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Publications:  Prof David Clayton

George JM, Bell ZW, Condliffe D, Dohrer K, Abaurrea T, Spencer K, Leitão A, Gahr M et al.(2019). Acute social isolation alters neurogenomic state in songbird forebrain. Proc Natl Acad Sci U S A
Clayton DF, Anreiter I, Aristizabal M, Frankland PW, Binder EB, Citri A(2019). The role of the genome in experience-dependent plasticity: Extending the analogy of the genomic action potential. Proc Natl Acad Sci U S A
Lansverk AL, Schroeder KM, London SE, Griffith SC, Clayton DF, Balakrishnan CN(2019). The variability of song variability in zebra finch (Taeniopygia guttata) populations. Royal Society Open Science vol. 6, (5)
Bell ZW, Lovell P, Mello CV, Yip PK, George JM, Clayton DF(2019). Urotensin-related gene transcripts mark developmental emergence of the male forebrain vocal control system in songbirds. Sci Rep vol. 9, (1)
Lansverk A, London S, Griffith S, Clayton D, Balakrishnan C(2018). The variability of song variability in wild and domesticated zebra finches Taeniopygia guttata.
Bukhari SA, Saul MC, Seward CH, Zhang H, Bensky M, James N, Zhao SD, Chandrasekaran S et al.(2017). Temporal dynamics of neurogenomic plasticity in response to social interactions in male threespined sticklebacks. PLOS Genetics vol. 13, (7) e1006840-e1006840.
Griffith SC, Crino OL, Andrew SC, Nomano FY, Adkins-Regan E, Alonso-Alvarez C, Bailey IE, Bittner SS et al.(2016). Variation in Reproductive Success Across Captive Populations: Methodological Differences, Potential Biases and Opportunities. Ethology vol. 123, (1) 1-29.
STOWELL DF, Gill LF, Clayton D(2016). Detailed temporal structure of communication networks in groups of songbirds. Journal of the Royal Society Interface vol. 13, (119)
Stowell D, Clayton D (2015). Acoustic event detection for multiple overlapping similar sources. 2015 IEEE Workshop on Applications of Signal Processing to Audio and Acoustics, WASPAA 2015.
Mello CV, Clayton DF(2015). The opportunities and challenges of large-scale molecular approaches to songbird neurobiology. Neurosci Biobehav Rev vol. 50, 70-76.
Clayton DF, London SE(2014). Advancing avian behavioral neuroendocrinology through genomics. Front Neuroendocrinol vol. 35, (1) 58-71.
Balakrishnan CN, Mukai M, Gonser RA, Wingfield JC, London SE, Tuttle EM, Clayton DF(2014). Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior. PeerJ vol. 2,
Lin Y-C, Balakrishnan CN, Clayton DF(2014). Functional genomic analysis and neuroanatomical localization of miR-2954, a song-responsive sex-linked microRNA in the zebra finch. Front Neurosci vol. 8,
Clayton DF(2013). Genomics of memory and learning in songbirds. Annual Review of Genomics and Human Genetics
Balakrishnan CN, Chapus C, Brewer MS, Clayton DF(2013). Brain transcriptome of the violet-eared waxbill Uraeginthus granatina and recent evolution in the songbird genome. Open Biology vol. 3, (SEP)
Kültz D, Clayton DF, Robinson GE, Albertson C, Carey HV, Cummings ME, Dewar K, Edwards SV et al.(2013). New frontiers for organismal biology. BioScience vol. 63, (6) 464-471.
Lee JV, Maclin EL, Low KA, Gratton G, Fabiani M, Clayton DF(2013). Noninvasive diffusive optical imaging of the auditory response to birdsong in the zebra finch. J Comp Physiol A Neuroethol Sens Neural Behav Physiol vol. 199, (3) 227-238.
Balakrishnan CN, Lin Y-C, London SE, Clayton DF(2012). RNA-seq transcriptome analysis of male and female zebra finch cell lines. Genomics vol. 100, (6) 363-369.
