The Grizzly, February 11, 2016

Campus Safety Officers to Increase Reimert Presence • Preparing for More Snow • Ursinus Hires New VP of Admissions • Improv Troupe Set to Perform • UC Hosts Title IX Meeting • International Perspective: School vs. Work • Exploring the 80\u27s • New Spin on SPINT • Opinions: End the 21-Meal Plan; Is it Appropriate to Culturally Appropriate? • More Than Just a Trainer • Women\u27s Swimming Posts Third Perfect Seasonhttps://digitalcommons.ursinus.edu/grizzlynews/1682/thumbnail.jp

The Grizzly, February 4, 2016

Ursinus to Host Popular Author • Clearing the Path to a Career • Companies and Grad Schools Seek Out Ursinus Alumni • International Perspective: Cultural Differences in Parties • Businesses Offer Student Discounts • Talking About Depression with Nuance • Fighting Off the Freshman Fifteen • Ups and Downs of Being an RA in Reimert • New Face on Campus • Opinion: The Elephants Aren\u27t in the Room: Poll Probes Pupils on Pressing Politics • From Across the Atlantic • Dynamic Duohttps://digitalcommons.ursinus.edu/grizzlynews/1681/thumbnail.jp

Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG)

MicroRNAs (miRNA) are endogenous tissue-specific short RNAs that regulate gene expression. Discriminating each let-7 family member expression is especially important due to let-7's abundance and connection with development and cancer. However, short lengths (22 nt) and similarities between multiple sequences have prevented identification of individual members. Here, we present ProDeG, a computational algorithm which designs imperfectly matched sequences (previously yielding only noise levels in microarray experiments) for genome-wide microarray “signal” probes to discriminate single nucleotide differences and to improve probe qualities. Our probes for the entire let-7 family are both homogeneous and specific, verified using microarray signals from fluorescent dye-tagged oligonucleotides corresponding to the let-7 family, demonstrating the power of our algorithm. In addition, false let-7c signals from conventional perfectly-matched probes were identified in lymphoblastoid cell-line samples through comparison with our probe-set signals, raising concerns about false let-7 family signals in conventional microarray platform

Critical role for iron accumulation in the pathogenesis of fibrotic lung disease

Increased iron levels and dysregulated iron homeostasis, or both, occur in several lung diseases. Here, the effects of iron accumulation on the pathogenesis of pulmonary fibrosis and associated lung function decline was investigated using a combination of murine models of iron overload and bleomycin-induced pulmonary fibrosis, primary human lung fibroblasts treated with iron, and histological samples from patients with or without idiopathic pulmonary fibrosis (IPF). Iron levels are significantly increased in iron overloaded transferrin receptor 2 (Tfr2) mutant mice and homeostatic iron regulator (Hfe) gene–deficient mice and this is associated with increases in airway fibrosis and reduced lung function. Furthermore, fibrosis and lung function decline are associated with pulmonary iron accumulation in bleomycin-induced pulmonary fibrosis. In addition, we show that iron accumulation is increased in lung sections from patients with IPF and that human lung fibroblasts show greater proliferation and cytokine and extracellular matrix responses when exposed to increased iron levels. Significantly, we show that intranasal treatment with the iron chelator, deferoxamine (DFO), from the time when pulmonary iron levels accumulate, prevents airway fibrosis and decline in lung function in experimental pulmonary fibrosis. Pulmonary fibrosis is associated with an increase in Tfr1+ macrophages that display altered phenotype in disease, and DFO treatment modified the abundance of these cells. These experimental and clinical data demonstrate that increased accumulation of pulmonary iron plays a key role in the pathogenesis of pulmonary fibrosis and lung function decline. Furthermore, these data highlight the potential for the therapeutic targeting of increased pulmonary iron in the treatment of fibrotic lung diseases such as IPF

Auroral Current and Electrodynamics Structure Measured by Two SOunding Rockets in Flight Simultaneously

On January 29, 2009, two identically instrumented sounding rockets were launched into a sub-storm auroral arc from Poker Flat Alaska. Labeled the Auroral Currents and Electrodynamics Structure (ACES) mission, the payloads were launched to different apogees (approx.350km and approx.120km) and staggered in time so as to optimize their magnetic conjunctions. The different altitudes provided simultaneous in-situ measurements of magnetospheric input and output to the ionosphere and the ionospheric response in the lower F and E region. Measurements included 3-axis magnetic field, 2-axis electric field nominally perpendicular to the magnetic field, energetic particles, electron and ion, up to 15keV, cold plasma temperature and density. In addition, PFISR was also operating in a special designed mode to measure electric field and density profiles in the plane defined by the rocket trajectories and laterally to either side of the trajectories. Observation of the measured currents and electrodynamics structure of the auroral form encountered are presented in the context of standard auroral models and the temporal/spatial limitations of mission designs

A Rocket-Base Study of Auroral Electrodynamics Within the Current Closure Ionosphere

The Auroral Current and Electrodynamics Structure (ACES) mission consisted of two sounding rockets launched nearly simultaneously from Poker Flat Research Range, AK on January 29, 2009 into a dynamic multiple-arc aurora. The ACES rocket mission, in conjunction with the PFISR Radar, was designed to observe the three-dimensional current system of a stable auroral arc system. ACES utilized two well instrumented payloads flown along very similar magnetic field footprints, at various altitudes with small temporal separation between both payloads. ACES High, the higher altitude payload (apogee 360 km), took in-situ measurements of the plasma parameters above the current closure region to provide the input signature into the lower ionosphere. ACES Low, the low-altitude payload (apogee 130 km), took similar observations within the current closure region, where cross-field currents can flow. We present results comparing observations of the electric fields, magnetic fields, electron flux, and the electron temperature at similar magnetic footpoints between both payloads. We further present data from all-sky imagers and PFISR detailing the evolution of the auroral event as the payloads traversed regions connected by similar magnetic footpoints. Current measurements derived from the magnetometers on both payloads are further compared. We examine data from both PFISR and observations on the high-altitude payload which we interpreted as a signature of electron acceleration by means of Alfv n waves. We further examine all measurements to understand ionospheric conductivity and how energy is being deposited into the ionosphere through Joule heating. Data from ACES is compared against models of Joule heating to make inferences regarding the effect of collisions at various altitudes

LSST Science Book, Version 2.0

A survey that can cover the sky in optical bands over wide fields to faint magnitudes with a fast cadence will enable many of the exciting science opportunities of the next decade. The Large Synoptic Survey Telescope (LSST) will have an effective aperture of 6.7 meters and an imaging camera with field of view of 9.6 deg^2, and will be devoted to a ten-year imaging survey over 20,000 deg^2 south of +15 deg. Each pointing will be imaged 2000 times with fifteen second exposures in six broad bands from 0.35 to 1.1 microns, to a total point-source depth of r~27.5. The LSST Science Book describes the basic parameters of the LSST hardware, software, and observing plans. The book discusses educational and outreach opportunities, then goes on to describe a broad range of science that LSST will revolutionize: mapping the inner and outer Solar System, stellar populations in the Milky Way and nearby galaxies, the structure of the Milky Way disk and halo and other objects in the Local Volume, transient and variable objects both at low and high redshift, and the properties of normal and active galaxies at low and high redshift. It then turns to far-field cosmological topics, exploring properties of supernovae to z~1, strong and weak lensing, the large-scale distribution of galaxies and baryon oscillations, and how these different probes may be combined to constrain cosmological models and the physics of dark energy.Comment: 596 pages. Also available at full resolution at http://www.lsst.org/lsst/sciboo

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts