Digital Commons Network^™

Curating Gene Sets: Challenges And Opportunities For Integrative Analysis., Jason A. Bubier, David P. Hill, Gaurab Mukherjee, Timothy Reynolds, Erich J Baker, Alexander Berger, Jake Emerson, Judith A. Blake, Elissa J Chesler

Faculty Research 2019

Genomic data interpretation often requires analyses that move from a gene-by-gene focus to a focus on sets of genes that are associated with biological phenomena such as molecular processes, phenotypes, diseases, drug interactions or environmental conditions. Unique challenges exist in the curation of gene sets beyond the challenges in curation of individual genes. Here we highlight a literature curation workflow whereby gene sets are curated from peer-reviewed published data into GeneWeaver (GW), a data repository and analysis platform. We describe the system features that allow for a flexible yet precise curation procedure. We illustrate the value of curation by gene …

An Effective Biomedical Document Classification Scheme In Support Of Biocuration: Addressing Class Imbalance., Xiangying Jiang, Martin Ringwald, Judith A. Blake, Cecilia Arighi, Gongbo Zhang, Hagit Shatkay

Faculty Research 2019

Published literature is an important source of knowledge supporting biomedical research. Given the large and increasing number of publications, automated document classification plays an important role in biomedical research. Effective biomedical document classifiers are especially needed for bio-databases, in which the information stems from many thousands of biomedical publications that curators must read in detail and annotate. In addition, biomedical document classification often amounts to identifying a small subset of relevant publications within a much larger collection of available documents. As such, addressing class imbalance is essential to a practical classifier. We present here an effective classification scheme for automatically …

Cd11c+ Cells Are Gatekeepers For Lymphocyte Trafficking To Infiltrated Islets During Type 1 Diabetes., Adam M Sandor, Robin S Lindsay, Nathan Dyjack, Jennifer C Whitesell, Cydney Rios, Brenda J Bradley, Kathryn Haskins, David V. Serreze, Aron M Geurts, Yi-Guang Chen, Max A Seibold, Jordan Jacobelli, Rachel S Friedman

Faculty Research 2019

Type 1 diabetes (T1D) is a T cell mediated autoimmune disease that affects more than 19 million people with incidence increasing rapidly worldwide. For T cells to effectively drive T1D, they must first traffic to the islets and extravasate through the islet vasculature. Understanding the cues that lead to T cell entry into inflamed islets is important because diagnosed T1D patients already have established immune infiltration of their islets. Here we show that CD11c

A Microbial-Based Cancer Vaccine For Induction Of Egfrviii-Specific Cd8+ T Cells And Anti-Tumor Immunity., Lauren Zebertavage, Shelly Bambina, Jessica Shugart, Alejandro Alice, Kyra D Zens, Peter Lauer, Bill Hanson, Michael J. Gough, Marka R Crittenden, Keith S Bahjat

Articles, Abstracts, and Reports

Dysregulated signaling via the epidermal growth factor receptor (EGFR)-family is believed to contribute to the progression of a diverse array of cancers. The most common variant of EGFR is EGFRvIII, which results from a consistent and tumor-specific in-frame deletion of exons 2-7 of the EGFR gene. This deletion generates a novel glycine at the junction and leads to constitutive ligand-independent activity. This junction forms a novel shared tumor neo-antigen with demonstrated immunogenicity in both mice and humans. A 21-amino acid peptide spanning the junctional region was selected, and then one or five copies of this 21-AA neo-peptide were incorporated into …

Participation In An Innovative Patient Support Program Reduces Prescription Abandonment For Adalimumab-Treated Patients In A Commercial Population., Diana Brixner, Manish Mittal, David T Rubin, Philip Mease, Harry H Liu, Matthew Davis, Arijit Ganguli, A Mark Fendrick

Articles, Abstracts, and Reports

Purpose: Nonadherence to indicated therapy reduces treatment effectiveness and may increase cost of care. HUMIRA Complete, a Patient Support Program (PSP), aims to reduce nonadherence in patients prescribed adalimumab (ADA). The objective of this study was to assess the relationship between participation in the PSP and prescription abandonment rates among ADA-treated patients.

