Digital Commons Network^™

Effects Of Rootstock And Location On Open Field ‘Bhn 589’ And ‘Nebraska Wedding’ Grafted Tomato Yield, Raihanah H. Shonerd, Ashley A. Thompson, Samuel E. Wortman

Department of Agronomy and Horticulture: Faculty Publications

Grafted tomato (Solanum lycopersicum) production is popular, particularly in high tunnels, because grafted plants can mitigate soilborne disease incidence in highly infested soils and increase water and nutrient use efficiency and crop yield and quality. However, these potential benefits are not as well documented in open field production systems with less disease pressure. The objective of this study was to quantify the effect of tomato grafting on fruit yield, number, and size across 2 years (2018 and 2019) and three diverse open-field production environments in Nebraska (Lincoln, North Platte, and Dwight). At each location, a scion from one …

Statistical And Machine Learning Approaches To Describe Factors Affecting Preweaning Mortality Of Piglets, Md Towfiqur Rahman, Tami M. Brown-Bandl, Gary A. Rohrer, Sudhendu R. Sharma, Vamsi Manthena, Yeyin Shi

Department of Agricultural and Biological Systems Engineering: Faculty Publications

High preweaning mortality (PWM) rates for piglets are a significant concern for the worldwide pork industries, causing economic loss and well-being issues. This study focused on identifying the factors affecting PWM, overlays, and predicting PWM using historical production data with statistical and machine learning models. Data were collected from 1,982 litters from the U.S. Meat Animal Research Center, Nebraska, over the years 2016 to 2021. Sows were housed in a farrowing building with three rooms, each with 20 farrowing crates, and taken care of by well-trained animal caretakers. A generalized linear model was used to analyze the various sow, litter, …

Temperature And Predators As Interactive Drivers Of Community Properties, John Delong, Kyle E. Coblentz, Stella F. Uiterwaal, Chika Akwani, Miranda E. Salsbery

School of Biological Sciences: Faculty Publications

The effects of warming on ecological communities emerge from a range of potentially asymmetric impacts on individual physiology and development. Understanding these responses, however, is limited by our ability to connect mechanisms or emergent patterns across the many processes that drive variation in demography. Further complicating this understanding is the gain or loss of predators to many communities, which may interact with changes in temperature to drive community change. Here we conducted a factorial warming and predation experiment to test generalized predictions about responses to warming. We used microcosms with a range of protists, rotifers, and a gastrotrich, with and …

Temperature And Predators As Interactive Drivers Of Community Properties, John P. Delong, Kyle E. Coblentz, Stella F. Uiterwaal, Chika Akwani, Miranda E. Salsbery

School of Biological Sciences: Faculty Publications

The effects of warming on ecological communities emerge from a range of potentially asymmetric impacts on individual physiology and development. Understanding these responses, however, is limited by our ability to connect mechanisms or emergent patterns across the many processes that drive variation in demography. Further complicating this understanding is the gain or loss of predators to many communities, which may interact with changes in temperature to drive community change. Here we conducted a factorial warming and predation experiment to test generalized predictions about responses to warming. We used microcosms with a range of protists, rotifers, and a gastrotrich, with and …

Machine Learning‑Assisted Low‑Dimensional Electrocatalysts Design For Hydrogen Evolution Reaction, Jin Li, Naiteng Wu, Jian Zhang, Hong‑Hui Wu, Kunming Pan, Yingxue Wang, Guilong Liu, Xianming Liu, Zhenpeng Yao, Qiaobao Zhang

Department of Chemistry: Faculty Publications

Efficient electrocatalysts are crucial for hydrogen generation from electrolyzing water. Nevertheless, the conventional "trial and error" method for producing advanced electrocatalysts is not only cost-ineffective but also time-consuming and labor-intensive. Fortunately, the advancement of machine learning brings new opportunities for electrocatalysts discovery and design. By analyzing experimental and theoretical data, machine learning can effectively predict their hydrogen evolution reaction (HER) performance. This review summarizes recent developments in machine learning for low-dimensional electrocatalysts, including zero-dimension nanoparticles and nanoclusters, one-dimensional nanotubes and nanowires, two-dimensional nanosheets, as well as other electrocatalysts. In particular, the effects of descriptors and algorithms on screening low-dimensional electrocatalysts …

