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Jané Kondev - Publications

Affiliations: 
Brandeis University, Waltham, MA, United States 
Area:
Theoretical Physics--Condensed Matter
Website:
https://www.brandeis.edu/departments/physics/people/faculty/kond.html

52/96 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Tenenbaum D, Inlow K, Friedman LJ, Cai A, Gelles J, Kondev J. RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons. Proceedings of the National Academy of Sciences of the United States of America. 120: e2301402120. PMID 37459525 DOI: 10.1073/pnas.2301402120  0.617
2023 Inlow K, Tenenbaum D, Friedman LJ, Kondev J, Gelles J. Recycling of bacterial RNA polymerase by the Swi2/Snf2 ATPase RapA. Proceedings of the National Academy of Sciences of the United States of America. 120: e2303849120. PMID 37406096 DOI: 10.1073/pnas.2303849120  0.625
2023 Inlow K, Tenenbaum D, Friedman LJ, Kondev J, Gelles J. Recycling of Bacterial RNA Polymerase by the Swi2/Snf2 ATPase RapA. Biorxiv : the Preprint Server For Biology. PMID 36993374 DOI: 10.1101/2023.03.22.533849  0.626
2023 Tenenbaum D, Inlow K, Friedman L, Cai A, Gelles J, Kondev J. RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons. Biorxiv : the Preprint Server For Biology. PMID 36798213 DOI: 10.1101/2023.02.10.528045  0.618
2020 Harden TT, Herlambang KS, Chamberlain M, Lalanne JB, Wells CD, Li GW, Landick R, Hochschild A, Kondev J, Gelles J. Alternative transcription cycle for bacterial RNA polymerase. Nature Communications. 11: 448. PMID 31974358 DOI: 10.1038/S41467-019-14208-9  0.645
2019 McInally SG, Kondev J, Dawson SC. Length-dependent disassembly maintains four different flagellar lengths in . Elife. 8. PMID 31855176 DOI: 10.7554/Elife.48694  0.33
2019 Shekhar S, Chung J, Kondev J, Gelles J, Goode BL. Synergy between Cyclase-associated protein and Cofilin accelerates actin filament depolymerization by two orders of magnitude. Nature Communications. 10: 5319. PMID 31757952 DOI: 10.1038/S41467-019-13268-1  0.569
2019 Fai TG, Mohapatra L, Kar P, Kondev J, Amir A. Length regulation of multiple flagella that self-assemble from a shared pool of components. Elife. 8. PMID 31596235 DOI: 10.7554/eLife.42599  0.326
2019 Bashor CJ, Patel N, Choubey S, Beyzavi A, Kondev J, Collins JJ, Khalil AS. Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies. Science (New York, N.Y.). PMID 31000590 DOI: 10.1126/Science.Aau8287  0.313
2018 Choubey S, Kondev J, Sanchez A. Distribution of Initiation Times Reveals Mechanisms of Transcriptional Regulation in Single Cells. Biophysical Journal. 114: 2072-2082. PMID 29742401 DOI: 10.1016/J.Bpj.2018.03.031  0.649
2017 Mohapatra L, Lagny TJ, Harbage D, Jelenkovic PR, Kondev J. The Limiting-Pool Mechanism Fails to Control the Size of Multiple Organelles. Cell Systems. 4: 559-567.e14. PMID 28544883 DOI: 10.1016/j.cels.2017.04.011  0.315
2017 Rauch J, Kondev J, Sanchez A. Cooperators trade off ecological resilience and evolutionary stability in public goods games. Journal of the Royal Society, Interface. 14. PMID 28148770 DOI: 10.1098/Rsif.2016.0967  0.518
2016 Mohapatra L, Goode BL, Jelenkovic P, Phillips R, Kondev J. Design Principles of Length Control of Cytoskeletal Structures. Annual Review of Biophysics. PMID 27145876 DOI: 10.1146/Annurev-Biophys-070915-094206  0.309