Patients and methods: This longitudinal study using patient-level data from AbbVie's PSP linked with medical and pharmacy claims data included patients ≥18 years with an ADA-approved indication, ≥1 pharmacy claim for ADA, and available data ≥3 months before and ≥6 months after the index date (defined as the …

Reproducible Big Data Science: A Case Study In Continuous Fairness., Ravi Madduri, Kyle Chard, Mike D'Arcy, Segun C Jung, Alexis Rodriguez, Dinanath Sulakhe, Eric W Deutsch, Cory C Funk, Ben Heavner, Matthew A Richards, Paul Shannon, Gustavo Glusman, Nathan D Price, Carl Kesselman, Ian Foster

Articles, Abstracts, and Reports

Big biomedical data create exciting opportunities for discovery, but make it difficult to capture analyses and outputs in forms that are findable, accessible, interoperable, and reusable (FAIR). In response, we describe tools that make it easy to capture, and assign identifiers to, data and code throughout the data lifecycle. We illustrate the use of these tools via a case study involving a multi-step analysis that creates an atlas of putative transcription factor binding sites from terabytes of ENCODE DNase I hypersensitive sites sequencing data. We show how the tools automate routine but complex tasks, capture analysis algorithms in understandable and …

Lipid-Polymer Hybrid Nanoparticles As A Next-Generation Drug Delivery Platform: State Of The Art, Emerging Technologies, And Perspectives., Anubhab Mukherjee, Ariana K Waters, Pranav Kalyan, Achal Singh Achrol, Santosh Kesari, Venkata Yenugonda

Articles, Abstracts, and Reports

Lipid-polymer hybrid nanoparticles (LPHNPs) are next-generation core-shell nanostructures, conceptually derived from both liposome and polymeric nanoparticles (NPs), where a polymer core remains enveloped by a lipid layer. Although they have garnered significant interest, they remain not yet widely exploited or ubiquitous. Recently, a fundamental transformation has occurred in the preparation of LPHNPs, characterized by a transition from a two-step to a one-step strategy, involving synchronous self-assembly of polymers and lipids. Owing to its two-in-one structure, this approach is of particular interest as a combinatorial drug delivery platform in oncology. In particular, the outer surface can be decorated in multifarious ways …

An Inflammatory Landscape For Preoperative Neurologic Deficits In Glioblastoma., Amal Katrib, Hyun-Hwan Jeong, Nina L Fransen, Kristin S Henzel, Jeremy A Miller

Articles, Abstracts, and Reports

No abstract provided.

Unh: The Magazine Of The University Of New Hampshire, Winter 2019, Unh Magazine

UNH Magazine

No abstract provided.

Biol 2085 Human Anatomy & Physiology I, Steelman Library, Aimee Franklin Dr

Syllabus Repository

No abstract provided.

Fisheries Management In American Samoa And The Expanding Application Of Parens Patriae Standing To Challenge Federal Administrative Action, Kamaile A.N. Turčan

Notre Dame Journal of Law, Ethics & Public Policy

No abstract provided.

Nell2 Regulates The Contralateral-Versus-Ipsilateral Visual Projection As A Domain-Specific Positional Cue, Chizu Nakamoto, Elaine Durward, Masato Horie, Masaru Nakamoto

Biology Faculty Publications

In mammals with binocular vision, retinal ganglion cell (RGC) axons from each eye project to eye-specific domains in the contralateral and ipsilateral dorsal lateral geniculate nucleus (dLGN), underpinning disparity-based stereopsis. Although domain-specific axon guidance cues that discriminate contralateral and ipsilateral RGC axons have long been postulated as a key mechanism for development of the eye-specific retinogeniculate projection, the molecular nature of such cues has remained elusive. Here, we show that the extracellular glycoprotein Nell2 (neural epidermal growth factor-like-like 2) is expressed in the dorsomedial region of the dLGN, which ipsilateral RGC axons terminate in and contralateral axons avoid. In Nell2 …

Business In Engineering Education: Issues, Identities, Hybrids, And Limits, Mike Murphy, Pat O'Donnell, John Jameson

Books/Book chapters

This chapter explores how engineering students are broadened in their education through the teaching of non-engineering subjects, such as business subjects, in order to develop critical thinking skills and self-knowledge of what it means to be an engineer. The goal of the chapter is to provide a commentary on the level of interaction, from design of courses to design of curricula, between business faculty and engineering faculty, and the results of that interaction. This chapter sets out to (i) explore whether there appears to be a place in engineering education curricula for reflective critique of assumptions related to business thinking, …

School-Based Child Sexual Abuse Prevention: Implications For Professional School Counselors, Rebecca G. Cowan, Rebekah F. Cole, Laurie Craigen

Walden Faculty and Staff Publications

The purpose of this qualitative collective case study was to explore the experiences of four key internal stakeholders who are involved with a school-based child sexual abuse prevention program in a southeastern state in the United States. In order to explore the experiences of participants, in-depth, semi-structured interviews were conducted. After the data were collected, transcribed, and coded by a qualified research team, three main themes emerged from this study. These themes highlighted the importance of school-based child sexual abuse prevention education, various program impacts resulting from child sexual abuse prevention and intervention within a school setting, and barriers to …

