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Benoit Roux

Professor
roux@uchicago.edu
Publications

  1. Engineering Dirhodium Artificial Metalloenzymes for Diazo Coupling Cascade Reactions*. Angew Chem Int Ed Engl. 2021 10 25; 60(44):23672-23677. View in: PubMed

  2. Editorial: Advances in computational molecular biophysics. Biochim Biophys Acta Gen Subj. 2021 06; 1865(6):129888. View in: PubMed

  3. Biochemical patterns of antibody polyreactivity revealed through a bioinformatics-based analysis of CDR loops. Elife. 2020 11 10; 9. View in: PubMed

  4. Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field. J Chem Theory Comput. 2020 May 12; 16(5):3221-3239. View in: PubMed

  5. Calculating the Effect of Membrane Thickness on?the Lifetime of the Gramicidin A Channel: A?Landmark. Biophys J. 2019 11 19; 117(10):1779-1780. View in: PubMed

  6. Long intergenic non-coding RNAs regulate human lung fibroblast function: Implications for idiopathic pulmonary fibrosis. Sci Rep. 2019 04 15; 9(1):6020. View in: PubMed

  7. Long Non-coding RNAs Are Central Regulators of the IL-1?-Induced Inflammatory Response in Normal and Idiopathic Pulmonary Lung Fibroblasts. Front Immunol. 2018; 9:2906. View in: PubMed

  8. Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages. J Chem Theory Comput. 2018 Nov 13; 14(11):5567-5582. View in: PubMed

  9. Catalog of Differentially Expressed Long Non-Coding RNA following Activation of Human and Mouse Innate Immune Response. Front Immunol. 2017; 8:1038. View in: PubMed

  10. Transcriptional profiling identifies differential expression of long non-coding RNAs in Jo-1 associated and inclusion body myositis. Sci Rep. 2017 08 14; 7(1):8024. View in: PubMed

  11. Ion channels and ion selectivity. Essays Biochem. 2017 05 09; 61(2):201-209. View in: PubMed

  12. Inversion of the Side-Chain Stereochemistry of Indvidual Thr or Ile Residues in a Protein Molecule: Impact on the Folding, Stability, and Structure of the ShK Toxin. Angew Chem Int Ed Engl. 2017 03 13; 56(12):3324-3328. View in: PubMed

  13. Molecular Structure of Canonical Liquid Crystal Interfaces. J Am Chem Soc. 2017 03 15; 139(10):3841-3850. View in: PubMed

  14. Knockdown of Nuclear-Located Enhancer RNAs and Long ncRNAs Using Locked Nucleic Acid GapmeRs. Methods Mol Biol. 2017; 1468:11-8. View in: PubMed

  15. Long Intergenic Noncoding RNAs Mediate the Human Chondrocyte Inflammatory Response and Are Differentially Expressed in Osteoarthritis Cartilage. Arthritis Rheumatol. 2016 Apr; 68(4):845-56. View in: PubMed

  16. The Solvation Structure of Na(+) and K(+) in Liquid Water Determined from High Level ab Initio Molecular Dynamics Simulations. J Chem Theory Comput. 2012 Oct 09; 8(10):3526-35. View in: PubMed

  17. Special Issue on Free Energy. J Chem Theory Comput. 2014 Jul 08; 10(7):2631. View in: PubMed

  18. Determination of cholesterol oxides by gas chromatography-flame ionization detection/mass selective detection and their occurence in lanolin-containing cosmetics and ointments. Int J Cosmet Sci. 2016 Feb; 38(1):93-9. View in: PubMed

  19. Perspective on computational and structural aspects of kinase discovery from IPK2014. Biochim Biophys Acta. 2015 Oct; 1854(10 Pt B):1595-604. View in: PubMed

  20. Corrigendum: Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes. Nat Commun. 2015 Apr 09; 6:6814. View in: PubMed

