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1.  Baseline characteristics of patients in the Reduction of Events with Darbepoetin alfa in Heart Failure trial (RED-HF) 
McMurray, John J.V. | Anand, Inder S. | Diaz, Rafael | Maggioni, Aldo P. | O'Connor, Christopher | Pfeffer, Marc A. | Solomon, Scott D. | Tendera, Michal | van Veldhuisen, Dirk J. | Albizem, Moetaz | Cheng, Sunfa | Scarlata, Debra | Swedberg, Karl | Young, James B. | Amuchastegui, M. | Belziti, C. | Bluguermann, J. | Caccavo, M. | Cartasegna, L. | Colque, R. | Cuneo, C. | Fernandez, A. | Gabito, A. | Goicochea, R. | Gonzalez, M. | Gorosito, V. | Grinfeld, L. | Hominal, M. | Kevorkian, R. | Litvak Bruno, M. | Llanos, J. | Mackinnon, I. | Manuale, O. | Marzetti, E. | Nul, D. | Perna, E. | Riccitelli, M. | Sanchez, A. | Santos, D. | Schygiel, P. | Toblli, J. | Vogel, D. | Aggarwal, A. | Amerena, J. | De Looze, F. | Fletcher, P. | Hare, D. | Ireland, M. | Krum, H. | Lattimore, J. | Marwick, T. | Sindone, A. | Thompson, P. | Waites, J. | Altenberger, J. | Ebner, C. | Lenz, K. | Pacher, R. | Poelzl, G. | Charlier, F. | de Ceuninck, M. | De Keulenaer, G. | Dendale, P. | Maréchal, P. | Mullens, W. | Thoeng, J. | Vanderheyden, M. | Vanhaecke, J. | Weytjens, C. | Wollaert, B. | Albuquerque, D. | Almeida, D. | Aspe y Rosas, J. | Bocchi, E. | Bordignon, S. | Clausell, N. | Kaiser, S. | Leaes, P. | Martins Alves, S. | Montera, M. | Moura, L. | Pereira de Castro, R. | Rassi, S. | Reis, A. | Saraiva, J. | Simões, M. | Souza Neto, J. | Teixeira, M. | Benov, H. | Chompalova, B. | Donova, T. | Georgiev, P. | Gotchev, D. | Goudev, A. | Grigorov, M. | Guenova, D. | Hergeldjieva, V. | Ivanov, D. | Kostova, E. | Manolova, A. | Marchev, S. | Nikolov, F. | Popov, A. | Raev, D. | Tzekova, M. | Czarnecki, W. | Giannetti, N. | Haddad, H. | Heath, J. | Huynh, T. | Lepage, S. | Liu, P. | Lonn, E. | Ma, P. | Manyari, D. | Moe, G. | Parker, J. | Pesant, Y. | Rajda, M. | Ricci, J. | Roth, S. | Sestier, F. | Sluzar, V. | Sussex, B. | Vizel, S. | Antezana, G. | Bugueno, C. | Castro, P. | Conejeros, C. | Manriquez, L. | Martinez, D. | Potthoff, S. | Stockins, B. | Vukasovic, J. | Gregor, P. | Herold, M. | Jerabek, O. | Jirmar, R. | Kuchar, R. | Linhart, A. | Podzemska, B. | Soucek, M. | Spac, J. | Spacek, R. | Vodnansky, P. | Bronnum-Schou, J. | Clemmensen, K. | Egstrup, K. | Jensen, G. | Kjoller-Hansen, L. | Kober, L. | Markenvard, J. | Rokkedal, J. | Skagen, K. | Torp-Pedersen, C. | Tuxen, C. | Videbak, L. | Laks, T. | Vahula, V. | Harjola, V. | Kettunen, R. | Kotila, M. | Bauer, F. | Cohen Solal, A. | Coisne, D. | Davy, J. | De Groote, P. | Dos Santos, P. | Funck, F. | Galinier, M. | Gibelin, P. | Isnard, R. | Neuder, Y. | Roul, G. | Sabatier, R. | Trochu, J. | Anker, S. | Denny, S. | Dreykluft, T. | Flesch, M. | Genth-Zotz, S. | Hambrecht, R. | Hein, J. | Jeserich, M. | John, M. | Kreider-Stempfle, H. | Laufs, U. | Muellerleile, K. | Natour, M. | Sandri, M. | Schäufele, T. | von Hodenberg, E. | Weyland, K. | Winkelmann, B. | Tse, H. | Yan, B. | Barsi, B. | Csikasz, J. | Dezsi, C. | Edes, I. | Forster, T. | Karpati, P. | Kerekes, C. | Kis, E. | Kosa, I. | Lupkovics, G. | Nagy, A. | Preda, I. | Ronaszeki, A. | Tomcsanyi, J. | Zamolyi, K. | Agarwal, D. | Bahl, V. | Bordoloi, A. | Chockalingam, K. | Chopda, M. | Chopra, V. | Dugal, J. | Ghaisas, N. | Ghosh, S. | Grant, P. | Hiremath, S. | Iyengar, S. | Jagadeesa Subramania, B. | Jain, P. | Joshi, A. | Khan, A. | Mullasari, A. | Naik, S. | Oomman, A. | Pai, V. | Pareppally Gopal, R. | Parikh, K. | Patel, T. | Prakash, V. | Sastry, B. | Sathe, S. | Sinha, N. | Srikanthan, V. | Subburamakrishnan, P. | Thacker, H. | Wander, G. | Admon, D. | Katz, A. | Klainman, E. | Lewis, B. | Marmor, A. | Moriel, M. | Mosseri, M. | Shotan, A. | Weinstein, J. | Zimlichman, R. | Agostoni, P. | Albanese, M. | Alunni, G. | Bini, R. | Boccanelli, A. | Bolognese, L. | Campana, C. | Carbonieri, E. | Carpino, C. | Checco, L. | Cosmi, F. | D'Angelo, G. | De Cristofaro, M. | Floresta, A. | Fucili, A. | Galvani, M. | Ivleva, A. | Marra, S. | Musca, G. | Peccerillo, N. | Perrone Filardi, P. | Picchio, E. | Russo, T. | Scelsi, L. | Senni, M. | Tavazzi, L. | Erglis, A. | Jasinkevica, I. | Kakurina, N. | Veze, I. | Volans, E. | Bagdonas, A. | Berukstis, E. | Celutkiene, J. | Dambrauskaite, A. | Jarasuniene, D. | Luksiene, D. | Rudys, A. | Sakalyte, G. | Sliaziene, S. | Aguilar-Romero, R. | Cardona-Muñoz, E. | Castro-Jimenez, J. | Chavez-Herrera, J. | Chuquiure Valenzuela, E. | De la Pena, G. | Herrera, E. | Leiva-Pons, J. | Lopez Alvarado, A. | Mendez Machado, G. | Ramos-Lopez, G. | Basart, D. | Buijs, E. | Cornel, J. | de Leeuw, M. | Dijkgraaf, R. | Dunselman, P. | Freericks, M. | Hamraoui, K. | Lenderlink, T. | Linssen, G. | Lodewick, P. | Lodewijks, C. | Lok, D. | Nierop, P. | Ronner, E. | Somsen, A. | van Dantzig, J. | van der Burgh, P. | van Kempen, L. | van Vlies, B. | Voors, A. | Wardeh, A. | Willems, F. | Dickstein, K. | Gundersen, T. | Hole, T. | Thalamus, J. | Westheim, A. | Dabrowski, M. | Gorski, J. | Korewicki, J. | Kuc, K. | Miekus, P. | Musial, W. | Niegowska, J. | Piotrowski, W. | Podolec, P. | Polonski, L. | Ponikowski, P. | Rynkiewicz, A. | Szelemej, R. | Trusz-Gluza, M. | Ujda, M. | Wojciechowski, D | Wysokinski, A. | Camacho, A. | Fonseca, C. | Monteiro, P. | Apetrei, E. | Bruckner, I. | Carasca, E. | Coman, I. | Datcu, M. | Dragulescu, S. | Ionescu, P. | Iordachescu-Petica, D. | Manitiu, I. | Popa, V. | Pop-Moldovan, A. | Radoi, M. | Stamate, S. | Tomescu, M. | Vita, I. | Aroutiounov, G. | Ballyuzek, M. | Bart, B. | Churina, S. | Glezer, M. | Goloshchekin, B. | Ivleva, A. | Kobalava, Z. | Kostenko, V. | Lopatin, Y. | Martynov, A. | Orlov, V. | Semernin, E. | Shogenov, Z. | Sidorenko, B. | Skvortsov, A. | Storzhakov, G. | Sulimov, V. | Talibov, O. | Tereshenko, S. | Tsyrline, V. | Zadionchenko, V. | Zateyshchikov, D. | Dzupina, A. | Hranai, M. | Kmec, J. | Micko, K. | Murin, J. | Pella, D. | Sojka, G. | Spisak, V. | Vahala, P. | Vinanska, D. | Badat, A. | Bayat, J. | Dawood, S. | Delport, E. | Ellis, G. | Garda, R. | Klug, E. | Mabin, T. | Naidoo, D. | Pretorius, M. | Ranjith, N. | Van Zyl, L. | Weich, H. | Anguita, M. | Berrazueta, J. | Bruguera i Cortada, J. | de Teresa, E. | Gómez Sánchez, M. | González Juanatey, J. | Gonzalez-Maqueda, I. | Jordana, R. | Lupon, J. | Manzano, L. | Pascual Figal, D. | Pulpón, L. | Recio, J. | Ridocci Soriano, F. | Rodríguez Lambert, J. | Roig Minguell, E. | Roig Minguell, E. | Romero, J. | Valdovinos, P. | Klintberg, L. | Kronvall, T. | Lycksell, M. | Morner, S. | Rydberg, E. | Swedberg, K. | Timberg, I. | Wikstrom, G. | Moccetti, T.4 | Ashok, J. | Banerjee, P. | Carr-White, G. | Cleland, J. | Connolly, E. | Francis, M. | Greenbaum, R. | Kadr, H. | Lindsay, S. | McMurray, J. | Megarry, S. | Memon, A. | Murdoch, D. | Senior, R. | Squire, I. | Tan, L. | Witte, K. | Adams, K. | Adamson, P. | Adler, A. | Altschul, L. | Altschuller, A. | Amirani, H. | Anand, I. | Andreou, C. | Ansari, M. | Antonishen, M. | Banchs, H. | Banerjee, S. | Banish, D. | Bank, A. | Barbagelata, A. | Barnard, D. | Bellinger, R. | Benn, A. | Berk, M. | Berry, B. | Bethala, V. | Bilazarian, S. | Bisognano, J. | Bleyer, F. | Blum, M. | Boehmer, J. | Bouchard, A. | Boyle, A. | Bozkurt, B. | Brown, C. | Burlew, B. | Burnham, K. | Butler, J. | Call, J. | Cambier, P. | Cappola, T. | Carlson, R. | Chandler, B. | Chandra, R. | Chandraratna, P. | Chernick, R. | Colan, D. | Colfer, H. | Colucci, W. | Connelly, T. | Costantini, O. | Dadkhah, S. | Dauber, I. | Davis, J. | Davis, S. | Denning, S. | Drazner, M. | Dunlap, S. | Egbujiobi, L. | Elkayam, U. | Elliott, J. | El-Shahawy, M. | Essandoh, L. | Ewald, G. | Fang, J. | Farhoud, H. | Felker, G. | Fernandez, J. | Festin, R. | Fishbein, G. | Florea, V. | Flores, E. | Floro, J. | Gabris, M. | Garg, M. | Gatewood, R. | Geller, M. | Ghali, J. | Ghumman, W. | Gibbs, G. | Gillespie, E. | Gilmore, R. | Gogia, H. | Goldberg, L. | Gradus-Pizlo, I. | Grainger, T. | Gudmundsson, G. | Gunawardena, D. | Gupta, D. | Hack, T. | Hall, S. | Hamroff, G. | Hankins, S. | Hanna, M. | Hargrove, J. | Haught, W. | Hauptman, P. | Hazelrigg, M. | Herzog, C. | Heywood, J. | Hill, T. | Hilton, T. | Hirsch, H. | Hunter, J. | Ibrahim, H. | Imburgia, M. | Iteld, B. | Jackson, B. | Jaffrani, N. | Jain, D. | Jain, A. | James, M. | Jimenez, J. | Johnson, E. | Kale, P. | Kaneshige, A. | Kapadia, S. | Karia, D. | Karlsberg, R. | Katholi, R. | Kerut, E. | Khoury, W. | Kipperman, R. | Klapholz, M. | Kosinski, E. | Kozinn, M. | Kraus, D. | Krueger, S. | Krum, H. | Kumar, S. | Lader, E. | Lee, C. | Levy, W. | Lewis, E. | Light-McGroary, K. | Loh, I. | Lombardi, W. | Machado, C. | Maislos, F. | Mancini, D. | Markus, T. | Mather, P. | McCants, K. | McGrew, F. | McLaurin, B. | McMillan, E. | McNamara, D. | Meyer, T. | Meymandi, S. | Miller, A. | Minami, E. | Modi, M. | Mody, F. | Mohanty, P. | Moscoso, R. | Moskowitz, R. | Moustafa, M. | Mullen, M. | Naz, T. | Noonan, T. | O'Brien, T. | Oellerich, W. | Oren, R. | Pamboukian, S. | Pereira, N. | Pitt, W. | Porter, C. | Prabhu, S. | Promisloff, S. | Ratkovec, R. | Richardson, R. | Ross, A. | Saleh, N. | Saltzberg, M. | Sarkar, S. | Schmedtje, J. | Schneider, R. | Schuyler, G. | Shanes, J. | Sharma, A. | Siegel, C. | Siegel, R. | Silber, D. | Singh, V. | Singh, N. | Singh, J. | Sklar, J. | Small, R. | Smith, A. | Smith, E. | Smith, E. | Smull, D. | Sotolongo, R. | Staniloae, C. | Stapleton, D. | Steele, P. | Stehlik, J. | Stein, M. | Tang, W. | Thadani, U. | Torre-Amoine, G. | Trichon, B. | Tsai, C. | Tummala, R. | Van Bakel, A. | Vicari, R. | Vijay, N. | Vijayaraghavan, K. | Vittorio, T. | Vossler, M. | Wagoner, L. | Wallis, D. | Ward, N. | Widmer, M. | Wight, J. | Wilkins, C. | Williams, C. | Williams, G. | Winchester, M. | Winkel, E. | Wittmer, B. | Wood, D. | Wormer, D. | Wright, R. | Xu, Z. | Yasin, M. | Zolty, R.
