Digital Commons Network^™

Assessing Selective Export Of Fluorescent Ssa4 Reporters, Caroline Firmin, Rebecca Adams

Science University Research Symposium (SURS)

The process of creating proteins from mRNA is necessary for cell viability. Importantly, the proteins that are generated are differentially regulated so that the cell makes specific proteins in response to its environment. For example, mRNA is selectively exported during stress conditions to allow response to this stress. During heat shock at 42°C, in which proteins are denatured, the gene SSA4 encodes a selectively transported protein chaperone that allows refolding of denatured proteins. This study sought to explore the mechanisms of this selective export. To do this, I analyzed the expression of a fluorescent reporter wherein GFP is expressed with …

Independence Testing-Based Approach To Causal Discovery Under Measurement Error And Linear Non-Gaussian Models, Haoyue Dai, Peter Spirtes, Kun Zhang

Machine Learning Faculty Publications

Causal discovery aims to recover causal structures generating the observational data. Despite its success in certain problems, in many real-world scenarios the observed variables are not the target variables of interest, but the imperfect measures of the target variables. Causal discovery under measurement error aims to recover the causal graph among unobserved target variables from observations made with measurement error. We consider a specific formulation of the problem, where the unobserved target variables follow a linear non-Gaussian acyclic model, and the measurement process follows the random measurement error model. Existing methods on this formulation rely on non-scalable over-complete independent component …

Design, Synthesis, And Evaluation Of N-Methylated H2r2w4, Talal Alrubaie

Pharmaceutical Sciences (MS) Theses

Antimicrobial peptides (AMPs) are potential candidates for developing antibiotics against multidrug-resistant bacteria. We have recently developed a potent cyclic AMP containing histidine (H), arginine (R), and tryptophan (W) residues named [H₂R₂W₄]. This peptide showed antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus aureus (SA) with a minimum inhibitor concentration (MIC) of 3.1 μg/mL and a MIC of 6.2 μg/mL for Escherichia coli (E. coli). However, it displayed a mild cytotoxicity with cell viability of approximately 80% against normal human lung cells (MRC-5) and ~60% against normal human kidney cells (HEK-293) at the …

Developing Novel Remote Camera Approaches To Assess And Monitor The Population Status Of Australian Sea Lions, Mathew Hourston, Daniela Waltrick, Stuart Blight, Ainslie Denham, Alex Hesp, Steve Taylor

Fisheries Research Reports

This project trialled the use of remote cameras to monitor the relative abundance of Australian sea lions (ASLs, Neophoca cinerea) at three Western Australian (WA) breeding colonies. The research was undertaken by the Department of Primary Industries and Regional Development (DPIRD) to assess whether the analysis of camera footage could be used to estimate ASL relative abundance, providing an alternative to the traditional “boots on the ground” approach (hereon in “BoG”) of visiting colonies to count animals. This report outlines the strengths and limitations of this novel approach rather than providing an update on the population status of ASLs. …

Columbia Chronicle (09/26/2022), Columbia College Chicago

Columbia Chronicle

Student newspaper from September 26, 2022 entitled The Columbia Chronicle. This issue is 20 pages. Cover story: "The Creatives". Editors-in-Chief: Anna Busalacchi & Noah Jennings.

Structural Covariance Of The Ventral Visual Stream Predicts Posttraumatic Intrusion And Nightmare Symptoms: A Multivariate Data Fusion Analysis, Nathaniel G. Harnett, Katherine E. Finegold, Lauren A.M. Lebois, Sanne J.H. Van Rooij, Timothy D. Ely, Vishnu P. Murty, Tanja Jovanovic, Steven E. Bruce, Stacey L. House, Francesca L. Beaudoin, Xinming An, Donglin Zeng, Thomas C. Neylan, Gari D. Clifford, Sarah D. Linnstaedt, Laura T. Germine, Kenneth A. Bollen, Scott L. Rauch, John P. Haran, Alan B. Storrow, Christopher Lewandowski, Paul I. Musey, Phyllis L. Hendry, Sophia Sheikh, Christopher W. Jones, Brittany E. Punches, Michael C. Kurz, Robert A. Swor, Lauren A. Hudak, Jose L. Pascual, Mark J. Seamon, Erica Harris

