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  • 1
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    Cap homeostasis is independent of poly(A) tail length (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-09
    Description: Cap homeostasis is a cyclical process of decapping and recapping that maintains the cap on a subset of the cytoplasmic transcriptome. Interfering with cytoplasmic capping results in the redistribution of target transcripts from polysomes to non-translating mRNPs, where they accumulate in an uncapped but nonetheless stable form. It is generally thought that decapping is preceded by shortening of the poly(A) tail to a length that can no longer support translation. Therefore recapped target transcripts would either have to undergo cytoplasmic polyadenylation or retain a reasonably long poly(A) tail if they are to return to the translating pool. In cells that are inhibited for cytoplasmic capping there is no change in the overall distribution of poly(A) lengths or in the elution profile of oligo(dT)-bound targets. Poly(A) tail lengths were similar for target mRNAs on polysomes or in non-translating mRNPs, and the presence of polyadenylated uncapped mRNA in mRNPs was confirmed by separation into capped and uncapped pools prior to assay. Finally, in silico analysis of cytoplasmic capping targets revealed significant correlations with genes encoding transcripts with uridylated or multiply modified 3' ends, and genes possessing multiple 3'-untranslated regions (UTRs) generated by alternative cleavage and polyadenylation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Pitch angle distributions of energetic electrons at Saturn (2011)
    Wiley
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    Publication Date: 2011-01-29
    Description: Pitch angle distributions of energetic electrons (110–365 keV) at Saturn are statistically analyzed for 2005–2009. Using a nondipolar model magnetic field, pitch angle distributions are mapped to the magnetospheric equator and sorted by equatorial crossing distance. The results are quantified using a standard function for the pitch angle distribution, f(α) = AsinKα (where α is the pitch angle and K is the power). Inside of ∼10 RS, the distributions are mostly peaked at 90° (K 〈 0), signifying a trapping distribution. Outside of this distance, the distributions are mostly field aligned (K 〉 0) with maxima near 0° and 180°. The 10 RS boundary maps to Saturn's ionosphere at latitudes equatorward of the aurora. Very few “flat” distributions are observed (K ≈ 0). The pitch angle distributions are not as well organized in local time as they are in radial distance, but over the 5 year survey between 10 and 20 RS field-aligned distributions appear most often near midnight, while trapping distributions are found elsewhere.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 3
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    Differential electrophysiological response during rest, self-referential, and non-self-referential tasks in human posteromedial cortex [Neuroscience] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-02-16
    Description: The electrophysiological basis for higher brain activity during rest and internally directed cognition within the human default mode network (DMN) remains largely unknown. Here we use intracranial recordings in the human posteromedial cortex (PMC), a core node within the DMN, during conditions of cued rest, autobiographical judgments, and arithmetic processing. We found a heterogeneous profile of PMC responses in functional, spatial, and temporal domains. Although the majority of PMC sites showed increased broad gamma band activity (30–180 Hz) during rest, some PMC sites, proximal to the retrosplenial cortex, responded selectively to autobiographical stimuli. However, no site responded to both conditions, even though they were located within the boundaries of the DMN identified with resting-state functional imaging and similarly deactivated during arithmetic processing. These findings, which provide electrophysiological evidence for heterogeneity within the core of the DMN, will have important implications for neuroimaging studies of the DMN.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 4
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    Effect of separate sampling on classification accuracy (2014)
    Oxford University Press
    Details
    Publication Date: 2014-01-16
    Description: Motivation: Measurements are commonly taken from two phenotypes to build a classifier, where the number of data points from each class is predetermined, not random. In this ‘separate sampling’ scenario, the data cannot be used to estimate the class prior probabilities. Moreover, predetermined class sizes can severely degrade classifier performance, even for large samples. Results: We employ simulations using both synthetic and real data to show the detrimental effect of separate sampling on a variety of classification rules. We establish propositions related to the effect on the expected classifier error owing to a sampling ratio different from the population class ratio. From these we derive a sample-based minimax sampling ratio and provide an algorithm for approximating it from the data. We also extend to arbitrary distributions the classical population-based Anderson linear discriminant analysis minimax sampling ratio derived from the discriminant form of the Bayes classifier. Availability: All the codes for synthetic data and real data examples are written in MATLAB. A function called mmratio, whose output is an approximation of the minimax sampling ratio of a given dataset, is also written in MATLAB. All the codes are available at: http://gsp.tamu.edu/Publications/supplementary/shahrokh13b . Contact: edward@ece.tamu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 5
