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  • 1
    Publication Date: 2013-12-20
    Description: A major challenge for the development of a highly effective AIDS vaccine is the identification of mechanisms of protective immunity. To address this question, we used a nonhuman primate challenge model with simian immunodeficiency virus (SIV). We show that antibodies to the SIV envelope are necessary and sufficient to prevent infection. Moreover, sequencing of viruses from breakthrough infections revealed selective pressure against neutralization-sensitive viruses; we identified a two-amino-acid signature that alters antigenicity and confers neutralization resistance. A similar signature confers resistance of human immunodeficiency virus (HIV)-1 to neutralization by monoclonal antibodies against variable regions 1 and 2 (V1V2), suggesting that SIV and HIV share a fundamental mechanism of immune escape from vaccine-elicited or naturally elicited antibodies. These analyses provide insight into the limited efficacy seen in HIV vaccine trials.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3946913/" 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/PMC3946913/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roederer, Mario -- Keele, Brandon F -- Schmidt, Stephen D -- Mason, Rosemarie D -- Welles, Hugh C -- Fischer, Will -- Labranche, Celia -- Foulds, Kathryn E -- Louder, Mark K -- Yang, Zhi-Yong -- Todd, John-Paul M -- Buzby, Adam P -- Mach, Linh V -- Shen, Ling -- Seaton, Kelly E -- Ward, Brandy M -- Bailer, Robert T -- Gottardo, Raphael -- Gu, Wenjuan -- Ferrari, Guido -- Alam, S Munir -- Denny, Thomas N -- Montefiori, David C -- Tomaras, Georgia D -- Korber, Bette T -- Nason, Martha C -- Seder, Robert A -- Koup, Richard A -- Letvin, Norman L -- Rao, Srinivas S -- Nabel, Gary J -- Mascola, John R -- AI100645/AI/NIAID NIH HHS/ -- HHSN261200800001E/PHS HHS/ -- HHSN27201100016C/PHS HHS/ -- UM1 AI100645/AI/NIAID NIH HHS/ -- Z99 AI999999/Intramural NIH HHS/ -- ZIA AI005019-12/Intramural NIH HHS/ -- England -- Nature. 2014 Jan 23;505(7484):502-8. doi: 10.1038/nature12893. Epub 2013 Dec 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, NIAID, NIH, Bethesda, Maryland 20892, USA. ; SAIC-Frederick, Frederick National Laboratory, NIH, Frederick, Maryland 21702, USA. ; 1] Vaccine Research Center, NIAID, NIH, Bethesda, Maryland 20892, USA [2] George Washington University, Washington DC 20052, USA. ; Los Alamos National Laboratories, Los Alamos, New Mexico 87545, USA. ; Department of Surgery, Duke University, Durham, North Carolina 27710, USA. ; 1] Vaccine Research Center, NIAID, NIH, Bethesda, Maryland 20892, USA [2] Sanofi-Pasteur, Cambridge, Massachusetts 02139, USA. ; Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA. ; Human Vaccine Institute, Duke University, Durham, North Carolina 27710, USA. ; Fred Hutchison Cancer Research Center, Seattle, Washington 98109, USA. ; Biostatistics Research Branch, NIAID, NIH, Bethesda, Maryland 20892, USA. ; 1] Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA [2].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24352234" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines/*immunology ; Amino Acid Sequence ; Animals ; Antibodies, Neutralizing/immunology ; Disease Susceptibility/immunology ; Female ; Founder Effect ; HIV Antibodies/immunology ; HIV Infections/immunology/*prevention & control/*virology ; HIV-1/chemistry/*immunology ; Humans ; Immune Evasion/immunology ; Macaca mulatta ; Male ; Molecular Sequence Data ; Phylogeny ; Risk ; SAIDS Vaccines/*immunology ; Simian Acquired Immunodeficiency Syndrome/immunology/prevention & ; control/virology ; Simian Immunodeficiency Virus/chemistry/genetics/*immunology/physiology ; env Gene Products, Human Immunodeficiency Virus/immunology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2012-06-16