2016 Harbage DW, Kondev J. Exact Length Distribution of Filamentous Structures Assembled from a Finite Pool of Subunits. The Journal of Physical Chemistry. B. PMID 27135597 DOI: 10.1021/acs.jpcb.6b02242  0.316
2016 Harden TT, Wells CD, Friedman LJ, Landick R, Hochschild A, Kondev J, Gelles J. Bacterial RNA polymerase can retain σ70 throughout transcription. Proceedings of the National Academy of Sciences of the United States of America. PMID 26733675 DOI: 10.1073/Pnas.1513899113  0.638
2015 Choubey S, Kondev J, Sanchez A. Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules. Plos Computational Biology. 11: e1004345. PMID 26544860 DOI: 10.1371/Journal.Pcbi.1004345  0.641
2015 Mohapatra L, Goode BL, Kondev J. Antenna Mechanism of Length Control of Actin Cables. Plos Computational Biology. 11: e1004160. PMID 26107518 DOI: 10.1371/Journal.Pcbi.1004160  0.319
2015 Paramanathan T, Reeves D, Friedman LJ, Kondev J, Gelles J. Competitor Effect on Molecular Complex Dissociation in the Absence of Ternary Complex Formation Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.905  0.585
2015 Harden TT, Friedman LJ, Wells CD, Hochschild A, Kondev J, Gelles J. Bacterial Transcript Elongation Complexes can Retain Sigma Factor throughout RNA Synthesis Biophysical Journal. 108: 535a. DOI: 10.1016/J.Bpj.2014.11.2933  0.652
2014 Paramanathan T, Reeves D, Friedman LJ, Kondev J, Gelles J. A general mechanism for competitor-induced dissociation of molecular complexes. Nature Communications. 5: 5207. PMID 25342513 DOI: 10.1038/Ncomms6207  0.587
2014 Choubey S, Sanchez A, Kondev J. Deciphering Transcriptional Dynamics in Vivo by Counting Nascent RNAs Biophysical Journal. 106: 375a. DOI: 10.1016/J.Bpj.2013.11.2123  0.645
2013 Sanchez A, Choubey S, Kondev J. Stochastic models of transcription: from single molecules to single cells. Methods (San Diego, Calif.). 62: 13-25. PMID 23557991 DOI: 10.1016/J.Ymeth.2013.03.026  0.651
2013 Sanchez A, Choubey S, Kondev J. Regulation of noise in gene expression. Annual Review of Biophysics. 42: 469-91. PMID 23527780 DOI: 10.1146/Annurev-Biophys-083012-130401  0.599
2013 Mohapatra L, Eskin J, Goode BL, Kondev J. Length Regulation of Actin Filament Arrays Biophysical Journal. 104: 139a. DOI: 10.1016/J.Bpj.2012.11.794  0.349
2013 Bronk G, Avsaroglu B, Ham J, Haber J, Kondev J. Rabl Organization of Chromosomes in the Yeast Nucleus Biophysical Journal. 104: 582a. DOI: 10.1016/J.Bpj.2012.11.3235  0.321
2012 Garcia HG, Sanchez A, Boedicker JQ, Osborne M, Gelles J, Kondev J, Phillips R. Operator sequence alters gene expression independently of transcription factor occupancy in bacteria. Cell Reports. 2: 150-61. PMID 22840405 DOI: 10.1016/J.Celrep.2012.06.004  0.694
2011 Sanchez A, Osborne ML, Friedman LJ, Kondev J, Gelles J. Mechanism of transcriptional repression at a bacterial promoter by analysis of single molecules. The Embo Journal. 30: 3940-6. PMID 21829165 DOI: 10.1038/Emboj.2011.273  0.723
2011 Sanchez A, Garcia HG, Jones D, Phillips R, Kondev J. Effect of promoter architecture on the cell-to-cell variability in gene expression. Plos Computational Biology. 7: e1001100. PMID 21390269 DOI: 10.1371/Journal.Pcbi.1001100  0.621
2011 Garcia HG, Kondev J, Orme N, Theriot JA, Phillips R. Thermodynamics of biological processes. Methods in Enzymology. 492: 27-59. PMID 21333788 DOI: 10.1016/B978-0-12-381268-1.00014-8  0.326
