Список использованной литературы

Список использованной литературы

Общий

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Глава 1

Katzourakis, A., Gifford, R.J. Macroevolution of complex retroviruses, 2009; 325:1512.

Ziegler, Anna, 51, theatre play.

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Eigen, M., Error catastrophe and antiviral strategy, 002; 99:13374.

Patel, B.H. Common origins of RNA, protein and lipid precursors in a protometabolism, . 2015; 4:301.

Sweetlove, L., Number of species on Earth at 8.7 million, 2011, doi:10.1038/news.2011498.

: Sharp, P.A., The discovery of split genes and RNA splicing, 2005; 30:279.

Глава 2

: Taubenberger, J.K., Influenza viruses: Breaking all the rules, . 2013; 4: p.ii: e00365–13.

Fouchier, R.A.M., Garcнa-Sastre, A., and Kawaoka, Y., H5N1 virus: Transmission studies resume for avian flu, 2013; 493:609.

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: Lane, H.C., La Montagne, H.L., and Fauci, A.S., Bioterrorism: A clear and present danger, . 2001; 7:1271.

: Cohen, J., AIDS research. More woes for struggling HIV vaccine field, 2013; 340:667.

: Weber, R., Bossart, W. Moelling, K., Phase I clinical trial with HIV-1 gp160 plasmid vaccine in HIV-1-infected asymptomatic subjects, . 2001; 11:800.

Lowrie, D.B. Moelling, K., Silva, C.L., Therapy of tuberculosis in mice by DNA vaccination, 1999; 400:269.

Schlitz, J.G., Salzer, U., Mohajeri, M.H. Moelling, K., Antibodies from a DNA peptide vaccination decrease the brain amyloid burden in a mouse model of Alzheimer`s disease, 2004; 82:706.

: Haase, A.T., Early events in sexual transmission of HIV for interventions, . 2011; 62:127.

Matzen, K. Moelling, K., RNase H-mediated retrovirus destruction in vivo triggered by oligodeoxynucleotides, . 2007; 25:669; : Johnson, W.E., Assisted suicide for retroviruses, 2007; 25:643.

Wittmer-Elzaouk, L. Moelling, K., Retroviral self-inactivation in the mouse vagina, . 2009; 82:22.

: H?tter, G., Transplantation of blood stem cells for HIV/AIDS?, 2009; 12:10.

Faria, N.R. HIV eipdemiology. The early spread and ignition of HIV-1 in human, 2014; 346:56.

Глава 3

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Moelling, K., RT and RNase H: In a murine virus and in both subunits of an avian virus, 975; 39:269.

Moelling, K., Targeting the RNase H by rational drug design, 012;26:1983.

Moelling, K. Relationship retroviral replication and RNA interference, 006; 71:365.

Simon, D.M. and Zimmerly, S., A diversity of uncharacterized RTs in bacteria, 008; 36:7219.

Lampson, B.C., Inouye, M., and Inouye, S., Retrons, msDNA, bacterial genome, . 2005; 110:491.

Moelling, K. and Broecker F., The RT-RNase H: From viruses to antiviral defense, 2015; 1341:126.

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Broecker, F., Andrae, K., and Moelling, K., Activation of HIV RNase H, suicide a novel microbicide?, 012; 28:1397.

Song, J.J. Structure of Argonaute and implications for RISC slicer, 2004; 305:1434.

Malik, H.S. and Eickbush, T.H., RNase H suggests a late origin of LTR from TE, 2001; 11:1187.

Crow, Y.J. Jackson, A.P., Mutations in genes encoding ribonuclease H2 subunits cause Aicardi-Gouti?re syndrome and mimic congenital viral brain infection. . 2006; 38:910.

Cerritelli, S.M. and Crouch, R.J., Ribonuclease H: The enzymes in eukaryotes, 2009; 276:1494.

Nowotny, M., Retroviral integrase superfamily: The structural perspective, 2009; 10:144.

Arshan Nasir, A., Sun, F.-J., Kim, K.M., and Caetano-Anolles, G., Untangling the origin of viruses and their impact on cellular evolution, . 2014; 1341:61.

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Skloot, R., (Crown Publishing Group, 2010).