European Journal of Heart Failure  2013;15(3):334-341.
Aims
This report describes the baseline characteristics of patients in the Reduction of Events with Darbepoetin alfa in Heart Failure trial (RED-HF) which is testing the hypothesis that anaemia correction with darbepoetin alfa will reduce the composite endpoint of death from any cause or hospital admission for worsening heart failure, and improve other outcomes.
Methods and results
Key demographic, clinical, and laboratory findings, along with baseline treatment, are reported and compared with those of patients in other recent clinical trials in heart failure. Compared with other recent trials, RED-HF enrolled more elderly [mean age 70 (SD 11.4) years], female (41%), and black (9%) patients. RED-HF patients more often had diabetes (46%) and renal impairment (72% had an estimated glomerular filtration rate <60 mL/min/1.73 m2). Patients in RED-HF had heart failure of longer duration [5.3 (5.4) years], worse NYHA class (35% II, 63% III, and 2% IV), and more signs of congestion. Mean EF was 30% (6.8%). RED-HF patients were well treated at randomization, and pharmacological therapy at baseline was broadly similar to that of other recent trials, taking account of study-specific inclusion/exclusion criteria. Median (interquartile range) haemoglobin at baseline was 112 (106–117) g/L.
Conclusion
The anaemic patients enrolled in RED-HF were older, moderately to markedly symptomatic, and had extensive co-morbidity.
doi:10.1093/eurjhf/hfs204
PMCID: PMC3576902  PMID: 23329651
Heart failure; Anaemia
2.  Hospital Career Structure 
Appleyard, W. J. | Barbor, P. R. H. | Barraclough, M. A. | Beeden, A. G. | Berger, P. | Black, A. J. | Blaxill, R. W. | Boggon, R. P. | Butler, M. J. | Chilvers, A. S. | Church, Armorel B. | Cobb, P. J. | Cochrane, A. M. G. | Condon, P. I. | Cove-Smith, J. R. | Cream, J. J. | Croft, D. N. | Crick, M. D. P. | Davidson, N. McD. | Davies, D. R. | Davies, R. J. | Devlin, H. B. | Dutton, N. M. | Eames, G. M. | Eisinger, A. J. | Eustace, P. | Evans, D. S. | Evans, J. M. G. | Evans, R. | Evans-Prosser, C. D. G. | Eykyn, Susannah J. | Fawcett, B. M. | Foley, T. H. | Follows, R. C. | Frommer, D. J. | Gardner, N. H. | Gent, A. E. | Gibbens, G. L. D. | Goldberg, D. P. B. | Grace, R. H. | Graham, J. M. | Gray, R. C. F. | Green, M. | Greenhalgh, R. M. | Gregory, I. C. | Griffiths, W. A. D. | Lee, D. M. Gruebel | Hall, J. H. | Hammond, K. C. | Haas, P. A. | Herzberg, L. | Heughan, C. | Hicks, E. P. | Hilary-Jones, E. P. | Hope, R. J. | Inman, S. E. | Jackson, R. K. | Jenkins, Esmé S. | Johnston, D. I. | Jones, D. J. | Joy, M. D. | Kaye, H. H. | Lloyd-Davies, R. W. | Logan, R. L. | Lord, Elizabeth J. A. | Marks, C. J. | Martin, E. C. | Mathews, J. A. | McCarthy, T. G. | McLachlan, R. | Melcher, D. H. | Milward, T. M. | Morgan, J. M. | Moul, D. J. | Negus, D. | Newman, C. G. H. | Nicholson, G. D. | Norton, R. | Nutting, M. G. | Nicholls, J. T. | Olver, R. E. | Orr, N. W. M. | Pratt, D. G. | Prasad, D. S. | Peachey, R. S. | Petch, M. C. | Phillips, D. J. | Pim, H. P. | Poole-Wilson, P. A. | Prenton, M. A. | Price, A. B. | Pulvertaft, R. W. | Rawlins, M. D. | Redman, L. R. | Reed, R. N. | Rees, R. | Rimmer, Diana M. D. | Rippey, J. J. | Rosenberg, M. T. | Rosendorff, C. | Rowland, R. | Salisbury, Jennifer A. | Sargent, N. W. | Saunders, P. G. | Shilling, J. S. | Singh, A. K. | Smith, M. E. | Solan, M. J. | Stephenson, R. H. | Torrens, M. | Trevelyan, H. | Walker, G. | Warden, N. J. | Watts, J. I. M. | Webb, D. A. | White, J. E. | Wight, D. G. D. | Williams, Jean O. | Willoughby, J. M. T. | Wilson, D. S.
British Medical Journal  1968;3(5611):188-189.
PMCID: PMC1986097
3.  DNA sequence and analysis of human chromosome 9 
Humphray, S. J. | Oliver, K. | Hunt, A. R. | Plumb, R. W. | Loveland, J. E. | Howe, K. L. | Andrews, T. D. | Searle, S. | Hunt, S. E. | Scott, C. E. | Jones, M. C. | Ainscough, R. | Almeida, J. P. | Ambrose, K. D. | Ashwell, R. I. S. | Babbage, A. K. | Babbage, S. | Bagguley, C. L. | Bailey, J. | Banerjee, R. | Barker, D. J. | Barlow, K. F. | Bates, K. | Beasley, H. | Beasley, O. | Bird, C. P. | Bray-Allen, S. | Brown, A. J. | Brown, J. Y. | Burford, D. | Burrill, W. | Burton, J. | Carder, C. | Carter, N. P. | Chapman, J. C. | Chen, Y. | Clarke, G. | Clark, S. Y. | Clee, C. M. | Clegg, S. | Collier, R. E. | Corby, N. | Crosier, M. | Cummings, A. T. | Davies, J. | Dhami, P. | Dunn, M. | Dutta, I. | Dyer, L. W. | Earthrowl, M. E. | Faulkner, L. | Fleming, C. J. | Frankish, A. | Frankland, J. A. | French, L. | Fricker, D. G. | Garner, P. | Garnett, J. | Ghori, J. | Gilbert, J. G. R. | Glison, C. | Grafham, D. V. | Gribble, S. | Griffiths, C. | Griffiths-Jones, S. | Grocock, R. | Guy, J. | Hall, R. E. | Hammond, S. | Harley, J. L. | Harrison, E. S. I. | Hart, E. A. | Heath, P. D. | Henderson, C. D. | Hopkins, B. L. | Howard, P. J. | Howden, P. J. | Huckle, E. | Johnson, C. | Johnson, D. | Joy, A. A. | Kay, M. | Keenan, S. | Kershaw, J. K. | Kimberley, A. M. | King, A. | Knights, A. | Laird, G. K. | Langford, C. | Lawlor, S. | Leongamornlert, D. A. | Leversha, M. | Lloyd, C. | Lloyd, D. M. | Lovell, J. | Martin, S. | Mashreghi-Mohammadi, M. | Matthews, L. | McLaren, S. | McLay, K. E. | McMurray, A. | Milne, S. | Nickerson, T. | Nisbett, J. | Nordsiek, G. | Pearce, A. V. | Peck, A. I. | Porter, K. M. | Pandian, R. | Pelan, S. | Phillimore, B. | Povey, S. | Ramsey, Y. | Rand, V. | Scharfe, M. | Sehra, H. K. | Shownkeen, R. | Sims, S. K. | Skuce, C. D. | Smith, M. | Steward, C. A. | Swarbreck, D. | Sycamore, N. | Tester, J. | Thorpe, A. | Tracey, A. | Tromans, A. | Thomas, D. W. | Wall, M. | Wallis, J. M. | West, A. P. | Whitehead, S. L. | Willey, D. L. | Williams, S. A. | Wilming, L. | Wray, P. W. | Young, L. | Ashurst, J. L. | Coulson, A. | Blöcker, H. | Durbin, R. | Sulston, J. E. | Hubbard, T. | Jackson, M. J. | Bentley, D. R. | Beck, S. | Rogers, J. | Dunham, I.
Nature  2004;429(6990):369-374.
Chromosome 9 is highly structurally polymorphic. It contains the largest autosomal block of heterochromatin, which is heteromorphic in 6–8% of humans, whereas pericentric inversions occur in more than 1% of the population. The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs and represents >99.6% of the region. Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block. We have annotated 1,149 genes, including genes implicated in male-to-female sex reversal, cancer and neurodegenerative disease, and 426 pseudogenes. The chromosome contains the largest interferon gene cluster in the human genome. There is also a region of exceptionally high gene and G + C content including genes paralogous to those in the major histocompatibility complex. We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection.
doi:10.1038/nature02465
PMCID: PMC2734081  PMID: 15164053
4.  FGF receptor genes and breast cancer susceptibility: results from the Breast Cancer Association Consortium 
Agarwal, D | Pineda, S | Michailidou, K | Herranz, J | Pita, G | Moreno, L T | Alonso, M R | Dennis, J | Wang, Q | Bolla, M K | Meyer, K B | Menéndez-Rodríguez, P | Hardisson, D | Mendiola, M | González-Neira, A | Lindblom, A | Margolin, S | Swerdlow, A | Ashworth, A | Orr, N | Jones, M | Matsuo, K | Ito, H | Iwata, H | Kondo, N | Hartman, M | Hui, M | Lim, W Y | T-C Iau, P | Sawyer, E | Tomlinson, I | Kerin, M | Miller, N | Kang, D | Choi, J-Y | Park, S K | Noh, D-Y | Hopper, J L | Schmidt, D F | Makalic, E | Southey, M C | Teo, S H | Yip, C H | Sivanandan, K | Tay, W-T | Brauch, H | Brüning, T | Hamann, U | Dunning, A M | Shah, M | Andrulis, I L | Knight, J A | Glendon, G | Tchatchou, S | Schmidt, M K | Broeks, A | Rosenberg, E H | van't Veer, L J | Fasching, P A | Renner, S P | Ekici, A B | Beckmann, M W | Shen, C-Y | Hsiung, C-N | Yu, J-C | Hou, M-F | Blot, W | Cai, Q | Wu, A H | Tseng, C-C | Van Den Berg, D | Stram, D O | Cox, A | Brock, I W | Reed, M W R | Muir, K | Lophatananon, A | Stewart-Brown, S | Siriwanarangsan, P | Zheng, W | Deming-Halverson, S | Shrubsole, M J | Long, J | Shu, X-O | Lu, W | Gao, Y-T | Zhang, B | Radice, P | Peterlongo, P | Manoukian, S | Mariette, F | Sangrajrang, S | McKay, J | Couch, F J | Toland, A E | Yannoukakos, D | Fletcher, O | Johnson, N | Silva, I dos Santos | Peto, J | Marme, F | Burwinkel, B | Guénel, P | Truong, T | Sanchez, M | Mulot, C | Bojesen, S E | Nordestgaard, B G | Flyer, H | Brenner, H | Dieffenbach, A K | Arndt, V | Stegmaier, C | Mannermaa, A | Kataja, V | Kosma, V-M | Hartikainen, J M | Lambrechts, D | Yesilyurt, B T | Floris, G | Leunen, K | Chang-Claude, J | Rudolph, A | Seibold, P | Flesch-Janys, D | Wang, X | Olson, J E | Vachon, C | Purrington, K | Giles, G G | Severi, G | Baglietto, L | Haiman, C A | Henderson, B E | Schumacher, F | Le Marchand, L | Simard, J | Dumont, M | Goldberg, M S | Labrèche, F | Winqvist, R | Pylkäs, K | Jukkola-Vuorinen, A | Grip, M | Devilee, P | Tollenaar, R A E M | Seynaeve, C | García-Closas, M | Chanock, S J | Lissowska, J | Figueroa, J D | Czene, K | Eriksson, M | Humphreys, K | Darabi, H | Hooning, M J | Kriege, M | Collée, J M | Tilanus-Linthorst, M | Li, J | Jakubowska, A | Lubinski, J | Jaworska-Bieniek, K | Durda, K | Nevanlinna, H | Muranen, T A | Aittomäki, K | Blomqvist, C | Bogdanova, N | Dörk, T | Hall, P | Chenevix-Trench, G | Easton, D F | Pharoah, P D P | Arias-Perez, J I | Zamora, P | Benítez, J | Milne, R L
British Journal of Cancer  2014;110(4):1088-1100.
Background:
Breast cancer is one of the most common malignancies in women. Genome-wide association studies have identified FGFR2 as a breast cancer susceptibility gene. Common variation in other fibroblast growth factor (FGF) receptors might also modify risk. We tested this hypothesis by studying genotyped single-nucleotide polymorphisms (SNPs) and imputed SNPs in FGFR1, FGFR3, FGFR4 and FGFRL1 in the Breast Cancer Association Consortium.
Methods:
Data were combined from 49 studies, including 53 835 cases and 50 156 controls, of which 89 050 (46 450 cases and 42 600 controls) were of European ancestry, 12 893 (6269 cases and 6624 controls) of Asian and 2048 (1116 cases and 932 controls) of African ancestry. Associations with risk of breast cancer, overall and by disease sub-type, were assessed using unconditional logistic regression.