Statistical And Machine Learning Approaches To Describe Factors Affecting Preweaning Mortality Of Piglets, Md Towfiqur Rahman, Tami M. Brown-Bandl, Gary A. Rohrer, Sudhendu R. Sharma, Vamsi Manthena, Yeyin Shi

Department of Agricultural and Biological Systems Engineering: Faculty Publications

High preweaning mortality (PWM) rates for piglets are a significant concern for the worldwide pork industries, causing economic loss and well-being issues. This study focused on identifying the factors affecting PWM, overlays, and predicting PWM using historical production data with statistical and machine learning models. Data were collected from 1,982 litters from the U.S. Meat Animal Research Center, Nebraska, over the years 2016 to 2021. Sows were housed in a farrowing building with three rooms, each with 20 farrowing crates, and taken care of by well-trained animal caretakers. A generalized linear model was used to analyze the various sow, litter, …

Separated By Geographical Location And Lineage: A Case Study Design Using Qualitative Methodology In Research On Hope, Love, And Resilience During A Family Reunion, Cynthia Dee Reece

Doctoral Dissertations and Projects

Family reunions are extensive functions in the African American community. The family members look forward to seeing one another, year after year, to share on various topics such as births, marriages, weddings, educational accomplishments, employment advancements, as well as deaths that have occurred. Often, some family members cannot attend reunions due to the distance or financial and economic hardships. Geographical location is a major hurdle to overcome when there is a lack of finances. Additionally, a mindset of not being accepted or assured of love in the family due to the perceived lineage of a family member or absence from …

Student And Parent/Guardian Perceptions Of The Effects Of Extra-Curricular Drumming Ensemble Participation On Social-Emotional Learning In A Title I Elementary School, Jennifer Nicole Gray

Doctoral Dissertations and Projects

The purpose of this phenomenological study was to examine the perceptions of students and parents/guardians regarding the effects on social-emotional learning of extra-curricular drumming ensemble participation while attending a Title I school in North Texas. The aim was to understand how participants and their parents/guardians perceived any changes to social and emotional development as a result of participating in a drumming ensemble beyond the traditional school day. The study was conducted at a Title I elementary school campus encompassing grades kindergarten through fifth in a suburban region of North Texas and concentrated on the fifth-grade students enrolled at that campus. …

To What Extent Do Environmental Regulations Curb Air Pollution And Enhance Production, Productivity, And Innovation?, Emmanuel Wabi Wangi

Doctoral Dissertations and Projects

This study delves into the fascinating relationship between environmental regulations, air pollution reduction, and their subsequent impact on production, productivity, and innovation. By adopting Porter’s hypothesis approach, the study aims to shed light on a crucial aspect overlooked in previous studies - the prerequisite of “well-designed environmental regulation,” as Porter’s hypothesis emphasizes. The study uses microeconomic principles, whose conclusions propose a novel framework for crafting effective policies that balance curbing air pollution and fostering economic growth. Specifically, the study advocates for a tax rate on pollution that aligns with the marginal cost of the polluter within the industry. This approach …

Perceptions Of Maternal Satisfaction Over The Course Of A Child’S Developmental Stages, Kristen Cartwright Ross

Doctoral Dissertations and Projects

Every motherhood experience comes with its own set of difficulties and experiences that might impact the level of life happiness for the women who inhabit it. Life satisfaction falls under the general heading of subjective well-being as it draws on comparison processes in which people assess how their present circumstances measure up to social norms and cultural ideals. This study aims to understand the changes in maternal satisfaction throughout the children's developmental years to understand potential avenues for improvement in the maternal experience, as well as provide clinical providers with the knowledge they need to help women experiencing either extreme …