Stevenson TJ, Replogle K, Drnevich J, Clayton DF, Ball GF(2012). High throughput analysis reveals dissociable gene expression profiles in two independent neural systems involved in the regulation of social behavior. BMC Neuroscience vol. 13, (1)
Drnevich J, Replogle KL, Lovell P, Hahn TP, Johnson F, Mast TG, Nordeen E, Nordeen K et al.(2012). Impact of experience-dependent and -independent factors on gene expression in songbird brain. Proc Natl Acad Sci U S A vol. 109 Suppl 2, 17245-17252.
Thompson CK, Meitzen J, Replogle K, Drnevich J, Lent KL, Wissman AM, Farin FM, Bammler TK et al.(2012). Seasonal changes in patterns of gene expression in avian song control brain regions. PLoS ONE vol. 7, (4)
Amaya KR, Sweedler JV, Clayton DF(2011). Small molecule analysis and imaging of fatty acids in the zebra finch song system using time-of-flight-secondary ion mass spectrometry. J Neurochem vol. 118, (4) 499-511.
Janes DE, Chapus C, Gondo Y, Clayton DF, Sinha S, Blatti CA, Organ CL, Fujita MK et al.(2011). Reptiles and mammals have differentially retained long conserved noncoding sequences from the amniote ancestor. Genome Biology and Evolution vol. 3, (1) 102-113.
Gunaratne PH, Lin YC, Benham AL, Drnevich J, Coarfa C, Tennakoon JB, Creighton CJ, Kim JH et al.(2011). Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain. BMC Genomics vol. 12,
Balakrishnan CN, Edwards SV, Clayton DF(2010). The Zebra Finch genome and avian genomics in the wild. Emu vol. 110, (3) 233-241.
London SE, Clayton DF(2010). The neurobiology of Zebra Finch song: Insights from gene expression studies. Emu vol. 110, (3) 219-232.
Nam K, Mugal C, Nabholz B, Schielzeth H, Wolf JBW, Backström N, Künstner A, Balakrishnan CN et al.(2010). Molecular evolution of genes in avian genomes. Genome Biology vol. 11, (6)
London SE, Clayton DF(2010). Genomic and neural analysis of the estradiol-synthetic pathway in the zebra finch. BMC Neurosci vol. 11,
Itoh Y, Replogle K, Kim YH, Wade J, Clayton DF, Arnold AP(2010). Sex bias and dosage compensation in the zebra finch versus chicken genomes: General and specialized patterns among birds. Genome Research vol. 20, (4) 512-518.
Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S et al.(2010). The genome of a songbird. Nature vol. 464, (7289) 757-762.
Xie F, London SE, Southey BR, Annangudi SP, Amare A, Rodriguez-Zas SL, Clayton DF, Sweedler JV(2010). The zebra finch neuropeptidome: prediction, detection and expression. BMC Biol vol. 8,
Mukai M, Replogle K, Drnevich J, Wang G, Wacker D, Band M, Clayton DF, Wingfield JC(2009). Seasonal differences of gene expression profiles in song sparrow (melospiza melodia) hypothalamus in relation to territorial aggression. PLoS ONE vol. 4, (12)
Clayton DF, Balakrishnan CN, London SE(2009). Integrating genomes, brain and behavior in the study of songbirds. Curr Biol vol. 19, (18) R865-R873.
Dong S, Clayton DF(2009). Habituation in songbirds. Neurobiol Learn Mem vol. 92, (2) 183-188.
Rankin CH, Abrams T, Barry RJ, Bhatnagar S, Clayton DF, Colombo J, Coppola G, Geyer MA et al. (2009). Habituation revisited: An updated and revised description of the behavioral characteristics of habituation. NEUROBIOLOGY OF LEARNING AND MEMORY. vol. 92, 135-138.
Dong S, Replogle KL, Hasadsri L, Imai BS, Yau PM, Rodriguez-Zas S, Southey BR, Sweedler JV et al.(2009). Discrete molecular states in the brain accompany changing responses to a vocal signal. Proc Natl Acad Sci U S A vol. 106, (27) 11364-11369.
London SE, Dong S, Replogle K, Clayton DF(2009). Developmental shifts in gene expression in the auditory forebrain during the sensitive period for song learning. Dev Neurobiol vol. 69, (7) 437-450.