Results:
Little evidence of association with breast cancer risk was observed for SNPs in the FGF receptor genes. The strongest evidence in European women was for rs743682 in FGFR3; the estimated per-allele odds ratio was 1.05 (95% confidence interval=1.02–1.09, P=0.0020), which is substantially lower than that observed for SNPs in FGFR2.
Conclusion:
Our results suggest that common variants in the other FGF receptors are not associated with risk of breast cancer to the degree observed for FGFR2.
doi:10.1038/bjc.2013.769
PMCID: PMC3929867  PMID: 24548884
breast cancer; SNP; FGF receptors; susceptibility; disease subtypes
5.  High Rate of HIV Resuppression After Viral Failure on First-line Antiretroviral Therapy in the Absence of Switch to Second-line Therapy 
Gupta, Ravindra K. | Goodall, Ruth L. | Ranopa, Michael | Kityo, Cissy | Munderi, Paula | Lyagoba, Fred | Mugarura, Lincoln | Gilks, Charles F. | Kaleebu, Pontiano | Pillay, Deenan | Grosskurth, H. | Munderi, P. | Kabuye, G. | Nsibambi, D. | Kasirye, R. | Zalwango, E. | Nakazibwe, M. | Kikaire, B. | Nassuna, G. | Massa, R. | Fadhiru, K. | Namyalo, M. | Zalwango, A. | Generous, L. | Khauka, P. | Rutikarayo, N. | Nakahima, W. | Mugisha, A. | Todd, J. | Levin, J. | Muyingo, S. | Ruberantwari, A. | Kaleebu, P. | Yirrell, D. | Ndembi, N. | Lyagoba, F. | Hughes, P. | Aber, M. | Medina Lara, A. | Foster, S. | Amurwon, J. | Mugyenyi, P. | Kityo, C. | Ssali, F. | Tumukunde, D. | Otim, T. | Kabanda, J. | Musana, H. | Akao, J. | Kyomugisha, H. | Byamukama, A. | Sabiiti, J. | Komugyena, J. | Wavamunno, P. | Mukiibi, S. | Drasiku, A. | Byaruhanga, R. | Labeja, O. | Katundu, P. | Tugume, S. | Awio, P. | Namazzi, A. | Bakeinyaga, T. G. | Katabira, H. | Abaine, D. | Tukamushaba, J. | Anywar, W. | Ojiambo, W. | Angweng, E. | Murungi, S. | Haguma, W. | Atwiine, S. | Kigozi, J. | Latif, A. | Hakim, J. | Robertson, V. | Reid, A. | Chidziva, E. | Bulaya-Tembo, R. | Musoro, G. | Taziwa, F. | Chimbetete, C. | Chakonza, L. | Mawora, A. | Muvirimi, C. | Tinago, G. | Svovanapasis, P. | Simango, M. | Chirema, O. | Machingura, J. | Mutsai, S. | Phiri, M. | Bafana, T. | Chirara, M. | Muchabaiwa, L. | Muzambi, M. | Katabira, E. | Ronald, A. | Kambungu, A. | Lutwama, F. | Nanfuka, A. | Walusimbi, J. | Nabankema, E. | Nalumenya, R. | Namuli, T. | Kulume, R. | Namata, I. | Nyachwo, L. | Florence, A. | Kusiima, A. | Lubwama, E. | Nairuba, R. | Oketta, F. | Buluma, E. | Waita, R. | Ojiambo, H. | Sadik, F. | Wanyama, J. | Nabongo, P. | Ochai, R. | Muhweezi, D. | Gilks, C. | Boocock, K. | Puddephatt, C. | Winogron, D. | Bohannon, J. | Darbyshire, J. | Gibb, M. D. | Burke, A. | Bray, D. | Babiker, A. | Walker, S. A. | Wilkes, H. | Rauchenberger, M. | Sheehan, S. | Peto, L. | Taylor, K. | Spyer, M. | Ferrier, A. | Naidoo, B. | Dunn, D. | Goodall, R. | Nanfuka, R. | Mufuka-Kapuya, C. | Kaleebu, P. | Pillay, D. | Awio, P. | Chirara, M. | Dunn, D. | Gilks, C. | Goodall, R. | Kapaata, A. | Katuramur, M. | Lyagoba, F. | Magala, R. | Magambo, B. | Mataruka, K. | McCormick, A. | Mugarura, L. | Musunga, T. | Nabankkema, M. | Nkalubo, J. | Nkurunziza, P. | Parry, C. | Robertson, V. | Spyer, M. | Yirrell, D. | Medina Lara, A. | Foster, S. | Amurwon, J. | Nyanzi Wakholi, B. | Kigozi, J. | Muchabaiwa, L. | Muzambi, M. | Weller, I. | Babiker, A. | Bahendeka, S. | Bassett, M. | Chogo Wapakhabulo, A. | Darbyshire, J. | Gazzard, B. | Gilks, C. | Hakim, J. | Latif, A. | Mapuchere, C. | Mugurungi, O. | Mugyenyi, P. | Burke, C. | Jones, S. | Newland, C. | Rahim, S. | Rooney, J. | Smith, M. | Snowden, W. | Steens, J.-M. | Breckenridge, A. | McLaren, A. | Hill, C. | Matenga, J. | Pozniak, A. | Serwadda, D. | Peto, T. | Palfreeman, A. | Borok, M.
In a randomized comparison of nevirapine or abacavir with zidovudine plus lamivudine, routine viral load monitoring was not performed, yet 27% of individuals with viral failure at week 48 experienced resuppression by week 96 without switching. This supports World Health Organization recommendations that suspected viral failure should trigger adherence counseling and repeat measurement before a treatment switch is considered.
doi:10.1093/cid/cit933
PMCID: PMC3952602  PMID: 24352348
HIV; failure; viral resuppression; resistance; Africa
6.  The DNA sequence and analysis of human chromosome 13 
Dunham, A. | Matthews, L. H. | Burton, J. | Ashurst, J. L. | Howe, K. L. | Ashcroft, K. J. | Beare, D. M. | Burford, D. C. | Hunt, S. E. | Griffiths-Jones, S. | Jones, M. C. | Keenan, S. J. | Oliver, K. | Scott, C. E. | Ainscough, R. | Almeida, J. P. | Ambrose, K. D. | Andrews, D. T. | Ashwell, R. I. S. | Babbage, A. K. | Bagguley, C. L. | Bailey, J. | Bannerjee, R. | Barlow, K. F. | Bates, K. | Beasley, H. | Bird, C. P. | Bray-Allen, S. | Brown, A. J. | Brown, J. Y. | Burrill, W. | Carder, C. | Carter, N. P. | Chapman, J. C. | Clamp, M. E. | Clark, S. Y. | Clarke, G. | Clee, C. M. | Clegg, S. C. M. | Cobley, V. | Collins, J. E. | Corby, N. | Coville, G. J. | Deloukas, P. | Dhami, P. | Dunham, I. | Dunn, M. | Earthrowl, M. E. | Ellington, A. G. | Faulkner, L. | Frankish, A. G. | Frankland, J. | French, L. | Garner, P. | Garnett, J. | Gilbert, J. G. R. | Gilson, C. J. | Ghori, J. | Grafham, D. V. | Gribble, S. M. | Griffiths, C. | Hall, R. E. | Hammond, S. | Harley, J. L. | Hart, E. A. | Heath, P. D. | Howden, P. J. | Huckle, E. J. | Hunt, P. J. | Hunt, A. R. | Johnson, C. | Johnson, D. | Kay, M. | Kimberley, A. M. | King, A. | Laird, G. K. | Langford, C. J. | Lawlor, S. | Leongamornlert, D. A. | Lloyd, D. M. | Lloyd, C. | Loveland, J. E. | Lovell, J. | Martin, S. | Mashreghi-Mohammadi, M. | McLaren, S. J. | McMurray, A. | Milne, S. | Moore, M. J. F. | Nickerson, T. | Palmer, S. A. | Pearce, A. V. | Peck, A. I. | Pelan, S. | Phillimore, B. | Porter, K. M. | Rice, C. M. | Searle, S. | Sehra, H. K. | Shownkeen, R. | Skuce, C. D. | Smith, M. | Steward, C. A. | Sycamore, N. | Tester, J. | Thomas, D. W. | Tracey, A. | Tromans, A. | Tubby, B. | Wall, M. | Wallis, J. M. | West, A. P. | Whitehead, S. L. | Willey, D. L. | Wilming, L. | Wray, P. W. | Wright, M. W. | Young, L. | Coulson, A. | Durbin, R. | Hubbard, T. | Sulston, J. E. | Beck, S. | Bentley, D. R. | Rogers, J. | Ross, M. T.
Nature  2004;428(6982):522-528.
Chromosome 13 is the largest acrocentric human chromosome. It carries genes involved in cancer including the breast cancer type 2 (BRCA2) and retinoblastoma (RB1) genes, is frequently rearranged in B-cell chronic lymphocytic leukaemia, and contains the DAOA locus associated with bipolar disorder and schizophrenia. We describe completion and analysis of 95.5 megabases (Mb) of sequence from chromosome 13, which contains 633 genes and 296 pseudogenes. We estimate that more than 95.4% of the protein-coding genes of this chromosome have been identified, on the basis of comparison with other vertebrate genome sequences. Additionally, 105 putative non-coding RNA genes were found. Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb.
doi:10.1038/nature02379
PMCID: PMC2665288  PMID: 15057823
7.  Physician-assessed and patient-reported outcome measures in chemotherapy-induced sensory peripheral neurotoxicity: two sides of the same coin 
Alberti, P. | Rossi, E. | Cornblath, D. R. | Merkies, I. S. J. | Postma, T. J. | Frigeni, B. | Bruna, J. | Velasco, R. | Argyriou, A. A. | Kalofonos, H. P. | Psimaras, D. | Ricard, D. | Pace, A. | Galiè, E. | Briani, C. | Dalla Torre, C. | Faber, C. G. | Lalisang, R. I. | Boogerd, W. | Brandsma, D. | Koeppen, S. | Hense, J. | Storey, D. | Kerrigan, S. | Schenone, A. | Fabbri, S. | Valsecchi, M. G. | Cavaletti, G. | Cavaletti, G. | Cornblath, D.R. | Merkies, I.S.J. | Postma, T.J. | Valsecchi, M.G | Galimberti, S. | Rossi, E. | Cavaletti, G. | Frigeni, B. | Lanzani, F. | Mattavelli, L. | Piatti, ML. | Alberti, P. | Binda, D. | Bidoli, P.. | Cazzaniga, M. | Cortinovis, D. | Bruna, J. | Velasco, R. | Argyriou, AA. | Kalofonos, HP. | Psimaras, D. | Ricard, D. | Pace, A. | Galiè, E. | Briani, C. | Lucchetta, M. | Campagnolo, M. | Dalla Torre, C. | Merkies, ISJ. | Faber, CG. | Merkies, ISJ. | Vanhoutte, EK. | Bakkers, M. | Brouwer, B. | Lalisang, RI. | Boogerd, W. | Brandsma, D. | Koeppen, S. | Hense, J. | Grant, R. | Storey, D. | Kerrigan, S. | Schenone, A. | Reni, L. | Piras, B. | Fabbri, S. | Padua, L. | Granata, G. | Leandri, M. | Ghignotti, I. | Plasmati, R.. | Pastorelli, F. | Postma, TJ. | Heimans, JJ. | Eurelings, M. | Meijer, RJ. | Grisold, W. | Lindeck Pozza, E. | Mazzeo, A. | Toscano, A. | Tomasello, C. | Altavilla, G. | Penas Prado, M. | Dominguez Gonzalez, C. | Dorsey, SG. | Brell, JM.
Annals of Oncology  2013;25(1):257-264.
The perception of the severity and relevance of Chemotherapy Induced Peripheral Neurotoxicity (CIPN) is different for physicians and patients. This study provides the basis for a rationale use of different physician assessed scales and of European Organization for Research and Treatment of Cancer CIPN specific self-report questionnaire (EORTC QOL-CIPN20).
Background
The different perception and assessment of chemotherapy-induced peripheral neurotoxicity (CIPN) between healthcare providers and patients has not yet been fully addressed, although these two approaches might eventually lead to inconsistent, possibly conflicting interpretation, especially regarding sensory impairment.
Patients and methods
A cohort of 281 subjects with stable CIPN was evaluated with the National Cancer Institute—Common Toxicity Criteria (NCI-CTC v. 2.0) sensory scale, the clinical Total Neuropathy Score (TNSc©), the modified Inflammatory Neuropathy Cause and Treatment (INCAT) sensory sumscore (mISS) and the European Organization for Research and Treatment of Cancer CIPN specific self-report questionnaire (EORTC QOL-CIPN20).
Results
Patients' probability estimates showed that the EORTC QLQ-CIPN20 sensory score was overall more highly related to the NCI-CTC sensory score. However, the vibration perception item of the TNSc had a higher probability to be scored 0 for EORTC QLQ-CIPN20 scores lower than 35, as vibration score 2 for EORTC QLQ-CIPN20 scores between 35 and 50 and as grade 3 or 4 for EORTC QLQ-CIPN20 scores higher than 50. The linear models showed a significant trend between each mISS item and increasing EORTC QLQ-CIPN20 sensory scores.
