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151. Skjaerven, Lars, Grant, Barry, Muga, Arturo, Teigen, Knut, McCammon, J. Andrew, Reuter, Nathalie, Martinez, Aurora, (2011), "Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations.", PLoS computational biology, 7, 3: pg: e1002004, 1553-7358 (Electronic)$\backslash$r1553-734X (Link, (DOI: 10.1371/journal.pcbi.1002004).
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152. Sinko, William, de Oliveira, Csar, Williams, Sarah and, (2011), "Applying molecular dynamics simulations to identify rarely sampled ligand-bound conformational states of undecaprenyl pyrophosphate synthase, an antibacterial target.", Chemical biology \& drug design, 77, 6: pg: 412--20, 1747-0285, (DOI: 10.1111/j.1747-0285.2011.01101.x).
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153. Sinko, William, de Oliveira, Csar, Williams, Sarah and, (2011), "Applying molecular dynamics simulations to identify rarely sampled ligand-bound conformational states of undecaprenyl pyrophosphate synthase, an antibacterial target.", Chemical biology \& drug design, 77, 6: pg: 412--20, 1747-0285, (DOI: 10.1111/j.1747-0285.2011.01101.x).
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154. Sander, Tommy, Frlund, Bente, Bruun, Anne Techau, Ivanov, Ivaylo, McCammon, James Andrew, Balle, Thomas, (2011), "New insights into the GABA(A) receptor structure and orthosteric ligand binding: receptor modeling guided by experimental data.", Proteins, 79, 5: pg: 1458--77, 4535336040 1097-0134, (DOI: 10.1002/prot.22975).
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155. Rane, Aboli A., Chuang, Joyce S., Shah, Amul, Hu, Diane P., Dalton, Nancy D., Gu, Yusu, Peterson, Kirk L., Omens, Jeffrey H., Christman, Karen L., (2011), "Increased infarct wall thickness by a bio-inert material is insufficient to prevent negative left ventricular remodeling after myocardial infarction.", PloS one, 6, 6: pg: e21571, 1932-6203 (Electronic)$\backslash$r1932-6203 (Link, (DOI: 10.1371/journal.pone.0021571).
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156. Quinn, T. A., Granite, S., Allessie, M. A., Antzelevitch, C., Bollensdorff, C., Bub, G., Burton, R. A. B., Cerbai, E., Chen, P. S., Delmar, M., Difrancesco, D., Earm, Y. E., Efimov, I. R., Egger, M., Entcheva, E., Fink, M., Fischmeister, R., Franz, M. R., Garny, A., Giles, W. R., Hannes, T., Harding, S. E., Hunter, P. J., Iribe, G., Jalife, J., Johnson, C. R., Kass, R. S., Kodama, I., Koren, G., Lord, P., Markhasin, V. S., Matsuoka, S., McCulloch, A. D., Mirams, G. R., Morley, G. E., Nattel, S., Noble, D., Olesen, S. P., Panfilov, A. V., Trayanova, N. A., Ravens, U., Richard, S., Rosenbaum, D. S., Rudy, Y., Sachs, F., Sachse, F. B., Saint, D. A., Schotten, U., Solovyova, O., Taggart, P., Tung, L., Varr, (2011), "Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): standardised reporting for model reproducibility, interoperability, and data sharing.", Progress in biophysics and molecular biology, 107, 1: pg: 4--10, 1873-1732 (Electronic)$\backslash$r0079-6107 (Link, (DOI: 10.1016/j.pbiomolbio.2011.07.001).
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157. Pierce, Levi C. T., Markwick, Phineus R. L., McCammon, J. Andrew, Doltsinis, Nikos L., (2011), "Accelerating chemical reactions: exploring reactive free-energy surfaces using accelerated ab initio molecular dynamics.", The Journal of chemical physics, 134, 17: pg: 174107, doi 10.1063/1.3581093 1089-7690, (DOI: 10.1063/1.3581093).