Augmented Reality Experience And Perception Theory: A Quantitative Study Using Eye Tracking To Investigate How Mobile Phone Users Perceive Multiple Layered Depths, Donna C. Templeton

Doctoral Dissertations and Projects

This research explores how mobile augmented reality experiences are perceived and interacted with by using a quantitative eye-tracking study to record user eye movement behavior. Visual communication is vital in today’s increasingly visual society and current technology gives evidence of much promise in adding additional engagement, information, and interactivity through augmented reality. Though smartphone technology allows all smartphone users to access and experience browser-based augmented reality, there is little research on design aspects from a user experience perspective, such as the influence of layered depths in an augmented scene. The purpose of this study was to explore the variable of …

Use And Effectiveness Of Wildlife Exits Designed For Ocelots And Other Mesocarnivores On A South Texas Highway, Zarina N. Sheikh, Jamie E. Langbein, Kevin W. Ryer, Md Saydur Rahman, Christopher A. Gabler, John H. Young Jr., Richard Kline

School of Earth, Environmental, & Marine Sciences Faculty Publications

Movement is a key component of survival and reproduction, often causing wildlife to cross heavily trafficked highways, resulting in road mortalities by oncoming vehicles. Fencing and crossing structures are commonly regarded as effective mitigation structures to reduce these mortalities. In south Texas, ten wildlife exits (WE) were installed along State Highway 100 in conjunction with existing mitigation structures to provide the US endangered ocelot (Leopardus pardalis), a medium-sized spotted wild cat, a safe option to escape the right of way (ROW). The objectives of this study were to determine the effectiveness and species usage and to estimate the …

The George-Anne Inkwell Edition, Georgia Southern University

The Inkwell

No abstract provided.

Guide-Specific Loss Of Efficiency And Off-Target Reduction With Cas9 Variants, Liang Zhang, Wei He, Rongjie Fu, Shuyue Wang, Yiwen Chen, Han Xu

Faculty, Staff and Student Publications

High-fidelity clustered regularly interspaced palindromic repeats (CRISPR)-associated protein 9 (Cas9) variants have been developed to reduce the off-target effects of CRISPR systems at a cost of efficiency loss. To systematically evaluate the efficiency and off-target tolerance of Cas9 variants in complex with different single guide RNAs (sgRNAs), we applied high-throughput viability screens and a synthetic paired sgRNA-target system to assess thousands of sgRNAs in combination with two high-fidelity Cas9 variants HiFi and LZ3. Comparing these variants against wild-type SpCas9, we found that ∼20% of sgRNAs are associated with a significant loss of efficiency when complexed with either HiFi or LZ3. …

Novobiocin Blocks Nucleic Acid Binding To Polθ And Inhibits Stimulation Of Its Atpase Activity, Aleem Syed, Frantisek Filandr, Jeffrey Patterson-Fortin, Albino Bacolla, Ramya Ravindranathan, Jia Zhou, Drew T Mcdonald, Mohammed E Albuhluli, Amy Verway-Cohen, Joseph A Newman, Miaw-Sheue Tsai, Darin E Jones, David C Schriemer, Alan D D'Andrea, John A Tainer

Faculty, Staff and Student Publications

Polymerase theta (Polθ) acts in DNA replication and repair, and its inhibition is synthetic lethal in BRCA1 and BRCA2-deficient tumor cells. Novobiocin (NVB) is a first-in-class inhibitor of the Polθ ATPase activity, and it is currently being tested in clinical trials as an anti-cancer drug. Here, we investigated the molecular mechanism of NVB-mediated Polθ inhibition. Using hydrogen deuterium exchange-mass spectrometry (HX-MS), biophysical, biochemical, computational and cellular assays, we found NVB is a non-competitive inhibitor of ATP hydrolysis. NVB sugar group deletion resulted in decreased potency and reduced HX-MS interactions, supporting a specific NVB binding orientation. Collective results revealed that NVB …

