Digital Commons Network^™

Predicting Sea Pen (Pennatulacea) Distribution On The Uk Continental Shelf: Evidence Of Range Modification By Benthic Trawling, Anna Leena Downie, Tamsyn Noble-James, Ana Chaverra, Kerry L. Howell

School of Biological and Marine Sciences

Sea pen communities are United Nations General Assembly-designated Vulnerable Marine Ecosystems which occur worldwide in soft-bottom sediments where trawling often occurs. However, the ability of marine managers to assess, monitor and mitigate impacts to sea pens at national scales has been constrained by a limited understanding of their environmental requirements, geographical distribution and responses to trawling. In this study, we used random forest species distribution modelling (SDM) to predict the distribution of suitable habitat for 3 sea pen species (tall sea pen Funiculina quadrangularis, slender sea pen Virgularia mirabilis and phosphorescent sea pen Pennatula phosphorea) on the UK continental shelf, …

Zebrafish Blunt-Force Tbi Induces Heterogenous Injury Pathologies That Mimic Human Tbi And Responds With Sonic Hedgehog-Dependent Cell Proliferation Across The Neuroaxis, James Hentig, Kaylee Cloghessy, Manuela Lahne, Yoo Jin Jung, Rebecca A. Petersen, Ann C. Morris, David R. Hyde

Biology Faculty Publications

Blunt-force traumatic brain injury (TBI) affects an increasing number of people worldwide as the range of injury severity and heterogeneity of injury pathologies have been recognized. Most current damage models utilize non-regenerative organisms, less common TBI mechanisms (penetrating, chemical, blast), and are limited in scalability of injury severity. We describe a scalable blunt-force TBI model that exhibits a wide range of human clinical pathologies and allows for the study of both injury pathology/progression and mechanisms of regenerative recovery. We modified the Marmarou weight drop model for adult zebrafish, which delivers a scalable injury spanning mild, moderate, and severe phenotypes. Following …

The Weekly Challenger, July 22, 2021, The Weekly Challenger, Et Al

Weekly Challenger Newspaper Collection

The July 22, 2021, issue of The Weekly Challenger.

12 Honored For Excellence In Teaching, Haley Herfurth

Browse All News

No abstract provided.

Structure And Function Of An Arabidopsis Thaliana Sulfate Transporter, Lie Wang, Kehan Chen, Ming Zhou

Faculty, Staff and Students Publications

Plant sulfate transporters (SULTR) mediate absorption and distribution of sulfate (SO42−) and are essential for plant growth; however, our understanding of their structures and functions remains inadequate. Here we present the structure of a SULTR from Arabidopsis thaliana, AtSULTR4;1, in complex with SO42− at an overall resolution of 2.8 Å. AtSULTR4;1 forms a homodimer and has a structural fold typical of the SLC26 family of anion transporters. The bound SO42− is coordinated by side-chain hydroxyls and backbone amides, and further stabilized electrostatically by the conserved Arg393 and two helix dipoles. Proton and SO42− are co-transported by AtSULTR4;1 and a …

Myeloid Cell Mediated Immune Suppression In Pancreatic Cancer, Samantha B. Kemp, Marina Pasca Di Magliano, Howard C. Crawford

Hematology/Oncology Articles

Pancreatic ductal adenocarcinoma (PDA), the most common pancreatic cancer, is a nearly-universally lethal malignancy. PDA is characterized by extensive infiltration of immunosuppressive myeloid cells, including tumor-associated macrophages (TAMs) and myeloid-derived suppressor cells (MDSCs). Myeloid cells in the tumor microenvironment (TME) inhibit cytotoxic T cell responses promoting carcinogenesis. Immune checkpoint therapy has not been effective in PDA, most likely due to this robust immune suppression, making it critical to elucidate mechanisms behind this phenomenon. Here, we review myeloid cell infiltration and cellular crosstalk in PDA progression and highlight current therapeutic approaches to target myeloid cell-driven immune suppression.