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158. Perkins, Guy A., Ellisman, Mark H., (2011), "Mitochondrial configurations in peripheral nerve suggest differential ATP production", Journal of Structural Biology, 173, 1: pg: 117--127, 8585348585 10478477, (DOI: 10.1016/j.jsb.2010.06.017).
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159. Olsen, Brett N., Schlesinger, Paul H., Ory, Daniel S., Baker, Nathan A., (2011), "25-Hydroxycholesterol increases the availability of cholesterol in phospholipid membranes.", Biophysical journal, 100, 4: pg: 948--56, 0006-3495 1542-0086, (DOI: 10.1016/j.bpj.2010.12.3728).
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160. Nichols, Sara E., Baron, Riccardo, Ivetac, Anthony, McCammon, J. Andrew, (2011), "Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening", Journal of Chemical Information and Modeling, 51, 6: pg: 1439--1446, 1549-9596, (DOI: 10.1021/ci200117n).
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161. Nguyen, D., Alavi, M. V., Kim, K. Y., Kang, T., Scott, R. T., Noh, Y. H., Lindsey, J. D., Wissinger, B., Ellisman, M. H., Weinreb, R. N., Perkins, G. a, Ju, W. K., (2011), "A new vicious cycle involving glutamate excitotoxicity, oxidative stress and mitochondrial dynamics.", Cell death \& disease, 2, 12: pg: e240, 2041-4889 (Electronic) 2041-4889, (DOI: 10.1038/cddis.2011.117).
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162. Nekouzadeh, Ali, Rudy, Yoram, (2011), "Continuum molecular simulation of large conformational changes during ion-channel gating.", PloS one, 6, 5: pg: e20186, 1932-6203, (DOI: 10.1371/journal.pone.0020186).
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163. Mereghetti, Paolo, Kokh, Daria, McCammon, J. Andrew, Wade, Rebecca C., (2011), "Diffusion and association processes in biological systems: theory, computation and experiment.", BMC biophysics, 4, 1: pg: 2, 2046-1682, (DOI: 10.1186/2046-1682-4-2).
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164. McCammon, J. Andrew, (2011), "Gated Diffusion-controlled Reactions.", BMC biophysics, 4, 1: pg: 4, 2046-1682, (DOI: 10.1186/2046-1682-4-4).
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165. Markwick, Phineus R. L., Pierce, Levi C. T., Goodin, David B., McCammon, J. Andrew, (2011), "Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam.", The journal of physical chemistry letters, 2, 3: pg: 158--164, 1948-7185, (DOI: 10.1021/jz101462n).
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166. Malmstrom, Robert D., Watowich, Stanley J., (2011), "Using free energy of binding calculations to improve the accuracy of virtual screening predictions.", Journal of chemical information and modeling, 51, 7: pg: 1648--55, 1549-960X (Electronic)$\backslash$r1549-9596 (Link, (DOI: 10.1021/ci200126v).
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167. Machanick, Philip, Bailey, Timothy L., (2011), "MEME-ChIP: motif analysis of large DNA datasets.", Bioinformatics (Oxford, England), 27, 12: pg: 1696--7, 1367-4811 (Electronic)$\backslash$n1367-4803 (Link, (DOI: 10.1093/bioinformatics/btr189).
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168. Lawrenz, Morgan, Baron, Riccardo, Wang, Yi, McCammon, J. Andrew, (2011), "Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies.", Journal of chemical theory and computation, 7, 7: pg: 2224--2232, 1858534291 1549-9626, (DOI: 10.1021/ct200230v).
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169. Johnson, Graham T., Autin, Ludovic, Goodsell, David S., Sanner, Michel F., Olson, Arthur J., (2011), "ePMV embeds molecular modeling into professional animation software environments.", Structure (London, England : 1993), 19, 3: pg: 293--303, 09692126 1878-4186, (DOI: 10.1016/j.str.2010.12.023).
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170. Ivetac, Anthony and, (2011), "Molecular Recognition in the Case of Flexible Targets", Current Pharmaceutical Design, 17, 17: pg: 1663--1671, 1873-4286 (Electronic)$\backslash$r1381-6128 (Link, (DOI: 10.2174/138161211796355056).