Reap-2: An Interactive Quantitative Tool For Robust And Efficient Dose-Response Curve Estimation, Xinying Fang, Xinyi Liu, Vernon M Chinchilli, Michael Wang, Hong-Gang Wang, Nikolay V Dokholyan, Chan Shen, J Jack Lee, Shouhao Zhou

Faculty, Staff and Student Publications

REAP-2 is an interactive dose-response curve estimation tool for Robust and Efficient Assessment of drug Potency. It provides user-friendly dose-response curve estimation for in vitro studies and conducts statistical testing for model comparisons with a redesigned user interface. We also make a major update of the underlying estimation method with penalized beta regression, which demonstrates great reliability and accuracy in dose estimation and uncertainty quantification. In this note, we describe the method and implementation of REAP-2 with a highlight on potency estimation and drug comparison.

Bacterial And Fungal Characterization Of Pancreatic Adenocarcinoma From Endoscopic Ultrasound-Guided Biopsies, Robin D Wright, Thais F Bartelli, Seyda Baydogan, James Robert White, Michael P Kim, Manoop S Bhutani, Florencia Mcallister

Faculty, Staff and Student Publications

INTRODUCTION: The tumor microbiome (TM) has been linked to pancreatic cancer prognosis. Specific microbes can confer tumor resistance to therapies. Early knowledge of the TM at time of diagnosis would be clinically relevant for precision therapy based on microbial composition. However, it is difficult to define the TM prior to surgical resection.

METHODS: In this pilot feasibility study, patients underwent Endoscopic Ultrasound-Fine Needle Aspiration (EUS-FNA) biopsy of pancreatic adenocarcinoma. These samples were analyzed using 16S rRNA and internal transcribed spacer (ITS) sequencing for characterization of the tumor bacteria and fungi.

RESULT: After in silico decontamination and comparison to non-matched tumor, …

Synthesis And Antitumor Activity Of Brominated-Ormeloxifene (Br-Orm) Against Cervical Cancer, Mohammed Sikander, Shabnam Malik, John Apraku, Sonam Kumari, Parvez Khan, Hassan Mandil, Sheema Khan, Murali M. Yallapu, Meena Jaggi, Subhash C. Chuahan

School of Medicine Publications

Aberrant regulation of β-catenin signaling is strongly linked with cancer proliferation, invasion, migration, and metastasis, thus, small molecules that can inhibit this pathway might have great clinical significance. Our molecular modeling studies suggest that ormeloxifene (ORM), a triphenylethylene molecule that docks with β-catenin, and its brominated analogue (Br-ORM) bind more effectively with relatively less energy (−7.6 kcal/mol) to the active site of β-catenin as compared to parent ORM. Herein, we report the synthesis and characterization of a Br-ORM by NMR and FTIR, as well as its anticancer activity in cervical cancer models. Br-ORM treatment effectively inhibited tumorigenic features (cell proliferation …

An Exploration Of Defensive Mediatization Strategies And Motherhood Media Decision-Making, Emily B. Young

Doctoral Dissertations and Projects

This quantitative study focused on media-related decision-making in motherhood, with mediatization theory serving as a framework for the research. The study began with an overview of recent changes to motherhood and family media use. The purpose of this study was to explore the problem of how mothers make decisions about their children’s media use. After providing a basic overview of the changes to motherhood and family media use, as well as establishing the purpose and problem for the study, the literature on relevant topics for this study was discussed. Primarily, the literature review focused on mediatization theory. Next, the survey …

Studying Borderline Personality Disorder And Childhood Trauma: Exploring Clinicians’ Lived Experiences And Attitudes Toward Treating Bpd Individuals, Tracy F. Coggins

Doctoral Dissertations and Projects

A recurring theme in research on borderline personality disorder (BPD) and childhood trauma was the stigma associated with a BPD diagnosis often resulting in barriers to recovery processes and challenges to treatment for this population. The purpose of this transcendental phenomenological study focused on the lived experience of licensed clinicians who work with BPD clients, with the aim to find common themes experienced by clinicians regarding clinicians’ BPD clients, what successes and challenges experienced by clinicians led to their attitudes and perspectives toward treating BPD clients, and what perspectives clinicians have regarding what resources (education, training, etc.) are available in …