Conclusion
None of the clinical items had a perfect relationship with patients' perception, and most of the discrepancies stood in the intermediate levels of CIPN severity. Our data indicate that to achieve a comprehensive knowledge of CIPN including a reliable assessment of both the severity and the quality of CIPN-related sensory impairment, clinical and PRO measures should be always combined.
doi:10.1093/annonc/mdt409
PMCID: PMC3868322  PMID: 24256846
chemotherapy; neuropathy; assessment; patient-reported outcome measure; neurotoxicity
8.  The chemotherapy-induced peripheral neuropathy outcome measures standardization study: from consensus to the first validity and reliability findings 
Cavaletti, G. | Cornblath, D. R. | Merkies, I. S. J. | Postma, T. J. | Rossi, E. | Frigeni, B. | Alberti, P. | Bruna, J. | Velasco, R. | Argyriou, A. A. | Kalofonos, H. P. | Psimaras, D. | Ricard, D. | Pace, A. | Galiè, E. | Briani, C. | Dalla Torre, C. | Faber, C. G. | Lalisang, R. I. | Boogerd, W. | Brandsma, D. | Koeppen, S. | Hense, J. | Storey, D. | Kerrigan, S. | Schenone, A. | Fabbri, S. | Valsecchi, M. G. | Mazzeo, A. | Pace, A. | Pessino, A. | Schenone, A. | Toscano, A. | Argyriou, A.A. | Brouwer, B. | Frigeni, B. | Piras, B. | Briani, C. | Dalla Torre, C. | Dominguez Gonzalez, C. | Faber, C. G. | Tomasello, C. | Binda, D. | Brandsma, D. | Cortinovis, D. | Psimaras, D. | Ricard, D. | Storey, D. | Cornblath, D.R. | Galiè, E. | Lindeck Pozza, E. | Rossi, E. | Vanhoutte, E.K. | Lanzani, F. | Pastorelli, F. | Altavilla, G. | Cavaletti, G. | Granata, G. | Kalofonos, H.P. | Ghignotti, I. | Merkies, I.S.J. | Bruna, J. | Hense, J. | Heimans, J.J. | Mattavelli, L. | Padua, L. | Reni, L. | Bakkers, M. | Boogerd, M. | Campagnolo, M. | Cazzaniga, M. | Eurelings, M. | Leandri, M. | Lucchetta, M. | Penas Prado, M. | Russo, M. | Valsecchi, M.G. | Piatti, M.L. | Alberti, P. | Bidoli, P. | Grant, R. | Plasmati, R. | Velasco, R. | Lalisang, R.I. | Meijer, R.J. | Fabbri, S. | Dorsey, S. G. | Galimberti, S. | Kerrigan, S. | Koeppen, S. | Postma, T.J. | Boogerd, W. | Grisold, W.
Annals of Oncology  2012;24(2):454-462.
Background
Chemotherapy-induced peripheral neuropathy (CIPN) is a debilitating and dose-limiting complication of cancer treatment. Thus far, the impact of CIPN has not been studied in a systematic clinimetric manner. The objective of the study was to select outcome measures for CIPN evaluation and to establish their validity and reproducibility in a cross-sectional multicenter study.
Patients and methods
After literature review and a consensus meeting among experts, face/content validity were obtained for the following selected scales: the National Cancer Institute-Common Toxicity Criteria (NCI-CTC), the Total Neuropathy Score clinical version (TNSc), the modified Inflammatory Neuropathy Cause and Treatment (INCAT) group sensory sumscore (mISS), the European Organization for Research and Treatment of Cancer (EORTC) QLQ-C30, and CIPN20 quality-of-life measures. A total of 281 patients with stable CIPN were examined. Validity (correlation) and reliability studies were carried out.
Results
Good inter-/intra-observer scores were obtained for the TNSc, mISS, and NCI-CTC sensory/motor subscales. Test–retest values were also good for the EORTC QLQ-C30 and CIPN20. Acceptable validity scores were obtained through the correlation among the measures.
Conclusion
Good validity and reliability scores were demonstrated for the set of selected impairment and quality-of-life outcome measures in CIPN. Future studies are planned to investigate the responsiveness aspects of these measures.
doi:10.1093/annonc/mds329
PMCID: PMC3551481  PMID: 22910842
assessment; chemotherapy; clinimetrics; peripheral neuropathy; reliability; validity
9.  Global, regional, and national incidence and mortality for HIV, tuberculosis, and malaria during 1990–2013: a systematic analysis for the Global Burden of Disease Study 2013 
Murray, Christopher J L | Ortblad, Katrina F | Guinovart, Caterina | Lim, Stephen S | Wolock, Timothy M | Roberts, D Allen | Dansereau, Emily A | Graetz, Nicholas | Barber, Ryan M | Brown, Jonathan C | Wang, Haidong | Duber, Herbert C | Naghavi, Mohsen | Dicker, Daniel | Dandona, Lalit | Salomon, Joshua A | Heuton, Kyle R | Foreman, Kyle | Phillips, David E | Fleming, Thomas D | Flaxman, Abraham D | Phillips, Bryan K | Johnson, Elizabeth K | Coggeshall, Megan S | Abd-Allah, Foad | Ferede, Semaw | Abraham, Jerry P | Abubakar, Ibrahim | Abu-Raddad, Laith J | Abu-Rmeileh, Niveen Me | Achoki, Tom | Adeyemo, Austine Olufemi | Adou, Arsène Kouablan | Adsuar, José C | Agardh, Emilie Elisabet | Akena, Dickens | Al Kahbouri, Mazin J | Alasfoor, Deena | Albittar, Mohammed I | Alcalá-Cerra, Gabriel | Alegretti, Miguel Angel | Alemu, Zewdie Aderaw | Alfonso-Cristancho, Rafael | Alhabib, Samia | Ali, Raghib | Alla, Francois | Allen, Peter J | Alsharif, Ubai | Alvarez, Elena | Alvis-Guzman, Nelson | Amankwaa, Adansi A | Amare, Azmeraw T | Amini, Hassan | Ammar, Walid | Anderson, Benjamin O | Antonio, Carl Abelardo T | Anwari, Palwasha | Ärnlöv, Johan | Arsenijevic, Valentina S Arsic | Artaman, Ali | Asghar, Rana J | Assadi, Reza | Atkins, Lydia S | Badawi, Alaa | Balakrishnan, Kalpana | Banerjee, Amitava | Basu, Sanjay | Beardsley, Justin | Bekele, Tolesa | Bell, Michelle L | Bernabe, Eduardo | Beyene, Tariku Jibat | Bhala, Neeraj | Bhalla, Ashish | Bhutta, Zulfiqar A | Abdulhak, Aref Bin | Binagwaho, Agnes | Blore, Jed D | Basara, Berrak Bora | Bose, Dipan | Brainin, Michael | Breitborde, Nicholas | Castañeda-Orjuela, Carlos A | Catalá-López, Ferrán | Chadha, Vineet K | Chang, Jung-Chen | Chiang, Peggy Pei-Chia | Chuang, Ting-Wu | Colomar, Mercedes | Cooper, Leslie Trumbull | Cooper, Cyrus | Courville, Karen J | Cowie, Benjamin C | Criqui, Michael H | Dandona, Rakhi | Dayama, Anand | De Leo, Diego | Degenhardt, Louisa | Del Pozo-Cruz, Borja | Deribe, Kebede | Jarlais, Don C Des | Dessalegn, Muluken | Dharmaratne, Samath D | Dilmen, Uğur | Ding, Eric L | Driscoll, Tim R | Durrani, Adnan M | Ellenbogen, Richard G | Ermakov, Sergey Petrovich | Esteghamati, Alireza | Faraon, Emerito Jose A | Farzadfar, Farshad | Fereshtehnejad, Seyed-Mohammad | Fijabi, Daniel Obadare | Forouzanfar, Mohammad H | Paleo, Urbano Fra. | Gaffikin, Lynne | Gamkrelidze, Amiran | Gankpé, Fortuné Gbètoho | Geleijnse, Johanna M | Gessner, Bradford D | Gibney, Katherine B | Ginawi, Ibrahim Abdelmageem Mohamed | Glaser, Elizabeth L | Gona, Philimon | Goto, Atsushi | Gouda, Hebe N | Gugnani, Harish Chander | Gupta, Rajeev | Gupta, Rahul | Hafezi-Nejad, Nima | Hamadeh, Randah Ribhi | Hammami, Mouhanad | Hankey, Graeme J | Harb, Hilda L | Haro, Josep Maria | Havmoeller, Rasmus | Hay, Simon I | Hedayati, Mohammad T | Pi, Ileana B Heredia | Hoek, Hans W | Hornberger, John C | Hosgood, H Dean | Hotez, Peter J | Hoy, Damian G | Huang, John J | Iburg, Kim M | Idrisov, Bulat T | Innos, Kaire | Jacobsen, Kathryn H | Jeemon, Panniyammakal | Jensen, Paul N | Jha, Vivekanand | Jiang, Guohong | Jonas, Jost B | Juel, Knud | Kan, Haidong | Kankindi, Ida | Karam, Nadim E | Karch, André | Karema, Corine Kakizi | Kaul, Anil | Kawakami, Norito | Kazi, Dhruv S | Kemp, Andrew H | Kengne, Andre Pascal | Keren, Andre | Kereselidze, Maia | Khader, Yousef Saleh | Khalifa, Shams Eldin Ali Hassan | Khan, Ejaz Ahmed | Khang, Young-Ho | Khonelidze, Irma | Kinfu, Yohannes | Kinge, Jonas M | Knibbs, Luke | Kokubo, Yoshihiro | Kosen, S | Defo, Barthelemy Kuate | Kulkarni, Veena S | Kulkarni, Chanda | Kumar, Kaushalendra | Kumar, Ravi B | Kumar, G Anil | Kwan, Gene F | Lai, Taavi | Balaji, Arjun Lakshmana | Lam, Hilton | Lan, Qing | Lansingh, Van C | Larson, Heidi J | Larsson, Anders | Lee, Jong-Tae | Leigh, James | Leinsalu, Mall | Leung, Ricky | Li, Yichong | Li, Yongmei | De Lima, Graça Maria Ferreira | Lin, Hsien-Ho | Lipshultz, Steven E | Liu, Shiwei | Liu, Yang | Lloyd, Belinda K | Lotufo, Paulo A | Machado, Vasco Manuel Pedro | Maclachlan, Jennifer H | Magis-Rodriguez, Carlos | Majdan, Marek | Mapoma, Christopher Chabila | Marcenes, Wagner | Marzan, Melvin Barrientos | Masci, Joseph R | Mashal, Mohammad Taufiq | Mason-Jones, Amanda J | Mayosi, Bongani M | Mazorodze, Tasara T | Mckay, Abigail Cecilia | Meaney, Peter A | Mehndiratta, Man Mohan | Mejia-Rodriguez, Fabiola | Melaku, Yohannes Adama | Memish, Ziad A | Mendoza, Walter | Miller, Ted R | Mills, Edward J | Mohammad, Karzan Abdulmuhsin | Mokdad, Ali H | Mola, Glen Liddell | Monasta, Lorenzo | Montico, Marcella | Moore, Ami R | Mori, Rintaro | Moturi, Wilkister Nyaora | Mukaigawara, Mitsuru | Murthy, Kinnari S | Naheed, Aliya | Naidoo, Kovin S | Naldi, Luigi | Nangia, Vinay | Narayan, K M Venkat | Nash, Denis | Nejjari, Chakib | Nelson, Robert G | Neupane, Sudan Prasad | Newton, Charles R | Ng, Marie | Nisar, Muhammad Imran | Nolte, Sandra | Norheim, Ole F | Nowaseb, Vincent | Nyakarahuka, Luke | Oh, In-Hwan | Ohkubo, Takayoshi | Olusanya, Bolajoko O | Omer, Saad B | Opio, John Nelson | Orisakwe, Orish Ebere | Pandian, Jeyaraj D | Papachristou, Christina | Caicedo, Angel J Paternina | Patten, Scott B | Paul, Vinod K | Pavlin, Boris Igor | Pearce, Neil | Pereira, David M | Pervaiz, Aslam | Pesudovs, Konrad | Petzold, Max | Pourmalek, Farshad | Qato, Dima | Quezada, Amado D | Quistberg, D Alex | Rafay, Anwar | Rahimi, Kazem | Rahimi-Movaghar, Vafa | Rahman, Sajjad Ur | Raju, Murugesan | Rana, Saleem M | Razavi, Homie | Reilly, Robert Quentin | Remuzzi, Giuseppe | Richardus, Jan Hendrik | Ronfani, Luca | Roy, Nobhojit | Sabin, Nsanzimana | Saeedi, Mohammad Yahya | Sahraian, Mohammad Ali | Samonte, Genesis May J | Sawhney, Monika | Schneider, Ione J C | Schwebel, David C | Seedat, Soraya | Sepanlou, Sadaf G | Servan-Mori, Edson E | Sheikhbahaei, Sara | Shibuya, Kenji | Shin, Hwashin Hyun | Shiue, Ivy | Shivakoti, Rupak | Sigfusdottir, Inga Dora | Silberberg, Donald H | Silva, Andrea P | Simard, Edgar P | Singh, Jasvinder A | Skirbekk, Vegard | Sliwa, Karen | Soneji, Samir | Soshnikov, Sergey S | Sreeramareddy, Chandrashekhar T | Stathopoulou, Vasiliki Kalliopi | Stroumpoulis, Konstantinos | Swaminathan, Soumya | Sykes, Bryan L | Tabb, Karen M | Talongwa, Roberto Tchio | Tenkorang, Eric Yeboah | Terkawi, Abdullah Sulieman | Thomson, Alan J | Thorne-Lyman, Andrew L | Towbin, Jeffrey A | Traebert, Jefferson | Tran, Bach X | Dimbuene, Zacharie Tsala | Tsilimbaris, Miltiadis | Uchendu, Uche S | Ukwaja, Kingsley N | Uzun, Selen Begüm | Vallely, Andrew J | Vasankari, Tommi J | Venketasubramanian, N | Violante, Francesco S | Vlassov, Vasiliy Victorovich | Vollset, Stein Emil | Waller, Stephen | Wallin, Mitchell T | Wang, Linhong | Wang, XiaoRong | Wang, Yanping | Weichenthal, Scott | Weiderpass, Elisabete | Weintraub, Robert G | Westerman, Ronny | White, Richard A | Wilkinson, James D | Williams, Thomas Neil | Woldeyohannes, Solomon Meseret | Wong, John Q | Xu, Gelin | Yang, Yang C | Yano, Yuichiro | Yentur, Gokalp Kadri | Yip, Paul | Yonemoto, Naohiro | Yoon, Seok-Jun | Younis, Mustafa | Yu, Chuanhua | Jin, Kim Yun | El Sayed Zaki, Maysaa | Zhao, Yong | Zheng, Yingfeng | Zhou, Maigeng | Zhu, Jun | Zou, Xiao Nong | Lopez, Alan D | Vos, Theo
Lancet  2014;384(9947):1005-1070.