  21. LincRNA signatures in human lymphocytes. Nat Immunol. 2015 Mar; 16(3):220-2. View in: PubMed

  22. Divergent signalling pathways regulate lipopolysaccharide-induced eRNA expression in human monocytic THP1 cells. FEBS Lett. 2015 Jan 30; 589(3):396-406. View in: PubMed

  23. Insights into the molecular foundations of electrical excitation. J Mol Biol. 2015 Jan 16; 427(1):1-2. View in: PubMed

  24. Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes. Nat Commun. 2014 Jun 09; 5:3979. View in: PubMed

  25. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B. 1998 Apr 30; 102(18):3586-616. View in: PubMed

  26. Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations. J Chem Phys. 2014 May 14; 140(18):184114. View in: PubMed

  27. Virtual high-throughput ligand screening. Methods Mol Biol. 2014; 1140:251-61. View in: PubMed

  28. Dynamics transitions at the outer vestibule of the KcsA potassium channel during gating. Proc Natl Acad Sci U S A. 2014 Feb 04; 111(5):1831-6. View in: PubMed

  29. Self-Learning Adaptive Umbrella Sampling Method for the Determination of Free Energy Landscapes in Multiple Dimensions. J Chem Theory Comput. 2013 Apr 09; 9(4):1885-1895. View in: PubMed

  30. Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field. Faraday Discuss. 2013; 160:135-49; discussion 207-24. View in: PubMed

  31. Restrained-ensemble molecular dynamics simulations based on distance histograms from double electron-electron resonance spectroscopy. J Phys Chem B. 2013 May 02; 117(17):4733-9. View in: PubMed

  32. On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method. J Chem Phys. 2013 Feb 28; 138(8):084107. View in: PubMed

  33. Nano-positioning system for structural analysis of functional homomeric proteins in multiple conformations. Structure. 2012 Oct 10; 20(10):1629-40. View in: PubMed

  34. Multi-ion distributions in the cytoplasmic domain of inward rectifier potassium channels. Biophys J. 2012 Aug 08; 103(3):434-443. View in: PubMed

  35. Ion binding sites and their representations by reduced models. J Phys Chem B. 2012 Jun 14; 116(23):6966-79. View in: PubMed

  36. Ouabain binding site in a functioning Na+/K+ ATPase. J Biol Chem. 2011 Nov 04; 286(44):38177-38183. View in: PubMed

  37. Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail. Biophys J. 2011 Aug 17; 101(4):755-6. View in: PubMed

  38. Biogenesis of the pore architecture of a voltage-gated potassium channel. Proc Natl Acad Sci U S A. 2011 Feb 22; 108(8):3240-5. View in: PubMed

  39. Structural dynamics of the magnesium-bound conformation of CorA in a lipid bilayer. Structure. 2010 Jul 14; 18(7):868-78. View in: PubMed

  40. Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications. Theor Chem Acc. 2009 Sep; 124(1-2):11-28. View in: PubMed

  41. Assessing the accuracy of approximate treatments of ion hydration based on primitive quasichemical theory. J Chem Phys. 2010 Jun 21; 132(23):234101. View in: PubMed

  42. Exploring the ion selectivity properties of a large number of simplified binding site models. Biophys J. 2010 Jun 16; 98(12):2877-85. View in: PubMed

  43. Perspectives on: molecular dynamics and computational methods. J Gen Physiol. 2010 Jun; 135(6):547-8. View in: PubMed

  44. CHARMM: the biomolecular simulation program. J Comput Chem. 2009 Jul 30; 30(10):1545-614. View in: PubMed

  45. Nanosculpting reversed wavelength sensitivity into a photoswitchable iGluR. Proc Natl Acad Sci U S A. 2009 Apr 21; 106(16):6814-9. View in: PubMed

  46. Using Markov models to simulate electron spin resonance spectra from molecular dynamics trajectories. J Phys Chem B. 2008 Sep 04; 112(35):11014-27. View in: PubMed

  47. The membrane potential and its representation by a constant electric field in computer simulations. Biophys J. 2008 Nov 01; 95(9):4205-16. View in: PubMed

