Digital Commons Network^™

Replacing Fallow With Field Pea In Wheat Production Systems Across Western Nebraska, Samuel T. Koeshall, Amanda Easterly, Rodrigo Werle, Strahinja Stepanovic, Cody F. Creech

Department of Agronomy and Horticulture: Faculty Publications

Integration of field pea (Pisum sativum L.) (FP) into dryland cropping systems has increased due to ecological and economic benefits, paired with a growing market for pea-derived products. Challenges exist in the High Plains that limit the integration of crop rotations to replace fallow periods with FP in wheat (Triticum aestivum L.)- based systems. This experiment compares chemical summer fallow to FP in a fallow– wheat rotation at two locations in western Nebraska. Soil water content, soil fertility, N mineralization, FP yield, and subsequent hard red winter wheat (HWW) yields were recorded. Subsequent HWW yields were not different …

Hybrid Conferences: Opportunities, Challenges And Ways Forward, Eleonora Puccinelli, Daniela Zeppilli, Paris V. Stefanoudis, Annaig Wittische-Helou, Marjorie Kermorgant, Sandra Fuchs, Lenaick Menot, Erin E. Easton, Alexandra A-T. Weber

School of Earth, Environmental, & Marine Sciences Faculty Publications

Hybrid conferences are in-person events that have an online component. This type of meeting format was rare before the COVID-19 pandemic, but started to become more common recently given the asynchronous global progression of the pandemic, the uneven access to vaccines and different travel regulations among countries that led to a large proportion of participants being unable to attend conferences in person. Here we report the organization of a middle-sized (581 participants: 159 onsite, 422 online) international hybrid conference that took place in France in September 2021. We highlight particular organizational challenges inherent to this relatively new type of meeting …

Artificial Neural Network Concepts And Examples, Harcharan Kabbay

Theses

Artificial Neural Networks have gained much media attention in the last few years. Every day, numer- ous articles on Artificial Intelligence, Machine Learning, and Deep Learning exist. Both academics and business are becoming increasingly interested in deep learning. Deep learning has innumerable uses, in- cluding autonomous driving, computer vision, robotics, security and surveillance, and natural language processing. The recent development and focus have primarily been made possible by the convergence of related research efforts and the introduction of APIs like Keras. The availability of high-speed compute resources such as GPUs and TPUs has also been instrumental in developing deep learning …

Profiling A Community-Specific Function Landscape For Bacterial Peptides Through Protein-Level Meta-Assembly And Machine Learning, Mitra Vajjala, Brady Johnson, Lauren Kasparek, Michael Leuze, Qiuming Yao

School of Computing: Faculty Publications

Small proteins, encoded by small open reading frames, are only beginning to emerge with the current advancement of omics technology and bioinformatics. There is increasing evidence that small proteins play roles in diverse critical biological functions, such as adjusting cellular metabolism, regulating other protein activities, controlling cell cycles, and affecting disease physiology. In prokaryotes such as bacteria, the small proteins are largely unexplored for their sequence space and functional groups. For most bacterial species from a natural community, the sample cannot be easily isolated or cultured, and the bacterial peptides must be better characterized in a metagenomic manner. The bacterial …

The Future Of Synbiotics: Rational Formulation And Design, David Fabian Gomez Gomez, Car Reen Kok, Robert Hutkins

Department of Food Science and Technology: Faculty Publications

Synbiotics, mixtures of live microbes and substrates selectively utilized by host organisms, are of considerable interest due to their ability to improve gastrointestinal health. However, formulating synbiotics remains challenging, due in part, to the absence of rational strategies to assess these products for synbiotic activities prior to clinical trials. Currently, synbiotics are formulated as either complementary or synergistic. Complementary synbiotics are made by combining probiotics and prebiotics, with each component acting independently and with the combination shown to provide a clinical health benefit. Most commercial synbiotics as well as those used in clinical trials have been of the complementary type. …