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171. Hoshijima, Masahiko, Hayashi, Takeharu, Jeon, Young E., Fu, Zhenxing, Gu, Yusu, Dalton, Nancy D., Ellisman, Mark H., Xiao, Xiao, Powell, Frank L., Ross, John, (2011), "Delta-sarcoglycan gene therapy halts progression of cardiac dysfunction, improves respiratory failure, and prolongs life in myopathic hamsters.", Circulation. Heart failure, 4, 1: pg: 89--97, 1941-3297 (Electronic)$\backslash$n1941-3289 (Link, (DOI: 10.1161/CIRCHEARTFAILURE.110.957258).
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172. Grant, Charles E., Bailey, Timothy L., Noble, William Stafford, (2011), "FIMO: scanning for occurrences of a given motif.", Bioinformatics (Oxford, England), 27, 7: pg: 1017--8, 1367-4811 (Electronic)$\backslash$n1367-4803 (Link, (DOI: 10.1093/bioinformatics/btr064).
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173. Grant, Barry J., Lukman, Suryani, Hocker, Harrison J., Sayyah, Jaqueline, Brown, Joan Heller, McCammon, J. Andrew, Gorfe, Alemayehu A., (2011), "Novel allosteric sites on Ras for lead generation.", PloS one, 6, 10: pg: e25711, 1932-6203 (Electronic)$\backslash$n1932-6203 (Link, (DOI: 10.1371/journal.pone.0025711).
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174. Grant, Barry J., Gheorghe, Dana M., Zheng, Wenjun, Alonso, Maria, Huber, Gary, Dlugosz, Maciej, McCammon, J. Andrew, Cross, Robert A., (2011), "Electrostatically biased binding of kinesin to microtubules.", PLoS biology, 9, 11: pg: e1001207, 1545-7885 (Electronic)$\backslash$r1544-9173 (Link, (DOI: 10.1371/journal.pbio.1001207).
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175. Durrant, Jacob D., McCammon, J. Andrew, (2011), "Molecular dynamics simulations and drug discovery", BMC Biology, 9, 1: pg: 71, 1741-7007, (DOI: 10.1186/1741-7007-9-71).
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176. Durrant, Jacob D., McCammon, J. Andrew, (2011), "Towards the development of novel Trypanosoma brucei RNA editing ligase 1 inhibitors.", BMC pharmacology, 11, 1: pg: 9, 1471-2210 (Electronic)$\backslash$r1471-2210 (Link, (DOI: 10.1186/1471-2210-11-9).
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177. Durrant, Jacob D., McCammon, J. Andrew, (2011), "NNScore 2.0: a neural-network receptor-ligand scoring function.", Journal of chemical information and modeling, 51, 11: pg: 2897--903, 1549-960X, (DOI: 10.1021/ci2003889).
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178. Durrant, Jacob D., McCammon, J. Andrew, (2011), "BINANA: a novel algorithm for ligand-binding characterization.", Journal of molecular graphics \& modelling, 29, 6: pg: 888--93, 1093-3263 1873-4243, (DOI: 10.1016/j.jmgm.2011.01.004).
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179. Durrant, Jacob D., McCammon, J. Andrew, (2011), "HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis.", Journal of molecular graphics \& modelling, 31: pg: 5--9, 1093-3263 1873-4243, (DOI: 10.1016/j.jmgm.2011.07.008).
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180. Durrant, Jacob D., Friedman, Aaron J., McCammon, J. Andrew, (2011), "CrystalDock: a novel approach to fragment-based drug design.", Journal of chemical information and modeling, 51, 10: pg: 2573--80, 1549-960X (Electronic)$\backslash$r1549-9596 (Link, (DOI: 10.1021/ci200357y).
