Digital Commons Network^™

Assessing The Similarity Of Ligand Binding Conformations With The Contact Mode Score, Yun Ding, Ye Fang, Juana Moreno, J. Ramanujam, Mark Jarrell, Michal Brylinski

Faculty Publications

© 2016 Elsevier Ltd Structural and computational biologists often need to measure the similarity of ligand binding conformations. The commonly used root-mean-square deviation (RMSD) is not only ligand-size dependent, but also may fail to capture biologically meaningful binding features. To address these issues, we developed the Contact Mode Score (CMS), a new metric to assess the conformational similarity based on intermolecular protein-ligand contacts. The CMS is less dependent on the ligand size and has the ability to include flexible receptors. In order to effectively compare binding poses of non-identical ligands bound to different proteins, we further developed the eXtended Contact …

A Geometrical Model For Testing Bilateral Symmetry Of Bamboo Leaf With A Simplified Gielis Equation, Shuyan Lin, Li Zhang, Gadi V.P. Reddy, Cang Hui, Johan Gielis, Yulong Ding, Peijian Shi

Faculty Publications

The size and shape of plant leaves change with growth, and an accurate description of leaf shape is crucial for describing plant morphogenesis and development. Bilateral symmetry, which has been widely observed but poorly examined, occurs in both dicot and monocot leaves, including all nominated bamboo species (approximately 1,300 species), of which at least 500 are found in China. Although there are apparent differences in leaf size among bamboo species due to genetic and environmental profiles, bamboo leaves have bilateral symmetry with parallel venation and appear similar across species. Here, we investigate whether the shape of bamboo leaves can be …

The Genetics Of Blood Pressure Regulation And Its Target Organs From Association Studies In 342,415 Individuals, Georg B. Ehret, Teresa Ferreira, Daniel I. Chasman, Anne U. Jackson, Ellen M. Schmidt, Toby Johnson, Gudmar Thorleifsson, Jian'an Luan, Louise A. Donnelly, Stavroula Kanoni, Ann Kristin Petersen, Vasyl Pihur, Rona J. Strawbridge, Dmitry Shungin, Maria F. Hughes, Osorio Meirelles, Marika Kaakinen, Nabila Bouatia-Naji, Kati Kristiansson, Sonia Shah, Marcus E. Kleber, Xiuqing Guo, Leo Pekka Lyytikäinen, Cristiano Fava, Niclas Eriksson, Ilja M. Nolte, Patrik K. Magnusson, Elias L. Salfati, Loukianos S. Rallidis, Elizabeth Theusch, Andrew J.P. Smith, Lasse Folkersen, Kate Witkowska

Faculty Publications

To dissect the genetic architecture of blood pressure and assess effects on target organ damage, we analyzed 128,272 SNPs from targeted and genome-wide arrays in 201,529 individuals of European ancestry, and genotypes from an additional 140,886 individuals were used for validation. We identified 66 blood pressure-associated loci, of which 17 were new; 15 harbored multiple distinct association signals. The 66 index SNPs were enriched for cis-regulatory elements, particularly in vascular endothelial cells, consistent with a primary role in blood pressure control through modulation of vascular tone across multiple tissues. The 66 index SNPs combined in a risk score showed comparable …

Lsu Research Fall 2016, Louisiana State University And Agricultural & Mechanical College

Research Magazine

LSU Research is published annually by the Office of Research & Economic Development, Louisiana State University.

Amine Reactive Dyes: An Alternative To Estimate Membrane Integrity In Fish Sperm Cells, Leticia Torres, Terrence R. Tiersch

Faculty Publications

Fluorescent dyes that binds irreversibly to cellular amines, come in several available emission spectra, and do not poses health concerns were used to evaluate membrane integrity in fish sperm cells. The objectives of the present study were to determine: (1) a working dye concentration for fish sperm samples, and (2) if the traditional propidium iodide/SYBR-14 staining combination was comparable with the amine reactive dye (ARD) methods at identifying cell populations with intact and compromised membranes after sperm activation, refrigerated storage, and exposure to cryoprotectant and surfactant. Zebrafish (Danio rerio) sperm were obtained by stripping, and pooled samples (in triplicate) were …