Immobilization Of A Bifidobacterial Endo-Ss-N-Acetylglucosaminidase To Generate Bioactive Compounds For Food Industry, Burcu Pekdemir, Hatice Duman, Ayşenur Arslan, Merve Kaplan, Melda Karyelioğlu, Tolgahan Özer, Hacı Mehmet Kayılı, Bekir Salih, Bethany M. Henrick, Rebbeca M. Duar, Sercan Karav

Department of Food Science and Technology: Faculty Publications

Conjugated N-glycans are considered next-generation bioactive prebiotic compounds due to their selective stimulation of beneficial microbes. These compounds are glycosidically attached to proteins through N-acetylglucosamines via specific asparagine residue (AsN-X-Ser/Thr). Certain bacteria such as Bifidobacterium longum subspecies infantis (B. infantis) have been shown to be capable of utilizing conjugated N-glycans, owing to their specialized genomic abilities. B. infantis possess a unique enzyme, Endo-ß-N-acetylglucosaminidase (EndoBI-1), which cleaves all types of conjugated N-glycans from glycoproteins. In this study, recombinantly cloned EndoBI- 1 enzyme activity was investigated using various immobilization methods: 1) adsorption, 2) entrapment-based alginate immobilization, …

Advance In Contextualizing Focal Structure Sets In Complex Network Analysis, Mustafa Alassad

Theses and Dissertations

Focal Structures are key sets of individuals who may be responsible for online socially minded events, protests, or leading citizen engagement efforts on social media networks. Discovering focal structure sets who able to promote online social campaigns is important, but complex, as they are typically active locally, globally, and acting unlike central users and influencers, focal structure sets can influence large social media networks. Researchers applied a greedy algorithm to discover focal structure sets in social media networks. However, the outcomes were lacking on the users’ activities and interests that made the analysis incomplete. In this research, I present a …

Tdp1-Independent Pathways In The Process And Repair Of Top1-Induced Dna Damage, Huimin Zhang, Yun Xiong, Dan Su, Chao Wang, Mrinal Srivastava, Mengfan Tang, Xu Feng, Min Huang, Zhen Chen, Junjie Chen

Faculty, Staff and Student Publications

Anticancer drugs, such as camptothecin (CPT), trap topoisomerase I (TOP1) on DNA and form TOP1 cleavage complexes (TOP1cc). Alternative repair pathways have been suggested in the repair of TOP1cc. However, how these pathways work with TDP1, a key repair enzyme that specifically hydrolyze the covalent bond between TOP1 catalytic tyrosine and the 3'-end of DNA and contribute to the repair of TOP1cc is poorly understood. Here, using unbiased whole-genome CRISPR screens and generation of co-deficient cells with TDP1 and other genes, we demonstrate that MUS81 is an important factor that mediates the generation of excess double-strand breaks (DSBs) in TDP1 …

Construction And Operation Of A Pilot-Scale Odor Control Device, Brendan Bunker

Department of Environmental Engineering: Theses and Other Student Research

Hydrogen sulfide (H₂S) is a naturally occurring by-product of anaerobic digestion and causes an odor that can be a nuisance and a public health risk at higher concentrations. This compound can be treated through various means, but one of particular interest is a biotrickling filter (BTF). Such devices have excellent H₂S treatment efficiencies, but start-up costs can be steep. The primary goal of this study is to explain the design and operation of a low-cost odor control device for improving environmental air quality in Nebraska using a BTF. This device has the potential for application as …

Influenza Activity And Composition Of The 2022-23 Influenza Vaccine - United States, 2021-22 Season, Angiezel Merced-Morales, Peter Daly, Anwar Isa Abd Elal, Noreen Ajayi, Ekow Annan, Alicia Budd, John Barnes, Arielle Colon, Charisse N Cummings, A Danielle Iuliano, Juliana Dasilva, Nick Dempster, Shikha Garg, Larisa Gubareva, Daneisha Hawkins, Amanda Howa, Stacy Huang, Marie Kirby, Krista Kniss, Rebecca Kondor, Jimma Liddell, Shunte Moon, Ha T Nguyen, Alissa O'Halloran, Catherine Smith, Thomas Stark, Katie Tastad, Dawud Ujamaa, Dave E Wentworth, Alicia M Fry, Vivien G Dugan, Lynnette Brammer