Nandakumar, J. and Cech, T.R., Finding the end: Recruitment of telomerase, 2013; 14:69.

Budin, I. and Szostak, J.W., Transition from primitive to modern cell membranes, 011; 108:5249.

Глава 4

: Martin, G. S., The hunting of the Src, 2001; 2:467.

Yeatman, T.J. and Roskoski, R. Jr., A renaissance for SRC, 2004; 4: 470.

: Donner, P., Greiser-Wilke, I. and Moelling, K., Nuclear localization and DNA binding of Myc, 1982; 296:262 and Moelling, K. 1984, 312:551, Myb, 1985; 40:983.

Axel, R., Schlom, J., and Spiegelman, S., Presence in human breast cancer of RNA homologous to MMTV1972; 235:32.

 Moelling, K. Serine–threonine PK activities of Mil/Raf, 1984; 312:558.

Zimmermann, S. and Moelling, K., Phosphorylation and regulation of Raf by Akt, 1999; 286:1741.

Rommel, C. Differentiation specific inhibition of Raf-MEK-ERK by Akt, 1999; 286:1738.

Zimmermann, S., Moelling K., and Radziwil, G., MEK1 mediates positive feedback on Raf, 1997; 15:1503.

Dummer, R. and Flaherty, K.T., Resistance with tyrosine kinase inhibitors in melanoma, . 2012; 24:150.

Das Thakur, M., Modelling Vemurafenib resistance in melanoma, 2013; 494:251.

Holderfield, M. Targeting RAF kinases for cancer therapy: BRAF-mutated melanoma and beyond, 2014; 14:455.

McMahon, M., Parsing out the complexity of RAF inhibitor resistance, . 2011; 24:361.

Sun, C. Bernards, R., Reversible resistance to BRAF(V600E) inhibition in melanoma, 2014; 508:118.

: Liu, J. and Levens, D., Making Myc, . 2006; 302:1.

: Gateff E: Malignant neoplasms of genetic origin in Drosophila, 1978; 200:1448.

Sherr, C.J. and McCormick, F., The RB and p53 pathways in cancer. 2002; 2:103.

Yi, L. Multiple roles of p53 in somatic and stem cell differentiation, . 2012; 72:563.

Wang, T. Retroviruses shape the transcriptional network of p53. 007; 104:18613.

: Baumgartner, M. Moelling, K., SRC-migration and invasion by PDZ, 008; 28:642.

Broecker, F. Moelling, K., Transcription of C-terminal metastatic c-Src mutant, 2016; 283:1669.

: Vogelstein, B. Cancer genome landscape, 2013; 339:1546

Hanahan, D. and Weinberg, R.A., Hallmarks of cancer: The next generation, 2011; 144:646.

zur Hausen, H., Papillomaviruses and cancer: From basics to clinical application, 2002; 2:342.

: Han, Y.C. Ventura, A., miR-17–92-mutant mice, . 2015; 47:766–75.

: Kearney, M. Coffin, J.M., Multiple sources of contamination in XMRV infection, 012; 7: e30889.

 Salama, N. Life in the human stomach: Helicobacter pylori, . 2013; 11:385.

Глава 5

: Suttle, C.A., Viruses in the sea, 2005; 437:356.

Reardon, S., News: Phage therapy: Phage therapy gets revitalized, 2014; 510:15.

Young, R.Y. and Gill, J.J., Phage therapy redux – What is to be done?, 2015; 350:1163.

Delwart, E., A roadmap to the human virome, . 2013; 9: e1003146.

Zarowiecki, M., Metagenomics with guts, . 2012; 10:674.

Turroni, F. Human gut microbiota and bifidobacteria, 2008; 94:35.

 Turnbaugh, P.J. Gordon, J.I., The effect of diet on human gut microbiome, . 2009; 1:6ra14.

Qin, J. A human gut microbial gene catalogue by metagenomic sequencing, 2010; 464:59.

Katsnelson, A. Twin study surveys genome for cause of multiple sclerosis, 2010; 464: 1259.

Mokili, J.L., Rohwer, F. and Dutilh, B.E., Metagenomics and future virus discovery, . 2012; 2:63.

