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Mon Jul 31 15:56:19 2006

Hillier LW, Miller W, Birney E, et al.
Sequence and comparative analysis of the chicken genome
provide unique perspectives on vertebrate evolution
NATURE 432 (7018): 695-716 DEC 9 2004
and the citing papers
Nodes: 203, Authors: 1483, Journals: 94, Outer References: 8307, Words: 911
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Collection span: 2004 - 2006
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#LCRNCRNode / Date / Journal / AuthorLCSGCS
1137140 2005 CYTOGENETIC AND GENOME RESEARCH 109 (4): 415-479
Schmid M; Nanda I; Hoehn H; Schartl M; Haaf T; et al.
Second report on chicken genes and chromosomes 2005
22
2122327 2005 CHROMOSOMA 114 (4): 212-229
Foster HA; Bridger JM
The genome and the nucleus: a marriage made by evolution - Genome organisation and nuclear architecture
01
31223138 2006 CURRENT DRUG METABOLISM 7 (4): 349-365
Reschly EJ; Krasowski MD
Evolution and function of the NR1I nuclear hormone receptor subfamily (VDR, PXR, and CAR) with respect to metabolism of xenobiotics and endogenous compounds
00
41184175 2006 JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 306B (3): 295-316
Kawasaki K; Weiss KM
Evolutionary genetics of vertebrate tissue mineralization: The origin secretory calcium-binding and evolution of the phosphoprotein family
01
5117287 2005 NATURE 437 (7055): 69-87
Mikkelsen TS; Hillier LW; Eichler EE; Zody MC; Jaffe DB; et al.
Initial sequence of the chimpanzee genome and comparison with the human genome
490
601652 2004 NATURE 432 (7018): 695-716
Hillier LW; Miller W; Birney E; Warren W; Hardison RC; et al.
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
202202
711594 2005 ADVANCES IN PARASITOLOGY, VOL 60 60: 285-330
Shirley MW; Smith AL; Tomley FM
The biology of avian Eimeria with an emphasis on their control by vaccination
01
811455 2005 ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS 77 (4): 627-650
Salzano FM
Evolutionary change - patterns and processes
00
9114171 2005 IMMUNOLOGICAL INVESTIGATIONS 34 (3): 295-323
Appenheimer MM; Chen Q; Girard RA; Wang WC; Evans SS
Impact of fever-range thermal stress on lymphocyte-endothelial adhesion and lymphocyte trafficking
01
102140187 2006 MOLECULAR ECOLOGY 15 (5): 1299-1320
Dawson DA; Burke T; Hansson B; Pandhal J; Hale MC; et al.
A predicted microsatellite map of the passerine genome based on chicken-passerine sequence similarity
01
#LCRNCRNode / Date / Journal / AuthorLCSGCS
111135189 2006 NATURE REVIEWS MICROBIOLOGY 4 (4): 283-294
Osterrieder N; Kamil JP; Schumacher D; Tischer BK; Trapp S
Marek's disease virus: from miasma to model
01
121133119 2005 TRENDS IN GENETICS 21 (12): 673-682
Coghlan A; Eichler EE; Oliver SG; Paterson AH; Stein L
Chromosome evolution in eukaryotes: a multi-kingdom perspective
01
13212836 2005 CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY 40 (6): 313-330
Khil PR; Camerini-Otero RD
Molecular features and functional constraints in the evolution of the mammalian X chromosome
00
141126102 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102: 6550-6557
Edwards SV; Kingan SB; Calkins JD; Balakrishnan CN; Jennings WB; et al.
Speciation in birds: Genes, geography, and sexual selection
05
151124109 2005 PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 272 (1567): 979-992
Edwards SV; Jennings WB; Shedlock AM
Phylogenetics of modern birds in the era of genomics
22
16112183 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (11): 2275-2284
Blair JE; Hedges SB
Molecular phylogeny and divergence times of deuterostome animals
07
17411989 2005 NATURE 438 (7069): 803-819
Lindblad-Toh K; Wade CM; Mikkelsen TS; Karlsson EK; Jaffe DB; et al.