Quantitative Gender And Ethnicity Differences In Emergency Medicine Residency Applications, Steven Jay Warrington

Doctoral Dissertations and Projects

The purpose of this quantitative causal-comparative study is to examine if gender affects a medical student’s electronic Standardized Letters of Evaluation, or the characteristics of language used, in their application materials to an emergency medicine residency program through the Electronic Residency Application Service. This study is important as research is needed to determine if there is a difference in ratings or language used in emergency residency applications based on a medical student’s gender. The participants include 173 applicants from the 2022-2023 cycle that submitted material to a single emergency medicine residency program through the Electronic Residency Application Service. Instruments used …

A Phenomenological Study On Perceived Academic And Social Factors That Attribute To The Collegiate Success Or Failure Of Low-Income, First-Generation Black Males, Tre' Antonio Finklea

Doctoral Dissertations and Projects

The purpose of this phenomenological study was to analyze and discover the factors that contributed to the success or failure of first-generation Black male collegiates at four-year institutions and effectively provide an in-depth understanding of these issues. The theory guiding this study was Tinto’s theory of integration, which focuses on the norms of academic and social integration. Related to this theory was a series of studies that presented the idea that students’ involvement in the social environment and educational setups were critical to their success and retention in college. Participants completed a questionnaire to determine their eligibility for the study. …

A Comparison Of Adult Black And White Male Killers' Behaviors, Their Motives For Murder, And What They Do With Their Victims' Bodies, Tracy Sargent

Doctoral Dissertations and Projects

Studies involving murder are often focused on one offender group or a specific victim type. Due to focused research on this topic, there is a need to explore homicidal research between two offender groups in order to compare deviant behaviors of persons who commit murder. The comparison of adult black male offenders and adult white male offenders, their motivations for murder, and what offenders do with their victims’ bodies is explored in the study. A total of 300 solved homicide cases, which consists primarily of adult male and female victims, and several child murders was collected. Such murder motivations of …

A Phenomenological Study Exploring The Lack Of Baptist Church Participation In Seminole County, Florida, Ismael Melendez

Doctoral Dissertations and Projects

This phenomenological study explores the reasons for a lack of participation in in-person Baptist churches and the rise of participation in online Baptist churches in Seminole County, Florida. The theory guiding this study was Martin Heidegger’s hermeneutical framework which focuses on the commonality of experiences. Heidegger believed that to arrive at the essence of a phenomenon a researcher must go through the revisionary process of what Heidegger termed the Hermeneutic Circle. The principal research question in this study explored existing relationship(s) between in-person and online Baptist church leaders and how such relationship(s) contributed to a lack of church participation. The …

Negative Predictive Value Of Circulating Tumor Tissue Modified Viral (Ttmv)-Hpv Dna For Hpv-Driven Oropharyngeal Cancer Surveillance, Noah Kalman, Sreenija Yarlagadda

All Publications

Purpose: Human papillomavirus (HPV) is causally linked to oropharyngeal squamous cell carcinoma (OPSCC). Consensus guidelines recommend clinical exams and imaging in decreasing frequency as part of posttreatment surveillance for recurrence. Plasma tumor tissue modified viral (TTMV)-HPV DNA testing has emerged as a biomarker which can inform disease status during surveillance.

Experimental design: This retrospective observational cohort study involved 543 patients who completed curative-intent therapy for HPV-associated OPSCC between February 2020 and January 2022 at eight U.S. cancer care institutions. We determined the negative predictive value (NPV) of TTMV-HPV DNA for recurrence when matched to physician-reported clinical outcome data (median follow-up …

Negative Predictive Value Of Circulating Tumor Tissue Modified Viral (Ttmv)-Hpv Dna For Hpv-Driven Oropharyngeal Cancer Surveillance, Noah Kalman, Sreenija Yarlagadda

All Publications

Purpose: Human papillomavirus (HPV) is causally linked to oropharyngeal squamous cell carcinoma (OPSCC). Consensus guidelines recommend clinical exams and imaging in decreasing frequency as part of posttreatment surveillance for recurrence. Plasma tumor tissue modified viral (TTMV)-HPV DNA testing has emerged as a biomarker which can inform disease status during surveillance.