: Dominguez-Bello, Microbiota of cesarean-born infants, 2016; doi:10.1038/nm.4039.

: Weiss, R.A. and Stoye, J.P., Virology. Our viral inheritance, 2013; 340:820.

Feschotte, C. and Gilbert, C., Endogenous viruses: Viral evolution and host biology, 2012; 13:283.

: Roossinck, M.J., The good viruses: Viral mutualistic symbioses. . 2011; 9:99.

Roossinck, M.J., Lifestyles of plant viruses, 2010; 365:1899.

: Mi, S. Syncytin – a retroviral envelope in human placenta. 2000; 403:785.

: Bezier, A. Polydnaviruses of braconid wasps derive from an ancestral nudivirus, 2009; 323: 926.

Strand, M.R. and Burke, G.R., Polydnaviurses as symbionts and gene delivery systems, 012; Pathog 8: e1002757.

: Mahal, S.P. Transfer of a prion strain leads to emergence of strain variants, 010; 107:22653.

Глава 6

: Van Etten, J., Giant viruses; 2011.

Van Etten, J., Lane, L.C. and Dunigan, D., DNA viruses: The really big ones (Giruses), 2010;64:83.

Broecker, F. Viral composition in the intestine after FT, 2016; 2: a000448.

Moelling, K. (Ed.), Nutrition and microbiome, (2016).

: Boyer, M. Mimivirus genome reduction after intraamoebal culture, 011; 108:10296.

Raoult, D. and Forterre, P., Redefining viruses: Lessons from mimivirus, 2006; 6:315.

Raoult, D. Claverie, J.M., The 1.2-megabase genome sequence of mimivirus, 2004; 306:1344.

Philippe, N. Pandoraviruses: Amoeba viruses with genomes up to 2.5 Mb, 2013; 341:281.

La Scola, B. Raoult, D., A giant virus in amoebae, 2003; 299:2033.

: Legendre, M. Mollivirus sib. 30,000y giant virus in Acanthamoea, 015; 112:10795

: Campos, R. K., Sambavirus: Mimivirus from rain forest, The Brazilian Amazon, 2014; 11:95.

: Pennisi, E., Ever bigger viruses shake tree of life, 2013; 341:226.

Yutin, N., Wolf, Y.I., and Koonin, E.V., Origin of giant viruses from smaller DNA viruses, 2014; 466–467:38.

 Yutin, N., Raoult, D. and Koonin, E., Virophages, polintons, and transpovirons: A complex evolutionary network of diverse selfish genetic elements with different reproduction strategies, 2013; 1:15.

Fischer, M.G. and Suttle, C.A., A virophage at the origin of large DNA transposons, 2011; 332:231.

Forterre, P., The origin of viruses and their possible roles in major evolutionary transitions, . 2006; 117:5.

: Huber, H. A new phylum of archaea represented by a nanosized hyperthermophilic symbiont, 2002; 417:63.

Slimani, M. Amoebae as battlefields for bacteria, giant viruses, and virophages. . 2013; 87:4783.

: Yutin, N. and Koonin, E.V., Proteorhodopsin genes in giant viruses, 2012; 7:34

: Stetter, K.O., A brief history of the discovery of hyperthermophilic life, . 2013; 41:416.

Podar, M. A genomic analysis of the archaeal system –, 2008; 9: R158.

Mochizuki, T. Archaeal virus with exceptional architecture, largest ssDNA genome, 012; 109:13386.

Prangishvili, D., Forterre, P. and Garrett, R.A., Viruses of the archaea: A unifying view, 2006; 4:837.

Глава 7

: Weiss, R.A., The discovery of endogenous retroviruses, 2006; 3:67.

: Katzourakis, A. Discovery of first endogenous lentivirus, 007; 10:6261.

Katzourakis, A. and Gifford, R.J., Endogenous viral elements in animal genomes, 2010: 6: e1001191.

Dewannieux, M. Identification of an infectious progenitor for the HERV-K, 2006; 16:1548.

: Tarlinton, R.E., Meers, J., and Young, P.R., Retroviral invasion of the koala genome, 2006; 442:79

: Belyi, V.A., Levine, A.J. and Skalka, A.M., Sequences from ancestral ssDNA viruses in vertebrate genomes: The parvoviridae and circoviridae are more than 40 to 50 mio years old, 2010; 84:12458

Gifford, R.J., A transitional endogenous lentivirus from a basal primate for lentivirus evolution, PNAS2008; 105:20362.