2010 Garcia HG, Sanchez A, Kuhlman T, Kondev J, Phillips R. Transcription by the numbers redux: experiments and calculations that surprise. Trends in Cell Biology. 20: 723-33. PMID 20801657 DOI: 10.1016/J.Tcb.2010.07.002  0.641
2010 Wiggins PA, Cheveralls K, Kondev J. Strong Intra-Nucleoid Interactions Organize the E. Coli Chromosome into a Nucleoid Filament Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.3613  0.319
2009 Reeves D, Cheveralls K, Kondev J. Biochemistry on a Leash: Confinement as a Regulatory Mechanism for Bimolecular Reaction Rates Biophysical Journal. 96. DOI: 10.1016/J.Bpj.2008.12.3121  0.327
2009 Sanchez A, Hol F, Kondev J, Wiggins P. Exploiting stochastic gene expression to infer promoter regulatory mechanisms: The Moment Analysis Method Biophysical Journal. 96: 305a. DOI: 10.1016/J.Bpj.2008.12.1522  0.625
2009 Wiggins P, Martin J, Kondev J. Chromatin Organization in E.coli Biophysical Journal. 96. DOI: 10.1016/J.Bpj.2008.12.1006  0.302
2008 Sánchez A, Kondev J. Transcriptional control of noise in gene expression. Proceedings of the National Academy of Sciences of the United States of America. 105: 5081-6. PMID 18353986 DOI: 10.1073/Pnas.0707904105  0.61
2007 Garcia HG, Grayson P, Han L, Inamdar M, Kondev J, Nelson PC, Phillips R, Widom J, Wiggins PA. Biological consequences of tightly bent DNA: the other life of a macromolecular celebrity. Biopolymers. 85: 115-30. PMID 17103419 DOI: 10.1002/Bip.20627  0.3
2005 Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Kuhlman T, Phillips R. Transcriptional regulation by the numbers: applications. Current Opinion in Genetics & Development. 15: 125-35. PMID 15797195 DOI: 10.1016/J.Gde.2005.02.006  0.737
2005 Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Phillips R. Transcriptional regulation by the numbers: models. Current Opinion in Genetics & Development. 15: 116-24. PMID 15797194 DOI: 10.1016/J.Gde.2005.02.007  0.753
2004 Majumdar SN, Das D, Kondev J, Chakraborty B. Landau-like theory of glassy dynamics. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 70: 060501. PMID 15697333 DOI: 10.1103/Physreve.70.060501  0.304
2004 Sandler N, Maei HR, Kondev J. Correlated quantum percolation in the lowest Landau level Physical Review B - Condensed Matter and Materials Physics. 70: 045309-1-045309-13. DOI: 10.1103/Physrevb.70.045309  0.734
2003 Purohit PK, Kondev J, Phillips R. Mechanics of DNA packaging in viruses. Proceedings of the National Academy of Sciences of the United States of America. 100: 3173-8. PMID 12629206 DOI: 10.1073/Pnas.0737893100  0.305
2003 Sandler N, Maei HR, Kondev J. Quantum and classical localization in the lowest Landau level Physical Review B - Condensed Matter and Materials Physics. 68: 2053151-2053154. DOI: 10.1103/Physrevb.68.205315  0.727
2003 Chakraborty B, Das D, Kondev J. Jamming in a model glass: Interplay of dynamics and thermodynamics Physica a: Statistical Mechanics and Its Applications. 318: 23-29. DOI: 10.1016/S0378-4371(02)01397-3  0.322
2002 Chakraborty B, Das D, Kondev J. Topological jamming and the glass transition in a frustrated system. The European Physical Journal. E, Soft Matter. 9: 227-32. PMID 15010912 DOI: 10.1140/Epje/I2002-10071-7  0.3
2000 Kondev J, Henley CL, Salinas DG. Nonlinear measures for characterizing rough surface morphologies Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 61: 104-25. PMID 11046246 DOI: 10.1103/Physreve.61.104  0.553