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    Outflow and plasma acceleration in Titan's induced magnetotail: Evidence of magnetic tension forces (2014)
    Wiley
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    Publication Date: 2014-11-28
    Description: Cassini plasma wave and particle observations are combined with magnetometer measurements to study Titan's induced magnetic tail. In this study, we report and analyze the plasma acceleration in Titan's induced magnetotail observed in flybys T17, T19 and T40. Radio and Plasma Wave Science (RPWS) observations show regions of cold plasma with electron densities between 0.1 and a few tens of electrons per cubic centimeter. The Cassini Plasma Spectrometer-Ion Mass Spectrometer (CAPS-IMS) measurements suggest that ionospheric plasma in this region is composed of ions with masses ranging from 15 to 17 amu and from 28 to 31 amu. From these measurements, we determine the bulk velocity of the plasma and the Alfvén velocity in Titan's tail region. Finally, a Walén test of such measurements suggest that the progressive acceleration of the ionospheric plasma shown by CAPS can be interpreted in terms of magnetic tension forces.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 6
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    Seeing the herpesvirus capsid at 8.5 A (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-05-08
    Description: Human herpesviruses are large and structurally complex viruses that cause a variety of diseases. The three-dimensional structure of the herpesvirus capsid has been determined at 8.5 angstrom resolution by electron cryomicroscopy. More than 30 putative alpha helices were identified in the four proteins that make up the 0.2 billion-dalton shell. Some of these helices are located at domains that undergo conformational changes during capsid assembly and DNA packaging. The unique spatial arrangement of the heterotrimer at the local threefold positions accounts for the asymmetric interactions with adjacent capsid components and the unusual co-dependent folding of its subunits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Z H -- Dougherty, M -- Jakana, J -- He, J -- Rixon, F J -- Chiu, W -- New York, N.Y. -- Science. 2000 May 5;288(5467):877-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology and Laboratory Medicine, University of Texas-Houston Medical School, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10797014" target="_blank"〉PubMed〈/a〉
    Keywords: Capsid/*chemistry/*ultrastructure ; Capsid Proteins ; Cryoelectron Microscopy ; Herpesvirus 1, Human/chemistry/*ultrastructure ; Image Processing, Computer-Assisted ; Models, Molecular ; Molecular Weight ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Jovian-like aurorae on Saturn (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-06-20
    Description: Planetary aurorae are formed by energetic charged particles streaming along the planet's magnetic field lines into the upper atmosphere from the surrounding space environment. Earth's main auroral oval is formed through interactions with the solar wind, whereas that at Jupiter is formed through interactions with plasma from the moon Io inside its magnetic field (although other processes form aurorae at both planets). At Saturn, only the main auroral oval has previously been observed and there remains much debate over its origin. Here we report the discovery of a secondary oval at Saturn that is approximately 25 per cent as bright as the main oval, and we show this to be caused by interaction with the middle magnetosphere around the planet. This is a weak equivalent of Jupiter's main oval, its relative dimness being due to the lack of as large a source of ions as Jupiter's volcanic moon Io. This result suggests that differences seen in the auroral emissions from Saturn and Jupiter are due to scaling differences in the conditions at each of these two planets, whereas the underlying formation processes are the same.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stallard, Tom -- Miller, Steve -- Melin, Henrik -- Lystrup, Makenzie -- Cowley, Stan W H -- Bunce, Emma J -- Achilleos, Nicholas -- Dougherty, Michele -- England -- Nature. 2008 Jun 19;453(7198):1083-5. doi: 10.1038/nature07077.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics and Astronomy, University of Leicester, Leicester LE1 7RH, UK. tss@ion.le.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18563160" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 8
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    Mechanism of folding chamber closure in a group II chaperonin (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-01-22
