Digital Commons Network^™

Integrated Analysis Of Genomic And Transcriptomic Data For The Discovery Of Splice-Associated Variants In Cancer, Kelsy C Cotto, Yang-Yang Feng, Avinash Ramu, Megan Richters, Sharon L Freshour, Zachary L Skidmore, Huiming Xia, Joshua F Mcmichael, Jason Kunisaki, Katie M Campbell, Timothy Hung-Po Chen, Emily B Rozycki, Douglas Adkins, Siddhartha Devarakonda, Sumithra Sankararaman, Yiing Lin, William C Chapman, Christopher A Maher, Vivek Arora, Ramaswamy Govindan, Obi L Griffith, Malachi Griffith, Et Al.

2020-Current year OA Pubs

Somatic mutations within non-coding regions and even exons may have unidentified regulatory consequences that are often overlooked in analysis workflows. Here we present RegTools ( www.regtools.org ), a computationally efficient, free, and open-source software package designed to integrate somatic variants from genomic data with splice junctions from bulk or single cell transcriptomic data to identify variants that may cause aberrant splicing. We apply RegTools to over 9000 tumor samples with both tumor DNA and RNA sequence data. RegTools discovers 235,778 events where a splice-associated variant significantly increases the splicing of a particular junction, across 158,200 unique variants and 131,212 unique …

Effect Of Type Of Mulch And Biological Soil Amendments Of Animal Origin (Bsaao) On Microbial Food Safety Risk On Cucumbers And Carrots Irrigated With Contaminated Or Chlorinated Water, Juan Fernando Moreira Calix

LSU Doctoral Dissertations

A comprehensive understanding of the effect biological soil amendments of animal origin and physical soil amendments have on produce contamination is important for developing strategies to mitigate this risk. Our studies investigated the persistence of generic E. coli, E. coli O157:H7 and Salmonella spp. in soil and produce surfaces with different BSAAO and mulch applications, as well as the effectiveness of chlorine treatments in reducing enteric bacteria in the field. Cucumbers harvested from plots with paper mulch had the highest levels of E. coli (3.76 Log CFU/cm²) while samples from maize mulch had the lowest levels (1.68 …

Workplace Violence Prevention Training: A Cross-Sectional Study Of Home Healthcare Workers, Tamara F. Small

Dissertations

HHCWs are at increased risk for WPV due to working alone in unsupervised, unpredictable, and potentially dangerous work environments. Similar to healthcare workers employed in institutionalized settings, HHCWs primarily experience Type II, verbal abuse from patients. Little is known about how HHCWs promote personal safety while at work. Guided by Haddon's Matrix, the purpose of this manuscript option dissertation was to estimate WPV exposures and identify interventions and resources used by HHCWs to promote personal safety and mitigate and prevent WPV. For this manuscript option dissertation, there are three distinct projects, all related to HHCWs and exposure to WPV.

Modular Design Of A Polymer-Bilayer-Based Mechanically Compliant Worm-Like Robot, Austin S. Mills, Shane Riddle, Hillel J. J. Chiel, Roger D. Quinn, Kathryn A. Daltorio

Faculty Scholarship

Soft earthworm-like robots that exhibit mechanical compliance can, in principle, navigate through uneven terrains and constricted spaces that are inaccessible to traditional legged and wheeled robots. However, unlike the biological originals that they mimic, most of the worm-like robots reported to date contain rigid components that limit their compliance, such as electromotors or pressure-driven actuation systems. Here, a mechanically compliant worm-like robot with a fully modular body that is based on soft polymers is reported. The robot is composed of strategically assembled, electrothermally activated polymer bilayer actuators, which are based on a semicrystalline polyurethane with an exceptionally large nonlinear thermal …

Small Rnas >26 Nt In Length Associate With Ago1 And Are Upregulated By Nutrient Deprivation In The Alga Chlamydomonas, Yingshan Li, Eun-Jeong Kim, Adam Voshall, Etsuko Moriyama, Heriberto D. Cerutti

School of Biological Sciences: Faculty Publications

Small RNAs (sRNAs) associate with ARGONAUTE (AGO) proteins forming effector complexes with key roles in gene regulation and defense responses against molecular parasites. In multicellular eukaryotes, extensive duplication and diversification of RNA interference (RNAi) components have resulted in intricate pathways for epigenetic control of gene expression. The unicellular alga Chlamydomonas reinhardtii also has a complex RNAi machinery, including 3 AGOs and 3 DICER-like proteins. However, little is known about the biogenesis and function of most endogenous sRNAs. We demonstrate here that Chlamydomonas contains uncommonly long (>26 nt) sRNAs that associate preferentially with AGO1. Somewhat reminiscent of animal PIWI-interacting RNAs, …

Housing And Space Guidelines For Livestock, Kendall Kunelius

Advisory Council

Following best management practices can help eliminate problems that arise between farming activities and other land uses in urban environments. There are several factors to consider when planning adequate livestock shelter.

