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    • Several versions

    The feasibility of axial and coronal combined imaging using multi-detector row computed tomography for the diagnosis and treatment of a primary spontaneous pneumothorax

    Kim Do
    Journal of cardiothoracic surgery, 01 May 2011, Vol.6(1), p.71 [Peer Reviewed Journal]
    Directory of Open Access Journals (DOAJ)
    • Several versions

    Origin of thickness dependent spin reorientation transition of B2 type FeCo alloy films

    Kim, Do-Kyung, Hong, J.
    Journal of Applied Physics, 2013, Vol.114(21), pp.213911 [Peer Reviewed Journal]

    • Several versions

    Structural Basis for Elastic Mechanical Properties of the DNA Double Helix

    Kim, Young-Joo, Kim, Do-Nyun
    PLoS ONE, 2016, Vol.11(4) [Peer Reviewed Journal]

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    Assembly and dynamics of the autophagy-initiating Atg1 complex

    Stjepanovic, Goran, Davies, Christopher W., Stanley, Robin E., Ragusa, Michael J., Kim, Do Jin, Hurley, James H.
    Proceedings of the National Academy of Sciences of the United States of America, 2 September 2014, Vol.111(35), pp.12793-12798 [Peer Reviewed Journal]
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    Title: Assembly and dynamics of the autophagy-initiating Atg1 complex
    Author: Stjepanovic, Goran; Davies, Christopher W.; Stanley, Robin E.; Ragusa, Michael J.; Kim, Do Jin; Hurley, James H.
    Description: The autophagy-related 1 (Atg1) complex of Saccharomyces cerevisiae has a central role in the initiation of autophagy following starvation and TORC1 inactivation. The complex consists of the protein kinase Atg1, the TORC1 substrate Atg13, and the trimeric Atg17-Atg31-Atg29 scaffolding subcomplex. Autophagy is triggered when Atg1 and Atg13 assemble with the trimeric scaffold. Here we show by hydrogen-deuterium exchange coupled to mass spectrometry that the mutually interacting Atg1 early autophagy targeting/tethering domain and the Atg13 central domain are highly dynamic in isolation but together form a stable complex with ~ 100-nM affinity. The Atg1-Atg13 complex in turn binds as a unit to the Atg17-Atg31-Atg29 scaffold with ~ 10-µM affinity via Atg13. The resulting complex consists primarily of a dimer of pentamers in solution. These results lead to a model for autophagy initiation in which Atg1 and Atg13 are tightly associated with one another and assemble transiently into the pentameric Atg1 complex during starvation.
    Is part of: Proceedings of the National Academy of Sciences of the United States of America, 2 September 2014, Vol.111(35), pp.12793-12798
    Identifier: 00278424 (ISSN)

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    Deep RNA Sequencing Reveals Novel Cardiac Transcriptomic Signatures for Physiological and Pathological Hypertrophy (RNA-Seq in Hypertrophy)

    Song, Hong Ki, Hong, Seong-Eui, Kim, Taeyong, Kim, Do Han
    PLoS ONE, 2012, Vol.7(4), p.e35552 [Peer Reviewed Journal]
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    Title: Deep RNA Sequencing Reveals Novel Cardiac Transcriptomic Signatures for Physiological and Pathological Hypertrophy (RNA-Seq in Hypertrophy)
    Author: Song, Hong Ki; Hong, Seong-Eui; Kim, Taeyong; Kim, Do Han
    Contributor: Schönbach, Christian (Editor)
    Subject: Research Article ; Biology ; Medicine ; Genetics And Genomics ; Molecular Biology ; Physiology ; Computational Biology
    Description: Although both physiological hypertrophy (PHH) and pathological hypertrophy (PAH) of the heart have similar morphological appearances, only PAH leads to fatal heart failure. In the present study, we used RNA sequencing (RNA-Seq) to determine the transcriptomic signatures for both PHH and PAH. Approximately 13–20 million reads were obtained for both models, among which PAH showed more differentially expressed genes (DEGs) (2,041) than PHH (245). The expression of 417 genes was barely detectable in the normal heart but was suddenly activated in PAH. Among them, Foxm1 and Plk1 are of particular interest, since Ingenuity Pathway Analysis (IPA) using DEGs and upstream motif analysis showed that they are essential hub proteins that regulate the expression of downstream proteins associated with PAH. Meanwhile, 52 genes related to collagen, chemokines, and actin showed opposite expression patterns between PHH and PAH. MAZ-binding motifs were enriched in the upstream region of the participating genes. Alternative splicing (AS) of exon variants was also examined using RNA-Seq data for PAH and PHH. We found 317 and 196 exon inclusions and exon exclusions, respectively, for PAH, and 242 and 172 exon inclusions and exclusions, respectively for PHH. The AS pattern was mostly related to gains or losses of domains, changes in activity, and localization of the encoded proteins. The splicing variants of 8 genes (i.e., Fhl1 , Rcan1 , Ndrg2 , Synpo , Ttll1 , Cxxc5 , Egfl7 , and Tmpo ) were experimentally confirmed. Multilateral pathway analysis showed that the patterns of quantitative (DEG) and qualitative (AS) changes differ depending on the type of pathway in PAH and PHH. One of the most significant changes in PHH is the severe downregulation of autoimmune pathways accompanied by significant AS. These findings revealed the unique transcriptomic signatures of PAH and PHH and also provided a more comprehensive understanding at both the quantitative and qualitative levels.
    Is part of: PLoS ONE, 2012, Vol.7(4), p.e35552
    Identifier: 1932-6203 (E-ISSN); 10.1371/journal.pone.0035552 (DOI)