Tomaszycki ML, Peabody C, Replogle K, Clayton DF, Tempelman RJ, Wade J(2009). Sexual differentiation of the zebra finch song system: Potential roles for sex chromosome genes. BMC Neuroscience vol. 10,
Clayton DF, George JM, Mello CV, Siepka SM(2009). Conservation and expression of IQ-domain-containing calpacitin gene products (neuromodulin/GAP-43, neurogranin/RC3) in the adult and developing oscine song control system. Dev Neurobiol vol. 69, (2-3) 124-140.
Mukai M, Replogle K, Wang G, Wacker D, Clayton D, Wingfield JC(2009). Effect of season and territorial aggression on hypothalamic gene expression in song sparrows. INTEGRATIVE AND COMPARATIVE BIOLOGY vol. 49, E120-E120.
Winograd C, Clayton D, Ceman S(2008). Expression of fragile X mental retardation protein within the vocal control system of developing and adult male zebra finches. Neuroscience vol. 157, (1) 132-142.
Robinson GE, Fernald RD, Clayton DF(2008). Genes and social behavior. Science vol. 322, (5903) 896-900.
Lovell PV, Clayton DF, Replogle KL, Mello CV(2008). Birdsong "transcriptomics": Neurochemical specializations of the oscine song system. PLoS ONE vol. 3, (10)
Dong S, Clayton DF(2008). Partial dissociation of molecular and behavioral measures of song habituation in adult zebra finches. Genes Brain Behav vol. 7, (7) 802-809.
Axelsson E, Hultin-Rosenberg L, Brandström M, Zwahlén M, Clayton DF, Ellegren H(2008). Natural selection in avian protein-coding genes expressed in brain. Molecular Ecology vol. 17, (12) 3008-3017.
London SE, Clayton DF(2008). Functional identification of sensory mechanisms required for developmental song learning. Nat Neurosci vol. 11, (5) 579-586.
Replogle K, Arnold AP, Ball GF, Band M, Bensch S, Brenowitz EA, Dong S, Drnevich J et al.(2008). The Songbird Neurogenomics (SoNG) Initiative: community-based tools and strategies for study of brain gene function and evolution. BMC Genomics vol. 9,
Naurin S, Bensch S, Hansson B, Johansson T, Clayton DF, Albrekt AS, Von Schantz T, Hasselquist D(2008). A microarray for large-scale genomic and transcriptional analyses of the zebra finch (Taeniopygia guttata) and other passerines. Molecular Ecology Resources vol. 8, (2) 275-281.
Naurin S, Bensch S, Hansson B, Johansson T, Clayton DF, Albrekt A-S, VON Schantz T, Hasselquist D(2008). TECHNICAL ADVANCES: A microarray for large-scale genomic and transcriptional analyses of the zebra finch (Taeniopygia guttata) and other passerines. Mol Ecol Resour vol. 8, (2) 275-281.
Clayton DF, Arnold AP(2008). Studies of songbirds in the age of genetics: What to expect from genomic approaches in the next 20 years. Neuroscience of Birdsong, Editors: Zeigler, HP, Marler, P, Cambridge University Press (Cambridge),
Clayton DF(2007). Molecular neurobiology of bird song. 373-417.
Sloley S, Smith S, Gandhi S, Caldwell Busby JA, London S, Luksch H, Clayton DF, Bhattacharya SK(2007). Proteomic analyses of zebra finch optic tectum and comparative histochemistry. Journal of Proteome Research vol. 6, (6) 2341-2350.
Itoh Y, Melamed E, Yang X, Kampf K, Wang S, Yehya N, Van Nas A, Replogle K et al.(2007). Dosage compensation is less effective in birds than in mammals. Journal of Biology vol. 6, (1)
Sloley S, Smith S, Algeciras M, Cavett V, Caldwell Busby JA, London S, Clayton DF, Bhattacharya SK(2007). Proteomic analyses of songbird (Zebra finch; Taeniopygia guttata) retina. Journal of Proteome Research vol. 6, (3) 1093-1100.
Amaya KR, Monroe EB, Sweedler JV, Clayton DF(2007). Lipid imaging in the zebra finch brain with secondary ion mass spectrometry. International Journal of Mass Spectrometry vol. 260, (2-3) 121-127.
Huesmann GR, Clayton DF(2006). Dynamic role of postsynaptic caspase-3 and BIRC4 in zebra finch song-response habituation. Neuron vol. 52, (6) 1061-1072.