Faculty, Staff and Student Publications

Before the emergence of SARS-CoV-2, the virus that causes COVID-19, influenza activity in the United States typically began to increase in the fall and peaked in February. During the 2021-22 season, influenza activity began to increase in November and remained elevated until mid-June, featuring two distinct waves, with A(H3N2) viruses predominating for the entire season. This report summarizes influenza activity during October 3, 2021-June 11, 2022, in the United States and describes the composition of the Northern Hemisphere 2022-23 influenza vaccine. Although influenza activity is decreasing and circulation during summer is typically low, remaining vigilant for influenza infections, performing testing …

Sirpα Mediates Igf1 Receptor In Cardiomyopathy-Induced By Chronic Kidney Disease, Sandhya S Thomas, Jiao Wu, Giovanni Davogustto, Michael W Holliday, Kristin Eckel-Mahan, Daniela Verzola, Giacomo Garibotto, Zhaoyong Hu, William E Mitch, Heinrich Taegtmeyer

Faculty, Staff and Student Publications

BACKGROUND: Chronic kidney disease (CKD) is characterized by increased myocardial mass despite near-normal blood pressure, suggesting the presence of a separate trigger. A potential driver is SIRPα (signal regulatory protein alpha)-a mediator impairing insulin signaling. The objective of this study is to assess the role of circulating SIRPα in CKD-induced adverse cardiac remodeling.

METHODS: SIRPα expression was evaluated in mouse models and patients with CKD. Specifically, mutant, muscle-specific, or cardiac muscle-specific SIRPα KO (knockout) mice were examined after subtotal nephrectomy. Cardiac function was assessed by echocardiography. Metabolic responses were confirmed in cultured muscle cells or cardiomyocytes.

RESULTS: We demonstrate that …

Multiplex Pcr Assay To Detect High Risk Lineages Of Salmonella Typhi And Paratyphi A, Fahad Khokhar, Derek Pickard, Zoe Dyson, Junaid Iqbal, Agila Pragasam, Jobin Jacob John, Balaji Veeraraghavan, Farah Qamar, Gordon Dougan, Hilary Macqueen

Department of Paediatrics and Child Health

Enteric fever infections remain a significant public health issue, with up to 20 million infections per year. Increasing rates of antibiotic resistant strains have rendered many first-line antibiotics potentially ineffective. Genotype 4.3.1 (H58) is the main circulating lineage of S. Typhi in many South Asian countries and is associated with high levels of antibiotic resistance. The emergence and spread of extensively drug resistant (XDR) typhoid strains has increased the need for a rapid molecular test to identify and track these high-risk lineages for surveillance and vaccine prioritisation. Current methods require samples to be cultured for several days, followed by DNA …

“Under Her Feet”: A Case Study On Motherhood Discourse In An American Muslim Community, Joanna Boudreaux

Electronic Theses and Dissertations Archive

This dissertation explores U.S. American Muslim mothers’ communicative experiences of identity. This investigation was undertaken by a Muslim woman researcher and insider to the research topic and founded on the premise that discussions of motherhood within the mainstream U.S. American Muslim community do not center the perspectives and lived experiences of actual mothers. Findings of this study are based on interviews with nine Muslim women who shared detailed thoughts about what Islamic scripture says about motherhood, the role of culture, rights and obligations of different family members, and details about their day-to-day lives. Data was critically analyzed, and themes were …

Iron And Magnesium Impregnation Of Avocado Seed Biochar For Aqueous Phosphate Removal, James Jihoon Kang, Jason Parsons, Sampath Gunukula, Dat T. Tran