Do Movement Behaviors Identify Reproductive Habitat Sampling For Wild Turkeys?, Mason D. Conley, Nathan A. Yeldell, Michael J. Chamberlain, Bret A. Collier

Faculty Publications

Selection of habitats has regularly been suggested to influence species demography at both local and broad scales. The expectation is that selection behaviors have positive benefits via greater fitness or increased survival. The current paradigm of habitat selection theory suggests a hierarchical process, where an individual first selects where they choose to live (e.g., range) and then searches and selects locations within this range meeting life history needs. Using high-frequency GPS data collected from reproductively active Rio Grande (n = 21) and Eastern (n = 23) wild turkeys, we evaluated a long-standing theory for ground-nesting galliformes, in that movements during …

Genetic Vulnerability And The Relationship Of Commercial Germplasms Of Maize In Brazil With The Nested Association Mapping Parents, Luciano Rogério Braatz De Andrade, Roberto Fritsche Neto, Ítalo Stefanine Correia Granato, Gustavo César Sant'ana, Pedro Patric Pinho Morais, Aluízio Borém

Faculty Publications

A few breeding companies dominate the maize (Zea mays L.) hybrid market in Brazil: Monsanto ® (35%), DuPont Pioneer® (30%), Dow Agrosciences® (15%), Syngenta® (10%) and Helix Sementes (4%). Therefore, it is important to monitor the genetic diversity in commercial germplasms as breeding practices, registration and marketing of new cultivars can lead to a significant reduction of the genetic diversity. Reduced genetic variation may lead to crop vulnerabilities, food insecurity and limited genetic gains following selection. The aim of this study was to evaluate the genetic vulnerability risk by examining the relationship between the commercial Brazilian maize germplasms and the …

Sexually Dimorphic Gene Expression In Bovine Conceptuses At The Initiation Of Implantation, Niamh Forde, Veronica Maillo, Peadar O'Gaora, Constantine A. Simintiras, Roger G. Sturmey, Alan D. Ealy, Thomas E. Spencer, Alfonso Gutierrez-Adan, Dimitrios Rizos, Patrick Lonergan

Faculty Publications

In cattle, maternal recognition of pregnancy occurs on Day 16 via secretion of interferon tau (IFNT) by the conceptus. The endometrium can distinguish between embryos with different developmental competencies. In eutherian mammals, X-chromosome inactivation (XCI) is required to ensure an equal transcriptional level of most X-linked genes for both male and female embryos in adult tissues, but this process is markedly different in cattle than mice. We examined how sexual dimorphism affected conceptus transcript abundance and amino acid composition as well as the endometrial transcriptome during the peri-implantation period of pregnancy. Of the 5132 genes that were differentially expressed on …

Impact : Issue 9, Patients Behbud

IMPACT – The Aga Khan University Hospital Archives

Content

- The Killer Disease

- Courage from the Heart

- Diagnosis, Early Detection and Treatment of Breast Cancer at AKUH

- "Whenever I Came Here, They Supported Me and..." - Mrs. Tazeen Mehkari

Labrad : Vol 42, Issue 2 - October 2016, Aga Khan University Hospital, Karachi

LABRAD - Departments of Pathology & Laboratory Medicine and Radiology Archives

• Revised Nomenclature of Encapsulated Follicular Variant of Papillary Carcinoma; Now NIFTP in 2016
• Heritable Thrombophilia Screening: When & in Whom
• Massive Transfusion
• A Review of Innovance PFA-200 System
• Radiologic-Pathologic Correlation Osteogenic Tumors
• Pre Albumin or Transthyretin - A Useful Biomarker in the Assessment of Malnutrition
• Urinary Tract Infections (UTIs) in Children: A Pictorial Guide
• Validation of Test Methods in a Clinical Laboratory: A Brief Overview of the Concepts, Aims and Procedures
• Clinical Significance of Stone Composition Analysis in Urolithiasis Management

Monarch, Philip Walzer (Editor)

Monarch Magazine

Fall 2016 issue of Monarch, the Old Dominion University Magazine.