Wade J, Peabody C, Coussens P, Tempelman RJ, Clayton DF, Liu L, Arnold AP, Agate R(2005). A cDNA microarray from the telencephalon of juvenile male and female zebra finches (vol 138, pg 199, 2004). JOURNAL OF NEUROSCIENCE METHODS vol. 142, (2) 327-327.
Clayton DF, Arnold AP, Warren W, Dodgson J (2005). Proposal for Construction of a Physical Map of the Genome of the Zebra Finch (Taeniopygia guttata).
Clayton DF, Arnold AP, Warren W, Jarvis E, Burt DW, Ellegren H (2005). Proposal to Sequence the Genome of the Zebra Finch (Taeniopygia guttata).
Wade J, Peabody C, Coussens P, Tempelman RJ, Clayton DF, Liu L, Arnold AP, Agate R(2004). A cDNA microarray from the telencephalon of juvenile male and female zebra finches. Journal of Neuroscience Methods vol. 138, (1-2) 199-206.
Kruse AA, Stripling R, Clayton DF(2004). Context-specific habituation of the zenk gene response to song in adult zebra finches. Neurobiol Learn Mem vol. 82, (2) 99-108.
Cheng H-Y, Clayton DF(2004). Activation and habituation of extracellular signal-regulated kinase phosphorylation in zebra finch auditory forebrain during song presentation. J Neurosci vol. 24, (34) 7503-7513.
Clayton DF(2004). Songbird genomics: methods, mechanisms, opportunities, and pitfalls. Ann N Y Acad Sci vol. 1016, 45-60.
Clayton DF(2003). A memoir on memory. Cell vol. 111,
Stripling R, Milewski L, Kruse AA, Clayton DF(2003). Rapidly learned song-discrimination without behavioral reinforcement in adult male zebra finches (Taeniopygia guttata). Neurobiol Learn Mem vol. 79, (1) 41-50.
Park KHJ, Clayton DF(2002). Influence of restraint and acute isolation on the selectivity of the adult zebra finch zenk gene response to acoustic stimuli. Behav Brain Res vol. 136, (1) 185-191.
Arnold AP, Clayton DF (2002). Proposal for Construction of a BAC library of the Genome of the Zebra Finch (Taeniopygia guttata).
Perrin RJ, Woods WS, Clayton DF, George JM(2001). Exposure to long chain polyunsaturated fatty acids triggers rapid multimerization of synucleins. J Biol Chem vol. 276, (45) 41958-41962.
Payton JE, Perrin RJ, Clayton DF, George JM(2001). Protein-protein interactions of alpha-synuclein in brain homogenates and transfected cells. Brain Res Mol Brain Res vol. 95, (1-2) 138-145.
Stripling R, Kruse AA, Clayton DF(2001). Development of song responses in the zebra finch caudomedial neostriatum: role of genomic and electrophysiological activities. J Neurobiol vol. 48, (3) 163-180.
Hartman VN, Miller MA, Clayton DF, Liu WC, Kroodsma DE, Brenowitz EA(2001). Testosterone regulates α-synuclein mRNA in the avian song system. NeuroReport vol. 12, (5) 943-946.
Holloway CC, Clayton DF(2001). Estrogen synthesis in the male brain triggers development of the avian song control pathway in vitro. Nat Neurosci vol. 4, (2) 170-175.
Perrin RJ, Woods WS, Clayton DF, George JM(2000). Interaction of human alpha-Synuclein and Parkinson's disease variants with phospholipids. Structural analysis using site-directed mutagenesis. J Biol Chem vol. 275, (44) 34393-34398.
Kruse AA, Stripling R, Clayton DF(2000). Minimal experience required for immediate-early gene induction in zebra finch neostriatum. Neurobiol Learn Mem vol. 74, (3) 179-184.
Clayton DF(2000). The genomic action potential. Neurobiol Learn Mem vol. 74, (3) 185-216.
Clayton DF(2000). Neural basis of avian song learning and perception. Brain, Perception, Memory: Advances in Cognitive Neuroscience, Editors: Bolhuis, J, Oxford Univ. Press (London),
Clayton DF, George JM(1999). Synucleins in synaptic plasticity and neurodegenerative disorders. J Neurosci Res vol. 58, (1) 120-129.