Genome sequence, comparative analysis and haplotype structure of the domestic dog
329
18211713 2005 ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS 6: 381-406
Giallourakis C; Henson C; Reich M; Xie XH; Mootha VK
Disease gene discovery through integrative genomics
01
19111194 2005 NATURE REVIEWS GENETICS 6 (9): 699-708
Gregory TR
Synergy between sequence and size in large-scale genomics
01
201110131 2006 BMC GENOMICS 7: Art. No. 83
Chakravarti R; Adams JC
Comparative genomics of the syndecans defines an ancestral genomic context associated with matrilins in vertebrates
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
211105135 2006 CELLULAR AND MOLECULAR LIFE SCIENCES 63 (10): 1125-1140
Cruciani V; Mikalsen SO
The vertebrate connexin family
00
22110359 2005 GENOME RESEARCH 15 (8): 1051-1060
King DC; Taylor J; Elnitski L; Chiaromonte F; Miller W; et al.
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences
06
23210395 2005 NEURON 48 (3): 455-464
Scott K
Taste recognition: Food for thought
02
24110212 2005 ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS 6: 143-164
Stone EA; Cooper GM; Sidow A
Trade-offs in detecting evolutionarily constrained sequence by comparative genomics
13
25199173 2006 JOURNAL OF BIOMEDICAL INFORMATICS 39 (1): 51-61
Kosiol C; Bofkin L; Whelan S
Phylogenetics by likelihood: Evolutionary modeling as a tool for understanding the genome
01
2619367 2005 GROWTH FACTORS 23 (4): 263-272
Clump DA; Qazi IH; Sudol M; Flynn DC
c-Yes response to growth factor activation
00
2749258 2005 GENOME RESEARCH 15 (8): 1034-1050
Siepel A; Bejerano G; Pedersen JS; Hinrichs AS; Hou MM; et al.
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
333
28192179 2006 JOURNAL OF MOLECULAR EVOLUTION 62 (5): 630-644
Piskurek O; Austin CC; Okada N
Sauria SINEs: Novel short interspersed retroposable elements that are widespread in reptile genomes
00
29191129 2006 BMC GENOMICS 7: Art. No. 20
Steinke D; Salzburger W; Braasch I; Meyer A
Many genes in fish have species-specific asymmetric rates of molecular evolution
00
30190203 2006 VETERINARY RESEARCH 37 (3): 311-324
Reese S; Dalamani G; Kaspers B
The avian lung-associated immune system: a review
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
3118615 2005 AUSTRALIAN JOURNAL OF EXPERIMENTAL AGRICULTURE 45 (7-8): 749-756
Moore RJ; Doran TJ; Wise TG; Riddell S; Granger K; et al.
Chicken functional genomics: an overview
00
32284110 2005 PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 272 (1578): 2289-2298
Hansson B; Akesson M; Slate J; Pemberton JM
Linkage mapping reveals sex-dimorphic map distances in a passerine bird
00
33182118 2005 TRENDS IN GENETICS 21 (10): 573-581
Mitreva M; Blaxter ML; Bird DM; McCarter JP
Comparative genomics of nematodes
05
34181172 2006 JOURNAL OF BIOLOGICAL CHEMISTRY 281 (3): 1698-1713
Odom EW; Vasta GR
Characterization of a binary tandem domain F-type lectin from striped bass (Morone saxatilis)
01
3517714 2005 ANNUAL REVIEW OF MICROBIOLOGY 59: 191-209
Snel B; Huynen MA; Dutilh BE
Genome trees and the nature of genome evolution
06
3617749 2005 GENE 359: 1-17
Edelstein LC; Collins T
The SCAN domain family of zinc finger transcription
00
37275132 2006 BMC NEUROSCIENCE 7: Art. No. 12
Scholz B; Kultima K; Mattsson A; Axelsson J; Brunstrom B; et al.