  48. Neuropeptide FF-sensitive confinement of mu opioid receptor does not involve lipid rafts in SH-SY5Y cells. Biochem Biophys Res Commun. 2008 Aug 15; 373(1):80-4. View in: PubMed

  49. Lonely arginine seeks friendly environment. J Gen Physiol. 2007 Aug; 130(2):233-6. View in: PubMed

  50. Extracellular blockade of potassium channels by TEA+: the tip of the iceberg? J Gen Physiol. 2006 Dec; 128(6):635-6. View in: PubMed

  51. Dissecting the coupling between the voltage sensor and pore domains. Neuron. 2006 Nov 22; 52(4):568-9. View in: PubMed

  52. Optimized atomic radii for protein continuum electrostatics solvation forces. Biophys Chem. 1999 Apr 05; 78(1-2):89-96. View in: PubMed

  53. Implicit solvent models. Biophys Chem. 1999 Apr 05; 78(1-2):1-20. View in: PubMed

  54. Structural properties of barley nucleosomes. Biophys Chem. 1984 Aug; 20(1-2):111-9. View in: PubMed

  55. Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels. Biophys Chem. 2006 Dec 01; 124(3):251-67. View in: PubMed

  56. Ion permeation through a narrow channel: using gramicidin to ascertain all-atom molecular dynamics potential of mean force methodology and biomolecular force fields. Biophys J. 2006 May 15; 90(10):3447-68. View in: PubMed

  57. On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation. J Gen Physiol. 2004 Dec; 124(6):679-90. View in: PubMed

  58. Computational studies of membrane channels. Structure. 2004 Aug; 12(8):1343-51. View in: PubMed

  59. Insertion of a glycosylphosphatidylinositol-anchored enzyme into liposomes. J Membr Biol. 2004 Feb 01; 197(3):169-77. View in: PubMed

  60. Structure of gramicidin a in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data. J Am Chem Soc. 2003 Aug 13; 125(32):9868-77. View in: PubMed

  61. Atomic proximity between S4 segment and pore domain in Shaker potassium channels. Neuron. 2003 Jul 31; 39(3):467-81. View in: PubMed

  62. Role of GPI-anchored enzyme in liposome detergent-resistance. J Membr Biol. 2003 Feb 01; 191(3):215-21. View in: PubMed

  63. Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus. J Mol Biol. 2002 Aug 16; 321(3):459-78. View in: PubMed

  64. Cysteine mutagenesis and computer modeling of the S6 region of an intermediate conductance IKCa channel. J Gen Physiol. 2002 Jul; 120(1):99-116. View in: PubMed

  65. What can be deduced about the structure of Shaker from available data? Novartis Found Symp. 2002; 245:84-101; discussion 101-8, 165-8. View in: PubMed

  66. Imaging the electrostatic potential of transmembrane channels: atomic probe microscopy of OmpF porin. Biophys J. 2002 Mar; 82(3):1667-76. View in: PubMed

  67. Energetics of ion conduction through the K+ channel. Nature. 2001 Nov 01; 414(6859):73-7. View in: PubMed

  68. Extracellular blockade of K(+) channels by TEA: results from molecular dynamics simulations of the KcsA channel. J Gen Physiol. 2001 Aug; 118(2):207-18. View in: PubMed

  69. Lipid-mediated interactions between intrinsic membrane proteins: dependence on protein size and lipid composition. Biophys J. 2001 Jul; 81(1):276-84. View in: PubMed

  70. Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell. 2001 Apr 06; 105(1):115-26. View in: PubMed

  71. Framework model for single proton conduction through gramicidin. Biophys J. 2001 Jan; 80(1):12-30. View in: PubMed

  72. Lipid-mediated interactions between intrinsic membrane proteins: a theoretical study based on integral equations. Biophys J. 2000 Dec; 79(6):2867-79. View in: PubMed