Subtitled: A New Era in Dining

Fall 2016, University Of North Dakota Alumni Association

ALL: UND Alumni Review Master List

Fall 2016 issue of "The University of North Dakota Alumni Review." 52 pages

Volume 99, Number 3

Discriminative Stimulus Properties Of 1.25 Mg/Kg Clozapine In Rats: Mediation By Serotonin 5-Ht2 And Dopamine D4 Receptors, Adam J. Prus, Laura E. Wise, Alan Pehrson, Scott D. Philibin, Benny Bang-Andersen, Jørn Arnt, Joseph H. Porter

Department of Psychology Faculty Scholarship and Creative Works

The atypical antipsychotic drug clozapine remains one of most effective treatments for schizophrenia, given a lack of extrapyramidal side effects, improvements in negative symptoms, cognitive impairment, and in symptoms in treatment-resistant schizophrenia. The adverse effects of clozapine, including agranulocytosis, make finding a safe clozapine-like a drug a goal for drug developers. The drug discrimination paradigm is a model of interoceptive stimulus that has been used in an effort to screen experimental drugs for clozapine-like atypical antipsychotic effects. The present study was conducted to elucidate the receptor-mediated stimulus properties that form this clozapine discriminative cue by testing selective receptor ligands in …

Pathways To College Preparatory Advanced Academic Offerings In The Anchorage School District, Rosyland Frazier

CAEPR Reports

There are many ways a child in the Anchorage School District (ASD) can access advanced course offerings. To a parent these pathways may seem complex. ASD offers options for gifted and highly gifted students at the elementary and middle school level, and accelerated, and enriched learning opportunities such as honors and advanced placement courses at the secondary level. These opportunities, though linked, are not the same, nor do they necessarily follow from one to another in a straight path. Moreover, pathways to and through these opportunities can be quite different. Offerings are different at the elementary, middle and high school …

2016 Fall Nutshell, Morehead State University. Institutional Research & Analysis.

Office of Institutional Research & Analysis Publication Archive

Fall 2016 issue of the Nutshell.

Behavioral And Emotional Consequences Of Thought Listing Versus Cognitive Restructuring During Discarding Decisions In Hoarding Disorder, Randy O. Frost, Clarissa Ong, Gail Steketee, David F. Tolin

Psychology: Faculty Publications

An essential criterion for hoarding disorder (HD) is difficulty discarding or parting with possessions, yet few studies have examined reactions to actual discarding behaviors. The present study examined whether individuals with HD differed from non-hoarding community controls (CC) in discarding behavior and emotional reactions to discarding. A second purpose was to examine the course of experienced distress following discarding. A third purpose was to determine whether HD participants responded differently to a simple thought listing (TL) instruction or to a cognitive restructuring (CR) protocol. Participants were asked to decide whether to keep or discard (a) a personal possession and (b) …

Wooster Magazine: Fall 2016, Karol Crosbie

Wooster Magazine: 2011-2020

The fall 2016 issue of the Wooster magazine features a section dedicated to Sarah Bolton, the College of Wooster’s 12th President, the renovations to the Cornerstone Playlab, and voices from the past, a creative endeavor with portraits by Mattie Cannon ’14 of John H. Gault, George C. Nimmons, Carlo Nolletti, Maria Sexton, Theodore “Ted” Williams, Lucy Lillian Notestein. This issue also remembers Stan Gault ’48, who passed in 2016, introduces Brush Hall, named in honor of donor Doug Brush ’77, and details the construction work beginning on Ruth W. Williams Hall of Life Science. This issue also includes a list …

Annual Report Of The Indiana University Maurer School Of Law Digital Repository, 2015/16, Richard Vaughan

Digital Repository Annual Reports

A brief annual report documenting the use and growth of the Indiana University Maurer School of Law, Jerome Hall Law Library, Digital Repository. Includes lists of the most downloaded documents and attached Excel spreadsheets of data.

