Digital Commons Network^™

Decision-Tree Based Meta-Strategy Improved Accuracy Of Disorder Prediction And Identified Novel Disordered Residues Inside Binding Motifs, Bi Zhao, Bin Xue

Molecular Biosciences Faculty Publications

Using computational techniques to identify intrinsically disordered residues is practical and effective in biological studies. Therefore, designing novel high-accuracy strategies is always preferable when existing strategies have a lot of room for improvement. Among many possibilities, a meta-strategy that integrates the results of multiple individual predictors has been broadly used to improve the overall performance of predictors. Nonetheless, a simple and direct integration of individual predictors may not effectively improve the performance. In this project, dual-threshold two-step significance voting and neural networks were used to integrate the predictive results of four individual predictors, including: DisEMBL, IUPred, VSL2, and ESpritz. The …

Poly Cystic Ovarian Syndrome In India: A Socio-Cultural Perspective, Hannah Wickham

Independent Study Project (ISP) Collection

This study examines the ways in which cultural determinants affect the health-seeking, diagnosis and treatment process of women with Poly Cystic Ovarian Syndrome (PCOS) as well as the underlying socio-cultural causes of the illness. Often coined as a “lifestyle disease”, PCOS is becoming a growing concern of physicians and women alike as its prevalence is on the rise with no signs of slowing down. Lifestyle, stigmas/taboos, PCOS’s effect on identity, and quality of life are all areas that are examined throughout this paper. A mixture of patients’ and doctors’ perspectives on PCOS were gathered throughout a three-week time period in …

Ursinus Magazine, Fall 2018, Brock Blomberg, Ed Moorhouse, Jack Croft, Mary Lobo, Richard L. Wallace

Ursinus Magazine, 1995–Present

Breaking ground on the Commons • Levinthal photographs donated to the Berman • First Abele scholarships awarded • Fostering inclusive conversations • Paying it forward • Then and now: Marzella's Pizzeria • Getting to know: Leah Joseph • Beneath the soil • Field of streams • The modern mapmakers • Burning question: Is our relationship with nature catastrophic? • Sustainability by the numbers • Lost and found • Homecoming and Family Weekend • Class notes • In memoriam • Births • Deaths • Weddings • Alumnus chronicles life as "reckless but lucky"

Toxoplasma Gondii Seropositivity And Substance Use In Us Adults, Bruce L. Brown, Andrew N. Berrett, Shawn D. Gale, Lance D. Erickson, Evan L. Thacker, Dawson W. Hedges

Faculty Publications

The intracellular parasite Toxoplasma gondii (Nicolle et Manceaux, 1908) infects humans resulting in acute toxoplasmosis, an infection that in immunocompetent people is typically mild but results in persistent latent toxoplasmosis. In that T. gondii appears to affect dopamine synthesis and because addicting drugs affect midbrain dopamine transmission, latent toxoplasmosis could influence substance use. Using both the third and continuous National Health and Nutrition Examination Surveys from the US Centers for Disease Control and Prevention, we used logistic regression to test for associations between T. gondii seropositivity and subject self-report of having ever used tobacco, alcohol, marijuana, cocaine, heroin, or methamphetamine. …

Bayesian And Semi-Bayesian Estimation Of The Parameters Of Generalized Inverse Weibull Distribution, Kamaljit Kaur, Kalpana K. Mahajan, Sangeeta Arora

Journal of Modern Applied Statistical Methods

Bayesian and semi-Bayesian estimators of parameters of the generalized inverse Weibull distribution are obtained using Jeffreys’ prior and informative prior under specific assumptions of loss function. Using simulation, the relative efficiency of the proposed estimators is obtained under different set-ups. A real life example is also given.

Synthesis And Evaluation Of Densely-Functionalized Troponoids, Danielle R. Hirsch

Dissertations, Theses, and Capstone Projects

Herein, we document our efforts to expand the scope of troponoid synthetic methodology towards densely-substituted scaffolds. This body of work has focused primarily on an oxidopyrylium cycloaddition/ring-opening strategy for the synthesis and biochemical evaluation of troponoids for assistance in a variety of medicinal chemistry studies. In Chapter 1, we outline the use of this synthetic strategy in the profiling of a library of synthetic αHTs against an aminoglycoside antibiotic resistance enzyme known as aminoglycoside-2’’-O-nucleotidyltransferase [ANT(2’’)-Ia]. Enzymatic mechanistic insights have been gleaned from an assessment of troponoid/antibiotic synergistic potential. In particular, two synthetic constructs were identified as promising antibiotic adjuvant candidates, …