Clayton DF, George JM(1998). The synucleins: a family of proteins involved in synaptic function, plasticity, neurodegeneration and disease. Trends Neurosci vol. 21, (6) 249-254.
Irizarry MC, Growdon W, Gomez-Isla T, Newell K, Ingraham A, George J, Clayton D, Hyman BT(1998). alpha-synuclein immunoreactivity in Lewy bodies and abnormal neurites in Parkinson's disease and dementia with Lewy body brain. JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY vol. 57, (5) 509-509.
Davidson WS, Jonas A, Clayton DF, George JM(1998). Stabilization of alpha-synuclein secondary structure upon binding to synthetic membranes. J Biol Chem vol. 273, (16) 9443-9449.
Irizarry MC, Growdon W, Gomez-Isla T, Newell K, George JM, Clayton DF, Hyman BT(1998). Nigral and cortical Lewy bodies and dystrophic nigral neurites in Parkinson's disease and cortical Lewy body disease contain α-synuclein immunoreactivity. Journal of Neuropathology and Experimental Neurology vol. 57, (4) 334-337.
George JM, Clayton DF(1998). Songbirds, synelfin and neurodegenerative disease. Neuroscience News vol. 1, (2) 12-17.
Jin H, Clayton DF(1997). Localized changes in immediate-early gene regulation during sensory and motor learning in zebra finches. Neuron vol. 19, (5) 1049-1059.
Clayton DF(1997). Role of gene regulation in song circuit development and song learning. J Neurobiol vol. 33, (5) 549-571.
Jin H, Clayton DF(1997). Synelfin regulation during the critical period for song learning in normal and isolated juvenile zebra finches. Neurobiol Learn Mem vol. 68, (3) 271-284.
Stripling R, Volman SF, Clayton DF(1997). Response modulation in the zebra finch neostriatum: relationship to nuclear gene regulation. J Neurosci vol. 17, (10) 3883-3893.
Withers GS, George JM, Banker GA, Clayton DF(1997). Delayed localization of synelfin (synuclein, NACP) to presynaptic terminals in cultured rat hippocampal neurons. Developmental Brain Research vol. 99, (1) 87-94.
Irizarry MC, Kim TW, Mcnamara M, Tanzi RE, George JM, Clayton DF, Hyman BT(1996). Characterization of the precursor protein of the non-Aβ component of senile plaques (NACP) in the human central nervous system. Journal of Neuropathology and Experimental Neurology vol. 55, (8) 889-895.
George JM, Clayton DF (1996). The non-amyloid-beta component of Alzheimer's disease plaque amyloid: Comparative analysis suggests a normal function as a synaptic plasticizer. NEURODEGENERATIVE DISEASES. 109-112.
Mello C, Nottebohm F, Clayton D(1995). Repeated exposure to one song leads to a rapid and persistent decline in an immediate early gene's response to that song in zebra finch telencephalon. J Neurosci vol. 15, (10) 6919-6925.
Wallace CS, Withers GS, Weiler IJ, George JM, Clayton DF, Greenough WT(1995). Correspondence between sites of NGFI-A induction and sites of morphological plasticity following exposure to environmental complexity. Brain Res Mol Brain Res vol. 32, (2) 211-220.
George JM, Jin H, Woods WS, Clayton DF(1995). Characterization of a novel protein regulated during the critical period for song learning in the zebra finch. Neuron vol. 15, (2) 361-372.
Nastiuk KL, Clayton DF(1995). The canary androgen receptor mRNA is localized in the song control nuclei of the brain and is rapidly regulated by testosterone. J Neurobiol vol. 26, (2) 213-224.
Mello CV, Clayton DF(1995). Differential induction of the ZENK gene in the avian forebrain and song control circuit after metrazole-induced depolarization. J Neurobiol vol. 26, (1) 145-161.
Nastiuk KL, Mello CV, George JM, Clayton DF(1994). Immediate-early gene responses in the avian song control system: cloning and expression analysis of the canary c-jun cDNA. Brain Res Mol Brain Res vol. 27, (2) 299-309.