Dealloying Behavior Of Nico And Nicocu Thin Films, Benjamin Peecher, Jennifer R. Hampton

Faculty Publications

Porous metals and alloys, such as those fabricated via electrochemical dealloying, are of interest for a variety of energy applications, ranging from their potential for enhanced catalytic behavior to their use as high surface area supports for pseudocapacitor materials. Here, the electrochemical dealloying process was explored for electrodeposited binary NiCo and ternary NiCoCu thin films. For each of the four different metal ratios, films were dealloyed using linear sweep voltammetry to various potentials in order to gain insight into the evolution of the film over the course of the linear sweep. Electrochemical capacitance, scanning electron microscopy, and energy dispersive X-ray …

An Arginine Finger Regulates The Sequential Action Of Asymmetrical Hexameric Atpase In The Double-Stranded Dna Translocation Motor, Zhengyi Zhao, Gian Marco De-Donatis, Chad T. Schwartz, Huaming Fang, Jingyuan Li, Peixuan Guo

Pharmaceutical Sciences Faculty Publications

Biological motors are ubiquitous in living systems. Currently, how the motor components coordinate the unidirectional motion is elusive in most cases. Here, we report that the sequential action of the ATPase ring in the DNA packaging motor of bacteriophage ϕ29 is regulated by an arginine finger that extends from one ATPase subunit to the adjacent unit to promote noncovalent dimer formation. Mutation of the arginine finger resulted in the interruption of ATPase oligomerization, ATP binding/hydrolysis, and DNA translocation. Dimer formation reappeared when arginine mutants were mixed with other ATPase subunits that can offer the arginine to promote their interaction. Ultracentrifugation …

Otterbein Towers Fall 2016, Otterbein Towers

Towers Magazine

What We Stand For. Articles include: A Promise for the Future - Beth Daugherty, A Spotlight on Otterbein Values, The Faculty Student Connection with Alan Goff '75 and David Deever '61, A Campaign Update, and "A Place to Belong" about Annie Upper '86.

Fluid Dynamic Factors As A Cause And Effect Of Biofilm Formation Of Staphylococcus Aureus Biofilms, Erica Sherman

Department of Mechanical and Materials Engineering: Dissertations, Theses, and Student Research

Staphylococcus aureus bacteria are able to form biofilms and distinctive tower structures that facilitate their ability to tolerate treatment and to spread within the human body. The formation of towers, which break off, get carried downstream and serve to initiate biofilms in other parts of the body are of particular interest here. It is known that flow conditions play a role in the development, dispersion and propagation of biofilms. The influence of flow on tower formation and what factors lead to tower formation is not at all understood The hypothesis being examined is that tower structures form within a specific …

The Integrity Of Women In Re-Making A Nation: The Case Of Guinea-Bissau, Brandon Lundy, Raul Mendes Fernandes Jr., Kezia Lartley

Journal of Global Initiatives: Policy, Pedagogy, Perspective

This article both acknowledges and celebrates the role of women in re-making the nation of Guinea-Bissau. A gendered perspective and historical and multi-scalar framing demonstrates that women have played integral roles in nation-building over time and space in Guinea-Bissau. How have the women of Guinea-Bissau fashioned their agency? Where are the new forms of agency for women in Guinea-Bissau? An examination of nation-building shows the foundational roles of women, unique aspects of innovative economic enterprise before, during, and after the colonial period, and contemporary political efforts by women toward the production of a successful and inclusive country. Gender has opened …

Critical Pedagogy And Language Acquisition: Benefiting From A Country’S Crisis To Improve Second Language Instruction, Jamile Forcelini

Journal of Global Initiatives: Policy, Pedagogy, Perspective

Education has the power to influence learners to either accept reality or critically deliberate and change it. Critical thinking is vital to empower learners and society as a whole to move from a practice of inertia to Freire’s practice of freedom as well as humanization. Change, however is only attainable if pursued with one of the most powerful social tools: Language; the most perceptible manifestation of culture and culture is our connection to the world, what unites us in society, identifies us communally, and serves us as guidance for civic conduct (Larson and Smalley, 1972). The present article aims to …