1998 Jacobsen JL, Kondev J. Field theory of compact polymers on the square lattice Nuclear Physics B. 532: 635-688. DOI: 10.1016/S0550-3213(98)00571-9  0.307
1997 Kondev J. Liouville field theory of fluctuating loops Physical Review Letters. 78: 4320-4323. DOI: 10.1103/Physrevlett.78.4320  0.303
1996 Kondev J, De Gier J, Nienhuis B. Operator spectrum and exact exponents of the fully packed loop model Journal of Physics a: Mathematical and General. 29: 6489-6504. DOI: 10.1088/0305-4470/29/20/007  0.304
1996 Kondev J, Henley CL. Kac-Moody symmetries of critical ground states Nuclear Physics B. 464: 540-575. DOI: 10.1016/0550-3213(96)00064-8  0.572
1995 Kondev J, Henley CL. Geometrical exponents of contour loops on random Gaussian surfaces. Physical Review Letters. 74: 4580-4583. PMID 10058546 DOI: 10.1103/Physrevlett.74.4580  0.557
1995 Kondev J, Henley CL. Four-coloring model on the square lattice: A critical ground state. Physical Review. B, Condensed Matter. 52: 6628-6639. PMID 9981892 DOI: 10.1103/Physrevb.52.6628  0.551
1994 Kondev J, Henley CL. Conformal charge and exact exponents in the n=2 fully packed loop model. Physical Review Letters. 73: 2786. PMID 10057193 DOI: 10.1103/Physrevlett.73.2786  0.538
Low-probability matches (unlikely to be authored by this person)
1997 Kondev J, Marston JB. Supersymmetry and localization in the quantum hall effect Nuclear Physics B. 497: 639-657. DOI: 10.1016/S0550-3213(97)00300-3  0.3
2003 Das D, Kondev J, Chakraborty B. Activated dynamics at a non-disordered critical point Europhysics Letters. 61: 506-512. DOI: 10.1209/Epl/I2003-00158-3  0.299
2003 Purohit PK, Kondev J, Phillips R. Force steps during viral DNA packaging? Journal of the Mechanics and Physics of Solids. 51: 2239-2257. DOI: 10.1016/J.Jmps.2003.09.016  0.297
2020 Li K, Bronk G, Kondev J, Haber JE. Yeast ATM and ATR kinases use different mechanisms to spread histone H2A phosphorylation around a DNA double-strand break. Proceedings of the National Academy of Sciences of the United States of America. 117: 21354-21363. PMID 32817543 DOI: 10.1073/Pnas.2002126117  0.295
2005 Purohit PK, Inamdar MM, Grayson PD, Squires TM, Kondev J, Phillips R. Forces during bacteriophage DNA packaging and ejection. Biophysical Journal. 88: 851-66. PMID 15556983 DOI: 10.1529/Biophysj.104.047134  0.294
2010 Wiggins PA, Cheveralls KC, Martin JS, Lintner R, Kondev J. Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament. Proceedings of the National Academy of Sciences of the United States of America. 107: 4991-5. PMID 20194778 DOI: 10.1073/pnas.0912062107  0.289
1997 Kondev J. Loop models, marginally rough interfaces, and the coulomb gas International Journal of Modern Physics B. 11: 153-159. DOI: 10.1142/S0217979297000204  0.289
2004 Jacobsen JL, Kondev J. Conformal field theory of the Flory model of polymer melting. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 69: 066108. PMID 15244668 DOI: 10.1103/Physreve.69.066108  0.289
2005 Das D, Farrell G, Kondev J, Chakraborty B. Critical dynamics of dimers: implications for the glass transition. The Journal of Physical Chemistry. B. 109: 21413-8. PMID 16853778 DOI: 10.1021/Jp051636L  0.288
