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  • 2010-2014  (92)
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Year
  • 1
    Publication Date: 2012-11-11
    Description: : We have established an RNA mapping database (RMDB) to enable structural, thermodynamic and kinetic comparisons across single-nucleotide-resolution RNA structure mapping experiments. The volume of structure mapping data has greatly increased since the development of high-throughput sequencing techniques, accelerated software pipelines and large-scale mutagenesis. For scientists wishing to infer relationships between RNA sequence/structure and these mapping data, there is a need for a database that is curated, tagged with error estimates and interfaced with tools for sharing, visualization, search and meta-analysis. Through its on-line front-end, the RMDB allows users to explore single-nucleotide-resolution mapping data in heat-map, bar-graph and colored secondary structure graphics; to leverage these data to generate secondary structure hypotheses; and to download the data in standardized and computer-friendly files, including the RDAT and community-consensus SNRNASM formats. At the time of writing, the database houses 53 entries, describing more than 2848 experiments of 1098 RNA constructs in several solution conditions and is growing rapidly. Availability: Freely available on the web at http://rmdb.stanford.edu Contact: rhiju@stanford.edu Supplementary information: Supplementary data are available at Bioinformatics Online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 2
    Publication Date: 2012-05-17
    Description: Antarctic ice sheet surface melting can regionally influence ice shelf stability, mass balance, and glacier dynamics, in addition to modulating near-surface physical and chemical properties over wide areas. Here, we investigate variability in surface melting from 1999 to 2009 using radar backscatter time series from the SeaWinds scatterometer aboard the QuikSCAT satellite. These daily, continent-wide observations are explored in concert with in situ meteorological records to validate a threshold-based melt detection method. Radar backscatter decreases during melting are significantly correlated with in situ positive degree-days as well as meltwater production determined from energy balance modeling at Neumayer Station, East Antarctica. These results support the use of scatterometer data as a diagnostic indicator of melt intensity (i.e., the relative liquid water production during melting). Greater spatial and temporal melting detected relative to previous passive microwave-based studies is attributed to a higher sensitivity of the scatterometer instrument. Continental melt intensity variability can be explained in part by the dynamics of the Southern Annular Mode and the Southern Oscillation Index, and extreme melting events across the Ross Ice Shelf region may be associated with El Niño conditions. Furthermore, we find that the Antarctic Peninsula accounts for only 20% of Antarctic melt extent but greater than 50% of the total Antarctic melt intensity. Over most areas, annual melt duration and intensity are proportional. However, regional and localized distinctions exist where the melt intensity metric provides greater insight into melting dynamics than previously obtainable with other remote sensing techniques.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 3
    Publication Date: 2013-12-06
    Description: A candidate anti-HIV reservoir compound, auranofin, exerts a selective ‘anti-memory’ effect by exploiting the baseline oxidative status of lymphocytes Cell Death and Disease 4, e944 (December 2013). doi:10.1038/cddis.2013.473 Authors: B Chirullo, R Sgarbanti, D Limongi, I L Shytaj, D Alvarez, B Das, A Boe, S DaFonseca, N Chomont, L Liotta, E III Petricoin, S Norelli, E Pelosi, E Garaci, A Savarino & A T Palamara
    Keywords: auranofinHIV curememory compartmentapoptosisdifferentiation effectoxidative stress
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 4
    Publication Date: 2013-10-09
    Description: The Journal of Physical Chemistry B DOI: 10.1021/jp407154h
    Electronic ISSN: 1520-5207
    Topics: Chemistry and Pharmacology , Physics
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  • 5
    Publication Date: 2012-10-23
    Description: CXCR1 is one of two high-affinity receptors for the CXC chemokine interleukin-8 (IL-8), a major mediator of immune and inflammatory responses implicated in many disorders, including tumour growth. IL-8, released in response to inflammatory stimuli, binds to the extracellular side of CXCR1. The ligand-activated intracellular signalling pathways result in neutrophil migration to the site of inflammation. CXCR1 is a class A, rhodopsin-like G-protein-coupled receptor (GPCR), the largest class of integral membrane proteins responsible for cellular signal transduction and targeted as drug receptors. Despite its importance, the molecular mechanism of CXCR1 signal transduction is poorly understood owing to the limited structural information available. Recent structural determination of GPCRs has advanced by modifying the receptors with stabilizing mutations, insertion of the protein T4 lysozyme and truncations of their amino acid sequences, as well as addition of stabilizing antibodies and small molecules that facilitate crystallization in cubic phase monoolein mixtures. The intracellular loops of GPCRs are crucial for G-protein interactions, and activation of CXCR1 involves both amino-terminal residues and extracellular loops. Our previous nuclear magnetic resonance studies indicate that IL-8 binding to the N-terminal residues is mediated by the membrane, underscoring the importance of the phospholipid bilayer for physiological activity. Here we report the three-dimensional structure of human CXCR1 determined by NMR spectroscopy. The receptor is in liquid crystalline phospholipid bilayers, without modification of its amino acid sequence and under physiological conditions. Features important