Katzourakis, A. Macroevolution of complex retroviruses, 2009; 32:1512.

: Lander, E.S. Initial sequencing and analysis of the human genome, 2001; 409:860.

Cordaux, R. and Batzer, M.A., The impact of retrotransposons on human genome evolution, 2009; 10:691.

SnapSot, Transposons, 2008; 135:192

Singer, T. LINE-1 retrotransposons in neuronal genomes? 2010; 33:345.

Pollard, K.S. RNA expressed during cortical development evolved in humans, 2006; 443:167.

Finnegan, D.J., Retrotransposons, . 2012; 22: R432–7.

, Harshey, R.M., The Mu story: How a maverick phage moved the field forword, 2012; 3:21.

Sander, D.M. Intracisternal A-type retroviral particles in autoimmunity, . 2005; 68:222

 Dolinoy, D.C. The Agouti mouse model: An epigenetic biosensor for nutritional and environmental alterations on the fetal epigenome, . 2008, 66 Suppl. 1: S7–11.

Rassoulzadegan, M., RNA-mediated non-Mendelian inheritance of an epigenetic change in the mouse, 2006; 441:469.

: Luft, F.C. Sleeping Beauty jumps to new heights, 2010; 88:641.

: Amemiya, C.T. African coelacanth genome insights into tetrapod evolution, 2013; 496:311.

: Warren, W.C. Genome analysis of the platypus unique evolution, 2008; 453:175.

: Morris, K. and Mattick, J.S., The rise of regulatory RNA, . 2014; 15:423.

Chabannes, M. Three infectious viral species lying in wait in the banana genome, . 2013; 87:8624.

Bartel, D.P., MicroRNAs target recognition and regulatory functions, 2009; 136:215.

Zimmerly, S. GroupII intron mobility, 1995; 82:545.

Beauregard, A., Curcio, M.J. and Belfort M., The take and give RT elements and hosts, . 2008; 42:587.

Lambowitz, A.M. and Zimmerly S., Group II introns: Mobile ribozymes in DNA, . 2011; 3: a003616.

Galej, W.P. Crystal structure of Prp8 reveals active site of slicosome, 2013; 493:638.

Pena, V. Structure and function of an RNase H at the heart of the spliceosome, 2008; 27:2929.

: Biemont, C. and Vieira, C., Junk DNA as an evolutionary force, 2006; 443:521.

Venter, C., Multiple personal genomes await, 2010, 464:676

Lev, S. Venter, C., The diploid genome sequence of an individual human, . 2007; 5: e254.

Fukai, E. Derepression of the plant Chromovirus LORE1 induces germline transposition in regenerated plants, 2010; 6(3): e1000868.

Глава 8

: Eigen, M., Error catastrophe and antiviral strategy, 002; 99:13374.

Biebricher, C.K. and Eigen, M., What is a quasispecies, . 2006; 299:1.

Biebricher, C.K. and Eigen, M., The error threshold, 2005; 107:117.

Lincoln, T.A. and Joyce, G.F., Self-sustained replication of an RNA enzyme, 2009; 323:1229.

Doudna, J.A. and Szostak, J.W., RNA-catalysed synthesis of complementarystrand, 1989; 33:519.

: Steger, G. Structure of viroid replicative intermediates of PST viroid, . 1986; 14:9613.

Villarreal, L.P., The widespread evolutionary significance of viruses, 2008;10:2168.

Cech, T.R. Hammerhead nailed down, 1994; 372:39.

Koonin, E.V. and Dolja, V.V., A virocentric perspective on the evolution of life, 2013; 5:546.

Lambowitz, A.M. and Zimmerly, S., Mobile group II introns, 2004; 38:1.

Adamala, K., Engelhart, A.E., and Szostak, J.W., Generation of functional RNAs from inactive oligonucleotide complexes by non-enzymatic primer extension, . 2015; 137:483–489.

Forterre, P., Defining life: The virus viewpoint, 2010; 40:51.