Neutrosophic Model To Examine The Challenges Faced By Manufacturing Businesses In Adopting Green Supply Chain Practices And To Provide Potential Solutions, Zenat Mohamed, Mahmoud M. Ismail, Amal F. Abd El-Gawad

Neutrosophic Systems with Applications

Several obstacles stand in the way of companies trying to adopt green supply-chain practices. The purpose of this research is to examine the challenges faced by the industrial industry in adopting green supply chain practices and to provide potential solutions. The information for this research was gathered via in-depth, personal conversations with manufacturing sector managers who are well-versed in green supply chain practices. The Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) technique was used in the evaluation phase to evaluate obstacles and assess efficient options for introducing green supply chain practices. The TOPSIS method is integrated …

Rna Virus-Mediated Changes In Organismal Oxygen Consumption Rate In Young And Old Drosophila Melanogaster Males, Eli Hagedorn, Dean Bunnell, Beate Henschel, Daniel Smith Jr, Stephanie Dickinson, Andrew Brown, Maria De Luca, Ashley Turner, Stanislava Chtarbanova

Research, Publications & Creative Work

Aging is accompanied by increased susceptibility to infections including with viral pathogens resulting in higher morbidity and mortality among the elderly. Significant changes in host metabolism can take place following virus infection. Efficient immune responses are energetically costly, and viruses divert host molecular resources to promote their own replication. Virus-induced metabolic reprogramming could impact infection outcomes, however, how this is affected by aging and impacts organismal survival remains poorly understood. RNA virus infection of Drosophila melanogaster with Flock House virus (FHV) is an effective model to study antiviral responses with age, where older flies die faster than younger flies due …

Piece‐By‐Piece Shape‐Morphing: Engineering Compatible Auxetic And Non‐Auxetic Lattices To Improve Soft Robot Performance In Confined Spaces, Yusuf Dikici, Hao Jiang, Bo Li, Kathryn A. Daltorio, Ozan Akkus

Student Scholarship

No abstract provided.

Cc16 Augmentation Reduces Exaggerated Copd-Like Disease In Cc16-Deficient Mice, Joselyn Rojas-Quintero, Maria Eugenia Laucho-Contreras, Xiaoyun Wang, Quynh-Anh Fucci, Patrick R Burkett, Se-Jin Kim, Duo Zhang, Yohannes Tesfaigzi, Yuhong Li, Abhiram R Bhashyam, Zhang Li, Haider Khamas, Bartolome Celli, Aprile L Pilon, Francesca Polverino, Caroline A Owen

Faculty, Staff and Students Publications

Low Club Cell 16 kDa protein (CC16) plasma levels are linked to accelerated lung function decline in patients with chronic obstructive pulmonary disease (COPD). Cigarette smoke-exposed (CS-exposed) Cc16-/- mice have exaggerated COPD-like disease associated with increased NF-κB activation in their lungs. It is unclear whether CC16 augmentation can reverse exaggerated COPD in CS-exposed Cc16-/- mice and whether increased NF-κB activation contributes to the exaggerated COPD in CS-exposed Cc16-/- lungs. CS-exposed WT and Cc16-/- mice were treated with recombinant human CC16 (rhCC16) or an NF-κB inhibitor versus vehicle beginning at the midpoint of the exposures. COPD-like disease and NF-κB activation were …

Interleukins, Chemokines, And Tumor Necrosis Factor Superfamily Ligands In The Pathogenesis Of West Nile Virus Infection, Emna Benzarti, Kristy O Murray, Shannon E Ronca

Faculty, Staff and Students Publications

West Nile virus (WNV) is a mosquito-borne pathogen that can lead to encephalitis and death in susceptible hosts. Cytokines play a critical role in inflammation and immunity in response to WNV infection. Murine models provide evidence that some cytokines offer protection against acute WNV infection and assist with viral clearance, while others play a multifaceted role WNV neuropathogenesis and immune-mediated tissue damage. This article aims to provide an up-to-date review of cytokine expression patterns in human and experimental animal models of WNV infections. Here, we outline the interleukins, chemokines, and tumor necrosis factor superfamily ligands associated with WNV infection and …