School of Earth, Environmental, & Marine Sciences Faculty Publications

There has been increasing interest in using biochar for nutrient removal from water, and its application for anionic nutrient removal such as in phosphate (PO₄³⁻) necessitates surface modifications of raw biochar. This study produced avocado seed biochar (AB), impregnated Fe- or Mg-(hydr)oxide onto biochar (post-pyrolysis), and tested their performance for aqueous phosphate removal. The Fe- or Mg-loaded biochar was prepared in either high (1:8 of biochar to metal salt in terms of mass ratio) or low (1:2) loading rates via the co-precipitation method. A total of 5 biochar materials (unmodified AB, AB + High Fe, AB …

Effect Of Ultraviolet Light Treatment On Microbiological Safety And Quality Of Fresh Produce: An Overview, Veerachandra K. Yemmireddy, Achyut Adhikari, Juan Moreira

School of Earth, Environmental, & Marine Sciences Faculty Publications

Fresh and fresh-cut fruits and vegetables have been associated in several foodborne illness outbreaks. Although investigations from those outbreaks reported that the contamination with pathogenic microorganisms may occur at any point in the farm to fork continuum, effective control strategies are still being widely investigated. In that direction, the concept of hurdle technology involving a sequence of different interventions have been widely explored. Among those interventions, ultraviolet (UV) light alone or in combination with other treatments such as use of organic acids or sanitizer solutions, has found to be a promising approach to maintain the microbiological safety and quality of …

Butte Priority Soils Operable Unit (Bpsou) Draft Final Insufficiently Reclaimed Sites - Field Sampling Plan (Fsp) Bres No. 34 – Eveline., Mike Mcanulty

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Resilience And Protection Of Health Care And Research Laboratory Workers During The Sars-Cov-2 Pandemic: Analysis And Case Study From An Austrian High Security Laboratory, Martina Loibner, Paul Barach, Stella Wolfgruber, Christine Langner, Verena Stangl, Julia Rieger, Esther Föderl-Höbenreich, Melina Hardt, Eva Kicker, Silvia Groiss, Martin Zacharias, Philipp Wurm, Gregor Gorkiewicz, Peter Regitnig, Kurt Zatloukal

College of Population Health Faculty Papers

The SARS-CoV-2 pandemic has highlighted the interdependency of healthcare systems and research organizations on manufacturers and suppliers of personnel protective equipment (PPE) and the need for well-trained personnel who can react quickly to changing working conditions. Reports on challenges faced by research laboratory workers (RLWs) are rare in contrast to the lived experience of hospital health care workers. We report on experiences gained by RLWs (e.g., molecular scientists, pathologists, autopsy assistants) who significantly contributed to combating the pandemic under particularly challenging conditions due to increased workload, sickness and interrupted PPE supply chains. RLWs perform a broad spectrum of work with …

The Myths They Make Of Us, Kaitlin Stone

Dissertations and Theses

This thesis seeks to examine the relationship between myth and personhood. The societal constructs placed on us all, but specifically women, appear throughout cultures as mythology. How do these myths impact our identities? How can we utilize mythos and storytelling to reject, disrupt, or complicate those myths?

Development Of A Configurable Real-Time Event Detection Framework For Power Systems Using Swarm Intelligence Optimization, Umar Farooq

Dissertations and Theses

Modern power systems characterized by complex topologies require accurate situational awareness to maintain an adequate level of reliability. Since they are large and spread over wide geographical areas, occurrence of failures is inevitable in power systems. Various generation and transmission disturbances give rise to a mismatch between generation and demand, which manifest as frequency events. These events can take the form of negligible frequency deviations or more severe emergencies that can precipitate cascading outages, depending on the severity of the disturbance and efficacy of remedial action schema. The impacts of such events have become more critical with recent decline in …

Arbuscular Mycorrhizal Fungi Colonization Response To Dike Removal In The Salmon River Estuary, Elinore Webb