Improving A Dental School's Clinic Operations Using Lean Process Improvement, Fonda G. Robinson, Larry L. Cunningham, Sharon P. Turner, John E. Lindroth, Deborah Ray, Talib Khan, Audrey Yates

Oral Health Practice Faculty Publications

The term "lean production," also known as "Lean," describes a process of operations management pioneered at the Toyota Motor Company that contributed significantly to the success of the company. Although developed by Toyota, the Lean process has been implemented at many other organizations, including those in health care, and should be considered by dental schools in evaluating their clinical operations. Lean combines engineering principles with operations management and improvement tools to optimize business and operating processes. One of the core concepts is relentless elimination of waste (non-value-added components of a process). Another key concept is utilization of individuals closest to …

Faculty Tenure Report, Fall 2016, University Of Northern Iowa. Office Of Institutional Research And Effectiveness.

Institutional Effectiveness & Planning Documents

Statistical report showing the number of faculty that are tenured, on the tenure track, or not on the tenure track, broken down by college, department, gender, minority status, and if full or part time.

Structure-Function Relationships Of Archaeal Cbf5 During In Vivo Rna-Guided Pseudouridylation., Mrinmoyee Majumder, Michael S Bosmeny, Ramesh Gupta

Articles

In Eukarya and Archaea, in addition to protein-only pseudouridine (Ψ) synthases, complexes containing one guide RNA and four proteins can also produce Ψ. Cbf5 protein is the Ψ synthase in the complex. Previously, we showed that Ψ's at positions 1940, 1942, and 2605 of Haloferax volcanii 23S rRNA are absent in a cbf5-deleted strain, and a plasmid-borne copy of cbf5 can rescue the synthesis of these Ψ's. Based on published reports of the structure of archaeal Cbf5 complexed with other proteins and RNAs, we identified several potential residues and structures in H. volcanii Cbf5, which were expected to play important …

Population-Level Responses Of Life History Traits To Flow Regime In Three Common Stream Fish Species, Micah G. Bennett, Matt R. Whiles, Gregory Whitledge

Publications

Trait-based approaches may improve understanding in ecology by linking environmental variation to fitness-related characteristics of species. Most trait-environment studies focus on assemblage-level relationships; yet intraspecific trait variation is important for community, ecosystem, and evolutionary processes and has substantial implications for these approaches. Assessing population-level trait-environment relationships could test the generality of trait models while assessing intraspecific variation. We evaluated the generality of the trilateral life history model (TLHM of Winemiller and Rose 1992: opportunistic, periodic, and equilibrium endpoints) for fishes - a well-studied trait-environment model at the assemblage level - to populations of three stream fishes in the Midwestern United …

Library Newsletter Volume 12, Issue 2, Sacred Heart University

Library Newsletters

Highlights: Fake News and the Three Myths of Information --New Digital Commons Feature: Expert Gallery --New & Featured Library Resources: MarketLine Advantage, Criminal Justice Abstracts with Full Text, Literati by Credo, LearnTechLib, Browzine --Open Access Week October 24-28 --Some Recent SHU Faculty Publications in the Digital Commons@SHU --First Year Seminar Research Workshops --Library Trivia Contest --Library Mini Golf --Popular Reading --Book Reviews --What the Staff is Reading --Hours and Statistics.

The House Edge: On Gambling And Professional Discipline, Stacey A. Tovino

Washington Law Review

On March 26, 2014, the Iowa Supreme Court revoked the license to practice law of Cedar Rapids attorney Susan Hense. Admitted to the Iowa Bar in 1996, Hense subsequently misappropriated $837,000 in client trust funds to feed her addiction to casino gambling. This Article assesses how attorneys like Hense who are addicted to gambling are treated in professional disciplinary actions, including license suspension, revocation, and reinstatement proceedings. Themes that emerge include public misunderstanding of gambling disorder, stigma against individuals with gambling disorder, statutory recognition of substance addictions but not behavioral addictions, and mandatory attendance at religion-based fellowship meetings as a …