Mutational Analysis Reveals Potential Phosphorylation Sites In Eukaryotic Elongation Factor 1a That Are Important For Its Activity, Maria K. Mateyak, Dongming He, Pragati Sharma, Terri Goss Kinzy

Faculty Publications – Biological Sciences

Previous studies have suggested that phosphorylation of translation elongation factor 1A (eEF1A) can alter its function, and large-scale phospho-proteomic analyses in Saccharomyces cerevisiae have identified 14 eEF1A residues phosphorylated under various conditions. Here, a series of eEF1A mutations at these proposed sites were created and the effects on eEF1A activity were analyzed. The eEF1A-S53D and eEF1A-T430D phosphomimetic mutant strains were inviable, while corresponding alanine mutants survived but displayed defects in growth and protein synthesis. The activity of an eEF1A-S289D mutant was significantly reduced in the absence of the guanine nucleotide exchange factor eEF1Bα and could be restored by an exchange-deficient …

Bridging The 12-6-4 Model And The Fluctuating Charge Model, Pengfei Li

Chemistry: Faculty Publications and Other Works

Metal ions play important roles in various biological systems. Molecular dynamics (MD) using classical force field has become a popular research tool to study biological systems at the atomic level. However, meaningful MD simulations require reliable models and parameters. Previously we showed that the 12-6 Lennard-Jones nonbonded model for ions could not reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values simultaneously when ion has a charge of +2 or higher. We discussed that this deficiency arises from the overlook of the ion-induced dipole interaction in the 12-6 model, and this term is proportional to 1/r …

A Single Dose Of Replication-Competent Vsv-Vectored Vaccine Expressing Sars-Cov-2 S1 Protects Against Virus Replication In A Hamster Model Of Severe Covid-19., Delphine C. Malherbe, Drishya Kurup, Christoph Wirblich, Adam J. Ronk, Chad Mire, Natalia Kuzmina, Noor Shaik, Sivakumar Periasamy, Matthew A. Hyde, Julie M. Williams, Pei-Yong Shi, Matthias J. Schnell, Alexander Bukreyev

Department of Microbiology and Immunology Faculty Papers

The development of effective countermeasures against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the agent responsible for the COVID-19 pandemic, is a priority. We designed and produced ConVac, a replication-competent vesicular stomatitis virus (VSV) vaccine vector that expresses the S1 subunit of SARS-CoV-2 spike protein. We used golden Syrian hamsters as animal models of severe COVID-19 to test the efficacy of the ConVac vaccine. A single vaccine dose elicited high levels of SARS-CoV-2 specific binding and neutralizing antibodies; following intranasal challenge with SARS-CoV-2, animals were protected from weight loss and viral replication in the lungs. No enhanced pathology was observed …

Analysis Of The Role Of Akirin Interactions With Nuclear Body Proteins During Myogenesis, Laura Yorke

Master of Science in Integrative Biology Theses

Akirin is a highly conserved, small nuclear protein of indeterminate structure ubiquitously expressed in non-fungal eukaryotic species. It was first discovered in the innate immune response, but many other functions have since been found, including embryonic muscle patterning and myogenesis. Animals with either nonfunctional or missing Akirin have aberrations in embryonic muscle patterning, along with other defects. Akirin interacts with transcription factors such as Twist to coordinate development through interfacing between Twist and other complexes, such as the Brahma Chromatin Remodeling Complex (BRM). Therefore, Akirin likely plays a general role in transcription during early development, interfacing with other transcriptional machinery …

Semi Real-Time Detection Of Subsurface Consolidation Defects During Concrete Curing Stage, Chongsheng Cheng, Zhigang Shen