Experimental design: This retrospective observational cohort study involved 543 patients who completed curative-intent therapy for HPV-associated OPSCC between February 2020 and January 2022 at eight U.S. cancer care institutions. We determined the negative predictive value (NPV) of TTMV-HPV DNA for recurrence when matched to physician-reported clinical outcome data (median follow-up …

Deep Learning For Plant Bioinformatics: An Explainable Gradient-Based Approach For Disease Detection, Muhammad Shoaib, Babar Shah, Nasir Sayed, Farman Ali, Rafi Ullah, Irfan Hussain

All Works

Emerging in the realm of bioinformatics, plant bioinformatics integrates computational and statistical methods to study plant genomes, transcriptomes, and proteomes. With the introduction of high-throughput sequencing technologies and other omics data, the demand for automated methods to analyze and interpret these data has increased. We propose a novel explainable gradient-based approach EG-CNN model for both omics data and hyperspectral images to predict the type of attack on plants in this study. We gathered gene expression, metabolite, and hyperspectral image data from plants afflicted with four prevalent diseases: powdery mildew, rust, leaf spot, and blight. Our proposed EG-CNN model employs a …

The Overlap Of Skin And Blood T-Cell Clones In Early-Stage Mycosis Fungoides, Daniel Joffe, Safiyyah Bhatti, Lauren Banner, Romsin Zaya, Laura Gleason, Anjali Mishra, Ilan Kirsch, Pierluigi Porcu, Neda Nikbakht

Department of Dermatology and Cutaneous Biology Faculty Papers

No abstract provided.

A Retrospective, Observational Study Of 12 Cases Of Expanded-Access Customized Phage Therapy: Production, Characteristics, And Clinical Outcomes, Sabrina I Green, Justin R Clark, Haroldo H Santos, Kyle E Weesner, Keiko C Salazar, Saima Aslam, J William Campbell, Sarah B Doernberg, Emily Blodget, Michele I Morris, Gina A Suh, Karam Obeid, Fernanda P Silveira, Andrey A Filippov, Katrine L Whiteson, Barbara W Trautner, Austen L Terwilliger, Anthony Maresso

Faculty, Staff and Students Publications

BACKGROUND: Antimicrobial resistance (AMR) is undermining modern medicine, a problem compounded by bacterial adaptation to antibiotic pressures. Phages are viruses that infect bacteria. Their diversity and evolvability offer the prospect of their use as a therapeutic solution. Reported are outcomes of customized phage therapy for patients with difficult-to-treat antimicrobial resistant infections.

METHODS: We retrospectively assessed 12 cases of customized phage therapy from a phage production center. Phages were screened, purified, sequenced, characterized, and Food and Drug Administration-approved via the IND (investigational new drug) compassionate-care route. Outcomes were assessed as favorable or unfavorable by microbiologic and clinical standards. Infections were device-related …

Pptc7 Maintains Mitochondrial Protein Content By Suppressing Receptor-Mediated Mitophagy, Natalie M Niemi, Lianjie Wei, Andrew J Smith, Merima Forny, David J Pagliarini, Et Al.

2020-Current year OA Pubs

PPTC7 is a resident mitochondrial phosphatase essential for maintaining proper mitochondrial content and function. Newborn mice lacking Pptc7 exhibit aberrant mitochondrial protein phosphorylation, suffer from a range of metabolic defects, and fail to survive beyond one day after birth. Using an inducible knockout model, we reveal that loss of Pptc7 in adult mice causes marked reduction in mitochondrial mass and metabolic capacity with elevated hepatic triglyceride accumulation. Pptc7 knockout animals exhibit increased expression of the mitophagy receptors BNIP3 and NIX, and Pptc7