Psychology Faculty Works

Visual components of trauma memories are often vividly re-experienced by survivors with deleterious consequences for normal function. Neuroimaging research on trauma has primarily focused on threat-processing circuitry as core to trauma-related dysfunction. Conversely, limited attention has been given to visual circuitry which may be particularly relevant to posttraumatic stress disorder (PTSD). Prior work suggests that the ventral visual stream is directly related to the cognitive and affective disturbances observed in PTSD and may be predictive of later symptom expression. The present study used multimodal magnetic resonance imaging data (n = 278) collected two weeks after trauma exposure from the AURORA …

Phase Transitions In Evolutionary Dynamics, Adam D. Scott, Dawn M. King, Stephen W. Ordway, Sonya Bahar

Physics Faculty Works

Sharp changes in state, such as transitions from survival to extinction, are hallmarks of evolutionary dynamics in biological systems. These transitions can be explored using the techniques of statistical physics and the physics of nonlinear and complex systems. For example, a survival-to-extinction transition can be characterized as a non-equilibrium phase transition to an absorbing state. Here, we review the literature on phase transitions in evolutionary dynamics. We discuss directed percolation transitions in cellular automata and evolutionary models, and models that diverge from the directed percolation universality class. We explore in detail an example of an absorbing phase transition in an …

A Comparison Of Logistic, Ridge, And Lasso Regression With Heart Failure Risk Data: Effects Of Sample Size, Predictor Correlation, And Predictor Weight On Outcome Accuracy, Mahmoud M. Aljuhani

Electronic Theses and Dissertations

Logistic Regression (LR), LASSO regression, and RIDGE regression are standard classification techniques for predicting a dichotomous output. Since these methods are applied for similar purposes and have different features, it is crucial to evaluate the performance of these methods under different controlled conditions. With this information, researchers can apply the optimal method for specific conditions.

Following previous research, which reported the effects of conditions such as sample size and multicollinearity on the performance of the classification methods, this research focused on the effects of when sample size, level of predictor collinearity, and predictor variable weight are controlled on the performance …

Modeling Of Population Dynamics In Spatially Continuous And Heterogeneous Environments Using Partial Differential Equations, Ryan T. St. Clair

Masters Theses & Specialist Projects

This thesis provides an expansion of existing reaction diffusion population ecology models into patchy landscapes with greater spatial heterogeneity. The Sturm-Loiville eigenvalue problem for a heterogeneous 3 patch landscape is solved implicitly and the population growth rate and migration dynamics on such a landscape are thoroughly discussed. In addition a system of interface equations is found whose greatest solution is the dominant eigenvalue of an N-patch landscape. The results of this model agree well with previously published results and show the mathematical equivalence of two published approaches for incorporating organism behavior at habitat interfaces. Increased modeling capabilities in heterogeneous environments …

First-Generation Leaders: A Qualitative Examination Of Characteristics, Traits, And Identity Of First-Generation Graduates In Leadership, Jamie Woolery

Masters Theses & Specialist Projects

This study looked at first-generation college graduates and their paths to successful leadership roles. First-generation college students are defined by the National Association of Personnel Administrators (NASPA) as students from families in which their biological parents did not complete a four-year college degree (NASPA, 2017). An investigation was conducted on demographics, access to education, opportunity, and other factors that lend themselves to successful first-generation leaders who changed the narrative for themselves and their communities. This study looked at the previously conducted literature to provide background support for the need of the research, along with further recommendations and interviews which added …