Moelling, K., Are viruses our oldest ancestors? 2012; 13:1033.

Holmes, E.C., What does virus evolution tell us about virus origins? 2011; 85:5247.

: Lescot, M. and Ogata, H., Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages, 2015; 1–13.

: Memczak, S. Circular RNAs with regulatory potency, 2013; 495:333.

Hansen, T.B. Natural RNA circles function as efficient microRNA sponges, 2013; 495:384.

Hansen, T.B., Kjems, J., and Damgaard, C.K., Circular RNA and miR-7 in cancer, . 2013; 73:5609.

Ford, E. and Ares, M. Jr., Circular RNA using ribozymes from a T4 group I intron, 994; 12; 91:3117.

: Wilusz, J.E. and Sharp, P.A., A circuitous route to noncoding RNA. 2013; 340:44.

Navarro, B. Viroids: Infect a host and cause disease without encoding proteins, 2012; 94:1474.

Hammann, C. and Steger, G., Viroid-specific small RNA in plant disease, . 2012; 9:809.

Bartel, D.P., MicroRNAs target recognition and regulatory functions, 2009; 136:215.

Eilus, J.E. and Sharp, P.A., A circuitous route to non-coding RNA, 2013; 340:440.

: Moore, P.B., and Steitz, T.A., The ribosome revealed, 2005; 30:28.

Ma, B.G. Zhang, H.Y., Characters of very ancient proteins, 008; 366:607.

: Muller, G. NC protein of HIV-1 for increasing catalytic activity of a ribozyme, 1994; 242:422.

: Dreher, T.W., Viral tRNAs and tRNA-like structures, 2010; 1:402.

Hammond, J.A., Comparison and functional implications of viral tRNA-like structures, 2009; 15:294.

Witzany, G. (Editor), : (Springer 2012), p. 414.

: Eickbush, D.G., Retrotransposon ribozyme and its self-cleavage site, 2013; 8(9): e66441.

Webb, C.H. Widespread occurrence of self-cleaving ribozymes, 2009; 326:953.

Hammann, C. The ubiquitous hammerhead ribozyme, 2012; 18:871.

: Braza, R. and Ganem, D., The HDAg may be of human origin, 1996; 274:90.

Taylor, J., and Pelchat, M., Origin of hepatitis delta virus, 2010; 5:393.

Flores, R., Ruiz-Ruiz, S. and Serra, P., Viroids and hepatitis delta virus, 2012; 32:201.

: Liu, M. Bordetella bacteriophages encoding RT-mediated tropism-switching, 2004; 186:1503.

Doulatov, S. Tropism switching in Bordetella bacteriophage by diversity-generating retroelements, 2004; 431:476.

: Buck, K.W., Replication of tobacco mosaic virus RNA, 1999; 354:613

Beijerinck, M.W., Contagum vivum fluidum of tobacco leaves, Phytopathol Classics No. 7, ed. Johnson, J., Am. Phyto. Soc., 1898.

Dreher, T.W., Viral tRNAs and tRNA-like structures, 2010; 1:402.

Hammond, J.A. 3D architectures of viral tRNA-like structures, 2009; 15:294.

 Mitrovic, J. Sequences of Stolbur phytoplasma from DNA, 2014; 24:1.

Georgiades, K. Gene gain and loss events in and species, 2011; 6:6.

: Roossinck, M.J., Lifestyles of plant viruses, . 2010; 365:1899.

: Krupovic M. ., Geminiviruses: A tale of a plasmid becoming a virus, . 2009; 9:112.

: Lesnaw, J.A. and Ghabrial, S.A., Tulip breaking: Past, present and future, 2000; 84:1052.

Murray, J.D., How the leopard gets its spots, . 1988; 3:80–87.

Глава 9

: McNab, F. O’Garra, A., Type Interferons in infectious disease, 2015; 15:87–103.

: Baulcombe, D.C. and Dean, C., Epigenetic regulation in plant to the environment, 2014; 6(9): a019471.

Wilson, R.C. and Doudna, J.A., Molecular mechanisms of RNA interference, 2013; 42:217.

Moelling K., Matskevich A., and Jung J. S., Relationship between retroviral replication and RNA interference, 006; 71:365–8.