Catalyzing Next-Generation Artificial Intelligence Through Neuroai, Anthony Zador, Sean Escola, Blake Richards, Bence Ölveczky, Yoshua Bengio, Kwabena Boahen, Matthew Botvinick, Dmitri Chklovskii, Anne Churchland, Claudia Clopath, James Dicarlo, Surya Ganguli, Jeff Hawkins, Konrad Körding, Alexei Koulakov, Yann Lecun, Timothy Lillicrap, Adam Marblestone, Bruno Olshausen, Alexandre Pouget, Cristina Savin, Terrence Sejnowski, Eero Simoncelli, Sara Solla, David Sussillo, Andreas S Tolias, Doris Tsao

Faculty, Staff and Students Publications

Neuroscience has long been an essential driver of progress in artificial intelligence (AI). We propose that to accelerate progress in AI, we must invest in fundamental research in NeuroAI. A core component of this is the embodied Turing test, which challenges AI animal models to interact with the sensorimotor world at skill levels akin to their living counterparts. The embodied Turing test shifts the focus from those capabilities like game playing and language that are especially well-developed or uniquely human to those capabilities - inherited from over 500 million years of evolution - that are shared with all animals. Building …

Glia-Neuron Coupling Via A Bipartite Sialylation Pathway Promotes Neural Transmission And Stress Tolerance Iglia-Neuron Coupling Via A Bipartite Sialylation Pathway Promotes Neural Transmission And Stress Tolerance In Drosophila, Hilary Scott, Boris Novikov, Berrak Ugur, Brooke Allen, Ilya Mertsalov, Pedro Monagas-Valentin, Melissa Koff, Sarah Baas Robinson, Kazuhiro Aoki, Raisa Veizaj, Dirk J Lefeber, Michael Tiemeyer, Hugo Bellen, Vladislav Panin

Duncan NRI Faculty and Staff Publications

Modification by sialylated glycans can affect protein functions, underlying mechanisms that control animal development and physiology. Sialylation relies on a dedicated pathway involving evolutionarily conserved enzymes, including CMP-sialic acid synthetase (CSAS) and sialyltransferase (SiaT) that mediate the activation of sialic acid and its transfer onto glycan termini, respectively. In Drosophila, CSAS and DSiaT genes function in the nervous system, affecting neural transmission and excitability. We found that these genes function in different cells: the function of CSAS is restricted to glia, while DSiaT functions in neurons. This partition of the sialylation pathway allows for regulation of neural functions via …

Offshore Wind Energy Or Domestic Seafood? How The Department Of The Interior Can Facilitate Both Through Self-Binding Procedures, Adele Irwin

St. John's Law Review

(Excerpt)

The United States has many identities, including that of a coastal nation. With the largest Exclusive Economic Zone (“EEZ”) in the world, the United States has jurisdiction over more human activity in the ocean than any other country. Like people in most coastal nations, Americans are drawn to the ocean. Almost forty percent of the population lives in coastal counties that constitute less than ten percent of the nation’s land mass, and 58.3 million jobs and more than $9.5 trillion of gross domestic product are attributable to ocean resources annually. These figures have increased over time.

The diverse industries …

Effects Of Sowing Date And Phosphorus Fertiliser Application On Winter Survival Of Lucerne Cv. Aohan In The Northern Semi-Arid Region Of China, Z. L. Wang, Q. Zh. Sun, Y. W. Wang, Zh. Y. Li, Sh. F. Zhao

IGC Proceedings (1977-2023)

In the northern semi-arid region of China, winter survival is always a limiting factor for lucerne production, because low temperatures and a dry climate in winter (Zhou et al., 1993; Ma, 2000; Sun & Gui, 2001; Sun et al., 2003). An experiment was conducted to find an appropriate sowing date and P application rate in order to improve lucerne winter survival.

Finding Aid For The Fred Jackson Collection (Mum01761)

Archives & Special Collections: Finding Aids (alphabetical)

The collection contains 289 video tapes of blues performances around New York, filmed by Fred Jackson, and related files.

Finding Aid For The Miscellaneous 78s (Mum01740)

Archives & Special Collections: Finding Aids (alphabetical)

Collection of 78 rpm audio discs featuring blues, jazz, and popular music from the 1920s through the 1940s.