  73. A combined molecular dynamics and diffusion model of single proton conduction through gramicidin. Biophys J. 2000 Dec; 79(6):2840-57. View in: PubMed

  74. Anchoring of a monotopic membrane protein: the binding of prostaglandin H2 synthase-1 to the surface of a phospholipid bilayer. Eur Biophys J. 2000; 29(6):439-54. View in: PubMed

  75. Ion channels, permeation, and electrostatics: insight into the function of KcsA. Biochemistry. 2000 Nov 07; 39(44):13295-306. View in: PubMed

  76. A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels. Biophys J. 2000 Aug; 79(2):788-801. View in: PubMed

  77. Molecular dynamics of the KcsA K(+) channel in a bilayer membrane. Biophys J. 2000 Jun; 78(6):2900-17. View in: PubMed

  78. Protein inclusion in lipid membranes: a theory based on the hypernetted chain integral equation. Faraday Discuss. 1998; (111):165-72; discussion 225-46. View in: PubMed

  79. Role of metal ions on the secondary and quaternary structure of alkaline phosphatase from bovine intestinal mucosa. Proteins. 1999 Nov 01; 37(2):310-8. View in: PubMed

  80. Theories of ion permeation: a chaser. J Gen Physiol. 1999 Oct; 114(4):605-8. View in: PubMed

  81. Proton wires are different. Biophys J. 1999 Nov; 77(5):2331-2. View in: PubMed

  82. The binding site of sodium in the gramicidin A channel. Novartis Found Symp. 1999; 225:113-24; discussion 124-7. View in: PubMed

  83. A FTIR spectroscopy evidence of the interactions between wheat germ agglutinin and N-acetylglucosamine residues. FEBS Lett. 1999 Aug 13; 456(3):361-4. View in: PubMed

  84. The cavity and pore helices in the KcsA K+ channel: electrostatic stabilization of monovalent cations. Science. 1999 Jul 02; 285(5424):100-2. View in: PubMed

  85. Statistical mechanical equilibrium theory of selective ion channels. Biophys J. 1999 Jul; 77(1):139-53. View in: PubMed

  86. Simulation analysis of the retinal conformational equilibrium in dark-adapted bacteriorhodopsin. Biophys J. 1999 Apr; 76(4):1909-17. View in: PubMed

  87. Molecular dynamics study of calbindin D9k in the apo and singly and doubly calcium-loaded states. Proteins. 1998 Nov 01; 33(2):265-84. View in: PubMed

  88. Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane. Biophys J. 1998 Oct; 75(4):1603-18. View in: PubMed

  89. Free energy profiles for H+ conduction along hydrogen-bonded chains of water molecules. Biophys J. 1998 Jul; 75(1):33-40. View in: PubMed

  90. Molecular dynamics simulations of ion channels: how far have we gone and where are we heading? Biophys J. 1998 Jun; 74(6):2744-5. View in: PubMed

  91. High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints. Structure. 1997 Dec 15; 5(12):1655-69. View in: PubMed

  92. Structure and dynamics of an amphiphilic peptide in a lipid bilayer: a molecular dynamics study. Biophys J. 1997 Dec; 73(6):3039-55. View in: PubMed

  93. Influence of the membrane potential on the free energy of an intrinsic protein. Biophys J. 1997 Dec; 73(6):2980-9. View in: PubMed

  94. Mammalian GPI proteins: sorting, membrane residence and functions. Biochim Biophys Acta. 1997 Sep 08; 1331(2):153-86. View in: PubMed

  95. Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. J Mol Biol. 1997 Sep 26; 272(3):423-42. View in: PubMed

  96. The binding site of sodium in the gramicidin A channel: comparison of molecular dynamics with solid-state NMR data. Biophys J. 1997 May; 72(5):1930-45. View in: PubMed

  97. Small-angle neutron scattering by a strongly denatured protein: analysis using random polymer theory. Biophys J. 1997 Jan; 72(1):335-42. View in: PubMed