Interferon Priming Is Essential For Human Cd34+ Cell-Derived Plasmacytoid Dendritic Cell Maturation And Function, A. Lausten, R. O. Bak, C. Krapp, L. Kjær, J. H. Egedahl, C. C. Petersen, S. Pillai, H. Q. Tang, N. Uldbjerg, M. Porteus, N. R. Roan, M. Nyegaard, Paul W. Denton, M. R. Jakobsen

Biology Faculty Publications

Plasmacytoid dendritic cells (pDC) are essential for immune competence. Here we show that pDC precursor differentiated from human CD34+ hematopoietic stem and progenitor cells (HSPC) has low surface expression of pDC markers, and has limited induction of type I interferon (IFN) and IL-6 upon TLR7 and TLR9 agonists treatment; by contrast, cGAS or RIG-I agonists-mediated activation is not altered. Importantly, after priming with type I and II IFN, these precursor pDCs attain a phenotype and functional activity similar to that of peripheral blood-derived pDCs. Data from CRISPR/Cas9-mediated genome editing of HSPCs further show that HSPC-pDCs with genetic modifications can be …

New Robust Estimation In Compound Exponential Weibull-Poisson Distribution For Both Contaminated And Non-Contaminated Data, Intisar Uraybi Fadam Al-Duri

Journal of Economics and Administrative Sciences

The research Compared two methods for estimating fourparametersof the compound exponential Weibull - Poisson distribution which are the maximum likelihood method and the Downhill Simplex algorithm. Depending on two data cases, the first one assumed the original data (Non-polluting), while the second one assumeddata contamination. Simulation experimentswere conducted for different sample sizes and initial values of parameters and under different levels of contamination. Downhill Simplex algorithm was found to be the best method for in the estimation of the parameters, the probability function and the reliability function of the compound distribution in cases of natural and contaminateddata.

Redefining The Scope Of Prenylation: Discovery Of “Forbidden” Substrate Recognition And Development Of Methods Utilizing Prenylated Proteins, Melanie Jane Blanden

Dissertations - ALL

Post-translational modifications play a central role in controlling biological function and cell behavior through changes in protein structure, activity, and localization. Prenylation is one such modification wherein a 15- or 20-carbon isoprenoid group is attached to a cysteine residue near the C-terminus of a substrate protein by one of three enzymes: protein farnesyltransferase (FTase), protein geranylgeranyltransferase type I (GGTase-I) or protein geranylgeranyltransferase type II (GGTase-II, also known as Rab GGTase). These covalent modifications can aid in protein association with cellular membranes, with this localization necessary for function of many prenylated proteins. FTase and GGTase-I have been proposed to recognize a …

Microscopic Fungi On Cadavers And Skeletons From Cave And Mine Environments, Alena Nováková, Alena Kubátová, František Sklenář

KIP Articles

No abstract provided.

Tof-Sims Analysis Of Plant Seed Interactions With Plant Growth-Promoting Bacteria, Tammy Pheuphong, Rachel Komorek, Xiao-Ying Yu

STAR Program Research Presentations

The use of time-of-flight secondary ion mass spectrometry (ToF-SIMS) in plant biology is a relatively unexplored and quickly developing field. The majority of research in plant SIMS involves the application of ToF-SIMS to study dried wood tissues, and only a handful of studies apply SIMS on plant stems, roots, and/or seeds. Our project provides a brief description and review of previous work using SIMS on plant stems, roots, and/or seeds, along with an emphasis on the sample preparation in each study. Additionally, the use of Brachypodium distachyon (Brachypodium) as a model system for research on grasses has also become more …

Biodiversity And Conservation Study Of The St. Norbert Abbey, De Pere, Wisconsin - 2017 Annual Report, Mikaela Nowak, Mackenzie Hennes, Adam L. Brandt

Student Creative and Scholarly Works

Long term biological studies are rare but incredibly valuable for examining natural phenomena. Data collected over many years or decades allows for analyses of trends that would never be apparent in a single season. The research presented here is for the completion of the first field season in a long term study analyzing biodiversity trends at the St. Norbert Abbey. Using visual searches, live trapping, and trail cameras, the biodiversity and abundance of species was examined. Special emphasis was placed on small mammals, though other species were observed and documented. The goals of this project were to (1) provide preliminary …