Summary
Background
The Millennium Declaration in 2000 brought special global attention to HIV, tuberculosis, and malaria through the formulation of Millennium Development Goal (MDG) 6. The Global Burden of Disease 2013 study provides a consistent and comprehensive approach to disease estimation for between 1990 and 2013, and an opportunity to assess whether accelerated progress has occurred since the Millennium Declaration.
Methods
To estimate incidence and mortality for HIV, we used the UNAIDS Spectrum model appropriately modified based on a systematic review of available studies of mortality with and without antiretroviral therapy (ART). For concentrated epidemics, we calibrated Spectrum models to fit vital registration data corrected for misclassification of HIV deaths. In generalised epidemics, we minimised a loss function to select epidemic curves most consistent with prevalence data and demographic data for all-cause mortality. We analysed counterfactual scenarios for HIV to assess years of life saved through prevention of mother-to-child transmission (PMTCT) and ART. For tuberculosis, we analysed vital registration and verbal autopsy data to estimate mortality using cause of death ensemble modelling. We analysed data for corrected case-notifications, expert opinions on the case-detection rate, prevalence surveys, and estimated cause-specific mortality using Bayesian meta-regression to generate consistent trends in all parameters. We analysed malaria mortality and incidence using an updated cause of death database, a systematic analysis of verbal autopsy validation studies for malaria, and recent studies (2010–13) of incidence, drug resistance, and coverage of insecticide-treated bednets.
Findings
Globally in 2013, there were 1·8 million new HIV infections (95% uncertainty interval 1·7 million to 2·1 million), 29·2 million prevalent HIV cases (28·1 to 31·7), and 1·3 million HIV deaths (1·3 to 1·5). At the peak of the epidemic in 2005, HIV caused 1·7 million deaths (1·6 million to 1·9 million). Concentrated epidemics in Latin America and eastern Europe are substantially smaller than previously estimated. Through interventions including PMTCT and ART, 19·1 million life-years (16·6 million to 21·5 million) have been saved, 70·3% (65·4 to 76·1) in developing countries. From 2000 to 2011, the ratio of development assistance for health for HIV to years of life saved through intervention was US$4498 in developing countries. Including in HIV-positive individuals, all-form tuberculosis incidence was 7·5 million (7·4 million to 7·7 million), prevalence was 11·9 million (11·6 million to 12·2 million), and number of deaths was 1·4 million (1·3 million to 1·5 million) in 2013. In the same year and in only individuals who were HIV-negative, all-form tuberculosis incidence was 7·1 million (6·9 million to 7·3 million), prevalence was 11·2 million (10·8 million to 11·6 million), and number of deaths was 1·3 million (1·2 million to 1·4 million). Annualised rates of change (ARC) for incidence, prevalence, and death became negative after 2000. Tuberculosis in HIV-negative individuals disproportionately occurs in men and boys (versus women and girls); 64·0% of cases (63·6 to 64·3) and 64·7% of deaths (60·8 to 70·3). Globally, malaria cases and deaths grew rapidly from 1990 reaching a peak of 232 million cases (143 million to 387 million) in 2003 and 1·2 million deaths (1·1 million to 1·4 million) in 2004. Since 2004, child deaths from malaria in sub-Saharan Africa have decreased by 31·5% (15·7 to 44·1). Outside of Africa, malaria mortality has been steadily decreasing since 1990.
Interpretation
Our estimates of the number of people living with HIV are 18·7% smaller than UNAIDS’s estimates in 2012. The number of people living with malaria is larger than estimated by WHO. The number of people living with HIV, tuberculosis, or malaria have all decreased since 2000. At the global level, upward trends for malaria and HIV deaths have been reversed and declines in tuberculosis deaths have accelerated. 101 countries (74 of which are developing) still have increasing HIV incidence. Substantial progress since the Millennium Declaration is an encouraging sign of the effect of global action.
Funding
Bill & Melinda Gates Foundation.
doi:10.1016/S0140-6736(14)60844-8
PMCID: PMC4202387  PMID: 25059949
10.  The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation 
Pereyra, Florencia | Jia, Xiaoming | McLaren, Paul J. | Telenti, Amalio | de Bakker, Paul I.W. | Walker, Bruce D. | Jia, Xiaoming | McLaren, Paul J. | Ripke, Stephan | Brumme, Chanson J. | Pulit, Sara L. | Telenti, Amalio | Carrington, Mary | Kadie, Carl M. | Carlson, Jonathan M. | Heckerman, David | de Bakker, Paul I.W. | Pereyra, Florencia | de Bakker, Paul I.W. | Graham, Robert R. | Plenge, Robert M. | Deeks, Steven G. | Walker, Bruce D. | Gianniny, Lauren | Crawford, Gabriel | Sullivan, Jordan | Gonzalez, Elena | Davies, Leela | Camargo, Amy | Moore, Jamie M. | Beattie, Nicole | Gupta, Supriya | Crenshaw, Andrew | Burtt, Noël P. | Guiducci, Candace | Gupta, Namrata | Carrington, Mary | Gao, Xiaojiang | Qi, Ying | Yuki, Yuko | Pereyra, Florencia | Piechocka-Trocha, Alicja | Cutrell, Emily | Rosenberg, Rachel | Moss, Kristin L. | Lemay, Paul | O’Leary, Jessica | Schaefer, Todd | Verma, Pranshu | Toth, Ildiko | Block, Brian | Baker, Brett | Rothchild, Alissa | Lian, Jeffrey | Proudfoot, Jacqueline | Alvino, Donna Marie L. | Vine, Seanna | Addo, Marylyn M. | Allen, Todd M. | Altfeld, Marcus | Henn, Matthew R. | Le Gall, Sylvie | Streeck, Hendrik | Walker, Bruce D. | Haas, David W. | Kuritzkes, Daniel R. | Robbins, Gregory K. | Shafer, Robert W. | Gulick, Roy M. | Shikuma, Cecilia M. | Haubrich, Richard | Riddler, Sharon | Sax, Paul E. | Daar, Eric S. | Ribaudo, Heather J. | Agan, Brian | Agarwal, Shanu | Ahern, Richard L. | Allen, Brady L. | Altidor, Sherly | Altschuler, Eric L. | Ambardar, Sujata | Anastos, Kathryn | Anderson, Ben | Anderson, Val | Andrady, Ushan | Antoniskis, Diana | Bangsberg, David | Barbaro, Daniel | Barrie, William | Bartczak, J. | Barton, Simon | Basden, Patricia | Basgoz, Nesli | Bazner, Suzane | Bellos, Nicholaos C. | Benson, Anne M. | Berger, Judith | Bernard, Nicole F. | Bernard, Annette M. | Birch, Christopher | Bodner, Stanley J. | Bolan, Robert K. | Boudreaux, Emilie T. | Bradley, Meg | Braun, James F. | Brndjar, Jon E. | Brown, Stephen J. | Brown, Katherine | Brown, Sheldon T. | Burack, Jedidiah | Bush, Larry M. | Cafaro, Virginia | Campbell, Omobolaji | Campbell, John | Carlson, Robert H. | Carmichael, J. Kevin | Casey, Kathleen K. | Cavacuiti, Chris | Celestin, Gregory | Chambers, Steven T. | Chez, Nancy | Chirch, Lisa M. | Cimoch, Paul J. | Cohen, Daniel | Cohn, Lillian E. | Conway, Brian | Cooper, David A. | Cornelson, Brian | Cox, David T. | Cristofano, Michael V. | Cuchural, George | Czartoski, Julie L. | Dahman, Joseph M. | Daly, Jennifer S. | Davis, Benjamin T. | Davis, Kristine | Davod, Sheila M. | Deeks, Steven G. | DeJesus, Edwin | Dietz, Craig A. | Dunham, Eleanor | Dunn, Michael E. | Ellerin, Todd B. | Eron, Joseph J. | Fangman, John J.W. | Farel, Claire E. | Ferlazzo, Helen | Fidler, Sarah | Fleenor-Ford, Anita | Frankel, Renee | Freedberg, Kenneth A. | French, Neel K. | Fuchs, Jonathan D. | Fuller, Jon D. | Gaberman, Jonna | Gallant, Joel E. | Gandhi, Rajesh T. | Garcia, Efrain | Garmon, Donald | Gathe, Joseph C. | Gaultier, Cyril R. | Gebre, Wondwoosen | Gilman, Frank D. | Gilson, Ian | Goepfert, Paul A. | Gottlieb, Michael S. | Goulston, Claudia | Groger, Richard K. | Gurley, T. Douglas | Haber, Stuart | Hardwicke, Robin | Hardy, W. David | Harrigan, P. Richard | Hawkins, Trevor N. | Heath, Sonya | Hecht, Frederick M. | Henry, W. Keith | Hladek, Melissa | Hoffman, Robert P. | Horton, James M. | Hsu, Ricky K. | Huhn, Gregory D. | Hunt, Peter | Hupert, Mark J. | Illeman, Mark L. | Jaeger, Hans | Jellinger, Robert M. | John, Mina | Johnson, Jennifer A. | Johnson, Kristin L. | Johnson, Heather | Johnson, Kay | Joly, Jennifer | Jordan, Wilbert C. | Kauffman, Carol A. | Khanlou, Homayoon | Killian, Robert K. | Kim, Arthur Y. | Kim, David D. | Kinder, Clifford A. | Kirchner, Jeffrey T. | Kogelman, Laura | Kojic, Erna Milunka | Korthuis, P. Todd | Kurisu, Wayne | Kwon, Douglas S. | LaMar, Melissa | Lampiris, Harry | Lanzafame, Massimiliano | Lederman, Michael M. | Lee, David M. | Lee, Jean M.L. | Lee, Marah J. | Lee, Edward T.Y. | Lemoine, Janice | Levy, Jay A. | Llibre, Josep M. | Liguori, Michael A. | Little, Susan J. | Liu, Anne Y. | Lopez, Alvaro J. | Loutfy, Mono R. | Loy, Dawn | Mohammed, Debbie Y. | Man, Alan | Mansour, Michael K. | Marconi, Vincent C. | Markowitz, Martin | Marques, Rui | Martin, Jeffrey N. | Martin, Harold L. | Mayer, Kenneth Hugh | McElrath, M. Juliana | McGhee, Theresa A. | McGovern, Barbara H. | McGowan, Katherine | McIntyre, Dawn | Mcleod, Gavin X. | Menezes, Prema | Mesa, Greg | Metroka, Craig E. | Meyer-Olson, Dirk | Miller, Andy O. | Montgomery, Kate | Mounzer, Karam C. | Nagami, Ellen H. | Nagin, Iris | Nahass, Ronald G. | Nelson, Margret O. | Nielsen, Craig | Norene, David L. | O’Connor, David H. | Ojikutu, Bisola O. | Okulicz, Jason | Oladehin, Olakunle O. | Oldfield, Edward C. | Olender, Susan A. | Ostrowski, Mario | Owen, William F. | Pae, Eunice | Parsonnet, Jeffrey | Pavlatos, Andrew M. | Perlmutter, Aaron M. | Pierce, Michael N. | Pincus, Jonathan M. | Pisani, Leandro | Price, Lawrence Jay | Proia, Laurie | Prokesch, Richard C. | Pujet, Heather Calderon | Ramgopal, Moti | Rathod, Almas | Rausch, Michael | Ravishankar, J. | Rhame, Frank S. | Richards, Constance Shamuyarira | Richman, Douglas D. | Robbins, Gregory K. | Rodes, Berta | Rodriguez, Milagros | Rose, Richard C. | Rosenberg, Eric S. | Rosenthal, Daniel | Ross, Polly E. | Rubin, David S. | Rumbaugh, Elease | Saenz, Luis | Salvaggio, Michelle R. | Sanchez, William C. | Sanjana, Veeraf M. | Santiago, Steven | Schmidt, Wolfgang | Schuitemaker, Hanneke | Sestak, Philip M. | Shalit, Peter | Shay, William | Shirvani, Vivian N. | Silebi, Vanessa I. | Sizemore, James M. | Skolnik, Paul R. | Sokol-Anderson, Marcia | Sosman, James M. | Stabile, Paul | Stapleton, Jack T. | Starrett, Sheree | Stein, Francine | Stellbrink, Hans-Jurgen | Sterman, F. Lisa | Stone, Valerie E. | Stone, David R. | Tambussi, Giuseppe | Taplitz, Randy A. | Tedaldi, Ellen M. | Telenti, Amalio | Theisen, William | Torres, Richard | Tosiello, Lorraine | Tremblay, Cecile | Tribble, Marc A. | Trinh, Phuong D. | Tsao, Alice | Ueda, Peggy | Vaccaro, Anthony | Valadas, Emilia | Vanig, Thanes J. | Vecino, Isabel | Vega, Vilma M. | Veikley, Wenoah | Wade, Barbara H. | Walworth, Charles | Wanidworanun, Chingchai | Ward, Douglas J. | Warner, Daniel A. | Weber, Robert D. | Webster, Duncan | Weis, Steve | Wheeler, David A. | White, David J. | Wilkins, Ed | Winston, Alan | Wlodaver, Clifford G. | Wout, Angelique van’t | Wright, David P. | Yang, Otto O. | Yurdin, David L. | Zabukovic, Brandon W. | Zachary, Kimon C. | Zeeman, Beth | Zhao, Meng
Science (New York, N.Y.)  2010;330(6010):1551-1557.
