Andreas Schikc

United States Food and Drug Administration: Publications

The introduction of abuse-deterrent OxyContin in 2010 was intended to reduce its misuse by making it more tamper resistant. However, some studies have suggested that this reformulation might have had unintended consequences, such as increases in heroin-related deaths. We used the 2005–2014 cross-sectional U.S. National Survey on Drug Use and Health to explore the impact of this reformulation on intermediate outcomes that precede heroin-related deaths for individuals with a history of OxyContin misuse. Our study sample consisted of adults who misused any prescription pain reliever prior to the reformulation of OxyContin (n = 81,400). Those who misused OxyContin prior to …

Development Of A Nicotinic Acetylcholine Receptor Nachr Α7 Binding Activity Prediction Model, Sugunadevi Sakkiah, Carmine Leggett, Bohu Pan, Wenjing Guo, Luis G. Valerio Jr., Huixiao Hong

United States Food and Drug Administration: Publications

Despite the well-known adverse health effects associated with tobacco use, addiction to nicotine found in tobacco products causes difficulty in quitting among users. Nicotinic acetylcholine receptors (nAChRs) are the physiological targets of nicotine and facilitate addiction to tobacco products. The nAChR-α7 subtype plays an important role in addiction; therefore, predicting the binding activity of tobacco constituents to nAChR-α7 is an important component for assessing addictive potential of tobacco constituents. We developed an α7 binding activity prediction model based on a large training data set of 843 chemicals with human α7 binding activity data extracted from PubChem and ChEMBL. The model …

Perceived Neighborhood: Preferences Versus Actualities, Saeed Moradi, Ali Nejat, Da Hu, Souparno Ghosh

Department of Statistics: Faculty Publications

Housing recovery plays a key role in the overall restoration of a community. A multitude of factors affect housing recovery, many of which are associated with interactions of residents with their perceived neighborhoods. Targeting perceived neighborhoods rather than administratively defined measures of land helps with devising recovery plans that could better address social preferences of the residents. However, such measures are commonly subject to collection of information via expensive and time-consuming surveys. The current research aims to contribute to the domain by exploring the relationship between perception of households of their neighborhood anchors (perceived anchors) and the anchors that exist …

Tumor Ablation Due To Inhomogeneous Anisotropic Diffusion In Generic Three-Dimensional Topologies, Erdi Kara, Aminur Rahman, Eugenio Aulisa, Souparno Ghosh

Department of Statistics: Faculty Publications

In recent decades computer-aided technologies have become prevalent in medicine, however, cancer drugs are often only tested on in vitro cell lines from biopsies. We derive a full three-dimensional model of inhomogeneous -anisotropic diffusion in a tumor region coupled to a binary population model, which simulates in vivo scenarios faster than traditional cell-line tests. The diffusion tensors are acquired using diffusion tensor magnetic resonance imaging from a patient diagnosed with glioblastoma multiform. Then we numerically simulate the full model with finite element methods and produce drug concentration heat maps, apoptosis hotspots, and dose-response curves. Finally, predictions are made about optimal …

Examining How Rural Ecological Contexts Influence Children's Early Learning Opportunities, Iheoma U. Iruka, Mark Dekraai, Janell Walther, Susan M. Sheridan, Tarik Abdel-Monem

University of Nebraska Public Policy Center: Publications

According to Bronfenbrenner’s bioecological theory (Bronfenbrenner & Evans, 2000), children’s early development and learning are influenced by multiple systems, including the microsystem (e.g., family poverty level), mesosystem (e.g., home-school partnership), exosystem (e.g., community type, early education policies), and macrosystem (e.g., rural culture). Given the lack of early education studies focused on rural communities, we sought to explore how these ecological systems are linked to children’s early learning experiences, with a particular focus on educators’ perceptions of how these ecosystems influence children’s learning environments and opportunities. Based on interviews and focus groups with school leaders, educators, and parents in 10 rural …

Network Science: Insights For Pandemics, Julia Mcquillan, Patricia Wonch Hill

Worlds of Connections Resources

The focus of our current project is on helping members of the public to better understand the role of network science theories and tools for improving public health because often public health is connected to complex systems. We’ll focus today on the relevance of network science for understanding how to contain viruses that cause diseases.