Mello CV, Clayton DF(1994). Song-induced ZENK gene expression in auditory pathways of songbird brain and its relation to the song control system. Journal of Neuroscience vol. 14, (11 I) 6652-6666.
Mello CV, Clayton DF(1994). Song-induced ZENK gene expression in auditory pathways of songbird brain and its relation to the song control system. J Neurosci vol. 14, (11 Pt 1) 6652-6666.
Nastiuk KL, Clayton DF(1994). Seasonal and tissue-specific regulation of canary androgen receptor messenger ribonucleic acid. Endocrinology vol. 134, (2) 640-649.
Alvarez-Buylla A, Clayton DF(1993). Application of PEG sections for in situ hybridization studies. Polyethylene Glycol as an Embedding Medium for Microscopy and Histochemistry, CRC Press (Boca Raton, FL),
Mello CV, Vicario DS, Clayton DF(1992). Song presentation induces gene expression in the songbird forebrain. Proc Natl Acad Sci U S A vol. 89, (15) 6818-6822.
George JM, Clayton DF(1992). Differential regulation in the avian song control circuit of an mRNA predicting a highly conserved protein related to protein kinase C and the bcr oncogene. Brain Res Mol Brain Res vol. 12, (4) 323-329.
Collum RG, Clayton DF, Alt FW(1991). Structure and expression of canary myc family genes. Molecular and Cellular Biology vol. 11, 1770-1776.
Clayton DF, Huecas M(1990). Forebrain-enriched RNAs of the canary: a population analysis using hybridization kinetics. Brain Res Mol Brain Res vol. 7, (1) 23-30.
Clayton DF, Alvarez-Buylla A(1989). In situ hybridization using PEG-embedded tissue and riboprobes: increased cellular detail coupled with high sensitivity. J Histochem Cytochem vol. 37, (3) 389-393.
Clayton DF, Huecas ME, Sinclair-Thompson EY, Nastiuk KL, Nottebohm F(1988). Probes for rare mRNAs reveal distributed cell subsets in canary brain. Neuron vol. 1, (3) 249-261.
Allegra P, Sterner R, Clayton DF, Allfrey VG(1987). Affinity chromatographic purification of nucleosomes containing transcriptionally active DNA sequences. J Mol Biol vol. 196, (2) 379-388.
Friedman JM, Babiss LE, Clayton DF, Darnell JE(1986). Cellular promoters incorporated into the adenovirus genome: cell specificity of albumin and immunoglobulin expression. Molecular and Cellular Biology vol. 6, 3791-3797.
CLAYTON DF (1985). Coordinated control of liver-specific genes in cultured cells of mice and rats.
Clayton DF, Harrelson AL, Darnell JE(1985). Dependence of liver-specific transcription on tissue organization. Molecular and Cellular Biology vol. 5, (10) 2623-2632.
Narita M, Jefferson DM, Fujita M, Miller EJ, Clayton DF, Rosenberg LC, Reid L(1985). Hormonal and matrix regulation of differentiation in primary liver cultures. Growth and Differentiation of Cells in Defined Environments, Editors: Murakami, H, Yamane, I, Barnes, DW, Mather, JP et al., Springer-Verlag (New York),
Clayton DF, Weiss M, Darnell JE(1985). Liver-specific rna metabolism in hepatoma cells: variations in transcription rates and mrna levels. Molecular and Cellular Biology vol. 5, (10) 2633-2641.
Darnell JE, Clayton DF, Friedman JM, Powell DJ(1985). Notes on tissue-specific gene control. Genetics, Cell Differentiation and Cancer, Academic Press (New York),
Jefferson DM, Clayton DF, Darnell JEJ, Reid LM(1984). Posttranscriptional modulation of gene expression in cultured rat hepatocytes. Mol Cell Biol vol. 4, (9) 1929-1934.
Darnell JE, Salditt-Georgieff ME, Clayton DF, Krauter KS, Citron BA, Powell DJ, Hofer E(1984). Transcriptional control of beta-globin and liver-specific genes in mouse cells. Transfer and Expression of Eukaryotic Genes, Academic Press, Inc (New York),
CLAYTON DF, Darnell Jr JE(1983). Changes in liver-specific compared to common gene transcription during primary culture of mouse hepatocytes. Molecular and Cellular Biology vol. 3, 1552-1561.
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