  98. Valence selectivity of the gramicidin channel: a molecular dynamics free energy perturbation study. Biophys J. 1996 Dec; 71(6):3177-85. View in: PubMed

  99. Commentary: surface tension of biomembranes. Biophys J. 1996 Sep; 71(3):1346-7. View in: PubMed

  100. Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study. Biophys J. 1996 Aug; 71(2):670-81. View in: PubMed

  101. Structure and dynamics of a proton wire: a theoretical study of H+ translocation along the single-file water chain in the gramicidin A channel. Biophys J. 1996 Jul; 71(1):19-39. View in: PubMed

  102. Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer. Proteins. 1996 Jan; 24(1):92-114. View in: PubMed

  103. Configurational distribution of denatured phosphoglycerate kinase. J Mol Biol. 1993 Jun 05; 231(3):840-8. View in: PubMed

  104. Computer simulations of the flexibility of a series of synthetic cyclic peptide analogues. Biopolymers. 1993 Aug; 33(8):1249-70. View in: PubMed

  105. Structure and dynamics of bacteriorhodopsin. Comparison of simulation and experiment. FEBS Lett. 1993 Aug 02; 327(3):256-60. View in: PubMed

  106. p-Aminobenzoate synthesis in Escherichia coli: mutational analysis of three conserved amino acid residues of the amidotransferase PabA. Biochemistry. 1993 Apr 13; 32(14):3763-8. View in: PubMed

  107. Nuclear proteins interacting with DNA and tubulin. Study of the interaction of the High Mobility Group protein 1 with tubulin. Biochim Biophys Acta. 1994 Sep 13; 1219(1):39-46. View in: PubMed

  108. Thermal and pH stabilities of alkaline phosphatase from bovine intestinal mucosa: a FTIR study. Biochim Biophys Acta. 1995 Apr 27; 1248(2):186-92. View in: PubMed

  109. Functional interactions in bacteriorhodopsin: a theoretical analysis of retinal hydrogen bonding with water. Biophys J. 1995 Jan; 68(1):25-39. View in: PubMed

  110. Fine mapping of neutralization epitopes on duck hepatitis B virus (DHBV) pre-S protein using monoclonal antibodies and overlapping peptides. Virology. 1993 Jan; 192(1):217-23. View in: PubMed

  111. Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy. Biophys J. 1995 Mar; 68(3):876-92. View in: PubMed

  112. A molecular dynamics study of gating in dioxolane-linked gramicidin A channels. Biophys J. 1994 Oct; 67(4):1370-86. View in: PubMed

  113. Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer. Proc Natl Acad Sci U S A. 1994 Nov 22; 91(24):11631-5. View in: PubMed

  114. Molecular dynamics simulations of the gramicidin channel. Annu Rev Biophys Biomol Struct. 1994; 23:731-61. View in: PubMed

  115. Flexibility of nucleosomal DNA. Biochem Biophys Res Commun. 1980 Jul 16; 95(1):27-33. View in: PubMed

  116. Influence of histone H1 on chromatin structure. Biochem Biophys Res Commun. 1980 May 30; 94(2):535-41. View in: PubMed

  117. Effect of digestion with trypsin on chromatin structure. Biochem Biophys Res Commun. 1982 Oct 29; 108(4):1551-8. View in: PubMed

  118. Differences in the electric birefringence of spectrin dimers and tetramers as shown by the fast reversing electric pulse method. Biophys Chem. 1982 Nov; 16(3):193-8. View in: PubMed

  119. Role of histones H1 and H3 in the maintenance of chromatin in a compact conformation. Study with an immobilized enzyme. FEBS Lett. 1983 Jul 04; 157(2):317-21. View in: PubMed

  120. Electric birefringence of chromatin reconstituted with various histone H1 subfractions. Biochem Biophys Res Commun. 1984 Jun 15; 121(2):530-7. View in: PubMed

  121. Study of chromatin organization with trypsin immobilized on collagen membranes. Biochem Biophys Res Commun. 1983 Aug 12; 114(3):1169-75. View in: PubMed