How Do Trait-Mediated Non-Lethal Effects Of Predation Affect Population-Level Performance Of Mosquitoes?, Karthikeyan Chandrasegaran, Steven A. Juliano

Faculty Publications – Biological Sciences

Non-lethal, trait-mediated effects of predation impact prey behavior and life-history traits. Studying how these effects in turn influence prey demography is crucial to understand prey life-history evolution. Mosquitoes are important vectors that claim several million lives every year worldwide by transmitting a range of pathogens. Several ecological factors affect life-history traits of both larval and adult mosquitoes, creating effects that cascade to population-level consequences. Few studies have comprehensively explored the non-lethal effects of predation and its interactions with resources and competition on larval, adult, and population traits of mosquitoes. Understanding these interactions is important because the effects of predation are …

Exploring Faculty Perceptions About Classroom Technology Integration And Acceptance: A Literature Review., Zhanat Alma Burch, Shereeza Mohammed

Walden Faculty and Staff Publications

In examining the complexity of how higher education institutions integrate and adopt classroom technology, this study explores literature regarding classroom technology integration and acceptance that appears in research articles published from 2012 – 2018. The literature review of 148 articles was centered on a deeper understanding of faculty perceptions regarding classroom technology integration and acceptance. The evidence suggests that there is not a simple model when it comes to augmenting classrooms with classroom technology. Additionally, for the appropriate adoption of technology tools, it is important to understand how faculty perceive the integration of classroom technology tools.

Undergraduate Student Catalog 2019-2020, Nova Southeastern University

Undergraduate Programs Course Catalogs

No abstract provided.

Bachelor Of Science-Chemistry 2019-2020, Nova Southeastern University

Undergraduate Programs Course Catalogs

No abstract provided.

Lagosinema Tenuis Gen. Et Sp. Nov. (Prochlorotrichaceae, Cyanobacteria): A New Brackish Water Genus From Tropical Africa, Sandra C. Akagha, Jeffrey R. Johansen, Dike I. Nwankwo, Kedong Yin

2019 Faculty Bibliography

A novel filamentous, nonheterocytous cyanobacterium was isolated from Lagos Lagoon, Nigeria. The isolate was <3.0 μm wide, untapered, with small rounded polar bodies (aerotopes or cyanophycin granules) visible at the crosswalls, and consequently fit the morphological description of Limnothrix planctonica. Although morphologically inseparable from that species, it was molecularly distant from that taxon, with genetic identities between the two taxa ranging 90.73–92.49%, a degree of separation typical of different genera. Both taxa, as well as Limnothrix rosea, are phylogenetically in the Prochlorotrichaceae, distant from the type species of Limnothrix, L. redekei, which is in the Pseudanabaenaceae. The isolate is herein described as Lagosinema tenuis gen. et sp. nov.

A Field-Based Survey Of Fluorescence In Tropical Tree Frogs Using An Led Uv-B Flashlight, Michelle E. Thompson, Ralph Saporito, Diego H. Ruiz-Valderrama4, Guido F. Medina-Rangel, Maureen A. Donnelly

2019 Faculty Bibliography

No abstract provided.

Insight Into The Dynamics Of Apobec3g Protein In Complexes With Dna Assessed By High Speed Afm, Yangang Pan, Luda S. Shlyakhtenko, Yuri L. Lyubchenko

Journal Articles: Pharmaceutical Sciences

APOBEC3G (A3G) is a single-stranded DNA (ssDNA) binding protein that restricts the HIV virus by deamination of dC to dU during reverse transcription of the viral genome. A3G has two zinc-binding domains: the N-terminal domain (NTD), which efficiently binds ssDNA, and the C-terminal catalytic domain (CTD), which supports deaminase activity of A3G. Until now, structural information on A3G has been lacking, preventing elucidation of the molecular mechanisms underlying its interaction with ssDNA and deaminase activity. We have recently built a computational model for the full-length A3G monomer and validated its structure using data obtained by time-lapse High-Speed Atomic Force Microscopy …

2019 Bachelor's Degree Exit Survey, Southwestern Oklahoma State University

Assessment Center Reports

Exit Surveys produced by the SWOSU Assessment Center.