2011 Coïc E, Martin J, Ryu T, Tay SY, Kondev J, Haber JE. Dynamics of homology searching during gene conversion in Saccharomyces cerevisiae revealed by donor competition. Genetics. 189: 1225-33. PMID 21954161 DOI: 10.1534/Genetics.111.132738  0.286
2014 Kondev J. Bacterial decision making Physics Today. 67: 31-36. DOI: 10.1063/PT.3.2276  0.283
2011 Avsaroglu B, Gordon-Messer S, Haber JE, Kondev J. Polymer Model of the Spatial Organization of Interphase Chromosomes in Yeast Biophysical Journal. 100: 68a. DOI: 10.1016/J.Bpj.2010.12.573  0.282
2004 Jacobsen JL, Kondev J. Continuous melting of compact polymers. Physical Review Letters. 92: 210601. PMID 15245269 DOI: 10.1103/Physrevlett.92.210601  0.277
2014 Av?aro?lu B, Bronk G, Gordon-Messer S, Ham J, Bressan DA, Haber JE, Kondev J. Effect of chromosome tethering on nuclear organization in yeast. Plos One. 9: e102474. PMID 25020108 DOI: 10.1371/Journal.Pone.0102474  0.27
2001 Kondev J, Huber G. Critical geometry of two-dimensional passive scalar turbulence. Physical Review Letters. 86: 5890-3. PMID 11415387 DOI: 10.1103/Physrevlett.86.5890  0.269
2016 Avşaroğlu B, Bronk G, Li K, Haber JE, Kondev J. Chromosome-refolding model of mating-type switching in yeast. Proceedings of the National Academy of Sciences of the United States of America. PMID 27791086 DOI: 10.1073/Pnas.1607103113  0.269
2009 Gordon-Messer S, Martin JS, Kondev J, Haber JE. Using Polymer Models To Understand The Structure Of Chromosome III In Budding Yeast Biophysical Journal. 96: 348a. DOI: 10.1016/J.Bpj.2008.12.1750  0.266
1998 Kondev J, Jacobsen JL. Conformational entropy of compact polymers Physical Review Letters. 81: 2922-2925. DOI: 10.1103/Physrevlett.81.2922  0.264
2011 Reeves D, Cheveralls K, Kondev J. Regulation of biochemical reaction rates by flexible tethers. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 84: 021914. PMID 21929027 DOI: 10.1103/PhysRevE.84.021914  0.259
2020 Levien E, Kondev J, Amir A. The interplay of phenotypic variability and fitness in finite microbial populations. Journal of the Royal Society, Interface. 17: 20190827. PMID 32396808 DOI: 10.1098/rsif.2019.0827  0.258
2009 Schmit JD, Kamber E, Kondev J. Lattice model of diffusion-limited bimolecular chemical reactions in confined environments. Physical Review Letters. 102: 218302. PMID 19519142 DOI: 10.1103/Physrevlett.102.218302  0.257
2007 Hori Y, Prasad A, Kondev J. Stretching short biopolymers by fields and forces. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 75: 041904. PMID 17500918 DOI: 10.1103/Physreve.75.041904  0.253
1998 Zeng C, Kondev J, McNamara D, Middleton AA. Statistical topography of glassy interfaces Physical Review Letters. 80: 109-112. DOI: 10.1103/Physrevlett.80.109  0.251
2005 Prasad A, Hori Y, Kondev J. Elasticity of semiflexible polymers in two dimensions. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 041918. PMID 16383431 DOI: 10.1103/Physreve.72.041918  0.247
2019 Fai TG, Mohapatra L, Kar P, Kondev J, Amir A. Author response: Length regulation of multiple flagella that self-assemble from a shared pool of components Elife. DOI: 10.7554/Elife.42599.026  0.246
2019 McInally SG, Kondev J, Dawson SC. Author response: Length-dependent disassembly maintains four different flagellar lengths in Giardia Elife. DOI: 10.7554/Elife.48694.Sa2  0.24
2006 Oberdorf R, Ferguson A, Jacobsen JL, Kondev J. Secondary structures in long compact polymers. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 74: 051801. PMID 17279930 DOI: 10.1103/Physreve.74.051801  0.239