Dissertations and Theses

Arbuscular mycorrhizal fungi (AMF) form symbiotic relationships with wetland plants and are important to the restoration of coastal estuaries. The purpose of this study was to assess the presence and colonization of arbuscular mycorrhizal fungi in Distichlis spicata from three formerly diked areas of the Salmon River Estuary to determine an initial understanding of the mycorrhizal community in tidal wetlands post-restoration. AMF were present in all four sample areas and total colonization ranged on average 39-72%. The reference site had the lowest levels of total colonization, which is contrary to the findings of studies of younger wetland restorations. Most importantly, …

Orthotrichum Lyellii As An Active Moss Biomonitor: Examining The Interplay Between Ambient Pm10, Bulk Deposition And Heavy Metals In An Urban Environment, Scott Bradley Kiel

Dissertations and Theses

The importance of monitoring and preventing pollution in the environment is a globally recognized issue. Of the criteria pollutants outlined by the United States Environmental Protection Agency, particulate matter is among these least understood in relation to toxicity and most wide-spread. Many governments have employed continuous air quality monitoring networks to track ambient levels of particulate matter, but are often too widespread to capture the heterogeneity of the urban environment, especially for heavy metal deposition. In Portland, OR, the epiphytic moss Orthotrichum lyellii was successfully used as a low-cost passive biomonitor to increase the spatial resolution of pollution around the …

Mtorc1 And Mtorc2 Complexes Regulate The Untargeted Metabolomics And Amino Acid Metabolites Profile Through Mitochondrial Bioenergetic Functions In Pancreatic Beta Cells, Ghada A. Soliman, Rinat Abzalimov, Ye He

Advanced Science Research Center

Background: Pancreatic beta cells regulate bioenergetics efficiency and secret insulin in response to glucose and nutrient availability. The mechanistic Target of Rapamycin (mTOR) network orchestrates pancreatic progenitor cell growth and metabolism by nucleating two complexes, mTORC1 and mTORC2. Objective: To determine the impact of mTORC1/mTORC2 inhibition on amino acid metabolism in mouse pancreatic beta cells (Beta-TC-6 cells, ATCC-CRL-11506) using high-resolution metabolomics (HRM) and live-mitochondrial functions. Methods: Pancreatic beta TC-6 cells were incubated for 24 h with either: RapaLink-1 (RL); Torin-2 (T); rapamycin (R); metformin (M); a combination of RapaLink-1 and metformin (RLM); Torin-2 and metformin (TM); compared to the control. …

Urinary Matrix Gla Protein Is Associated With Mortality Risk In Flemish Population: A Prospective Study, Dongmei Wei, Jesus D. Melgarejo, Thomas Vanassche, Lucas Van Aelst, Stefan Janssens, Peter Verhamme, Zhen-Yu Zhang

School of Medicine Publications

Background: Vascular calcification is strongly related to the risk of mortality and cardiovascular (CV) diseases. In vascular calcification, matrix Gla protein (MGP), a small vitamin K-dependent protein, is an important mineralization inhibitor. Recent studies showed that circulating MGP is associated with mortality risk. However, the longitudinal association between urinary excretion of MGP and all-cause mortality was not established.

Materials and methods: Urinary MGP was measured in 776 randomly recruited Flemish population (mean age: 51.2 years; 50.9% women) at baseline (during 2005–2010) using capillary electrophoresis coupled with mass spectrometry. Plasma inactive MGP [desphospho-uncarboxylated MGP (dp-ucMGP)] levels were quantified in 646 individuals …

Myt1l In The Making: Emerging Insights On Functions Of A Neurodevelopmental Disorder Gene, Jiayang Chen, Allen Yen, Colin P Florian, Joseph D Dougherty