Infectious and inflammatory diseases have repeatedly shown strong genetic associations within the major histocompatibility complex (MHC); however, the basis for these associations remains elusive. To define host genetic effects on the outcome of a chronic viral infection, we performed genome-wide association analysis in a multiethnic cohort of HIV-1 controllers and progressors, and we analyzed the effects of individual amino acids within the classical human leukocyte antigen (HLA) proteins. We identified >300 genome-wide significant single-nucleotide polymorphisms (SNPs) within the MHC and none elsewhere. Specific amino acids in the HLA-B peptide binding groove, as well as an independent HLA-C effect, explain the SNP associations and reconcile both protective and risk HLA alleles. These results implicate the nature of the HLA–viral peptide interaction as the major factor modulating durable control of HIV infection.
doi:10.1126/science.1195271
PMCID: PMC3235490  PMID: 21051598
11.  Evaluation of a candidate breast cancer associated SNP in ERCC4 as a risk modifier in BRCA1 and BRCA2 mutation carriers. Results from the Consortium of Investigators of Modifiers of BRCA1/BRCA2 (CIMBA) 
Osorio, A | Milne, R L | Pita, G | Peterlongo, P | Heikkinen, T | Simard, J | Chenevix-Trench, G | Spurdle, A B | Beesley, J | Chen, X | Healey, S | Neuhausen, S L | Ding, Y C | Couch, F J | Wang, X | Lindor, N | Manoukian, S | Barile, M | Viel, A | Tizzoni, L | Szabo, C I | Foretova, L | Zikan, M | Claes, K | Greene, M H | Mai, P | Rennert, G | Lejbkowicz, F | Barnett-Griness, O | Andrulis, I L | Ozcelik, H | Weerasooriya, N | Gerdes, A-M | Thomassen, M | Cruger, D G | Caligo, M A | Friedman, E | Kaufman, B | Laitman, Y | Cohen, S | Kontorovich, T | Gershoni-Baruch, R | Dagan, E | Jernström, H | Askmalm, M S | Arver, B | Malmer, B | Domchek, S M | Nathanson, K L | Brunet, J | Ramón y Cajal, T | Yannoukakos, D | Hamann, U | Hogervorst, F B L | Verhoef, S | García, EB Gómez | Wijnen, J T | van den Ouweland, A | Easton, D F | Peock, S | Cook, M | Oliver, C T | Frost, D | Luccarini, C | Evans, D G | Lalloo, F | Eeles, R | Pichert, G | Cook, J | Hodgson, S | Morrison, P J | Douglas, F | Godwin, A K | Sinilnikova, O M | Barjhoux, L | Stoppa-Lyonnet, D | Moncoutier, V | Giraud, S | Cassini, C | Olivier-Faivre, L | Révillion, F | Peyrat, J-P | Muller, D | Fricker, J-P | Lynch, H T | John, E M | Buys, S | Daly, M | Hopper, J L | Terry, M B | Miron, A | Yassin, Y | Goldgar, D | Singer, C F | Gschwantler-Kaulich, D | Pfeiler, G | Spiess, A-C | Hansen, Thomas v O | Johannsson, O T | Kirchhoff, T | Offit, K | Kosarin, K | Piedmonte, M | Rodriguez, G C | Wakeley, K | Boggess, J F | Basil, J | Schwartz, P E | Blank, S V | Toland, A E | Montagna, M | Casella, C | Imyanitov, E N | Allavena, A | Schmutzler, R K | Versmold, B | Engel, C | Meindl, A | Ditsch, N | Arnold, N | Niederacher, D | Deißler, H | Fiebig, B | Varon-Mateeva, R | Schaefer, D | Froster, U G | Caldes, T | de la Hoya, M | McGuffog, L | Antoniou, A C | Nevanlinna, H | Radice, P | Benítez, J
British Journal of Cancer  2009;101(12):2048-2054.
Background:
In this study we aimed to evaluate the role of a SNP in intron 1 of the ERCC4 gene (rs744154), previously reported to be associated with a reduced risk of breast cancer in the general population, as a breast cancer risk modifier in BRCA1 and BRCA2 mutation carriers.
Methods:
We have genotyped rs744154 in 9408 BRCA1 and 5632 BRCA2 mutation carriers from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA) and assessed its association with breast cancer risk using a retrospective weighted cohort approach.
Results:
We found no evidence of association with breast cancer risk for BRCA1 (per-allele HR: 0.98, 95% CI: 0.93–1.04, P=0.5) or BRCA2 (per-allele HR: 0.97, 95% CI: 0.89–1.06, P=0.5) mutation carriers.
Conclusion:
This SNP is not a significant modifier of breast cancer risk for mutation carriers, though weak associations cannot be ruled out.
doi:10.1038/sj.bjc.6605416
PMCID: PMC2795432  PMID: 19920816
BRCA1; BRCA2; ERCC4; breast cancer
12.  Phenotypic and genotypic analyses to guide selection of reverse transcriptase inhibitors in second-line HIV therapy following extended virological failure in Uganda 
Goodall, R. L. | Dunn, D. T. | Pattery, T. | van Cauwenberge, A. | Nkurunziza, P. | Awio, P. | Ndembi, N. | Munderi, P. | Kityo, C. | Gilks, C. F. | Kaleebu, P. | Pillay, D. | Kaleebu, P. | Pillay, D. | Awio, P. | Chirara, M. | Dunn, D. | Gibb, D. M. | Gilks, C. | Goodall, R. | Kapaata, A. | Katuramur, M. | Lyagoba, F. | Magala, R. | Magambo, B. | Mataruka, K. | McCormick, A. | Mugarura, L. | Musunga, T. | Nabankkema, M. | Nkalubo, J. | Nkurunziza, P. | Parry, C. | Robertson, V. | Spyer, M. | Yirrell, D. | Grosskurth, H. | Munderi, P. | Kabuye, G. | Nsibambi, D. | Kasirye, R. | Zalwango, E. | Nakazibwe, M. | Kikaire, B. | Nassuna, G. | Massa, R. | Fadhiru, K. | Namyalo, M. | Zalwango, A. | Generous, L. | Khauka, P. | Rutikarayo, N. | Nakahima, W. | Mugisha, A. | Todd, J. | Levin, J. | Muyingo, S. | Ruberantwari, A. | Kaleebu, P. | Yirrell, D. | Ndembi, N. | Lyagoba, F. | Hughes, P. | Aber, M. | Medina Lara, A. | Foster, S. | Amurwon, J. | Nyanzi Wakholi, B. | Mugyenyi, P. | Kityo, C. | Ssali, F. | Tumukunde, D. | Otim, T. | Kabanda, J. | Musana, H. | Akao, J. | Kyomugisha, H. | Byamukama, A. | Sabiiti, J. | Komugyena, J. | Wavamunno, P. | Mukiibi, S. | Drasiku, A. | Byaruhanga, R. | Labeja, O. | Katundu, P. | Tugume, S. | Awio, P. | Namazzi, A. | Bakeinyaga, G. T. | Katabira, H. | Abaine, D. | Tukamushaba, J. | Anywar, W. | Ojiambo, W. | Angweng, E. | Murungi, S. | Haguma, W. | Atwiine, S. | Kigozi, J. | Latif, A. | Hakim, J. | Robertson, V. | Reid, A. | Chidziva, E. | Bulaya-Tembo, R. | Musoro, G. | Taziwa, F. | Chimbetete, C. | Chakonza, L. | Mawora, A. | Muvirimi, C. | Tinago, G. | Svovanapasis, P. | Simango, M. | Chirema, O. | Machingura, J. | Mutsai, S. | Phiri, M. | Bafana, T. | Chirara, M. | Muchabaiwa, L. | Muzambi, M. | Katabira, E. | Ronald, A. | Kambungu, A. | Lutwama, F. | Nanfuka, A. | Walusimbi, J. | Nabankema, E. | Nalumenya, R. | Namuli, T. | Kulume, R. | Namata, I. | Nyachwo, L. | Florence, A. | Kusiima, A. | Lubwama, E. | Nairuba, R. | Oketta, F. | Buluma, E. | Waita, R. | Ojiambo, H. | Sadik, F. | Wanyama, J. | Nabongo, P.
Objectives
We investigated phenotypic and genotypic resistance after 2 years of first-line therapy with two HIV treatment regimens in the absence of virological monitoring.
Methods
NORA [Nevirapine OR Abacavir study, a sub-study of the Development of AntiRetroviral Therapy in Africa (DART) trial] randomized 600 symptomatic HIV-infected Ugandan adults (CD4 cell count <200 cells/mm3) to receive zidovudine/lamivudine plus abacavir (cABC arm) or nevirapine (cNVP arm). All virological tests were performed retrospectively, including resistance tests on week 96 plasma samples with HIV RNA levels ≥1000 copies/mL. Phenotypic resistance was expressed as fold-change in IC50 (FC) relative to wild-type virus.
Results
HIV-1 RNA viral load ≥1000 copies/mL at week 96 was seen in 58/204 (28.4%) cABC participants and 21/159 (13.2%) cNVP participants. Resistance results were available in 35 cABC and 17 cNVP participants; 31 (89%) cABC and 16 (94%) cNVP isolates had a week 96 FC below the biological cut-off for tenofovir (2.2). In the cNVP arm, 16/17 participants had resistance mutations synonymous with high-level resistance to nevirapine and efavirenz; FC values for etravirine were above the biological cut-off in 9 (53%) isolates. In multivariate regression models, K65R, Y115F and the presence of thymidine analogue-associated mutations were associated with increased susceptibility to etravirine in the cABC arm.
Conclusions
Our data support the use of tenofovir following failure of a first-line zidovudine-containing regimen and shed further light on non-nucleoside reverse transcriptase inhibitor hypersusceptibility.
doi:10.1093/jac/dku052
PMCID: PMC4054985  PMID: 24633208
resistance; Africa; hypersusceptibility
13.  TRY – a global database of plant traits 
Kattge, J | Díaz, S | Lavorel, S | Prentice, I C | Leadley, P | Bönisch, G | Garnier, E | Westoby, M | Reich, P B | Wright, I J | Cornelissen, J H C | Violle, C | Harrison, S P | Van Bodegom, P M | Reichstein, M | Enquist, B J | Soudzilovskaia, N A | Ackerly, D D | Anand, M | Atkin, O | Bahn, M | Baker, T R | Baldocchi, D | Bekker, R | Blanco, C C | Blonder, B | Bond, W J | Bradstock, R | Bunker, D E | Casanoves, F | Cavender-Bares, J | Chambers, J Q | Chapin, F S | Chave, J | Coomes, D | Cornwell, W K | Craine, J M | Dobrin, B H | Duarte, L | Durka, W | Elser, J | Esser, G | Estiarte, M | Fagan, W F | Fang, J | Fernández-Méndez, F | Fidelis, A | Finegan, B | Flores, O | Ford, H | Frank, D | Freschet, G T | Fyllas, N M | Gallagher, R V | Green, W A | Gutierrez, A G | Hickler, T | Higgins, S I | Hodgson, J G | Jalili, A | Jansen, S | Joly, C A | Kerkhoff, A J | Kirkup, D | Kitajima, K | Kleyer, M | Klotz, S | Knops, J M H | Kramer, K | Kühn, I | Kurokawa, H | Laughlin, D | Lee, T D | Leishman, M | Lens, F | Lenz, T | Lewis, S L | Lloyd, J | Llusià, J | Louault, F | Ma, S | Mahecha, M D | Manning, P | Massad, T | Medlyn, B E | Messier, J | Moles, A T | Müller, S C | Nadrowski, K | Naeem, S | Niinemets, Ü | Nöllert, S | Nüske, A | Ogaya, R | Oleksyn, J | Onipchenko, V G | Onoda, Y | Ordoñez, J | Overbeck, G | Ozinga, W A | Patiño, S | Paula, S | Pausas, J G | Peñuelas, J | Phillips, O L | Pillar, V | Poorter, H | Poorter, L | Poschlod, P | Prinzing, A | Proulx, R | Rammig, A | Reinsch, S | Reu, B | Sack, L | Salgado-Negret, B | Sardans, J | Shiodera, S | Shipley, B | Siefert, A | Sosinski, E | Soussana, J-F | Swaine, E | Swenson, N | Thompson, K | Thornton, P | Waldram, M | Weiher, E | White, M | White, S | Wright, S J | Yguel, B | Zaehle, S | Zanne, A E | Wirth, C
Global Change Biology  2011;17(9):2905-2935.
Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.
doi:10.1111/j.1365-2486.2011.02451.x
PMCID: PMC3627314
comparative ecology; database; environmental gradient; functional diversity; global analysis; global change; interspecific variation; intraspecific variation; plant attribute; plant functional type; plant trait; vegetation model
14.  Association of PHB 1630 C>T and MTHFR 677 C>T polymorphisms with breast and ovarian cancer risk in BRCA1/2 mutation carriers: results from a multicenter study 
Jakubowska, A | Rozkrut, D | Antoniou, A | Hamann, U | Scott, R J | McGuffog, L | Healy, S | Sinilnikova, O M | Rennert, G | Lejbkowicz, F | Flugelman, A | Andrulis, I L | Glendon, G | Ozcelik, H | Thomassen, M | Paligo, M | Aretini, P | Kantala, J | Aroer, B | von Wachenfeldt, A | Liljegren, A | Loman, N | Herbst, K | Kristoffersson, U | Rosenquist, R | Karlsson, P | Stenmark-Askmalm, M | Melin, B | Nathanson, K L | Domchek, S M | Byrski, T | Huzarski, T | Gronwald, J | Menkiszak, J | Cybulski, C | Serrano, P | Osorio, A | Cajal, T R | Tsitlaidou, M | Benítez, J | Gilbert, M | Rookus, M | Aalfs, C M | Kluijt, I | Boessenkool-Pape, J L | Meijers-Heijboer, H E J | Oosterwijk, J C | van Asperen, C J | Blok, M J | Nelen, M R | van den Ouweland, A M W | Seynaeve, C | van der Luijt, R B | Devilee, P | Easton, D F | Peock, S | Frost, D | Platte, R | Ellis, S D | Fineberg, E | Evans, D G | Lalloo, F | Eeles, R | Jacobs, C | Adlard, J | Davidson, R | Eccles, D | Cole, T | Cook, J | Godwin, A | Bove, B | Stoppa-Lyonnet, D | Caux-Moncoutier, V | Belotti, M | Tirapo, C | Mazoyer, S | Barjhoux, L | Boutry-Kryza, N | Pujol, P | Coupier, I | Peyrat, J-P | Vennin, P | Muller, D | Fricker, J-P | Venat-Bouvet, L | Johannsson, O Th | Isaacs, C | Schmutzler, R | Wappenschmidt, B | Meindl, A | Arnold, N | Varon-Mateeva, R | Niederacher, D | Sutter, C | Deissler, H | Preisler-Adams, S | Simard, J | Soucy, P | Durocher, F | Chenevix-Trench, G | Beesley, J | Chen, X | Rebbeck, T | Couch, F | Wang, X | Lindor, N | Fredericksen, Z | Pankratz, V S | Peterlongo, P | Bonanni, B | Fortuzzi, S | Peissel, B | Szabo, C | Mai, P L | Loud, J T | Lubinski, J
British Journal of Cancer  2012;106(12):2016-2024.
Background:
The variable penetrance of breast cancer in BRCA1/2 mutation carriers suggests that other genetic or environmental factors modify breast cancer risk. Two genes of special interest are prohibitin (PHB) and methylene-tetrahydrofolate reductase (MTHFR), both of which are important either directly or indirectly in maintaining genomic integrity.
Methods:
To evaluate the potential role of genetic variants within PHB and MTHFR in breast and ovarian cancer risk, 4102 BRCA1 and 2093 BRCA2 mutation carriers, and 6211 BRCA1 and 2902 BRCA2 carriers from the Consortium of Investigators of Modifiers of BRCA1 and BRCA2 (CIMBA) were genotyped for the PHB 1630 C>T (rs6917) polymorphism and the MTHFR 677 C>T (rs1801133) polymorphism, respectively.
Results:
There was no evidence of association between the PHB 1630 C>T and MTHFR 677 C>T polymorphisms with either disease for BRCA1 or BRCA2 mutation carriers when breast and ovarian cancer associations were evaluated separately. Analysis that evaluated associations for breast and ovarian cancer simultaneously showed some evidence that BRCA1 mutation carriers who had the rare homozygote genotype (TT) of the PHB 1630 C>T polymorphism were at increased risk of both breast and ovarian cancer (HR 1.50, 95%CI 1.10–2.04 and HR 2.16, 95%CI 1.24–3.76, respectively). However, there was no evidence of association under a multiplicative model for the effect of each minor allele.
Conclusion:
The PHB 1630TT genotype may modify breast and ovarian cancer risks in BRCA1 mutation carriers. This association need to be evaluated in larger series of BRCA1 mutation carriers.
doi:10.1038/bjc.2012.160
PMCID: PMC3388557  PMID: 22669161
BRCA1/2 mutation carriers; PHB 1630 C>T polymorphism; MTHFR 677 C>T polymorphism; breast/ovarian cancer risk
15.  The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses 
Young, Nevin D. | Debellé, Frédéric | Oldroyd, Giles E. D. | Geurts, Rene | Cannon, Steven B. | Udvardi, Michael K. | Benedito, Vagner A. | Mayer, Klaus F. X. | Gouzy, Jérôme | Schoof, Heiko | Van de Peer, Yves | Proost, Sebastian | Cook, Douglas R. | Meyers, Blake C. | Spannagl, Manuel | Cheung, Foo | De Mita, Stéphane | Krishnakumar, Vivek | Gundlach, Heidrun | Zhou, Shiguo | Mudge, Joann | Bharti, Arvind K. | Murray, Jeremy D. | Naoumkina, Marina A. | Rosen, Benjamin | Silverstein, Kevin A. T. | Tang, Haibao | Rombauts, Stephane | Zhao, Patrick X. | Zhou, Peng | Barbe, Valérie | Bardou, Philippe | Bechner, Michael | Bellec, Arnaud | Berger, Anne | Bergès, Hélène | Bidwell, Shelby | Bisseling, Ton | Choisne, Nathalie | Couloux, Arnaud | Denny, Roxanne | Deshpande, Shweta | Dai, Xinbin | Doyle, Jeff | Dudez, Anne-Marie | Farmer, Andrew D. | Fouteau, Stéphanie | Franken, Carolien | Gibelin, Chrystel | Gish, John | Goldstein, Steven | González, Alvaro J. | Green, Pamela J. | Hallab, Asis | Hartog, Marijke | Hua, Axin | Humphray, Sean | Jeong, Dong-Hoon | Jing, Yi | Jöcker, Anika | Kenton, Steve M. | Kim, Dong-Jin | Klee, Kathrin | Lai, Hongshing | Lang, Chunting | Lin, Shaoping | Macmil, Simone L | Magdelenat, Ghislaine | Matthews, Lucy | McCorrison, Jamison | Monaghan, Erin L. | Mun, Jeong-Hwan | Najar, Fares Z. | Nicholson, Christine | Noirot, Céline | O’Bleness, Majesta | Paule, Charles R. | Poulain, Julie | Prion, Florent | Qin, Baifang | Qu, Chunmei | Retzel, Ernest F. | Riddle, Claire | Sallet, Erika | Samain, Sylvie | Samson, Nicolas | Sanders, Iryna | Saurat, Olivier | Scarpelli, Claude | Schiex, Thomas | Segurens, Béatrice | Severin, Andrew J. | Sherrier, D. Janine | Shi, Ruihua | Sims, Sarah | Singer, Susan R. | Sinharoy, Senjuti | Sterck, Lieven | Viollet, Agnès | Wang, Bing-Bing | Wang, Keqin | Wang, Mingyi | Wang, Xiaohong | Warfsmann, Jens | Weissenbach, Jean | White, Doug D. | White, Jim D. | Wiley, Graham B. | Wincker, Patrick | Xing, Yanbo | Yang, Limei | Yao, Ziyun | Ying, Fu | Zhai, Jixian | Zhou, Liping | Zuber, Antoine | Dénarié, Jean | Dixon, Richard A. | May, Gregory D. | Schwartz, David C. | Rogers, Jane | Quétier, Francis | Town, Christopher D. | Roe, Bruce A.
Nature  2011;480(7378):520-524.
Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation 1. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Mya). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species 2. Medicago truncatula (Mt) is a long-established model for the study of legume biology. Here we describe the draft sequence of the Mt euchromatin based on a recently completed BAC-assembly supplemented with Illumina-shotgun sequence, together capturing ~94% of all Mt genes. A whole-genome duplication (WGD) approximately 58 Mya played a major role in shaping the Mt genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the Mt genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max (Gm) and Lotus japonicus (Lj). Mt is a close relative of alfalfa (M. sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the Mt genome sequence provides significant opportunities to expand alfalfa’s genomic toolbox.
doi:10.1038/nature10625
PMCID: PMC3272368  PMID: 22089132
16.  GATE - Geant4 Application for Tomographic Emission: a simulation toolkit for PET and SPECT 
Physics in Medicine and Biology  2004;49(19):4543-4561.
Monte Carlo simulation is an essential tool in emission tomography that can assist in the design of new medical imaging devices, the optimization of acquisition protocols, and the development or assessment of image reconstruction algorithms and correction techniques. GATE, the Geant4 Application for Tomographic Emission, encapsulates the Geant4 libraries to achieve a modular, versatile, scripted simulation toolkit adapted to the field of nuclear medicine. In particular, GATE allows the description of time-dependent phenomena such as source or detector movement, and source decay kinetics. This feature makes it possible to simulate time curves under realistic acquisition conditions and to test dynamic reconstruction algorithms. This paper gives a detailed description of the design and development of GATE by the OpenGATE collaboration, whose continuing objective is to improve, document, and validate GATE by simulating commercially available imaging systems for PET and SPECT. Large effort is also invested in the ability and the flexibility to model novel detection systems or systems still under design. A public release of GATE licensed under the GNU Lesser General Public License can be downloaded at the address http://www-lphe.ep.ch/GATE/. Two benchmarks developed for PET and SPECT to test the installation of GATE and to serve as a tutorial for the users are presented. Extensive validation of the GATE simulation platform has been started, comparing simulations and measurements on commercially available acquisition systems. References to those results are listed. The future prospects toward the gridification of GATE and its extension to other domains such as dosimetry are also discussed.
PMCID: PMC3267383  PMID: 15552416
17.  Epigenomic alterations define lethal CIMP-positive ependymomas of infancy 
Nature  2014;506(7489):445-450.
Ependymomas are common childhood brain tumours that occur throughout the nervous system, but are most common in the paediatric hindbrain. Current standard therapy comprises surgery and radiation, but not cytotoxic chemotherapy as it does not further increase survival. Whole-genome and whole-exome sequencing of 47 hindbrain ependymomas reveals an extremely low mutation rate, and zero significant recurrent somatic single nucleotide variants. Although devoid of recurrent single nucleotide variants and focal copy number aberrations, poor-prognosis hindbrain ependymomas exhibit a CpG island methylator phenotype. Transcriptional silencing driven by CpG methylation converges exclusively on targets of the Polycomb repressive complex 2 which represses expression of differentiation genes through trimethylation of H3K27. CpG island methylator phenotype-positive hindbrain ependymomas are responsive to clinical drugs that target either DNA or H3K27 methylation both in vitro and in vivo. We conclude that epigenetic modifiers are the first rational therapeutic candidates for this deadly malignancy, which is epigenetically deregulated but genetically bland.
doi:10.1038/nature13108
PMCID: PMC4174313  PMID: 24553142
18.  A comparative risk assessment of burden of disease and injury attributable to 67 risk factors and risk factor clusters in 21 regions, 1990–2010: a systematic analysis for the Global Burden of Disease Study 2010 
Lim, Stephen S | Vos, Theo | Flaxman, Abraham D | Danaei, Goodarz | Shibuya, Kenji | Adair-Rohani, Heather | Amann, Markus | Anderson, H Ross | Andrews, Kathryn G | Aryee, Martin | Atkinson, Charles | Bacchus, Loraine J | Bahalim, Adil N | Balakrishnan, Kalpana | Balmes, John | Barker-Collo, Suzanne | Baxter, Amanda | Bell, Michelle L | Blore, Jed D | Blyth, Fiona | Bonner, Carissa | Borges, Guilherme | Bourne, Rupert | Boussinesq, Michel | Brauer, Michael | Brooks, Peter | Bruce, Nigel G | Brunekreef, Bert | Bryan-Hancock, Claire | Bucello, Chiara | Buchbinder, Rachelle | Bull, Fiona | Burnett, Richard T | Byers, Tim E | Calabria, Bianca | Carapetis, Jonathan | Carnahan, Emily | Chafe, Zoe | Charlson, Fiona | Chen, Honglei | Chen, Jian Shen | Cheng, Andrew Tai-Ann | Child, Jennifer Christine | Cohen, Aaron | Colson, K Ellicott | Cowie, Benjamin C | Darby, Sarah | Darling, Susan | Davis, Adrian | Degenhardt, Louisa | Dentener, Frank | Des Jarlais, Don C | Devries, Karen | Dherani, Mukesh | Ding, Eric L | Dorsey, E Ray | Driscoll, Tim | Edmond, Karen | Ali, Suad Eltahir | Engell, Rebecca E | Erwin, Patricia J | Fahimi, Saman | Falder, Gail | Farzadfar, Farshad | Ferrari, Alize | Finucane, Mariel M | Flaxman, Seth | Fowkes, Francis Gerry R | Freedman, Greg | Freeman, Michael K | Gakidou, Emmanuela | Ghosh, Santu | Giovannucci, Edward | Gmel, Gerhard | Graham, Kathryn | Grainger, Rebecca | Grant, Bridget | Gunnell, David | Gutierrez, Hialy R | Hall, Wayne | Hoek, Hans W | Hogan, Anthony | Hosgood, H Dean | Hoy, Damian | Hu, Howard | Hubbell, Bryan J | Hutchings, Sally J | Ibeanusi, Sydney E | Jacklyn, Gemma L | Jasrasaria, Rashmi | Jonas, Jost B | Kan, Haidong | Kanis, John A | Kassebaum, Nicholas | Kawakami, Norito | Khang, Young-Ho | Khatibzadeh, Shahab | Khoo, Jon-Paul | Kok, Cindy | Laden, Francine | Lalloo, Ratilal | Lan, Qing | Lathlean, Tim | Leasher, Janet L | Leigh, James | Li, Yang | Lin, John Kent | Lipshultz, Steven E | London, Stephanie | Lozano, Rafael | Lu, Yuan | Mak, Joelle | Malekzadeh, Reza | Mallinger, Leslie | Marcenes, Wagner | March, Lyn | Marks, Robin | Martin, Randall | McGale, Paul | McGrath, John | Mehta, Sumi | Mensah, George A | Merriman, Tony R | Micha, Renata | Michaud, Catherine | Mishra, Vinod | Hanafiah, Khayriyyah Mohd | Mokdad, Ali A | Morawska, Lidia | Mozaff arian, Dariush | Murphy, Tasha | Naghavi, Mohsen | Neal, Bruce | Nelson, Paul K | Nolla, Joan Miquel | Norman, Rosana | Olives, Casey | Omer, Saad B | Orchard, Jessica | Osborne, Richard | Ostro, Bart | Page, Andrew | Pandey, Kiran D | Parry, Charles D H | Passmore, Erin | Patra, Jayadeep | Pearce, Neil | Pelizzari, Pamela M | Petzold, Max | Phillips, Michael R | Pope, Dan | Pope III, C Arden | Powles, John | Rao, Mayuree | Razavi, Homie | Rehfuess, Eva A | Rehm, Jürgen T | Ritz, Beate | Rivara, Frederick P | Roberts, Thomas | Robinson, Carolyn | Rodriguez-Portales, Jose A | Romieu, Isabelle | Room, Robin | Rosenfeld, Lisa C | Roy, Ananya | Rushton, Lesley | Salomon, Joshua A | Sampson, Uchechukwu | Sanchez-Riera, Lidia | Sanman, Ella | Sapkota, Amir | Seedat, Soraya | Shi, Peilin | Shield, Kevin | Shivakoti, Rupak | Singh, Gitanjali M | Sleet, David A | Smith, Emma | Smith, Kirk R | Stapelberg, Nicolas J C | Steenland, Kyle | Stöckl, Heidi | Stovner, Lars Jacob | Straif, Kurt | Straney, Lahn | Thurston, George D | Tran, Jimmy H | Van Dingenen, Rita | van Donkelaar, Aaron | Veerman, J Lennert | Vijayakumar, Lakshmi | Weintraub, Robert | Weissman, Myrna M | White, Richard A | Whiteford, Harvey | Wiersma, Steven T | Wilkinson, James D | Williams, Hywel C | Williams, Warwick | Wilson, Nicholas | Woolf, Anthony D | Yip, Paul | Zielinski, Jan M | Lopez, Alan D | Murray, Christopher J L | Ezzati, Majid
Lancet  2012;380(9859):2224-2260.