Parasitism, Host Behavior, And Invasive Species, Sarah N. Bevins

United States Department of Agriculture Wildlife Services: Staff Publications

Animal behavior and parasitism are inextricable linked. In many cases, host behavior can affect what parasites are encountered. In other cases, parasites can manipulate the behavior of the host in an attempt to maximize their own transmission. These long-standing interactions are now further complicated by species movement around the globe. The list of introduced species that have become invasive includes parasites that have adapted to new hosts in areas of introduction, as well as invasive hosts that alter the association between existing parasite–host assemblages. Researchers have documented differences in rates of parasitism and in the consequences of parasite infection between …

Use Of Surgical Tissue Adhesive And Body Mass Change To Assess Ring-Necked Pheasant Brood Foraging Habitat, Todd R. Bogenschutz, Chris S. Jennelle, Mark W. Mcinroy, Steven D. Roberts

Journal of the Iowa Academy of Science: JIAS

Foraging rates (arthropod consumption [g/min/chick]) of human-imprinted chicks provide a reasonable metric for assessing the quality of brood-rearing habitats for gallinaceous species. Arthropod foraging rates have been estimated using dry mass or allometric equations of crop and gizzard contents, and internal surgical ligature of the crop. Current methods are time- and labor-intensive. We describe a new method to estimate foraging rate using chick mass change (g/min) during a 30-min foraging trial. Our technique requires surgical tissue adhesive be applied to the cloaca to prevent bias in mass change measurements caused by defecation. We compare our mass change technique to a …

Celebrating Student Scholarship With An Undergraduate Research Prize, Kevin Ross, Carolyn Radcliff, Talia Cain

Library Books and Book Chapters

"The Leatherby Libraries at Chapman University started its research prize contest for undergraduate students in 2007. Having reached the tenth anniversary of the contest, we are well positioned to reflect on how the contest has changed in concert with new ways of inquiry and information creation and on its role in supporting and honoring student research. A decade of experience has taught us how to diversify the contest and reflect collectively on its merits. In this chapter, we present a case study of how the Kevin and Tam Ross Undergraduate Research Prize (URP) recognizes and honors student scholarship. We explain …

Data-Driven Intelligent Scheduling For Long Running Workloads In Large-Scale Datacenters, Guoyao Xu

Wayne State University Dissertations

Cloud computing is becoming a fundamental facility of society today. Large-scale public or private cloud datacenters spreading millions of servers, as a warehouse-scale computer, are supporting most business of Fortune-500 companies and serving billions of users around the world. Unfortunately, modern industry-wide average datacenter utilization is as low as 6% to 12%. Low utilization not only negatively impacts operational and capital components of cost efficiency, but also becomes the scaling bottleneck due to the limits of electricity delivered by nearby utility. It is critical and challenge to improve multi-resource efficiency for global datacenters.

Additionally, with the great commercial success of …

Arab American Women's Health Study: Correlational And Experimental Examination Of A Sexual Health Interview, Hannah Holmes

Wayne State University Dissertations

Arab Americans are a diverse group of Americans of Arab heritage or identity. Given the underrepresentation of Arab Americans in research and a taboo surrounding sexuality in Arab culture, it is not surprising that Arab American sexual health is understudied, even though sexuality is an important aspect of health. Arab American women face the challenging task of negotiating both their heritage and American culture, which may have implications for sexual health due to the two cultures’ disparate views on sexuality. Given the conflict and taboo likely to surround the topic of sexuality among Arab American women, confidential discussion of these …

Switching Diffusions: Applications To Ecological Models, And Numerical Methods For Games In Insurance, Trang Thi-Huyen Bui

Wayne State University Dissertations

Recently, a class of dynamic systems called ``hybrid systems" containing both continuous dynamics and discrete events has been adapted to treat a wide variety of situations arising in many real-world situations. Motivated by such development, this dissertation is devoted to the study of dynamical systems involving a Markov chain as the randomly switching process. The systems studied include hybrid competitive Lotka-Volterra ecosystems and non-zero-sum stochastic differential games between two insurance companies with regime-switching.

The first part is concerned with competitive Lotka-Volterra model with Markov switching. A novelty of the contribution is that the Markov chain has a countable state space. …

Modification Of Bruker Amazon Etd And Solarix Mass Spectrometers Towards Infrared Multiple Photon Dissociation: Structural Characterization Of Modified Nucleosides, Lucas Ash Hamlow

Wayne State University Dissertations

Infrared ion spectroscopy has become an increasingly powerful tool for examining

the intrinsic structures of gas-phase ions. Infrared multiple photon dissociation (IRMPD)

action spectroscopy has been particularly successful. Several free electron laser (FEL)

facilities across the world have helped facilitate the growth of the IRMPD technique and

increasing interest has driven the development of more accessible IRMPD

instrumentation. The development of one such IRMPD instrumentation system is

described in this work, based around commercially available 3D quadrupole ion trap mass

spectrometers and Fourier-transform ion cyclotron resonance mass spectrometers.

The intrinsic gas-phase structures of nucleic acid monomers have been

extensively studied …

The Graduate Review, Vol. Iv, 2018-2019

The Graduate Review

No abstract provided.