Functional Analysis Of Legionella Pneumophila Effector Protein, Shreya Neupane

Masters Theses & Specialist Projects

Legionella pneumophila is a gram-negative bacterium that causes Legionnaire’s disease (a severe form of pneumonia) in humans. L. pneumophila can cause infection by utilizing its Type IV secretion system, a protein secretion system that transports proteins from the bacterial cytosol into the infected macrophage. Effectors released from the Type Iv secretion system allow L. pneumophila to create a safe environment to survive, replicate and cause infection. One such effector, RavQ, inhibits cell proliferation of mammalian HEK 293T cells and localizes to the cell’s nucleus, leading us to hypothesize that RavQ interferes with cellular activity in the nucleus. To detect its …

Carbon Cycling And Critical Zone Dynamics In An Urbanized Karst Groundwater System, Amy Hourigan

Masters Theses & Specialist Projects

Increasing atmospheric CO₂ concentrations are correlated to rising global temperatures. Investigating the cumulative global carbon cycling processes is important to understand and quantify the global carbon cycle. By investigating basic geochemical parameters, EpCO₂, DIC, and δ¹³C_DIC, at four sites along Lost River Cave (LRC), in Bowling Green, Kentucky, concentrations, fluxes and sources of C dissolved in groundwater were determined. Urban karst groundwater systems, compared to more natural karst landscapes, typically exhibit widespread impervious, heat-absorbing surfaces, urban heat island effects, and increased anthropogenic groundwater inputs and localized CO₂ emissions. Carbonate hydrogeochemical …

Post Pandemic Cyberbiosecurity Threats From Terrorist Groups, Haley D. Dodge

Master's Theses

The research in this thesis explored the research question: Are United States (US) health systems accessible to cyber-bio terrorist attacks post-pandemic, within the context of the emerging discipline of cyberbiosecurity? Key findings of the analysis demonstrated how US health systems are more accessible to cyber-bio terrorist attacks specifically from cyber hacking groups based on the increasing sophistication of their cyber capabilities and the lack of cyber protection for biological systems. The concept of cyberbiosecurity was first introduced in 2018 by researchers exploring the converging threat landscape of the cyber and biology domains. As biology is growing more dependent upon vulnerable …

A Reference Human Induced Pluripotent Stem Cell Line For Large-Scale Collaborative Studies., Caroline B Pantazis, Andrian Yang, Erika Lara, Justin A Mcdonough, Cornelis Blauwendraat, Lirong Peng, Hideyuki Oguro, Jitendra Kanaujiya, Jizhong Zou, David Sebesta, Gretchen Pratt, Erin Cross, Jeffrey Blockwick, Philip Buxton, Lauren Kinner-Bibeau, Constance Medura, Christopher Tompkins, Stephen Hughes, Marianita Santiana, Faraz Faghri, Mike A Nalls, Daniel Vitale, Shannon Ballard, Yue A Qi, Daniel M Ramos, Kailyn M Anderson, Julia Stadler, Priyanka Narayan, Jason Papademetriou, Luke Reilly, Matthew P Nelson, Sanya Aggarwal, Leah U Rosen, Peter Kirwan, Venkat Pisupati, Steven L Coon, Sonja W Scholz, Theresa Priebe, Miriam Öttl, Jian Dong, Marieke Meijer, Lara J M Janssen, Vanessa S Lourenco, Rik Van Der Kant, Dennis Crusius, Dominik Paquet, Ana-Caroline Raulin, Guojun Bu, Aaron Held, Brian J Wainger, Rebecca M C Gabriele, Jackie M Casey, Selina Wray, Dad Abu-Bonsrah, Clare L Parish, Melinda S Beccari, Don W Cleveland, Emmy Li, Indigo V L Rose, Martin Kampmann, Carles Calatayud Aristoy, Patrik Verstreken, Laurin Heinrich, Max Y Chen, Birgitt Schüle, Dan Dou, Erika L F Holzbaur, Maria Clara Zanellati, Richa Basundra, Mohanish Deshmukh, Sarah Cohen, Richa Khanna, Malavika Raman, Zachary S Nevin, Madeline Matia, Jonas Van Lent, Vincent Timmerman, Bruce R Conklin, Katherine Johnson Chase, Ke Zhang, Salome Funes, Daryl A Bosco, Lena Erlebach, Marc Welzer, Deborah Kronenberg-Versteeg, Guochang Lyu, Ernest Arenas, Elena Coccia, Lily Sarrafha, Tim Ahfeldt, John C Marioni, William C Skarnes, Mark R Cookson, Michael E Ward, Florian T Merkle