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    Tuning Charge Transport in Solution-Sheared Organic Semiconductors Using Lattice Strain

    Giri, Guarav, Verploegen, Eric, Mannsfeld, Stefan C. B., Atahan, Sule, Kim, Do Hwam, Lee, Sang Yoon, Beccerril, Hector A., Aspuru-Guzik, Alan, Toney, Michael F., Bao, Zhenan
    Giri, Gaurav, Eric Verploegen, Stefan C. B. Mannsfeld, Sule Atahan-Evrenk, Do Hwan Kim, Sang Yoon Lee, Hector A. Becerril, Alán Aspuru-Guzik, Michael F. Toney, and Zhenan Bao. 2011. Tuning charge transport in solution-sheared organic semiconductors using lattice strain. Nature 480(7378): 504–508. [Peer Reviewed Journal]
    Harvard University Library
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    Title: Tuning Charge Transport in Solution-Sheared Organic Semiconductors Using Lattice Strain
    Author: Giri, Guarav; Verploegen, Eric; Mannsfeld, Stefan C. B.; Atahan, Sule; Kim, Do Hwam; Lee, Sang Yoon; Beccerril, Hector A.; Aspuru-Guzik, Alan; Toney, Michael F.; Bao, Zhenan
    Subject: Sciences (General) ; Physics;
    Description: Circuits based on organic semiconductors are being actively explored for flexible, transparent and low-cost electronic applications. But to realize such applications, the charge carrier mobilities of solution-processed organic semiconductors must be improved. For inorganic semiconductors, a general method of increasing charge carrier mobility is to introduce strain within the crystal lattice. Here we describe a solution-processing technique for organic semiconductors in which lattice strain is used to increase charge carrier mobilities by introducing greater electron orbital overlap between the component molecules. For organic semiconductors, the spacing between cofacially stacked, conjugated backbones (the π–π stacking distance) greatly influences electron orbital overlap and therefore mobility. Using our method to incrementally introduce lattice strain, we alter the π–π stacking distance of 6,13-bis(triisopropylsilylethynyl) pentacene (TIPS-pentacene) from 3.33Å to 3.08 Å. We believe that 3.08Å is the shortest π–π stacking distance that has been achieved in an organic semiconductor crystal lattice (although a π–π distance of 3.04Å has been achieved through intramolecular bonding). The positive charge carrier (hole) mobility in TIPS-pentacene transistors increased from \(0.8 cm^2 V^{−1} s^{−1}\) for unstrained films to a high mobility of \(4.6 cm^2 V^{−1} s^{−1}\) for a strained film. Using solution processing to modify molecular packing through lattice strain should aid the development of high-performance, low-cost organic semiconducting devices.
    Is part of: Giri, Gaurav, Eric Verploegen, Stefan C. B. Mannsfeld, Sule Atahan-Evrenk, Do Hwan Kim, Sang Yoon Lee, Hector A. Becerril, Alán Aspuru-Guzik, Michael F. Toney, and Zhenan Bao. 2011. Tuning charge transport in solution-sheared organic semiconductors using lattice strain. Nature 480(7378): 504–508.
    Identifier: 0028-0836 (ISSN); 10.1038/nature10683 (DOI)

    • Several versions

    Glycan variants of a respiratory syncytial virus antibody with enhanced effector function and in vivo efficacy

    Hiatt, Andrew, Bohorova, Natasha, Bohorov, Ognian, Goodman, Charles, Kim, Do, Pauly, Michael H, Velasco, Jesus, Whaley, Kevin J, Piedra, Pedro A, Gilbert, Brian E, Zeitlin, Larry
    Proceedings of the National Academy of Sciences of the United States of America, 22 April 2014, Vol.111(16), pp.5992-7 [Peer Reviewed Journal]

    • Several versions

    Enhanced potency of a fucose-free monoclonal antibody being developed as an Ebola virus immunoprotectant

    Zeitlin, Larry, Pettitt, James, Scully, Corinne, Bohorova, Natasha, Kim, Do, Pauly, Michael, Hiatt, Andrew, Ngo, Long, Steinkellner, Herta, Whaley, Kevin J, Olinger, Gene G
    Proceedings of the National Academy of Sciences of the United States of America, 20 December 2011, Vol.108(51), pp.20690-4 [Peer Reviewed Journal]

    • Several versions

    Effective production of fermentable sugars from brown macroalgae biomass

    Wang, Damao, Kim, Do, Kim, Kyoung
    Applied Microbiology and Biotechnology, 2016, Vol.100(22), pp.9439-9450 [Peer Reviewed Journal]

    • Several versions

    Accelerated deforestation in the humid tropics from the 1990s to the 2000s

    Kim, Do-Hyung, Sexton, Joseph O, Townshend, John R
    Geophysical research letters, 16 May 2015, Vol.42(9), pp.3495-3501 [Peer Reviewed Journal]