Department of Construction Engineering and Management: Faculty Publications

Subsurface consolidation defect is a common issue in concrete pavement construction, and the hidden defects often require costly repairs after project delivery. Therefore, being able to identify this type of defect during construction will enable contractor to conduct quick repairs to avoid costly post-construction rework. In this paper a semi real-time detection approach using infrared thermography is introduced. The developed approach utilizes the hydration heat during curing time to identify the subsurface voids based on the regional temperature contrast. Experimental studies were conducted using artificial void-defect in different sizes and depths. The thermographic analysis is employed to locate the void-defects …

Book Review: The Wildlife Techniques Manual, Eighth Edition, Justin Small

Human–Wildlife Interactions

Wildlife researchers and managers are consistently tackling ecological and conservation issues that are increasing in complexity and scope. Wildlife issues often span beyond singular research frameworks and management jurisdictions, preventing modern wildlife conservation from operating in mutually exclusive arenas (i.e., research or management). As a wildlife researcher whose research is conducted on both public and private rangelands, and across multiple stakeholder groups, techniques to answer difficult questions and offer time-sensitive solutions must pull from both research and management arenas. Historically, book or journal resources that wildlife professionals could readily access for necessary scientific guidance were contained in many documents, making …

Threshold Concepts In Web Development: The Impact Of Education And Experience On The Perceptions Of Practitioners, Michael Lee Mick

College of Computing and Digital Media Dissertations

The Threshold Concepts (TCs) framework posits characteristics of critical concepts that enable a learner to see things in a new and unforgettable way that allows the incorporation of cognitive approaches and skills needed by professionals in the discipline. All previous research has been qualitatively oriented toward discovery of candidate TCs, without, so far, quantitative studies of the candidate TCs recognition within the professional ranks. An underrepresented group in previous research is that of Web development professionals.

This proposal describes initial quantitative research utilizing the TCs framework in the Web development area to measure the perception of candidate TCs by professionals …

Integration Of Systemic Therapy And Stereotactic Radiosurgery For Brain Metastases, Raees Tonse, Martin Tom, Minesh Mehta, Manmeet Ahluwalia, Rupesh Kotecha

All Publications

Abstract: Brain metastasis (BM) represents a common complication of cancer, and in the modern era requires multi-modal management approaches and multi-disciplinary care. Traditionally, due to the limited efficacy of cytotoxic chemotherapy, treatment strategies are focused on local treatments alone, such as whole-brain radiotherapy (WBRT), stereotactic radiosurgery (SRS), and resection. However, the increased availability of molecular-based therapies with central nervous system (CNS) penetration now permits the individualized selection of tailored systemic therapies to be used alongside local treatments. Moreover, the introduction of immune checkpoint inhibitors (ICIs), with demonstrated CNS activity has further revolutionized the management of BM patients. The rapid introduction …

Seasonal Nutrient Limitations Of Cyanobacteria, Phytoplankton, And Cyanotoxins In Utah Lake, Gabriella Marie Lawson

Theses and Dissertations

Excess nutrients from human activity trigger toxic cyanobacterial and algal blooms, creating expansive hypoxic dead zones in lakes, damaging ecosystems, hurting local economies, undermining food and water security, and directly harming human health. To identify when and where nutrients limit phytoplankton and cyanobacterial growth, and cyanotoxin concentrations across Utah Lake, USA we conducted four in-situ bioassay studies (563 cubitainers or experimental units) that experimentally added N, P or N+P over the spring, early summer, summer, late summer, and fall in lake water from the top 20 cm of the water column. For our purpose, we defined total phytoplankton as all …

Raman Spectroscopy Reveals High Phloem Sugar Content In Leaves Of Canopy Red Oak Trees, Jess T. Gersony, Arthur Mcclelland, N Michele Holbrook