Faculty Research 2022

Human induced pluripotent stem cell (iPSC) lines are a powerful tool for studying development and disease, but the considerable phenotypic variation between lines makes it challenging to replicate key findings and integrate data across research groups. To address this issue, we sub-cloned candidate human iPSC lines and deeply characterized their genetic properties using whole genome sequencing, their genomic stability upon CRISPR-Cas9-based gene editing, and their phenotypic properties including differentiation to commonly used cell types. These studies identified KOLF2.1J as an all-around well-performing iPSC line. We then shared KOLF2.1J with groups around the world who tested its performance in head-to-head comparisons …

Identifying Susceptibility Genes For Essential Hypertension By Transcriptome-Wide Association Study., Lu-Jie Huang, Qiao-Xia Zhang, Robert K Valenzuela, Jia-Chen Xu, Fang Yan, Jie Ma

Faculty Research 2022

Hypertension is a leading risk factor of cardiovascular disease and mortality in the population worldwide. Recently, hundreds of genomic loci were reported for hypertension by GWAS, however, the most SNPs are located in intergenic regions of genome, where a functional cause is difficult to determine. In the current study, a TWAS of hypertension was conducted using 452,264 individuals including 84,640 patients. KEGG and GO enrichment analyses were performed for the hypertension-related genes identified via TWAS. PPI network analysis based on the STRING database was also performed to detect TWAS-identified genes in hypertension. We have identified 18,420 genes from the …

Chelonia Mydas Cranium, Celina Nelson-Jordan, Bryan Weber

Hirons Field Techniques

Chelonia mydas Cranium - Green Sea Turtle skull with jaw positioned agape for detail

South-To-North Migration Preceded The Advent Of Intensive Farming In The Maya Region, Douglas J. Kennett, Mark Lipson, Keith M. Prufer, David Mora-Marín, Richard J. George, Nadin Rohland, Mark Robinson, Willa R. Trask, Heather H. J. Edgar, Ethan C. Hill, Erin E. Ray, Paige Lynch, Emily Moes, Lexi O’Donnell, Thomas K. Harper, Emily J. Kate, Josue Ramos, John Morris, Said M. Gutierrez

Faculty and Student Publications

The genetic prehistory of human populations in Central America is largely unexplored leaving an important gap in our knowledge of the global expansion of humans. We report genome-wide ancient DNA data for a transect of twenty individuals from two Belize rock-shelters dating between 9,600-3,700 calibrated radiocarbon years before present (cal. BP). The oldest individuals (9,600-7,300 cal. BP) descend from an Early Holocene Native American lineage with only distant relatedness to present-day Mesoamericans, including Mayan-speaking populations. After ~5,600 cal. BP a previously unknown human dispersal from the south made a major demographic impact on the region, contributing more than 50% of …

Utah State Engineer, Fall 2022, College Of Engineering

College of Engineering Magazines

Annual magazine for the College of Engineering at Utah State University.

Interview With Michelle Baker, Utah State University Special Collections & Archives

Utah State University COVID-19 Oral History Collection

No abstract provided.

Interview With Patrick Belmont, Utah State University Special Collections & Archives

Utah State University COVID-19 Oral History Collection

No abstract provided.

Interview With Frank Galey, Utah State University Special Collections & Archives

Utah State University COVID-19 Oral History Collection

No abstract provided.