  122. Histone phosphorylation in native chromatin induces local structural changes as probed by electric birefringence. J Mol Biol. 1985 Nov 20; 186(2):367-79. View in: PubMed

  123. Association states of tubulin in the presence and absence of microtubule-associated proteins. Analysis by electric birefringence. Biophys Chem. 1985 Oct; 22(4):307-16. View in: PubMed

  124. Antibodies to Z DNA stabilized with polyarginine. FEBS Lett. 1985 Oct 21; 191(1):67-71. View in: PubMed

  125. The effect of histone H1 on the compaction of oligonucleosomes. A quasielastic light scattering study. Biophys Chem. 1985 Jun; 22(1-2):53-64. View in: PubMed

  126. Tubulin-chromatin interactions: evidence for tubulin-binding sites on chromatin and isolated oligonucleosomes. Biochim Biophys Acta. 1986 Aug 29; 888(1):49-61. View in: PubMed

  127. Temperature and external electric field influence in membrane permeability of Babesia infected erythrocytes. Int J Biochem. 1987; 19(11):1069-73. View in: PubMed

  128. ANTHEPROT: a package for protein sequence analysis using a microcomputer. Comput Appl Biosci. 1988 Aug; 4(3):351-6. View in: PubMed

  129. Phosphorylation- and ligand-induced conformational changes of rat liver fructose-1,6-bisphosphatase. Arch Biochem Biophys. 1986 Aug 01; 248(2):604-11. View in: PubMed

  130. Isolation and characterisation of five histone H1 subtypes from adult rat liver. Biochim Biophys Acta. 1989 Nov 02; 1009(2):121-8. View in: PubMed

  131. Epitope of OSCP oligomycin sensitivity conferring protein exposed at the surface of the mitochondrial ATPase-ATPsynthase complex. Biochimie. 1989 Aug; 71(8):917-29. View in: PubMed

  132. The normal modes of the gramicidin-A dimer channel. Biophys J. 1988 Mar; 53(3):297-309. View in: PubMed

  133. A general solution to the time interval omission problem applied to single channel analysis. Biophys J. 1985 Jul; 48(1):149-58. View in: PubMed

  134. Intrinsic tryptophan fluorescence of Schizosaccharomyces pombe mitochondrial F1-ATPase. A powerful probe for phosphate and nucleotide interactions. Biochemistry. 1991 Apr 02; 30(13):3256-62. View in: PubMed

  135. Ion transport in a model gramicidin channel. Structure and thermodynamics. Biophys J. 1991 May; 59(5):961-81. View in: PubMed

  136. The structure of gramicidin A in dimethylsulfoxide/acetone. Eur J Biochem. 1990 Nov 26; 194(1):57-60. View in: PubMed

  137. Histone H1a subtype presents structural differences compared to other histone H1 subtypes. Evidence for a specific motif in the C-terminal domain. Biochim Biophys Acta. 1992 Jul 31; 1122(2):167-77. View in: PubMed

  138. p-aminobenzoate synthesis in Escherichia coli: kinetic and mechanistic characterization of the amidotransferase PabA. Biochemistry. 1992 Aug 04; 31(30):6904-10. View in: PubMed

  139. Differential nucleotide binding to catalytic and noncatalytic sites and related conformational changes involving alpha/beta-subunit interactions as monitored by sensitive intrinsic fluorescence in Schizosaccharomyces pombe mitochondrial F1. Biochemistry. 1992 Jun 30; 31(25):5791-8. View in: PubMed

  140. Phenol-containing adsorbents for the affinity chromatography purification of some NAD(H)-dependent dehydrogenases. FEBS Lett. 1977 Apr 15; 76(2):246-9. View in: PubMed

  141. Intermolecular interaction studies on native and enzyme-treated acid-soluble collagen. Biochim Biophys Acta. 1978 Feb 15; 532(2):305-14. View in: PubMed
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