Biological Sciences: Faculty Publications

A robust understanding of phloem functioning in tall trees evades us because current methods for collecting phloem sap do not lend themselves to measuring actively photosynthesizing canopy leaves. We show that Raman spectroscopy can be used as a quantitative tool to assess sucrose concentration in leaf samples. Specifically, we found that Raman spectroscopy can predict physiologically relevant sucrose concentrations (adjusted R2 of 0.9) in frozen leaf extract spiked with sucrose. We then apply this method to estimate sieve element sucrose concentration in rapidly frozen petioles of canopy red oak (Quercus rubra) trees and found that sucrose concentrations are > 1100 mM …

Investigating Endocrine‐Disrupting Properties Of Chemicals In Fish And Amphibians: Opportunities To Apply The 3rs, N Burden, Mr Embry, Th Hutchinson, Sg Lynn, Sk Maynard, Ca Mitchell, F Pellizzato, F Sewell, Kl Thorpe, L Weltje, Jr Wheeler

School of Geography, Earth and Environmental Sciences

Many regulations are beginning to explicitly require investigation of a chemical's endocrine-disrupting properties as a part of the safety assessment process for substances already on or about to be placed on the market. Different jurisdictions are applying distinct approaches. However, all share a common theme requiring testing for endocrine activity and adverse effects, typically involving in vitro and in vivo assays on selected endocrine pathways. For ecotoxicological evaluation, in vivo assays can be performed across various animal species, including mammals, amphibians, and fish. Results indicating activity (i.e., that a test substance may interact with the endocrine system) from in vivo …

Global Initiative For Asthma (Gina): What’S New In Gina 2021?, Christopher Chambers, Md

Department of Family & Community Medicine Presentations and Grand Rounds

No abstract provided.

Effect Of Low Lactose Formula On The Short-Term Outcomes Of Neonatal Abstinence Syndrome: A Systematic Review., Mahdi Alsaleem, Jarrod Dusin, Gangaram Akangire

Manuscripts, Articles, Book Chapters and Other Papers

The use of low lactose formula (LLF) in term and near-term infants in infants with neonatal abstinence syndrome (NAS) has been increasing recently. However, the clinical evidence of such use is limited. Our aim in this paper was to systematically review the current literature about the use of LLF in infants with NAS. We searched PubMed, Embase, Cumulative Index to Nursing and Allied Health Literature, and Cochrane Database of Systematic Reviews for articles published between 2015 and 2020. Only randomized controlled trials, prospective, and retrospective studies. The risk of bias was assessed by using published tools appropriate for the study …

Ruminant Milk-Derived Extracellular Vesicles: A Nutritional And Therapeutic Opportunity?, Siew Ling Ong, Cherie Blenkiron, Stephen Haines, Alejandra Acevedo-Fani, Juliana A.S. Leite, Janos Zempleni, Rachel C. Anderson, Mark J. Mccann

Department of Nutrition and Health Sciences: Faculty Publications

Milk has been shown to contain a specific fraction of extracellular particles that are reported to resist digestion and are purposefully packaged with lipids, proteins, and nucleic acids to exert specific biological effects. These findings suggest that these particles may have a role in the quality of infant nutrition, particularly in the early phase of life when many of the foundations of an infant’s potential for health and overall wellness are established. However, much of the current research focuses on human or cow milk only, and there is a knowledge gap in how milk from other species, which may be …

Near-Optimal Learning Of Tree-Structured Distributions By Chow-Liu, Arnab Bhattacharyya, Sutanu Gayen, Eric Price, N. V. Vinodchandran

Department of Mathematics: Faculty Publications

We provide finite sample guarantees for the classical Chow-Liu algorithm (IEEE Trans. Inform. Theory, 1968) to learn a tree-structured graphical model of a distribution. For a distribution P on Σⁿ and a tree T on n nodes, we say T is an ε-approximate tree for P if there is a T-structured distribution Q such that D(P || Q) is at most ε more than the best possible tree-structured distribution for P. We show that if P itself is tree-structured, then the Chow-Liu algorithm with the plug-in estimator for mutual information with eO (|Σ| …