Interview With Jagath Kaluarachchi, Utah State University Special Collections & Archives

Utah State University COVID-19 Oral History Collection

No abstract provided.

Interview With Gina Landaverde, Utah State University Special Collections & Archives

Utah State University COVID-19 Oral History Collection

No abstract provided.

Interview With John Mortensen, Utah State University Special Collections & Archives

Utah State University COVID-19 Oral History Collection

No abstract provided.

Interview With Helen Bond Plylar, Utah State University Special Collections & Archives

Utah State University COVID-19 Oral History Collection

No abstract provided.

Interview With Kieth Roper, Utah State University Special Collections & Archives

Utah State University COVID-19 Oral History Collection

No abstract provided.

Defining Heroinism: Heartthrobs Refining Heroines In 18th And 19th Century Women's Literature, Grace M. Gibson

Honors College Theses

This project will explore the emergence of “heroinism,” a uniquely feminine way in which early female authors approached the heroine’s journey. Barred by male expectations of female conduct both in society and literature, eighteenth and nineteenth century women daring to “attempt the pen” forged stories of heroines with conventions and tropes distinctly, though not entirely, separate from those told of centuries of heroes. I intend to track the ways in which these early tales of heroines told by women strayed from the traditional heroic plot, with unique motivations, mentors, trials, and rewards, but also how they were shaped and confined …

Fetal Sex Impacts Birth To Placental Weight Ratio And Umbilical Cord Oxygen Values With Implications For Regulatory Mechanisms, Bryan S. Richardson, Akasham Rajagopaul, Barbra De Vrijer, Genevieve Eastabrook, Timothy R.H. Regnault

Obstetrics & Gynaecology Publications

Background: We determined the effect of fetal sex on birth/placental weight and umbilical vein and artery oxygen values with implications for placental efficiency and regulatory mechanisms underlying fetal–placental growth differences. Methods: A hospital database was used to obtain birth/placental weight, cord PO2 and other information on patients delivering between Jan 1, 1990 and Jun 15, 2011 with GA > 34 weeks (N = 69,836). Oxygen saturation was calculated from the cord PO2 and pH data, while fractional O2 extraction was calculated from the oxygen saturation data. The effect of fetal sex on birth/placental weight, cord PO2, O2 saturation, and fractional O2 …

Principles Of Dormancy Evident In High-Grade Serous Ovarian Cancer, Trevor G. Shepherd, Frederick A. Dick

Paediatrics Publications

In cancer, dormancy refers to a clinical state in which microscopic residual disease becomes non-proliferative and is largely refractory to chemotherapy. Dormancy was first described in breast cancer where disease can remain undetected for decades, ultimately leading to relapse and clinical presentation of the original malignancy. A long latency period can be explained by withdrawal from cell proliferation (cellular dormancy), or a balance between proliferation and cell death that retains low levels of residual disease (tumor mass dormancy). Research into cellular dormancy has revealed features that define this state. They include arrest of cell proliferation, altered cellular metabolism, and unique …

Deciphering The Role Of Spl12 And Agl6 From A Genetic Module That Functions In Nodulation And Root Regeneration In Medicago Sativa., Vida Nasrollahi, Ze-Chun Yuan, Qing Shi Mimmie Lu, Tim Mcdowell, Susanne Kohalmi, Abdelali Hannoufa

Biology Publications

Our results show that SPL12 plays a crucial role in regulating nodule development in Medicago sativa L. (alfalfa), and that AGL6 is targeted and downregulated by SPL12. Root architecture in plants is critical because of its role in controlling nutrient cycling, water use efficiency and response to biotic and abiotic stress factors. The small RNA, microRNA156 (miR156), is highly conserved in plants, where it functions by silencing a group of SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors. We previously showed that transgenic Medicago sativa (alfalfa) plants overexpressing miR156 display increased nodulation, improved nitrogen fixation and enhanced root regenerative capacity during vegetative …