    Description: Group II chaperonins are essential mediators of cellular protein folding in eukaryotes and archaea. These oligomeric protein machines, approximately 1 megadalton, consist of two back-to-back rings encompassing a central cavity that accommodates polypeptide substrates. Chaperonin-mediated protein folding is critically dependent on the closure of a built-in lid, which is triggered by ATP hydrolysis. The structural rearrangements and molecular events leading to lid closure are still unknown. Here we report four single particle cryo-electron microscopy (cryo-EM) structures of Mm-cpn, an archaeal group II chaperonin, in the nucleotide-free (open) and nucleotide-induced (closed) states. The 4.3 A resolution of the closed conformation allowed building of the first ever atomic model directly from the single particle cryo-EM density map, in which we were able to visualize the nucleotide and more than 70% of the side chains. The model of the open conformation was obtained by using the deformable elastic network modelling with the 8 A resolution open-state cryo-EM density restraints. Together, the open and closed structures show how local conformational changes triggered by ATP hydrolysis lead to an alteration of intersubunit contacts within and across the rings, ultimately causing a rocking motion that closes the ring. Our analyses show that there is an intricate and unforeseen set of interactions controlling allosteric communication and inter-ring signalling, driving the conformational cycle of group II chaperonins. Beyond this, we anticipate that our methodology of combining single particle cryo-EM and computational modelling will become a powerful tool in the determination of atomic details involved in the dynamic processes of macromolecular machines in solution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2834796/" 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/PMC2834796/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Junjie -- Baker, Matthew L -- Schroder, Gunnar F -- Douglas, Nicholai R -- Reissmann, Stefanie -- Jakana, Joanita -- Dougherty, Matthew -- Fu, Caroline J -- Levitt, Michael -- Ludtke, Steven J -- Frydman, Judith -- Chiu, Wah -- P41 RR002250/RR/NCRR NIH HHS/ -- P41 RR002250-23/RR/NCRR NIH HHS/ -- P41 RR002250-237254/RR/NCRR NIH HHS/ -- P41 RR002250-24/RR/NCRR NIH HHS/ -- P41 RR002250-247897/RR/NCRR NIH HHS/ -- PN2 EY016525/EY/NEI NIH HHS/ -- PN2 EY016525-02S1/EY/NEI NIH HHS/ -- PN2 EY016525-03/EY/NEI NIH HHS/ -- PN2 EY016525-04/EY/NEI NIH HHS/ -- PN2 EY016525-05/EY/NEI NIH HHS/ -- R01 GM063817/GM/NIGMS NIH HHS/ -- R01 GM079429/GM/NIGMS NIH HHS/ -- R01 GM079429-03/GM/NIGMS NIH HHS/ -- R01 GM080139/GM/NIGMS NIH HHS/ -- R01 GM080139-03/GM/NIGMS NIH HHS/ -- R01 GM080139-04/GM/NIGMS NIH HHS/ -- R90 DK071504/DK/NIDDK NIH HHS/ -- R90 DK071504-03/DK/NIDDK NIH HHS/ -- T32 GM007276-30/GM/NIGMS NIH HHS/ -- T32 GM007276-31/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Jan 21;463(7279):379-83. doi: 10.1038/nature08701.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20090755" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/chemistry/metabolism/pharmacology ; Allosteric Regulation ; Binding Sites ; Cryoelectron Microscopy ; Group II Chaperonins/*chemistry/*metabolism/ultrastructure ; Hydrolysis/drug effects ; Methanococcus/*chemistry ; Models, Molecular ; Protein Binding ; Protein Conformation/drug effects ; *Protein Folding ; Protein Subunits/chemistry/metabolism ; Structure-Activity Relationship
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 9
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    A response to comments on stress and sexual signaling: a systematic review and meta-analysis (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-19
    Print ISSN: 1045-2249
    Electronic ISSN: 1465-7279
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Stress and sexual signaling: a systematic review and meta-analysis (2016)
    Oxford University Press
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    Publication Date: 2016-03-19
    Description: The vertebrate stress response has been shown to suppress investment in reproductive and immune function and may also lead to a reduced investment in the production of secondary sexual traits. However, it has been difficult to model roles of stress in sexual selection due to the inconsistent results seen in empirical studies testing for the effect of stress on the expression of secondary sexual traits. We conducted a phylogenetically controlled meta-analysis of published associations between physiological correlates of stress and sexual signaling in vertebrates in order to identify any consistent patterns. Our analysis included signaling in both males and females, 4 stress measures, and 4 categories of sexually selected traits (vocalizations, traits that varied in size, traits that varied in coloration, and opposite-sex preference). Across 38 studies of 26 species, there was no significant relationship between physiological correlates of stress and the expression of sexual signals. Mean effect size, however, varied significantly across the 4 types of sexually selected trait. We propose development of a model that incorporates the nuanced effects of species ecology, trait type, ecological context, and the complex nature of the physiological stress response, on the expression of sexually selected traits.
    Print ISSN: 1045-2249
    Electronic ISSN: 1465-7279
    Topics: Biology
    Published by Oxford University Press
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