Similar Bird Communities Across Grazing Systems In The Nebraska Sandhills, M. Sliwinski, L.A. Powell, W. Schacht

School of Natural Resources: Faculty Publications

No abstract provided.

Changes In Students’ Mental Models From Computational Modeling Of Gene Regulatory Networks, Jenny Dauer, Heather E. Bergan-Roller, Gretchen P. King, Mckenzie Kjose, Nicholas Galt, Tomas Helikar

School of Natural Resources: Faculty Publications

Background: Computational modeling is an increasingly common practice for disciplinary experts and therefore necessitates integration into science curricula. Computational models afford an opportunity for students to investigate the dynamics of biological systems, but there is significant gap in our knowledge of how these activities impact student knowledge of the structures, relationships, and dynamics of the system. We investigated how a computational modeling activity affected introductory biology students’ mental models of a prokaryotic gene regulatory system (lac operon) by analyzing conceptual models created before and after the activity.

Results: Students’ pre-lesson conceptual models consisted of provided, system-general structures (e.g., activator, repressor) …

Long-Term Negative Emotional Outcomes Of Warzone Tbi, Jennifer J. Vasterling, Mihaela Aslan, Susan P. Proctor, John Ko, Xenia Leviyah, John Concato

United States Food and Drug Administration: Publications

Objective: Many veterans of the Iraq and Afghanistan Wars have experienced traumatic brain injury (TBI). Although prior work has examined associations between TBI and development of psychi- atric syndromes, less is known about associations between TBI and component emotions constituting these syndromes, especially in the long term. The purpose of this study was to examine the long-term emotional consequences of deployment-related TBI.

Methods: As part of VA Cooperative Studies Program #566, we assessed a sample of n1⁄4456US Army soldiers prior to an index deployment to Iraq, and again an average of 8.3 years (SD1⁄42.4years) after their deployment for a long-term …

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 …

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 …

Journey Through Science Club, Jacob Sorensen, Riha Karney

Honors Program: Expanded Learning Clubs

A science-based after school club that navigates the wonders of science while tying into fun activities for young students to enjoy, all while expanding their scientific knowledge and understanding in the process.

Critical Analysis Of The Value Of Drought Information And Impacts On Land Management And Public Health, Tingting Liu, Kelly Helm Smith, Richard Krop, Tonya Haigh, Mark Svoboda

National Drought Mitigation Center: Faculty Publications

This paper reviews previous efforts to assign monetary value to climatic or meteorological information, such as public information on drought, climate, early warning systems, and weather forecast information. Methods and tools that have been explored to examine the benefits of climatic and meteorological information include the avoided cost, contingent valuation, choice experiments, benefit transfer, and descriptive approaches using surveys. The second part of this paper discusses specific considerations related to valuing drought information for public health and the Bureau of Land Management. We found a multitude of connections between drought and the land management and health sectors in the literature. …

Harvest–Release Decisions In Recreational Fisheries, Mark A. Kaemingk, Keith L. Hurley, Christopher J. Chizinski, Kevin L. Pope

Department of Finance: Faculty Publications

Most fishery regulations aim to control angler harvest. Yet, we lack a basic understanding of what actually determines the angler’s decision to harvest or release fish caught. We used XGBoost, a machine learning algorithm, to develop a predictive angler harvest–release model by taking advantage of an extensive recreational fishery data set (24 water bodies, 9 years, and 193 523 fish). We were able to successfully predict the harvest–release outcome for 99% of fish caught in the training data set and 96% of fish caught in the test data set. Unsuccessful predictions were mostly attributed to predicting harvest of fish that …

Food Policy: Stability, Sustainability, And Safety, Gary D. Lynne

Department of Agricultural Economics: Faculty Publications

Everyone needs to eat, and eat well, as it is essential to the process of slowing down the pace to and time of our death, the point of maximum entropy for each person. As a result, it is perhaps the best example of the need to seek one’s Self-interest. It also puts us in the position, however, to more easily Empathize, walk-in-the-shoes of someone who may not have enough food, or the best kind of food, and help in forming a shared Other-interest, too. As a result, we might choose to support, with our tax money, some kind of a …