    Description: Author(s): X. W. Zhou, D. K. Ward, B. M. Wong, and F. P. Doty We use a new, quantum-mechanics-based bond-order potential (BOP) to reveal melt growth dynamics and fine scale defect formation mechanisms in CdTe crystals. Previous molecular dynamics simulations of semiconductors have shown qualitatively incorrect behavior due to the lack of an interatomic potenti... [Phys. Rev. Lett. 108, 245503] Published Fri Jun 15, 2012
    Keywords: Condensed Matter: Structure, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
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  • 3
    Publication Date: 2012-06-23
    Description: Author(s): J. J. Chavez, D. K. Ward, B. M. Wong, F. P. Doty, J. L. Cruz-Campa, G. N. Nielson, V. P. Gupta, D. Zubia, J. McClure, and X. W. Zhou The presence of atomic-scale defects at multilayer interfaces significantly degrades performance in CdTe-based photovoltaic technologies. The ability to accurately predict and understand defect formation mechanisms during overlayer growth is, therefore, a rational approach for improving the efficien... [Phys. Rev. B 85, 245316] Published Fri Jun 22, 2012
    Keywords: Semiconductors II: surfaces, interfaces, microstructures, and related topics
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 4
    Publication Date: 2012-06-02
    Description: Author(s): X. W. Zhou, D. K. Ward, B. M. Wong, F. P. Doty, J. A. Zimmerman, G. N. Nielson, J. L. Cruz-Campa, V. P. Gupta, J. E. Granata, J. J. Chavez, and D. Zubia CdTe has been a special semiconductor for constructing the lowest-cost solar cells, and the CdTe-based Cd 1− x Zn x Te alloy has been the leading semiconductor for radiation detection applications. The performance currently achieved for the materials, however, is still far below theoretical expectations.... [Phys. Rev. B 85, 245302] Published Fri Jun 01, 2012
    Keywords: Semiconductors II: surfaces, interfaces, microstructures, and related topics
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 5
    Publication Date: 2014-06-17
    Description: Motivation: The Expectation–Maximization (EM) algorithm has been successfully applied to the problem of transcription factor binding site (TFBS) motif discovery and underlies the most widely used motif discovery algorithms. In the wider field of probabilistic modelling, the stochastic EM (sEM) algorithm has been used to overcome some of the limitations of the EM algorithm; however, the application of sEM to motif discovery has not been fully explored. Results: We present MITSU (Motif discovery by ITerative Sampling and Updating), a novel algorithm for motif discovery, which combines sEM with an improved approximation to the likelihood function, which is unconstrained with regard to the distribution of motif occurrences within the input dataset. The algorithm is evaluated quantitatively on realistic synthetic data and several collections of characterized prokaryotic TFBS motifs and shown to outperform EM and an alternative sEM-based algorithm, particularly in terms of site-level positive predictive value. Availability and implementation: Java executable available for download at http://www.sourceforge.net/p/mitsu-motif/ , supported on Linux/OS X. Contact: a.m.kilpatrick@sms.ed.ac.uk
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 6
    Publication Date: 2017-11-10
    Description: The Cordilleran Ice Sheet (CIS) once covered an area comparable to that of Greenland. Previous geologic evidence and numerical models indicate that the ice sheet covered much of westernmost Canada as late as 12.5 thousand years ago (ka). New data indicate that substantial areas throughout westernmost Canada were ice free prior to 12.5 ka and some as early as 14.0 ka, with implications for climate dynamics and the timing of meltwater discharge to the Pacific and Arctic oceans. Early Bølling-Allerød warmth halved the mass of the CIS in as little as 500 years, causing 2.5 to 3.0 meters of sea-level rise. Dozens of cirque and valley glaciers, along with the southern margin of the CIS, advanced into recently deglaciated regions during the Bølling-Allerød and Younger Dryas.
    Keywords: Atmospheric Science
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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