Sex-dependent gene expression in early brain development of chicken embryos
00
38175185 2006 MOLECULAR BIOLOGY AND EVOLUTION 23 (6): 1203-1216
Webster MT; Axelsson E; Ellegren H
Strong regional biases in nucleotide substitution in the chicken genome
00
3917062 2005 GENOME RESEARCH 15 (12): 1777-1786
Brent MR
Genome annotation past, present, and future: How to define an ORF at each locus
01
40170116 2005 TRENDS IN ENDOCRINOLOGY AND METABOLISM 16 (9): 414-419
Dougherty DC; Sanders MM
Estrogen action: revitalization of the chick oviduct model
01
#LCRNCRNode / Date / Journal / AuthorLCSGCS
41169151 2006 GENE 365: 57-66
Watanabe M; Nikaido M; Tsuda TT; Inoko H; Mindell DP; et al.
The rise and fall of the CR1 subfamily in the lineage leading to penguins
00
4216878 2005 JOURNAL OF NEUROBIOLOGY 64 (2): 224-238
Wade J; Tang YP; Peabody C; Tempelman RJ
Enhanced gene expression in the forebrain of hatchling and juvenile male zebra finches
01
43168115 2005 TRENDS IN ECOLOGY & EVOLUTION 20 (4): 180-186
Ellegren H
The avian genome uncovered
23
44168199 2006 PROTEOMICS 6 (9): 2759-2771
McCarthy FM; Cooksey AM; Wang N; Bridges SM; Pharr GT; et al.
Modeling a whole organ using proteomics: The avian bursa of Fabricius
00
4516765 2005 GENOMICS 86 (6): 731-738
Liu WS; Eyer K; Yasue H; Roelofs B; Hiraiwa H; et al.
A 12,000-rad porcine radiation hybrid (IMNpRH2) panel refines the conserved synteny between SSC12 and HSA17
00
4616785 2005 NATURE 434 (7031): 325-337
Ross MT; Grafham DV; Coffey AJ; Scherer S; McLay K; et al.
The DNA sequence of the human X chromosome
360
47267183 2006 MOLECULAR BIOLOGY AND EVOLUTION 23 (3): 675-682
Chen FC; Wang SS; Chen CJ; Li WH; Chuang TJ
Alternatively and constitutively spliced exons are subject to different evolutionary forces
02
4816577 2005 JOURNAL OF LIPID RESEARCH 46 (10): 2151-2167
Sabol SL; Brewer HB; Santamarina-Fojo S
The human ABCG1 gene: identification of LXR response elements that modulate expression in macrophages and liver
04
49165158 2006 GENES CHROMOSOMES & CANCER 45 (7): 676-691
Angeloni D; ter Elst A; Wei MH; van der Veen AY; Braga EA; et al.
Analysis of a new homozygous deletion in the tumor suppressor region at 3p12.3 reveals two novel intronic noncoding RNA genes
00
5016444 2005 DEVELOPMENTAL CELL 8 (1): 9-17
Stern CD
The chick: A great model system becomes even greater
310
#LCRNCRNode / Date / Journal / AuthorLCSGCS
51164160 2006 GENOME BIOLOGY 7 (5): Art. No. R43
Blomme T; Vandepoele K; De Bodt S; Simillion C; Maere S; et al.
The gain and loss of genes during 600 million years of vertebrate evolution
00
52164186 2006 MOLECULAR ECOLOGY 15 (5): 1263-1273
Wang ZS; Farmer K; Hill GE; Edwards SV
A cDNA macroarray approach to parasite-induced gene expression changes in a songbird host: genetic response of house finches to experimental infection by Mycoplasma gallisepticum
01
5316357 2005 GENOME RESEARCH 15 (7): 901-913
Cooper GM; Stone EA; Asimenos G; Green ED; Batzoglou S; et al.