Play And Exhibitions: Expanding Definitions Within Museums, Helena Sizemore

Electronic Theses and Dissertations

This thesis is an exploration of the utilization of play, as a method for visitor engagement, within the context of the museum. Play, as a method for learning and engagement, is often a contested topic between scholars and practitioners within the museum field. This is in part due to the ambiguous nature of defining play, the ever-present dichotomy between work and play, and the struggles museums find in balancing education and entertainment. The Denver Museum of Nature and Science in Denver, Colorado names play as part of one of its core values. Using anthropological theoretical and methodological approaches, I examine …

Essential Market Squid (Doryteuthis Opalescens) Embryo Habitat: A Baseline For Anticipated Ocean Climate Change., Navarro, P.E. Parnell, L.A. Levin

Faculty, Staff, and Students

The market squid Doryteuthis opalescens deposits embryo capsules onto the continental shelf from Baja Californiato southern Alaska, yet little is known about the environment of embryo habitat. This study provides a baseline of environmental data and insights on factors underlying site selection for embryo deposition off southern California, and defines current essential embryo habitat using (1) remotely operated vehicle–supported surveys of benthos and environmental variables, (2) SCUBA surveys, and (3) bottom measurements of T, S, pH, and O2. Here, embryo habitat is defined using embryo capsule density, capsule bed area, consistent bed footprint, and association with [O2] and pH (pCO2) …

Empirical Bayesian Approach To Testing Multiple Hypotheses With Separate Priors For Left And Right Alternatives, Naveen K. Bansal, Mehdi Maadooliat, Steven J. Schrodi

Mathematics, Statistics and Computer Science Faculty Research and Publications

We consider a multiple hypotheses problem with directional alternatives in a decision theoretic framework. We obtain an empirical Bayes rule subject to a constraint on mixed directional false discovery rate (mdFDR≤α) under the semiparametric setting where the distribution of the test statistic is parametric, but the prior distribution is nonparametric. We proposed separate priors for the left tail and right tail alternatives as it may be required for many applications. The proposed Bayes rule is compared through simulation against rules proposed by Benjamini and Yekutieli and Efron. We illustrate the proposed methodology for two sets of …

Environmental Factors Influencing Amphibian Community Assemblage In Dune Wetlands On The Lake Michigan Coast, Alex H. Jouney

Masters Theses

Wetlands in dune landscapes provide important breeding habitat for amphibians along the Lake Michigan Coast. Unfortunately, these unique habitats and the corresponding amphibian metapopulations are understudied and threatened. We assessed amphibian species richness and terrestrial habitat type in 16 permanent and ephemeral wetlands along the coast of Lake Michigan in Grand Haven, MI. Wetland area, terrestrial habitat type, depth, hydroperiod, shade, and degree of isolation were measured from April to September of 2017. Nine species of amphibian were found; Green Frog (Rana clamitans melanota) and Spring Peepers (Pseudacris crucifer crucifer) were most abundant and Fowlers Toad …

Shame, Aggression, And Self-Compassion In At-Risk Adolescents, Sara Ashline Hofmann

Dissertations

Prior research has identified a strong link between experiences of shame and aggressive behavior in at-risk and offender populations but the mechanisms of this relationship are unclear. One potential interrupter of this relationship is self-compassion, a teachable emotional regulation skill. The purpose of this study was to investigate whether nonoffender at-risk youth differed significantly in levels of self-compassion, shame, and aggression from nonviolent offender and violent offender youth with the goal of evaluating these relationships to aid in the future development of more tailored and effective interventions for court-involved youth. One hundred and six at-risk adolescents in the Rocky Mountain …

Development And Commissioning Of An Independent Peer Review System For A Small Animal Irradiator, Mary Peters

Dissertations and Theses (Open Access)

Dosimetry for small animal irradiators lacks the standardization of clinical radiotherapy practice, yet plays a central translational role in human trial design. The purpose of this work was to improve the dosimetric accuracy and consistency of animal studies by developing an independent peer review system to verify dose delivery from animal irradiators. This study focused on the development of a mouse phantom and characterization of the thermoluminescent dosimetry system for a commonly used small animal irradiator.