A Smartphone App For Individual Xylazine/Ketamine Calculation Decreased Anesthesia-Related Mortality In Mice, Carlos Poblete Jara, Rodrigo S. Carraro, Ariane Zanesco, Beatriz Andrade, Karina Moreira, Guilherme Nogueira, Bruno L. Souza, Thais Paulino Prado, Valeria Povoa, William Velander, Licio A. Velloso, Eliana P. Araujo

Department of Chemical and Biomolecular Engineering: Faculty Publications

Currently, experimental animals are widely used in biological and medical research. However, the scientific community has raised several bioethical concerns, such as the number of animals required to achieve reproducible and statistically relevant results. These concerns involve aspects related to pain, discomfort, and unwanted animal loss. Retrospectively, we compare two different approaches for anesthesia dosage: a mobile app for dose calculation and a standard dose calculation. A total of 939 C57BL/6J and Swiss mice were analyzed. We collected data on intraoperative and anesthesia-related mortality as described in electronic or physical handwritten records. Our results showed that the mobile app approach …

Vertical Profiles Of Trace Gas And Aerosol Properties Over The Eastern North Atlantic: Variations With Season And Synoptic Condition, Yang Wang, Guangjie Zheng, Michael P. Jensen, Daniel A. Knopf, Alexander Laskin, Alyssa A. Matthews, For Full List Of Authors, See Publisher's Website.

Civil, Architectural and Environmental Engineering Faculty Research & Creative Works

Because of their extensive coverage, marine low clouds greatly impact the global climate. Presently, the response of marine low clouds to the changes in atmospheric aerosols remains a major source of uncertainty in climate simulations. One key contribution to this large uncertainty derives from the poor understanding of the properties and processes of marine aerosols under natural conditions and the perturbation by anthropogenic emissions. The eastern North Atlantic (ENA) is a region of persistent but diverse subtropical marine boundary layer (MBL) clouds, where cloud albedo and precipitation are highly susceptible to perturbations in aerosol properties. Here we examine the key …

Effects Of Microplastic On Freshwater Benthic Ecosystems: Toxicity And Impacts On Biogeochemical Cycling, Kristina Chomiak

Theses

The accumulation of plastic debris in waterways is an increasingly complex environmental problem due to the ubiquity and magnitude of plastic debris across freshwater ecosystems, along with the unknown impacts on ecosystems and public health. However, “plastic” is a catchall term for numerous polymers with unique physical and chemical properties. Further complicating the prediction of risk, plastic characteristics may change from environmental exposure, with changes in density, adsorption or leaching of toxins, and accumulation of biofilms that further influence material properties, fate and impact. Recent studies suggest that a substantial proportion of plastic entering freshwater systems is deposited in the …

Evaluation Of Damage To Forest Tree Plantations By Wild Boar In The Czech Republic, Vlastimil Skoták, Jakub Drimaj, Jiří Kamler

Human–Wildlife Interactions

Wild boar (Sus scrofa) populations in Central Europe have been growing long-term, and damages to crops and forests where boars damage freshly planted tree seedlings are growing too. In addition to having a significant economic impact, these damages worsen the prospect of successful restoration of bare land. This study presents an analysis of damage to tree seedling plantations caused by wild boar in the Czech Republic. We used data from an extensive questionnaire survey among forest owners, our own survey of the extent of damage in model areas, and experiments in locations with a large boar population. Damage …

Utility Of Visual Counts For Determining Efficacy Of Management Tools For California Ground Squirrels, Roger A. Baldwin, Theresa A. Becchetti, Niamh Quinn, Ryan Meinerz

Human–Wildlife Interactions

Visual counts are frequently used to assess efficacy of management tools for ground squirrels (Marmotini), but the effectiveness of this approach has not been assessed for many ground squirrel species including California ground squirrels (Otospermophilus spp.). As such, we used visual counts of California ground squirrels to determine the efficacy of diphacinone-treated oat groat applications in rangelands in central California, USA, and compared those results to efficacy values derived from the use of radio-collared ground squirrels in the same plots. We also used location data of radio-collared ground squirrels to explore the size of buffer zone needed around census …