for intracellular G-protein activation and signal transduction are revealed. The structure of human CXCR1 in a lipid bilayer should help to facilitate the discovery of new compounds that interact with GPCRs and combat diseases such as breast cancer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3700570/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3700570/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, Sang Ho -- Das, Bibhuti B -- Casagrande, Fabio -- Tian, Ye -- Nothnagel, Henry J -- Chu, Mignon -- Kiefer, Hans -- Maier, Klaus -- De Angelis, Anna A -- Marassi, Francesca M -- Opella, Stanley J -- P01 AI074805/AI/NIAID NIH HHS/ -- P01AI074805/AI/NIAID NIH HHS/ -- P41 EB002031/EB/NIBIB NIH HHS/ -- P41EB002031/EB/NIBIB NIH HHS/ -- R01 EB005161/EB/NIBIB NIH HHS/ -- R01 GM099986/GM/NIGMS NIH HHS/ -- R01EB005161/EB/NIBIB NIH HHS/ -- R01GM075877/GM/NIGMS NIH HHS/ -- R21GM075917/GM/NIGMS NIH HHS/ -- R21GM94727/GM/NIGMS NIH HHS/ -- England -- Nature. 2012 Nov 29;491(7426):779-83. doi: 10.1038/nature11580. Epub 2012 Oct 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0307, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23086146" target="_blank"〉PubMed〈/a〉
    Keywords: Disulfides/chemistry/metabolism ; Enzyme Activation ; Heterotrimeric GTP-Binding Proteins/metabolism ; Humans ; Interleukin-8/chemistry/metabolism ; Lipid Bilayers/chemistry/*metabolism ; Models, Molecular ; Molecular Conformation ; Nuclear Magnetic Resonance, Biomolecular ; Phospholipids/chemistry/*metabolism ; Receptors, Interleukin-8A/*chemistry/*metabolism ; Signal Transduction
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2012-12-12
    Description: Osteoarthritis is one of the leading causes of chronic pain, but almost nothing is known about the mechanisms and molecules that mediate osteoarthritis-associated joint pain. Consequently, treatment options remain inadequate and joint replacement is often inevitable. Here, we use a surgical mouse model that captures the long-term progression of knee...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 7
    Publication Date: 2013-05-31
    Description: Nature Geoscience 6, 503 (2013). doi:10.1038/ngeo1833 Author: Maya P. Bhatia, Elizabeth B. Kujawinski, Sarah B. Das, Crystaline F. Breier, Paul B. Henderson & Matthew A. Charette
    Print ISSN: 1752-0894
    Electronic ISSN: 1752-0908
    Topics: Geosciences
    Published by Springer Nature
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  • 8
    Publication Date: 2013-07-02
    Description: [1]  We use an airborne-radar method, verified with ice-core accumulation records, to determine the spatio-temporal variations of snow accumulation over Thwaites Glacier, West Antarctica between 1980 and 2009. We also present a regional evaluation of modeled accumulation in Antarctica. Comparisons between radar-derived measurements and model outputs show that three global models capture the interannual variability well ( r  〉 0.9), but a high-resolution regional model (RACMO2) has better absolute accuracy and captures the observed spatial variability ( r  = 0.86). Neither the measured nor modeled accumulation records over Thwaites Glacier show any trend since 1980. Although an increase in accumulation may potentially accompany the observed warming in the region, the projected trend is too small to detect over the 30-year record.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 9
    Publication Date: 2013-11-20
    Description: [1]  This study generates novel satellite-derived estimates of Antarctic-wide annual (1999–2009) surface meltwater production using an empirical relationship between radar backscatter from the QuikSCAT (QSCAT) satellite and melt calculated from in situ energy balance observations. The resulting QSCAT-derived melt fluxes significantly agree with output from the regional climate model RACMO2.1 and with independent ground-based observations. The high-resolution (4.45-km) QSCAT-based melt fluxes uniquely detect interannually persistent and intense melt (〉400 mm w.e. year -1 ) on interior Larsen C Ice Shelf that is not simulated by RACMO2.1. This supports a growing understanding of the importance of a föhn effect in this region and quantifies the resulting locally enhanced melting that is spatially consistent with recently observed Larsen C thinning. These new results highlight important cryosphere-climate interactions and processes that are presently not fully captured by the coarser resolution (27-km) regional climate model.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 10
    Publication Date: 2014-07-29
    Description: Interior Antarctica is among the most remote places on Earth and was thought to be beyond the reach of human impacts when Amundsen and Scott raced to the South Pole in 1911. Here we show detailed measurements from an extensive array of 16 ice cores quantifying substantial toxic heavy metal lead pollution at South Pole and throughout Antarctica by 1889 – beating polar explorers by more than 22 years. Unlike the Arctic where lead pollution peaked in the 1970s, lead pollution in Antarctica was as high in the early 20th century as at any time since industrialization. The similar timing and magnitude of changes in lead deposition across Antarctica, as well as the characteristic isotopic signature of Broken Hill lead found throughout the continent, suggest that this single emission source in southern Australia was responsible for the introduction of lead pollution into Antarctica at the end of the 19th century and remains a significant source today. An estimated 660 t of industrial lead have been deposited over Antarctica during the past 130 years as a result of mid-latitude industrial emissions, with regional-to-global scale circulation likely modulating aerosol concentrations. Despite abatement efforts, significant lead pollution in Antarctica persists into the 21st century. Scientific Reports 4 doi: 10.1038/srep05848
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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