Matskevich, A. and Moelling, K., Dicer is involved in protection against influenza A virus infection, 2007; 88:2627–35.

Song J. J., The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNA effector complexes, . 2003; 10:1026–32.

Nowotny, M., Retroviral integrase superfamily: The structural perspective. 2009; 19:144–151.

Nasir, A. and Caetano-Anolles, G., Origin of viruses and their impact on cellular evolution, 2015; 1341:61.

Moelling, K. and Broecker, F., The RT-RNase H: From viruses to antiviral defense, . Sc2015; 1341:126–35.

: Sterken, M.G. A heritable antiviral RNAi response limits Orsay virus infection, 2014; 9(2).

: Doudna, J.A. and Charpentier, E., Genome editing. The new frontier of genome engineering with CRISPR-Cas9, 2014; 346 (6213):1258096.

Jinek, M. Structures of Cas9 endonucleases, 2014; 343, 1247997.

Hsu, P.D., Lander, E.S., and Zhang, F., Development and applications of CRISPRCas9 for genome engineering, 2014; 157:1262.

Barrangou, R. and Marraffini, L.A., CRISPR-Cas systems: Procaryotes to adaptive immunity, 2014; 54:234.

Krupovic, M. Casposons: Self-synthesizing DNA transposons of CRISPR-Cas immunity, 2014; 12:36.

Horvath, P. and Barrangou R., CRISPR/Cas9, the immune system of bacteria and archaea, 2010; 327:167.

Swarts, D.C. DNA-guides DNA interference by a procaryotic Argonaute, 2014; 507:258.

Moelling, K. Silencing of HIV by hairpin-loop DNA oligonucleotide (siDNA), 2006; 580:3545.

Zhou, L. Transposition of hAT elements links TE and V(D)J recombination, 2004; 432:995

Bateman, A., Eddy, S.R., and Chothia, C., Members of the immunoglobulin superfamily in bacteria, .1996; 5:1939.

Beauregard, A., Curcio, M.J. and Belfort M., The take and give between TE, 2008; 42:587.

: Isselbacher, K.J., Retrospective: Paul C. Zamecnik (1912–2009), 2009; 326:1359.

Citron, M. and Schuster, H., The c4 repressors of bacteriophages P1 and P7 are antisense RNAs, 1990; 62:591.

Глава 10

Reardon, S., Phage therapy gets revitalized, 2014; 510:15.

Young, Ry. and Gill, J.J., Phage therapy redux – What is to be done? 2015; 350:1163.

Viertel, T.M., Ritter, K. and Horz, H.P., Phage therapy against MDR pathogens, . 2014; 69:2326–36.

: EU program: The main objective of Phagoburn is to assess the safety, effectiveness and pharmacodynamics of two therapeutic phage cocktails to treat either or burn wound infections, 2013–2016.

Vanessa, K. Gut microbiota from twins discordant for obesity, 2013; 341:1079.

: Nьbel, U., MRSA transmission on a neonatal intensive care unit, . 2013;8(1): e54898.

Stower, H., Medical genetics: Narrowing down obesity genes, 2014;20:349.

Lepage, P. Dore, A., Metagenomic insight into our gut`s microbiome, 2013; 62:146.

Smemo, S., Obesity-associated variants within FTO and with IRX3, 2014; 507:371.

Blaser, M. and Bork, P. The microbiome explored: Recent insights and future challenges, . 2013;11:213.

: Tobie, E.W. DNA methylation to prenatal famine, 2009; 18;2:4046.

Bygren, L.O. Grandmothers’ early food supply influenced mortality of female grandchildren, 2014; 15:12.

Norman, J.M. Alterations in the enteric virome in inflammatory bowel disease, 2015;160: 447.

Grossniklaus, U. Transgenerational epigenetic inheritance: How important is it?, 2013; 14:228.

Pembrey, M.E. Sex-specific, male-line transgenerational responses in humans, . 2006; 14:159.

Arabidopsis Genome Initiative, Analysis of the genome sequence of , 2006; 441:469.

Waterland, R.A. and Jirtle, R.L., TE targets for early nutritional effects on epigenetic gene regulation. 003; 23:5293.

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