Characteristics Of Non-Fatal Attacks By Black Bears: Conterminous United States, 2000–2017, Janel M. Scharhag, Cady Sartini, Shawn M. Crimmins, Scott E. Hygnstrom, Jeffrey B. Stetz

Human–Wildlife Interactions

Attacks on humans by bears (Ursus spp.) have increased in recent decades, as both human and bear populations have increased. To help mitigate the risk of future attacks, it is important to understand the circumstances in past attacks. Information and analyses exist regarding fatal attacks by both American black bears (Ursus americanus) and brown bears (U. arctos) as well as non-fatal attacks by brown bears. No similarly thorough analyses on non-fatal attacks by black bears are available. Our study addressed this information gap by analyzing all (n = 210) agency-confirmed, non-fatal attacks by black …

Generalist Bird Exhibits Site-Dependent Resource Selection, Samantha M. Cady, Craig A. Davis, Samuel D. Fuhlendorf, Rheinhardt Scholtz, Daniel R. Uden, Dirac Twidwell

Department of Agronomy and Horticulture: Faculty Publications

Quantifying resource selection (an organism's disproportionate use of available resources) is essential to infer habitat requirements of a species, develop management recommendations, predict species responses to changing conditions, and improve our understanding of the processes that underlie ecological patterns. Because study sites, even within the same region, can differ in both the amount and the arrangement of cover types, our objective was to determine whether proximal sites can yield markedly different resource selection results for a generalist bird, northern bobwhite (Colinus virginianus). We used 5 years of telemetry locations and newly developed land cover data at two, geographically distinct but …

Characterization Of Hnrnpa1 Mutations Defines Diversity In Pathogenic Mechanisms And Clinical Presentation., Danique Beijer, Hong Joo Kim, Lin Guo, Kevin O'Donovan, Inès Mademan, Tine Deconinck, Kristof Van Schil, Charlotte M Fare, Lauren E Drake, Alice F Ford, Andrzej Kochański, Dagmara Kabzińska, Nicolas Dubuisson, Peter Van Den Bergh, Nicol C Voermans, Richard Jlf Lemmers, Silvère M Van Der Maarel, Devon Bonner, Jacinda B Sampson, Matthew T Wheeler, Anahit Mehrabyan, Steven Palmer, Peter De Jonghe, James Shorter, J Paul Taylor, Jonathan Baets

Department of Biochemistry and Molecular Biology Faculty Papers

Mutations in HNRNPA1 encoding heterogeneous nuclear ribonucleoprotein (hnRNP) A1 are a rare cause of amyotrophic lateral sclerosis (ALS) and multisystem proteinopathy (MSP). hnRNPA1 is part of the group of RNA-binding proteins (RBPs) that assemble with RNA to form RNPs. hnRNPs are concentrated in the nucleus and function in pre-mRNA splicing, mRNA stability, and the regulation of transcription and translation. During stress, hnRNPs, mRNA, and other RBPs condense in the cytoplasm to form stress granules (SGs). SGs are implicated in the pathogenesis of (neuro-)degenerative diseases, including ALS and inclusion body myopathy (IBM). Mutations in RBPs that affect SG biology, including FUS, …

“Gender (As Constant) Labor”: A Consciousness Raising Dialogue On Transfeminist Scholarship And Organizing, Melissa Autumn White

The Seneca Falls Dialogues Journal

This co-authored essay draws on student research conducted for an upper-level course called Trans*Studies that was originally presented at the Seneca Falls Dialogues Conference in October 2016. Drawing on Jane Ward's generative concept of "gender labor", our Dialogue highlights the material effects of representational politics, and articulates the need to centre a transfeminist critique of normative regimes of power, including the representation of "women's" history in the United States.