2020-Current year OA Pubs

Large scale human genetic studies have shown that loss of function (LoF) mutations in MYT1L are implicated in neurodevelopmental disorders (NDDs). Here, we provide an overview of the growing number of published MYT1L patient cases, and summarize prior studies in cells, zebrafish, and mice, both to understand MYT1L's molecular and cellular role during brain development and consider how its dysfunction can lead to NDDs. We integrate the conclusions from these studies and highlight conflicting findings to reassess the current model of the role of MYT1L as a transcriptional activator and/or repressor based on the biological context. Finally, we highlight additional …

Electro-Mechanical Coupling Of Kcnq Channels Is A Target Of Epilepsy-Associated Mutations And Retigabine, Nien-Du Yang, Richard Kanyo, Lu Zhao, Jingru Li, Po Wei Kang, Alex Kelly Dou, Kelli Mcfarland White, Jingyi Shi, Jeanne M Nerbonne, Harley T Kurata, Jianmin Cui

2020-Current year OA Pubs

KCNQ2 and KCNQ3 form the M-channels that are important in regulating neuronal excitability. Inherited mutations that alter voltage-dependent gating of M-channels are associated with neonatal epilepsy. In the homolog KCNQ1 channel, two steps of voltage sensor activation lead to two functionally distinct open states, the intermediate-open (IO) and activated-open (AO), which define the gating, physiological, and pharmacological properties of KCNQ1. However, whether the M-channel shares the same mechanism is unclear. Here, we show that KCNQ2 and KCNQ3 feature only a single conductive AO state but with a conserved mechanism for the electro-mechanical (E-M) coupling between voltage sensor activation and pore …

New Endorsements Offered, Bethany Van Voorst

The Voice

No abstract provided.

Speech And Language Developmental Delays And Early Intervention Programs, Deidre Douglas-Washington

LC Journal of Special Education

The purpose of this paper is to provide information about speech and language acquisition as it applies to children with developmental delays. Local education agencies, early interventionists, such as speech-language pathologists, and parents must provide literacy rich environments for pre-school aged children. The concerted effort among these individuals to provide speech and language services and activities for children in natural environments will be necessary to identify children who may need additional special education services and decrease the number of children being identified with a developmental disability. A review of the literature about early speech and language acquisition and intervention is …

Reading Comprehension Interventions For Students With Learning Disabilities Or Reading Difficulties In Grades 3-12: A Literature Review, 2006-2011, Jessica R. Scott

LC Journal of Special Education

The purpose of this review is to summarize recent scientific studies of various reading comprehension interventions for students with reading difficulties in grades 3-12 in order to provide a quick reference for administrators and educators who are interested in the latest research on reading comprehension interventions. Additionally, research findings are presented on how to increase the frequency of effective instruction of reading comprehension in the classroom.

Decreasing Self-Injurious Behaviors In Children With Autism Spectrum Disorders, Susan L. Mccorkle

LC Journal of Special Education

There has been increased concern in developing successful interventions for problem behaviors in ASD due to a rise in diagnoses of this disorder (Doughty & Doughty, 2008). This paper will explore applied behavior analysis research studies that have examined interventions used in the attempt to decrease or extinguish SIB in children with ASD. Procedural alternatives for behavioral reduction will be investigated and the results of research will be evaluated for significant influence on SIB. These include reinforcement-based strategies, extinction strategies, removal of desirable stimuli, and the presentation of aversive stimuli. The functional relationship between SIB and these alternatives for behavior …

Academic Interventions For Students With Asd, Deanna B. Cash

LC Journal of Special Education

Following the reauthorization of the Individuals with Disabilities Education Improvement Act in 2004 and its emphasis on inclusion of students with disabilities in the general education setting, students with Autism Spectrum Disorder are increasingly taught in general education classrooms (Leblanc, Richardson, & Burns, 2009; Simpson, Boer-Ott, & Smith-Myles, 2003). Data from the Annual Report to Congress on Implementation of IDEA (U.S. Department of Education, 2010) indicated that almost 90% of students with autism in public schools in the United States receive their education in general education classrooms for some part of the school day. Yet, both general education and special …