Distribution and intensity of constraint in mammalian genomic sequence
28
5426370 2005 IMMUNOGENETICS 57 (8): 590-600
Maruoka T; Tanabe H; Chiba M; Kasahara M
Chicken CD1 genes are located in the MHC: CD1 and endothelial protein C receptor genes constitute a distinct subfamily of class-I-like genes that predates the emergence of mammals
00
55163181 2006 MARINE BIOLOGY 149 (1): 107-115
Watanabe H; Iguchi T
Using ecotoxicogenomics to evaluate the impact of chemicals on aquatic organisms
00
56262192 2006 PHYSIOLOGICAL GENOMICS 25 (3): 414-425
Ellestad LE; Carre W; Muchow M; Jenkins SA; Wang XF; et al.
Gene expression profiling during cellular differentiation in the embryonic pituitary gland using cDNA microarrays
00
57161171 2006 JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 54 (11): 3901-3910
Guerin-Dubiard C; Pasco M; Molle D; Desert C; Croguennec T; et al.
Proteomic analysis of hen egg white
00
58161182 2006 MOLECULAR BIOLOGY AND EVOLUTION 23 (1): 10-22
Olinski RP; Lundin LG; Hallbook F
Conserved synteny between the Ciona genome and human paralogons identifies large duplication events in the molecular evolution of the insulin-relaxin gene family
01
59106061 2005 GENOME RESEARCH 15 (12): 1692-1698
Burt DW
Chicken genome: Current status and future opportunities
00
6016063 2005 GENOME RESEARCH 15 (12): 1787-1797
Webber C; Ponting CP
Hotspots of mutation and breakage in dog and human chromosomes
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
6115979 2005 JOURNAL OF VIROLOGY 79 (16): 10408-10419
Elleder D; Stepanets V; Melder DC; Senigl F; Geryk J; et al.
The receptor for the subgroup C avian sarcoma and leukosis viruses, Tvc, is related to mammalian butyrophilins, members of the immunoglobulin superfamily
03
62259136 2006 CHROMOSOME RESEARCH 14 (2): 187-202
Kuraku S; Ishijima J; Nishida-Umehara C; Agata K; Kuratani S; et al.
cDNA-based gene mapping and GC(3) profiling in the soft-shelled turtle suggest a chromosomal size-dependent GC bias shared by sauropsids
00
63158180 2006 JOURNAL OF THE AMERICAN DENTAL ASSOCIATION 137 (6): 743-752
Pemberton TJ; Gee J; Patel PI
Gene discovery for dental anomalies - A primer for the dental professional
01
64158196 2006 POULTRY SCIENCE 85 (4): 593-605
McElroy JP; Kim JJ; Harry DE; Brown SR; Dekkers JCM; et al.
Identification of trait loci affecting white meat percentage and other growth and carcass traits in commercial broiler chickens
00
6515724 2005 BMC GENOMICS 6: Art. No. 139
Otto H; Reche PA; Bazan F; Dittmar K; Haag F; et al.
In silico characterization of the family of PARP-like poly(ADP-ribosyl) transferases (pARTs)
02
66157112 2005 RETROVIROLOGY 2: Art. No. 50
Jern P; Sperber GO; Blomberg J
Use of Endogenous Retroviral Sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy
01
6715664 2005 GENOMICS 86 (5): 566-580
Zebhauser R; Kammerer R; Eisenried A; McLellan A; Moore T; et al.
Identification of a novel group of evolutionarily conserved members within the rapidly diverging murine Cea family
03
68256163 2006 GENOME RESEARCH 16 (7): 864-874
Nishihara H; Smit AFA; Okada N
Functional noncoding sequences derived from SINEs in the mammalian genome
00
69356167 2006 IMMUNOGENETICS 58 (5-6): 362-373
Cannon JP; Haire RN; Mueller MG; Litman RT; Eason DD; et al.