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181. Durrant, Jacob D., de Oliveira, Csar A. F., McCammon, J. Andrew, (2011), "Pyrone-based inhibitors of metalloproteinase types 2 and 3 may work as conformation-selective inhibitors.", Chemical biology \& drug design, 78, 2: pg: 191--8, 1747-0285, (DOI: 10.1111/j.1747-0285.2011.01148.x).
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182. Durrant, Jacob D., de Oliveira, Csar Augusto F., McCammon, J. Andrew, (2011), "POVME: an algorithm for measuring binding-pocket volumes.", Journal of molecular graphics \& modelling, 29, 5: pg: 773--6, 2156623929 1873-4243, (DOI: 10.1016/j.jmgm.2010.10.007).
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183. Durrant, Jacob D., Cao, Rong, Gorfe, Alemayehu A., Zhu, Wei, Li, Jikun, Sankovsky, Anna, Oldfield, Eric, McCammon, J. Andrew, (2011), "Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug design.", Chemical biology \& drug design, 78, 3: pg: 323--32, 1747-0285, (DOI: 10.1111/j.1747-0285.2011.01164.x).
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184. Demir, zlem, Baronio, Roberta, Salehi, Faezeh, Wassman, Christopher D., Hall, Linda, Hatfield, G. Wesley, Chamberlin, Richard, Kaiser, Peter, Lathrop, Richard H., Amaro, Rommie E., (2011), "Ensemble-based computational approach discriminates functional activity of p53 cancer and rescue mutants.", PLoS computational biology, 7, 10: pg: e1002238, 1553-7358 (Electronic)$\backslash$n1553-734X (Link, (DOI: 10.1371/journal.pcbi.1002238).
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185. de Oliveira, Csar Augusto F., Grant, Barry J., Zhou, Michelle, McCammon, J. Andrew, (2011), "Large-scale conformational changes of Trypanosoma cruzi proline racemase predicted by accelerated molecular dynamics simulation.", PLoS computational biology, 7, 10: pg: e1002178, 1553-7358 (Electronic)$\backslash$r1553-734X (Link, (DOI: 10.1371/journal.pcbi.1002178).
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186. Darshi, Manjula, Mendiola, Vincent L., Mackey, Mason R., Murphy, Anne N., Koller, Antonius, Perkins, Guy A., Ellisman, Mark H., Taylor, Susan S., (2011), "ChChd3, an inner mitochondrial membrane protein, is essential for maintaining crista integrity and mitochondrial function.", The Journal of biological chemistry, 286, 4: pg: 2918--32, 1083-351X (Electronic)$\backslash$r0021-9258 (Link, (DOI: 10.1074/jbc.M110.171975).
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187. Coatrieux, Jean-Louis, Frangi, Alejandro F., Peng, Grace C. Y., D'Argenio, David Z., Marmarelis, Vasilis Z., Michailova, Anushka, (2011), "Editorial: TBME Letters special issue on multiscale modeling and analysis in computational biology and medicine--part-2.", IEEE transactions on bio-medical engineering, 58, 12: pg: 3434--9, 1558-2531, (DOI: 10.1109/TBME.2011.2168990).
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188. Chen, Zhan, Baker, Nathan A., Wei, G. W., (2011), "Differential geometry based solvation model II: Lagrangian formulation.", Journal of mathematical biology, 63, 6: pg: 1139--200, 1432-1416 (Electronic)$\backslash$n0303-6812 (Link, (DOI: 10.1007/s00285-011-0402-z).
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189. Carstensen, Tommy, Farrell, Damien, Huang, Yong, Baker, Nathan A., Nielsen, Jens Erik, (2011), "On the development of protein pKa calculation algorithms.", Proteins, 79, 12: pg: 3287--98, 0887-3585 1097-0134, (DOI: 10.1002/prot.23091).
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190. Campbell, Stuart G., McCulloch, Andrew D., (2011), "Multi-scale computational models of familial hypertrophic cardiomyopathy: genotype to phenotype", Journal of The Royal Society Interface, 8, 64: pg: 1550--1561, 1742-5689, (DOI: 10.1098/rsif.2011.0184).