Finding Aid For The Elijah M. Walker Collection (Mum00460)

Archives & Special Collections: Finding Aids (alphabetical)

Collection consists of transcriptions of one diary of Caroline King (1851-1860) and 5 original diaries of Elijah Millington Walker (1848-1851).

Finding Aid For The Craft / Fort Family Letters (Mum00091)

Archives & Special Collections: Finding Aids (alphabetical)

Collection consists of transcribed correspondence related to the life of the Craft family written 1840-1878.

Chs Country Operations’ International Business Strategy, Robert A. Lloyd

Journal of the North American Management Society

In 2012, U.S.-based CHS Country Operations executed their first steps in an international business strategy with the acquisition of Canadian agriculture retail company, DynAgra. In 2014 they purchased more retail locations from CPS and Viterra, and in the time since these international acquisitions, management at CHS has worked to bring the company’s core values and business culture to their new employees, customers, and market. Through a qualitative analysis of the company through interviews with key stakeholders in the acquisition and operation of the Canadian assets, a case study is formed to better understand the overall international business strategy of CHS …

The Effects Of Tert-Butyl Hydroquinone (Tbhq) On Estrogen Receptor Alpha (Erα) And Tumor Suppressor Protein P53 In T-47d And Mcf-7 Breast Cancer Cell Lines, Samantha E. Pfiffner, Katelyn Farrar, Erin Hallman, Kaylin Whittaker, Aisha Zanib, Sumi Dinda Ph.D.

Medical Student Research Symposium

Tert-butyl hydroquinone (TBHQ) is an aromatic compound that is commonly used as a preservative in processed food to prevent rancidity and lengthen shelf life. TBHQ is known to act as an antioxidant by protecting cells from radical oxygen species and thus preventing DNA damage. Although previous studies have found TBHQ to cause cancer cell death at high concentrations, they have also contrastingly found TBHQ, when studied in animal models, to enhance carcinogenic effects. However, the effect of TBHQ on breast cancer has not been thoroughly explored. With the prevalence of breast cancer and the wide use of TBHQ in processed …

Surgical Management Of Velopharyngeal Dysfunction: Major Techniques And Trends For The 21st Century, Dominic Alessio-Bilowus, Sadaf Hashemian, Kylie Nikolli, Ahmed Hashem Md

Medical Student Research Symposium

INTRODUCTION: Surgical management of velopharyngeal dysfunction (VPD) has become increasingly complex over recent decades with advances in diagnosis, evaluation and technique, and research focus in this area is expected to shift accordingly. This study aims to educate readers on updates in management of VPD and explore changes in surgical methods through the 21st century.

METHODS: A systematic review was conducted of all literature published on surgical treatment of VPD since the year 2000, following PRISMA reporting guidelines. Adult-acquired VPD, any non-surgical management, implants and prosthetic devices, animal or cadaver models, and case series involving less than 10 subjects were excluded. …

Intravital Imaging Of Cellular Response Due To Traumatic Brain Injury Using Confocal Microscopy, Enoch G. Kim, Jeffrey Horbatiuk, Carolyn Harris

Medical Student Research Symposium

Introduction: Cellular reaction to traumatic brain injury is complex and involves considerable interactions between cells and reactivity to foreign bodies. Our objective was to assess neurons, microglia, astrocytes, and intracellular Ca²⁺ signaling by creating a novel confocal microscopy technique involving an air immersed lens that does not sacrifice resolution and limits signal attenuation. This study aimed to create a consistent dynamic methodology to observe the cortical cellular response using real-time intravital imaging as trauma is being induced.

Methods: Once surgical plane was achieved, rodent cortices were exposed via craniotomy and blunt insertion with a silicone shunt catheter into the …

Multi-Omics Analysis Identifies Drivers Of Protein Phosphorylation., Tian Zhang, Gregory R Keele, Isabela Gerdes Gyuricza, Matthew J Vincent, Catherine Brunton, Timothy A Bell, Pablo Hock, Ginger D Shaw, Steven C. Munger, Fernando Pardo-Manuel De Villena, Martin T Ferris, Joao A Paulo, Steven P Gygi, Gary Churchill

Faculty Research 2023

BACKGROUND: Phosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling cascades. The abundance of a phosphorylated peptide (phosphopeptide) is determined by the abundance of its parent protein and the proportion of target sites that are phosphorylated.