Ancient divergence of a complex family of immune-type receptor genes
00
70156200 2006 RNA-A PUBLICATION OF THE RNA SOCIETY 12 (1): 102-110
Weil JE; Beemon KL
A 3 ' UTR sequence stabilizes termination codons in the unspliced RNA of Rous sarcoma virus
01
#LCRNCRNode / Date / Journal / AuthorLCSGCS
7115522 2005 BMC EVOLUTIONARY BIOLOGY 5: Art. No. 54
Winter EE; Ponting CP
Mammalian BEX, WEX and GASP genes: Coding and non-coding chimaerism sustained by gene conversion events
00
72155178 2006 JOURNAL OF MOLECULAR EVOLUTION 62 (2): 226-U17
Berlin S; Brandstrom M; Backstrom N; Axelsson E; Smith NDC; et al.
Substitution rate heterogeneity and the male mutation bias
00
73655190 2006 NUCLEIC ACIDS RESEARCH 34 (9): Art. No. e65
Tran T; Havlak P; Miller J
MicroRNA enrichment among short 'ultraconserved' sequences in insects
00
7415381 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (10): 1992-1999
Backstrom N; Ceplitis H; Berlin S; Ellegren H
Gene conversion drives the evolution of HINTW, an ampliconic gene on the female-specific avian W chromosome
12
75153101 2005 POULTRY SCIENCE 84 (11): 1678-1688
McElroy JP; Dekkers JCM; Fulton JE; O'Sullivan NP; Soller M; et al.
Microsatellite markers associated with resistance to Marek's disease in commercial layer chickens
00
76153113 2005 RUSSIAN JOURNAL OF GENETICS 41 (5): 461-467
Sazanov AA; Romanov MN; Smirnov AF
Libraries of large-insert genomic clones as a tool for molecular cytogenetic analysis of avian genome
00
77153141 2006 CYTOGENETIC AND GENOME RESEARCH 113 (1-4): 159-164
Okamura K; Ito T
Lessons from comparative analysis of species-specific imprinted genes
00
78153177 2006 JOURNAL OF MOLECULAR EVOLUTION 62 (1): 66-U36
Berlin S; Ellegren H
Fast accumulation of nonsynonymous mutations on the female-specific W chromosome in birds
00
7915151 2005 GENETICAL RESEARCH 86 (2): 115-125
Jacobsson L; Park HB; Wahlberg P; Fredriksson R; Perez-Enciso M; et al.
Many QTLs with minor additive effects are associated with a large difference in growth between two selection lines in chickens
12
80151137 2006 COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY 144 (3): 345-350
Yoshimura T
Molecular mechanism of the photoperiodic response of gonads in birds and mammals
02
#LCRNCRNode / Date / Journal / AuthorLCSGCS
81351139 2006 CURRENT OPINION IN GENETICS & DEVELOPMENT 16 (3): 213-218
Ross MT; Bentley DR; Tyler-Smith C
The sequences of the human sex chromosomes
00
8215048 2005 FEBS LETTERS 579 (15): 3355-3361
Zdobnov EM; von Mering C; Letunic I; Bork P
Consistency of genome-based methods in measuring Metazoan evolution
12
8315086 2005 NATURE 434 (7034): 724-731
Hillier LW; Graves TA; Fulton RS; Fulton LA; Pepin KH; et al.
Generation and annotation of the DNA sequences of human chromosomes 2 and 4
310
84250164 2006 GENOMICS 87 (1): 181-190
Luo MZ; Yu YS; Kim HR; Kudrna D; Itoh Y; et al.
Utilization of a zebra finch BAC library to determine the structure of an avian androgen receptor genomic region
02
8514920 2005 BMC BIOLOGY 3: Art. No. 2
Jorgensen FG; Hobolth A; Hornshoj H; Bendixen C; Fredholm M; et al.