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191. Bucher, Denis, Pierce, Levi C. T., McCammon, J. Andrew, Markwick, Phineus R. L., (2011), "On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations.", Journal of chemical theory and computation, 7, 4: pg: 890--897, 1549-9626, (DOI: 10.1021/ct100605v).
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192. Bucher, Denis, Grant, Barry J., McCammon, J. Andrew, (2011), "Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein.", Biochemistry, 50, 48: pg: 10530--9, 1520-4995, (DOI: 10.1021/bi201481a).
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193. Bucher, Denis, Grant, Barry J., Markwick, Phineus R., McCammon, J. Andrew, (2011), "Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics.", PLoS computational biology, 7, 4: pg: e1002034, 1553-7358 (Electronic)$\backslash$r1553-734X (Link, (DOI: 10.1371/journal.pcbi.1002034).
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194. Berlanga, M. L., Price, D. L., Phung, B. S., Giuly, R., Terada, M., Yamada, N., Cyr, M., Caron, M. G., Laakso, A., Martone, M. E., Ellisman, M. H., (2011), "Multiscale imaging characterization of dopamine transporter knockout mice reveals regional alterations in spine density of medium spiny neurons.", Brain research, 1390: pg: 41--9, 0006-8993 1872-6240, (DOI: 10.1016/j.brainres.2011.03.044).
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195. Baron, Riccardo, Binda, Claudia, Tortorici, Marcello, McCammon, J. Andrew, Mattevi, Andrea, (2011), "Molecular mimicry and ligand recognition in binding and catalysis by the histone demethylase LSD1-CoREST complex.", Structure (London, England : 1993), 19, 2: pg: 212--20, 0969-2126 1878-4186, (DOI: 10.1016/j.str.2011.01.001).
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196. Bailey, Timothy L., (2011), "DREME: motif discovery in transcription factor ChIP-seq data.", Bioinformatics (Oxford, England), 27, 12: pg: 1653--9, 1367-4811 (Electronic)$\backslash$r1367-4803 (Link, (DOI: 10.1093/bioinformatics/btr261).
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197. Amaro, Rommie E., Swift, Robert V., Votapka, Lane, Li, Wilfred W., Walker, Ross C., Bush, Robin M., (2011), "Mechanism of 150-cavity formation in influenza neuraminidase.", Nature communications, 2: pg: 388, 2041-1723 (Electronic) 2041-1723 (Linking) 2041-1, (DOI: 10.1038/ncomms1390).
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198. Alexov, Emil, Mehler, Ernest L., Baker, Nathan, Baptista, Antnio M., Huang, Yong, Milletti, Francesca, Nielsen, Jens Erik, Farrell, Damien, Carstensen, Tommy, Olsson, Mats H. M., Shen, Jana K., Warwicker, Jim, Williams, Sarah, Word, J. Michael, (2011), "Progress in the prediction of pKa values in proteins.", Proteins, 79, 12: pg: 3260--75, 1097-0134 (Electronic)$\backslash$r0887-3585 (Link, (DOI: 10.1002/prot.23189).
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199. Aguado-Sierra, Jazmin, Krishnamurthy, Adarsh, Villongco, Christopher, Chuang, Joyce, Howard, Elliot, Gonzales, Matthew J., Omens, Jeff, Krummen, David E., Narayan, Sanjiv, Kerckhoffs, Roy C. P., McCulloch, Andrew D., (2011), "Patient-specific modeling of dyssynchronous heart failure: a case study.", Progress in biophysics and molecular biology, 107, 1: pg: 147--55, 1873-1732 (Electronic)$\backslash$r0079-6107 (Link, (DOI: 10.1016/j.pbiomolbio.2011.06.014).
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200. Williams, Sarah L., de Oliveira, Csar Augusto F., McCammon, J. Andrew, (2010), "Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics.", Journal of chemical theory and computation, 6, 2: pg: 560--568, 1549-9626, (DOI: 10.1021/ct9005294).
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