2008 Reeves D, Ursell T, Sens P, Kondev J, Phillips R. Membrane mechanics as a probe of ion-channel gating mechanisms. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 78: 041901. PMID 18999449 DOI: 10.1103/Physreve.78.041901  0.225
1999 Jacobsen JL, Kondev J. Transition from the compact to the dense phase of two-dimensional polymers Journal of Statistical Physics. 96: 21-48. DOI: 10.1023/A:1004512230458  0.223
2010 Phillips R, Kondev J. Biochemistry on a Leash Annual Review of Biophysics. 40: 110301095232019. DOI: 10.1146/Annurev-Biophys-042910-155230  0.215
2007 Prasad A, Kondev J, Stone HA. Drift in supported membranes Physics of Fluids. 19. DOI: 10.1063/1.2805843  0.215
2009 Peterson EL, Kondev J, Theriot JA, Phillips R. Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment. Bioinformatics (Oxford, England). 25: 1356-62. PMID 19351620 DOI: 10.1093/bioinformatics/btp164  0.211
2019 Kondev J. Decision letter: A minimal self-organisation model of the Golgi apparatus Elife. DOI: 10.7554/Elife.47318.Sa1  0.211
2020 Datta A, Harbage D, Kondev J. Control of filament length by a depolymerizing gradient. Plos Computational Biology. 16: e1008440. PMID 33275598 DOI: 10.1371/journal.pcbi.1008440  0.205
2023 McInally SG, Reading AJB, Rosario A, Jelenkovic PR, Goode BL, Kondev J. Length control emerges from cytoskeletal network geometry. Biorxiv : the Preprint Server For Biology. PMID 38076874 DOI: 10.1101/2023.11.28.569063  0.201
2018 Bauer G, Fakhri N, Kicheva A, Kondev J, Kruse K, Noji H, Riveline D, Saunders TE, Thattai M, Wieschaus E. The Science of Living Matter for Tomorrow. Cell Systems. 6: 400-402. PMID 29698645 DOI: 10.1016/J.Cels.2018.04.003  0.188
2021 Bauer D, Ishikawa H, Wemmer KA, Hendel NL, Kondev J, Marshall WF. Analysis of biological noise in the flagellar length control system. Iscience. 24: 102354. PMID 33898946 DOI: 10.1016/j.isci.2021.102354  0.175
2021 McInally SG, Kondev J, Goode BL. Scaling of subcellular actin structures with cell length through decelerated growth. Elife. 10. PMID 34114567 DOI: 10.7554/eLife.68424  0.163
2022 McInally SG, Kondev J, Goode BL. Quantitative Analysis of Actin Cable Length in Yeast. Bio-Protocol. 12: e4402. PMID 35800466 DOI: 10.21769/BioProtoc.4402  0.162
2022 Datta A, Ghosh S, Kondev J. How to assemble a scale-invariant gradient. Elife. 11. PMID 35311649 DOI: 10.7554/eLife.71365  0.159
2021 Levien E, Min J, Kondev J, Amir A. Non-genetic variability in microbial populations: survival strategy or nuisance? Reports On Progress in Physics. Physical Society (Great Britain). 84. PMID 34825896 DOI: 10.1088/1361-6633/ac2c92  0.138
2024 Shiff CE, Kondev J, Mohapatra L. Ultrasensitivity of microtubule severing due to damage repair. Iscience. 27: 108874. PMID 38327774 DOI: 10.1016/j.isci.2024.108874  0.12
2021 Belliveau NM, Chure G, Hueschen CL, Garcia HG, Kondev J, Fisher DS, Theriot JA, Phillips R. Fundamental limits on the rate of bacterial growth and their influence on proteomic composition. Cell Systems. PMID 34214468 DOI: 10.1016/j.cels.2021.06.002  0.118
2005 Phillips R, Purohit PK, Kondev J. Mechanics of biological nanotechnology Nanotribology and Nanomechanics: An Introduction. 693-729. DOI: 10.1007/3-540-28248-3_14  0.104
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