First, a mouse model and irradiation stand were designed with the purpose of being used in a mailable audit. Two mouse phantoms were machined …

Hyperspectral Imaging Of Chemical Composition, Jerald C. Martin

Open Access Theses

In this work, two different types of imaging are explored, one using fluorescence and another using X-rays. Hyperspectral imaging is a method of imaging materials that typically has three dimensions of information: x, y, and λ (wavelength). These measurements are useful for broad classes of imaging applications, including astronomy, geology, and medicine. However, the current methods used for hyperspectral imaging have significant drawbacks, including 1/f noise and complexity. Therefore, new methods have been recently developed to address these issues, such as new snapshot imaging systems. These systems, however, still often have high complexity, are expensive, and have limited applicability outside …

Diversification And Speciation Patterns Of Ground Beetles (Coleoptera, Carabidae) And Rove Beetles (Coleoptera, Staphylinidae, Pselaphinae) In The Highlands Of Ecuador, Sofia Isabel Muñoz Tobar

All Dissertations

The tropical Andes are a biodiversity hotspot for numerous evolutionary lineages. Allopatric speciation and paleoclimatical events are the major drivers for species diversification in the tropics, especially for páramo species which show high diversity and endemicity. This dissertation elucidates speciation and diversification patterns of widely distributed species of beetles from isolated páramo patches across Ecuador, to provide insight into basic evolutionary processes for Andean insect species. Sampling targeted 17 sites in the páramo ecosystem (3500 – 4000 m), with pitfall trapping, hand collecting and leaf litter sampling. One nuclear and one mitochondrial marker were used to assess the genetic diversity …

Development And Characterization Of Reporter-Expressing Zika Viruses, Michael E. Woolley

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In recent years, Zika virus (ZIKV) has garnered worldwide attention due to its epidemic spread throughout the Americas and due to the newly recognized link between ZIKV infection and neurological diseases, including microcephaly and Guillain-Barré syndrome. ZIKV is a mosquito-borne member of the genus Flavivirus, which includes the other prominent human pathogens Japanese encephalitis virus, West Nile virus, dengue virus, and yellow fever virus. Many questions about the biology of ZIKV and how it causes disease remain unanswered. Furthermore, there currently are no vaccines or licensed antiviral drugs available to treat ZIKV infection. The goal of this study was to …

Research News. Publications, 2018. Volume 1, University Of Mississippi. School Of Pharmacy, Soumyajit Majumdar

Publications (2015-)

Publications that appeared during the period January 1 through June 30, 2018

The Role Of Rad4 In Dna Repair And Its Interplay With Telomeres In Tetrahymena Thermophila, Emily Nischwitz

Graduate Theses/Dissertations

Telomeres are repetitive parts of the genome that act as a protective end cap to the chromosomes. Telomeres are critical to the integrity and stability of the genome, therefore, ensuring that their sequence is maintained, even after damage, is crucial. Much of the pioneering work responsible for explaining telomeres has been conducted in ciliates, specifically in Tetrahymena thermophila. Telomeres in T. thermophila have a high amount of tandem thymine repeats (GGGGTT) and, thus, are susceptible to ultraviolet light (UV) induced lesions called pyrimidine dimers, which must be repaired by nucleotide excision repair (NER). In humans, Xeroderma Pigmentosum C (XPC) …

Deciphering The Role Of Human Arylamine N-Acetyltransferase 1 (Nat1) In Breast Cancer Cell Metabolism Using A Systems Biology Approach., Samantha Marie Carlisle

Electronic Theses and Dissertations

Background: Human arylamine N-acetyltransferase 1 (NAT1) is a phase II xenobiotic metabolizing enzyme found in almost all tissues. NAT1 can additionally hydrolyze acetyl-coenzyme A (acetyl-CoA) in the absence of an arylamine substrate. NAT1 expression varies inter-individually and is elevated in several cancers including estrogen receptor positive (ER+) breast cancers. Additionally, multiple studies have shown the knockdown of NAT1, by both small molecule inhibition and siRNA methods, in breast cancer cells leads to decreased invasive ability and proliferation and decreased anchorage-independent colony formation. However, the exact mechanism by which NAT1 expression affects cancer risk and progression remains unclear. Additionally, consequences …

Directly Light-Regulated Binding Of Rgs-Lov Photoreceptors To Anionic Membrane Phospholipids, Spencer T. Glantz, Erin E. Berlew, Zaynab Jaber, Benjamin S. Schuster, Kevin H. Gardner, Brian Y. Chow

