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Bucharest: The Publishing House of the Romanian Academy. Ch. 2.3."},{"key":"ref23","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1002\/pbc.21831","article-title":"Developmental genes and cancer in children","volume":"52","author":"S Moore","year":"2009","journal-title":"Pediatr Blood Cancer"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1111\/j.1440-1843.2006.00838.x","article-title":"Developmental signalling pathways in lung cancer","volume":"11","author":"V Daniel","year":"2006","journal-title":"Respirology"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"580","DOI":"10.4161\/cc.8.4.7657","article-title":"Paths of FGFR-driven tumorigenesis","volume":"8","author":"V Acevedo","year":"2009","journal-title":"Cell Cycle"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1023\/A:1006369223282","article-title":"Wnt signalling in mammalian development and cancer","volume":"18","author":"M Smalley","year":"1999","journal-title":"Cancer Metastasis 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(2012) Born too soon: The global action report on preterm birth. Technical report, The World Health Organization."},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1203\/01.PDR.0000108691.21824.E5","article-title":"VEGFR-1: a safe target for prophylaxis of retinopathy of prematurity?","volume":"55","author":"F Sennlaub","year":"2004","journal-title":"Pediatr Res"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1097\/MOP.0b013e32832925f9","article-title":"Antivascular endothelial growth factor for retinopathy of prematurity","volume":"21","author":"H Mintz-Hittner","year":"2009","journal-title":"Curr Opin Pediatr"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1542\/peds.97.2.210","article-title":"Chorioamnionitis and early lung inammation in infants in whom bronchopulmonary dysplasia develops","volume":"97","author":"K Watterberg","year":"1996","journal-title":"Pediatrics"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1146\/annurev.physiol.67.040403.102229","article-title":"Lung vascular development: implications for the pathogenesis of bronchopulmonary dysplasia","volume":"67","author":"K Stenmark","year":"2005","journal-title":"Annu Rev Physiol"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"1795","DOI":"10.1111\/j.1651-2227.2010.01973.x","article-title":"The clustering of disorders in infants born before the 28th week of gestation","volume":"99","author":"A Leviton","year":"2010","journal-title":"Acta Paediatr"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1159\/000351040","article-title":"Low urine vascular endothelial growth factor levels are associated with mechanical ventilation, bronchopulmonary dysplasia and retinopathy of prematurity","volume":"104","author":"BM Levesque","year":"2013","journal-title":"Neonatology"},{"key":"ref52","doi-asserted-by":"crossref","unstructured":"Bhatt A, Pryhuber G, Huyck H, Watkins R, Metlay L, <etal>et al<\/etal>.. (2001) Disrupted pulmonary vasculature and decreased vascular endothelial growth factor, Flt-1, and TIE-2 in human infants dying with bronchopulmonary dysplasia. AmJRespirCritCare Med: 1971\u20131980.","DOI":"10.1164\/ajrccm.164.10.2101140"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1038\/nm1102-1329b","article-title":"Loss of HIF-2alpha and inhibition of VEGF impair fetal lung maturation, whereas treatment with VEGF prevents fatal respiratory distress in premature mice","volume":"8","author":"V Compernolle","year":"2002","journal-title":"Nat Med"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"L209","DOI":"10.1152\/ajplung.00185.2005","article-title":"Vascular endothelial growth factor in the lung","volume":"290","author":"NF Voelkel","year":"2006","journal-title":"Am J Physiol Lung Cell Mol Physiol"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"1516","DOI":"10.1164\/rccm.200210-1207OC","article-title":"Methylprednisolone causes matrix metalloproteinase-dependent emphysema in adult rats","volume":"167","author":"K Choe","year":"2003","journal-title":"Am J Respir Crit Care Med"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"R210","DOI":"10.1186\/gb-2007-8-10-r210","article-title":"Perturbation of gene expression of the chromatin remodeling pathway in premature newborns at risk for bronchopulmonary dysplasia","volume":"8","author":"J Cohen","year":"2007","journal-title":"Genome Biol"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"4289","DOI":"10.1172\/JCI45144","article-title":"Denitrosylation of HDAC2 by targeting Nrf2 restores glucocorticosteroid sensitivity in macrophages from COPD patients","volume":"121","author":"D Malhotra","year":"2011","journal-title":"J Clin Invest"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1016\/j.bbrc.2011.02.035","article-title":"De- creased histone deacetylase 2 impairs Nrf2 activation by oxidative stress","volume":"406","author":"N Mercado","year":"2011","journal-title":"Biochem Biophys Res Commun"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1056\/NEJM196702162760701","article-title":"Pulmonary disease following respirator therapy of hyaline-membrane disease: Bronchopulmonary dysplasia","volume":"276","author":"WH Northway","year":"1967","journal-title":"N Engl J Med"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1183\/09031936.00127107","article-title":"Emphysema in young adult survivors of moderate-to-severe bronchopulmonary dysplasia","volume":"32","author":"P Wong","year":"2008","journal-title":"Eur Respir J"},{"key":"ref61","first-page":"50","article-title":"Mining functionally relevant gene sets for analyzing physiologically novel clinical expression data","volume":"16","author":"S Turcan","year":"2011","journal-title":"Pac Symp Biocomput"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/aje\/kwj175","article-title":"Tracking the epidemiology of human genes in the literature: the HuGE published literature database","volume":"164","author":"B Lin","year":"2006","journal-title":"Am J Epidemiol"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1186\/1471-2105-9-205","article-title":"GAPscreener: an automatic tool for screening human genetic association literature in PubMed using the support vector machine technique","volume":"9","author":"W Yu","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref64","first-page":"28","article-title":"Mining gene-disease relationships from biomedical literature: Weighting protein-protein interactions and connectivity measures","volume":"12","author":"G Gonzalez","year":"2007","journal-title":"Pacific Symposium on Biocomputing"},{"key":"ref65","unstructured":"McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Bal- timore, MD) (2012). 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