Comparative analysis of protein coding sequences from human, mouse and the domesticated pig
04
8614921 2005 BMC EVOLUTIONARY BIOLOGY 5: Art. No. 40
Laukaitis CM; Dlouhy SR; Emes RD; Ponting CP; Karn RC
Diverse spatial, temporal, and sexual expression of recently duplicated androgen-binding protein genes in Mus musculus
00
8714932 2005 CHROMOSOME RESEARCH 13 (6): 601-615
Matsuda Y; Nishida-Umehara C; Tarui H; Kuroiwa A; Yamada K; et al.
Highly conserved linkage homology between birds and turtles: Bird and turtle chromosomes are precise counterparts of each other
23
8814974 2005 JOURNAL OF IMMUNOLOGY 174 (8): 4998-5006
Lynch NJ; Khan SUH; Stover CM; Sandrini SM; Marston D; et al.
Composition of the lectin pathway of complement in Gallus gallus: Absence of mannan-binding lectin-associated serine protease-1 in birds
01
89149126 2006 BMC BIOINFORMATICS 7: Art. No. 103
Shih ACC; Lee DT; Lin L; Peng CL; Chen SH; et al.
SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools
00
90249193 2006 PHYSIOLOGICAL GENOMICS 25 (3): 514-524
Carre W; Wang XF; Porter TE; Nys Y; Tang JS; et al.
Chicken genomics resource: sequencing and annotation of 35,407 ESTs from single and multiple tissue cDNA libraries and CAP3 assembly of a chicken gene index
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
9114823 2005 BMC GENOMICS 6: Art. No. 41
Niskanen EA; Hytonen VP; Grapputo A; Nordlund HR; Kulomaa MS; et al.
Chicken genome analysis reveals novel genes encoding biotin-binding proteins related to avidin family
01
9234831 2005 CHROMOSOME RESEARCH 13 (6): 581-591
Rodrigue KL; May BP; Famula TR; Delany ME
Meiotic instability of chicken ultra-long telomeres and mapping of a 2.8 megabase array to the W-sex chromosome
00
9334739 2005 CURRENT OPINION IN GENETICS & DEVELOPMENT 15 (6): 645-651
Fraser JA; Heitman J
Chromosomal sex-determining regions in animals, plants and fungi
02
9414775 2005 JOURNAL OF IMMUNOLOGY 175 (1): 385-393
Viertlboeck BC; Habermann FA; Schmitt R; Groenen MAM; Du Pasquier L; et al.
The chicken leukocyte receptor complex: A highly diverse multigene family encoding at least six structurally distinct receptor types
24
95146120 2005 WORLDS POULTRY SCIENCE JOURNAL 61 (2): 215-226
Hocking PM
Review of QTL mapping results in chickens
14
9614582 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (11): 2198-2208
Cusack BP; Wolfe KH
Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exons
17
97245134 2006 CELL AND TISSUE RESEARCH 324 (1): 41-53
Mozdziak PE; Wu Q; Bradford JM; Pardue SL; Borwornpinyo S; et al.
Identification of the lacZ insertion site and beta-galactosidase expression in transgenic chickens
00
98145142 2006 DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 30 (1-2): 93-100
Lundqvist ML; Middleton DL; Radford C; Warr GW; Magor KE
Immunoglobulins of the non-galliform birds: Antibody expression and repertoire in the duck
00
9914476 2005 JOURNAL OF IMMUNOLOGY 175 (3): 1724-1734
Oshiumi H; Shida K; Goitsuka R; Kimura Y; Katoh J; et al.
Regulator of complement activation (RCA) locus in chicken: Identification of chicken RCA gene cluster and functional RCA proteins
00
100144107 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (32): 11367-11372
Benarafa C; Remold-O'Donnell E
The ovalbumin serpins revisited: Perspective from the chicken genome of clade B serpin evolution in vertebrates
12

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