Publications and Research

We report natural light–oxygen–voltage (LOV) photoreceptors with a blue light-switched, high-affinity (KD ∼ 10−7 M), and direct electrostatic interaction with anionic phospholipids. Membrane localization of one such photoreceptor, BcLOV4 from Botrytis cinerea, is directly coupled to its flavin photocycle, and is mediated by a polybasic amphipathic helixinthelinker regionbetween the LOV sensor and its C-terminal domain of unknown function (DUF), as revealed through a combination of bioinformatics, computational protein modeling, structure–function studies, and optogenetic assays in yeast and mammalian cell line expression systems. In model systems, BcLOV4 rapidly translocates from the cytosol to plasma membrane (∼1 second). The reversible electrostatic interaction …

Computer-Based Instruction As A Form Of Differentiated Instruction In A Traditional, Teacher-Led, Low-Income, High School Biology Classroom, Cheryl Casey

Dissertations and Theses

In 2015 the U.S. continues to struggle with academic achievement in public schools. Average test scores from 15 year olds taking the Program for International Student Assessment placed the U.S. as 38th out of 71 countries (Drew Devlin, 2017). It is common to discuss elimination of the achievement gap as the single most effective way to improve the U.S.'s mediocre standing among the highest scoring countries in the world in primary and secondary student test scores (McGhee,2004; Flemming 2012). In the broadest sense of the term the "achievement gap" refers to the difference in academic success between different groups of …

The Effects Of Spinal Cord Injury On Expression Of Pain-Relevant Genes In The Colon, Noelle Mckearney

Master's Theses

Spinal cord injury (SCI) results in varying degrees of paralysis, loss of normal sensory function and, oftentimes, chronic pain originating below the level of injury. Post-SCI pain tends to be resistant to traditional analgesic therapies and has been shown to impair recovery of function, making it a significant healthcare concern. Approximately one third of SCI patients report abdominal pain as a primary and severe symptom with marked similarity to other functional gastrointestinal pain disorders (e.g. irritable bowel). The etiology of this intense pain phenotype is unclear given that visceral organs are left uninjured in SCI. Here we examine changes in …

Prototype Of A Fish Inspired Swimming Silk Robot, Cassandra M. Donatelli, Sarah A. Bradner, Juanita Mathews, Erin Sanders, Casey R. Culligan, David Kaplan, Eric D. Tytell

Engineering Faculty Articles and Research

Elongate fishes have evolved hundreds of times throughout the tree of life. They occupy many aquatic environments, from streams and ponds to the deepest parts of the ocean. Due to their long body and numerous vertebrae, they are also highly flexible animals, which makes them useful as bioinspiration for designs in the field of soft robotics. We present a biodegradable soft robot prototype, inspired by elongate fishes. The robot's body is primarily composed of a silk hydrogel with embedded fibers to mimic the structure of natural fish skin. When actuated at the front, the flexible gel prototype mimics the undulatory …

Effects Of Red Fruit (Pandanus Conoideus Lam) Oil On Malondialdehyde Level And Spermatozoa Quality In Mice (Mus Musculus) Exposed To Monosodium Glutamate, Widayati Agustina, Widjiati Widjiati, Alfiah Hayati

Folia Medica Indonesiana

This study aimed to determine the effects of red fruit (Pandanus conoideus Lam) oil on MDA levels and spermatozoa quality in mice (Mus musculus) exposed to MSG. The quality includes motility, viability, concentration, and morphology of spermatozoa. This experimental study used randomized post-test only control group design. The subjects of this study were 25 mice (Mus musculus), divided into 5 groups (5 mice per group). K- group received distilled water for 35 days. K+ group received 4 mg/g BW MSG for 21 days. P1, P2, and P3 treatment groups received 4 mg/g BW MSG for 21 days and 0.02; 0.04; …

Jefferson Digital Commons Quarterly Report: April-June 2018, Kelsey Duinkerken, Msi, James Copeland, Libt

Jefferson Digital Commons Reports

This quarterly report includes:

• New Feature: PlumX Metrics
• New Feature: CrossRef DOIs
• College Restructuring
• Articles
• CREATE Day Presentations
• Department of Surgery Resident Research Day
• Dissertations
• From the Archives
• Grand Rounds and Lectures
• Master of Public Health Capstones
• Newsletters
• Pathology Honors Program Student Research Symposium
• Posters
• What People are Saying About the JDC