RESULTS: We quantified phosphopeptides, proteins, and transcripts in heart, liver, and kidney tissue samples of mice from 58 strains of the Collaborative Cross strain panel. We mapped ~700 phosphorylation quantitative trait loci (phQTL) across the three tissues and applied genetic mediation analysis to identify causal drivers of phosphorylation. We identified kinases, phosphatases, cytokines, …

The Eye Of The King: Screenplay Adaptation As A Craft Tool, Nora Annette Graves

Masters Theses

Adaptation studies typically focus on a screenplay’s fidelity to its original text within the constraints imposed by the new genre. This thesis approaches adaptation as a craft tool: a rich source of fresh authorial insight into characters, settings, and plotlines. Experimentation, not fidelity, is the goal of the self-adapter; adaptations are valued and deemed successful based on the new levels of complexity they uncover or add to an ongoing story. The author’s screenplay adaptation of her original novel, The Eye of the King, served as a case study for testing the value of adaptation as a writer’s craft tool. Re-telling …

Urine Cell Transcriptomes Implicate Specific Renal Inflammatory Pathways Associated With Difficult-To-Control Hypertension, Kausik Umanath, Ruicong She, Clare Hassett, Indra Adrianto, Albert M. Levin, Gina Savickas, Jerry Yee, Pablo A. Ortiz

Hypertension and Vascular Research Articles

Background: The renal mechanisms involved in the maintenance of human hypertension and resistance to treatment are not well understood. Animal studies suggest that chronic renal inflammation contributes to hypertension. We studied cells shed in first-morning urine samples from individuals who were hypertensive who exhibited difficult-to-control blood pressure (BP). We performed bulk RNA sequencing of these shed cells to develop transcriptome-wide associations with BP. We also analyzed nephron-specific genes and used an unbiased bioinformatic approach to find signaling pathways activated in difficult-to-control hypertension.

Methods and Results: Participants who completed the SPRINT (Systolic Blood Pressure Intervention Trial) at a single trial site …

Movement, Behavior, And Trophic Ecology Of A Pelagic Predator Guild In The Eastern Tropical Pacific Ocean, Ryan Keith Logan

All HCAS Student Capstones, Theses, and Dissertations

Pelagic apex predators exert strong influences on ecological communities, and often support valuable commercial or recreational fisheries worldwide. Yet, due to their rarity and pelagic lifestyle, many species, such as billfishes, have proven particularly difficult to study at resolutions necessary to define dynamics of recovery from fishery interaction, physical interaction with environmental features and prey exploitation, and competitive interactions among other billfish predators. This leads to a paucity of knowledge on billfish ecology and habitat use, and hinders management efforts. With the ever-improving and miniaturization of technology and oceanographic datasets, the ability to define and quantify these interactions of fish …

Transformative Learning Theory As Applied To Worship Studies, Loueda B. Bleiler

Doctoral Dissertations and Projects

Despite extensive research regarding the application of Transformative Learning Theory in adult education, there is very little literature promoting applying these principles and practices within Christian Worship Studies. Transformative Learning Theory is an educational theory that researches and promotes perspective-changing teaching and learning. Structured educational opportunities and spiritual development through Christian worship both have the potential to be life-altering events in human experience. In each of these dimensions of learning, the final result may include a change in perspective which then leads to modified behaviors. Transformative change occurs in the life of the learner. This qualitative research study explores the …

A Model Of Evangelism For A Bilingual Worship Community, Dorkham Donovan See

Doctoral Dissertations and Projects

The purpose of this DMIN action research project is to develop a model of evangelism for the Lahu-English bilingual worship community at Calvary Evangelical Free Church in Rochester, Minnesota. This study claims that the Lahu-English bilingual worship community has not emphasized evangelism—to share the gospel beyond this group—due to the decline of Christian influence in general and the cultural and language barriers that first and second- generation Lahu Christians encounter. Most ethnic worship communities tend to congregate and remain in their sphere of social and worship gatherings as a haven and belonging. While this is not intrinsically wrong, it ignores …

Creating Habitat Suitability Models For Restoration Of Sesbania Tomentosa And Chenopodium Oahuense On Molokai, Hawaii, Bronwyn Meldrum

Undergraduate Honors Theses

Hawaii is home to incredible diversity in both plant and animal life. Nearly 90% of Hawaii’s 1,400 plant taxa are found nowhere else in the world, and in an ecosystem threatened by invasive species and terrain alteration, this puts them at risk of extinction. As pressures on global biodiversity intensify, conservation efforts and restoration of endangered species are of the utmost importance. The Molokai Land Trust is actively working to eradicate invasive kiawe (Prosopis pallida) forests and to restore endemic species and other native vegetation on the Mokio Preserve. These vital efforts are made more difficult because the …