Summary
Background
Quantification of the disease burden caused by different risks informs prevention by providing an account of health loss different to that provided by a disease-by-disease analysis. No complete revision of global disease burden caused by risk factors has been done since a comparative risk assessment in 2000, and no previous analysis has assessed changes in burden attributable to risk factors over time.
Methods
We estimated deaths and disability-adjusted life years (DALYs; sum of years lived with disability [YLD] and years of life lost [YLL]) attributable to the independent effects of 67 risk factors and clusters of risk factors for 21 regions in 1990 and 2010. We estimated exposure distributions for each year, region, sex, and age group, and relative risks per unit of exposure by systematically reviewing and synthesising published and unpublished data. We used these estimates, together with estimates of cause-specific deaths and DALYs from the Global Burden of Disease Study 2010, to calculate the burden attributable to each risk factor exposure compared with the theoretical-minimum-risk exposure. We incorporated uncertainty in disease burden, relative risks, and exposures into our estimates of attributable burden.
Findings
In 2010, the three leading risk factors for global disease burden were high blood pressure (7·0% [95% uncertainty interval 6·2–7·7] of global DALYs), tobacco smoking including second-hand smoke (6·3% [5·5–7·0]), and alcohol use (5·5% [5·0–5·9]). In 1990, the leading risks were childhood underweight (7·9% [6·8–9·4]), household air pollution from solid fuels (HAP; 7·0% [5·6–8·3]), and tobacco smoking including second-hand smoke (6·1% [5·4–6·8]). Dietary risk factors and physical inactivity collectively accounted for 10·0% (95% UI 9·2–10·8) of global DALYs in 2010, with the most prominent dietary risks being diets low in fruits and those high in sodium. Several risks that primarily affect childhood communicable diseases, including unimproved water and sanitation and childhood micronutrient deficiencies, fell in rank between 1990 and 2010, with unimproved water we and sanitation accounting for 0·9% (0·4–1·6) of global DALYs in 2010. However, in most of sub-Saharan Africa childhood underweight, HAP, and non-exclusive and discontinued breastfeeding were the leading risks in 2010, while HAP was the leading risk in south Asia. The leading risk factor in Eastern Europe, most of Latin America, and southern sub-Saharan Africa in 2010 was alcohol use; in most of Asia, North Africa and Middle East, and central Europe it was high blood pressure. Despite declines, tobacco smoking including second-hand smoke remained the leading risk in high-income north America and western Europe. High body-mass index has increased globally and it is the leading risk in Australasia and southern Latin America, and also ranks high in other high-income regions, North Africa and Middle East, and Oceania.
Interpretation
Worldwide, the contribution of different risk factors to disease burden has changed substantially, with a shift away from risks for communicable diseases in children towards those for non-communicable diseases in adults. These changes are related to the ageing population, decreased mortality among children younger than 5 years, changes in cause-of-death composition, and changes in risk factor exposures. New evidence has led to changes in the magnitude of key risks including unimproved water and sanitation, vitamin A and zinc deficiencies, and ambient particulate matter pollution. The extent to which the epidemiological shift has occurred and what the leading risks currently are varies greatly across regions. In much of sub-Saharan Africa, the leading risks are still those associated with poverty and those that affect children.
Funding
Bill & Melinda Gates Foundation.
doi:10.1016/S0140-6736(12)61766-8
PMCID: PMC4156511  PMID: 23245609
19.  Somatic CALR Mutations in Myeloproliferative Neoplasms with Nonmutated JAK2 
The New England journal of medicine  2013;369(25):2391-2405.
BACKGROUND
Somatic mutations in the Janus kinase 2 gene (JAK2) occur in many myeloproliferative neoplasms, but the molecular pathogenesis of myeloproliferative neoplasms with nonmutated JAK2 is obscure, and the diagnosis of these neoplasms remains a challenge.
METHODS
We performed exome sequencing of samples obtained from 151 patients with myeloproliferative neoplasms. The mutation status of the gene encoding calreticulin (CALR) was assessed in an additional 1345 hematologic cancers, 1517 other cancers, and 550 controls. We established phylogenetic trees using hematopoietic colonies. We assessed calreticulin subcellular localization using immunofluorescence and flow cytometry.
RESULTS
Exome sequencing identified 1498 mutations in 151 patients, with medians of 6.5, 6.5, and 13.0 mutations per patient in samples of polycythemia vera, essential thrombocythemia, and myelofibrosis, respectively. Somatic CALR mutations were found in 70 to 84% of samples of myeloproliferative neoplasms with nonmutated JAK2, in 8% of myelodysplasia samples, in occasional samples of other myeloid cancers, and in none of the other cancers. A total of 148 CALR mutations were identified with 19 distinct variants. Mutations were located in exon 9 and generated a +1 base-pair frameshift, which would result in a mutant protein with a novel C-terminal. Mutant calreticulin was observed in the endoplasmic reticulum without increased cell-surface or Golgi accumulation. Patients with myeloproliferative neoplasms carrying CALR mutations presented with higher platelet counts and lower hemoglobin levels than patients with mutated JAK2. Mutation of CALR was detected in hematopoietic stem and progenitor cells. Clonal analyses showed CALR mutations in the earliest phylogenetic node, a finding consistent with its role as an initiating mutation in some patients.
CONCLUSIONS
Somatic mutations in the endoplasmic reticulum chaperone CALR were found in a majority of patients with myeloproliferative neoplasms with nonmutated JAK2. (Funded by the Kay Kendall Leukaemia Fund and others.)
doi:10.1056/NEJMoa1312542
PMCID: PMC3966280  PMID: 24325359
20.  Extensive genetics of ALS 
Neurology  2012;79(19):1983-1989.
Objective:
To assess the frequency and clinical characteristics of patients with mutations of major amyotrophic lateral sclerosis (ALS) genes in a prospectively ascertained, population-based epidemiologic series of cases.
Methods:
The study population includes all ALS cases diagnosed in Piemonte, Italy, from January 2007 to June 2011. Mutations of SOD1, TARDBP, ANG, FUS, OPTN, and C9ORF72 have been assessed.
Results:
Out of the 475 patients included in the study, 51 (10.7%) carried a mutation of an ALS-related gene (C9ORF72, 32; SOD1, 10; TARDBP, 7; FUS, 1; OPTN, 1; ANG, none). A positive family history for ALS or frontotemporal dementia (FTD) was found in 46 (9.7%) patients. Thirty-one (67.4%) of the 46 familial cases and 20 (4.7%) of the 429 sporadic cases had a genetic mutation. According to logistic regression modeling, besides a positive family history for ALS or FTD, the chance to carry a genetic mutation was related to the presence of comorbid FTD (odds ratio 3.5; p = 0.001), and age at onset ≤54 years (odds ratio 1.79; p = 0.012).
Conclusions:
We have found that ∼11% of patients with ALS carry a genetic mutation, with C9ORF72 being the commonest genetic alteration. Comorbid FTD or a young age at onset are strong indicators of a possible genetic origin of the disease.
doi:10.1212/WNL.0b013e3182735d36
PMCID: PMC3484987  PMID: 23100398
21.  Longitudinal analysis of HIV-1 coreceptor tropism by single and triplicate HIV-1 RNA and DNA sequencing in patients undergoing successful first-line antiretroviral therapy 
Meini, Genny | Rossetti, Barbara | Bianco, Claudia | Ceccherini-Silberstein, Francesca | Di Giambenedetto, Simona | Sighinolfi, Laura | Monno, Laura | Castagna, Antonella | Rozera, Gabriella | D'Arminio Monforte, Antonella | Zazzi, Maurizio | De Luca, Andrea | Moroni, M. | Angarano, G. | Antinori, A. | Armignacco, O. | d'Arminio Monforte, A. | Castelli, F. | Cauda, R. | Di Perri, G. | Galli, M. | Iardino, R. | Ippolito, G. | Lazzarin, A. | Perno, C. F. | von Schloesser, F. | Viale, P. | d'Arminio Monforte, A. | Antinori, A. | Castagna, A. | Ceccherini-Silberstein, F. | Cozzi-Lepri, A. | Girardi, E. | Lo Caputo, S. | Mussini, C. | Puoti, M. | Andreoni, M. | Ammassari, A. | Antinori, A. | Balotta, C. | Bonfanti, P. | Bonora, S. | Borderi, M. | Capobianchi, M. R. | Castagna, A. | Ceccherini-Silberstein, F. | Cingolani, A. | Cinque, P. | Cozzi-Lepri, A. | d'Arminio Monforte, A | De Luca, A. | Di Biagio, A. | Girardi, E. | Gianotti, N. | Gori, A. | Guaraldi, G. | Lapadula, G. | Lichtner, M. | Lo Caputo, S. | Madeddu, G. | Maggiolo, F. | Marchetti, G. | Marcotullio, S. | Monno, L. | Mussini, C. | Puoti, M. | Quiros Roldan, E. | Rusconi, S. | Cozzi-Lepri, A. | Cicconi, P. | Fanti, I. | Formenti, T. | Galli, L. | Lorenzini, P. | Giacometti, A. | Costantini, A. | Angarano, G. | Monno, L. | Santoro, C. | Maggiolo, F. | Suardi, C. | Viale, P. | Vanino, E. | Verucchi, G. | Castelli, F. | Quiros Roldan, E. | Minardi, C. | Quirino, T. | Abeli, C. | Manconi, P.E. | Piano, P. | Vecchiet, J. | Falasca, K. | Sighinolfi, L. | Segala, D. | Mazzotta, F. | Lo Caputo, S. | Cassola, G. | Viscoli, G. | Alessandrini, A. | Piscopo, R. | Mazzarello, G. | Mastroianni, C. | Belvisi, V. | Bonfanti, P. | Caramma, I. | Castelli, A. P. | Galli, M. | Lazzarin, A. | Rizzardini, G. | Puoti, M. | d'Arminio Monforte, A. | Ridolfo, A. L. | Piolini, R. | Castagna, A. | Salpietro, S. | Carenzi, L. | Moioli, M. C. | Cicconi, P. | Marchetti, G. | Mussini, C. | Puzzolante, C. | Gori, A. | Lapadula, G. | Abrescia, N. | Chirianni, A. | Guida, M. G. | Gargiulo, M. | Baldelli, F. | Francisci, D. | Parruti, G. | Ursini, T. | Magnani, G. | Ursitti, M. A. | Cauda, R. | Andreoni, M. | Antinori, A. | Vullo, V. | Cingolani, A. | d'Avino, A. | Ammassari, A. | Gallo, L. | Nicastri, E. | Acinapura, R. | Capozzi, M. | Libertone, R. | Tebano, G. | Cattelan, A. | Mura, M. S. | Madeddu, G. | Caramello, P. | Di Perri, G. | Orofino, G. C. | Bonora, S. | Sciandra, M. | Pellizzer, G. | Manfrin, V.
Objectives
Maraviroc has been shown to be effective in patients harbouring CCR5-tropic HIV-1. While this CCR5 antagonist has initially been used in salvage therapy, its excellent safety profile makes it ideal for antiretroviral treatment simplification strategies in patients with suppressed plasma viraemia. The aim of this study was to compare HIV-1 tropism as detected in baseline plasma RNA and peripheral blood mononuclear cell (PBMC) DNA prior to first-line therapy and to analyse tropism evolution while on successful treatment.
Methods
HIV-1 tropism was determined using triplicate genotypic testing combined with geno2pheno[coreceptor] analysis at a 10% false positive rate in 42 patients. Paired pre-treatment plasma RNA and PBMC DNA and two subsequent PBMC DNA samples (the first obtained after reaching undetectable plasma HIV-1 RNA and the second after at least 2 years of suppression of plasma viraemia) were evaluated.
Results
Coreceptor tropism was completely concordant in paired pre-treatment RNA and DNA, with 26.2% of HIV-1 sequences predicted to be non-CCR5-tropic. During follow-up, coreceptor tropism switches were detected in 4 (9.5%) patients without any preferential direction. Although false positive rate discrepancies within triplicates were common, the rate of discordance of coreceptor tropism assignment among triplicate results in this mostly CCR5-tropic dataset was only 2.1%, questioning the added value of triplicate testing compared with single testing.
Conclusions
HIV-1 coreceptor tropism changes during virologically successful first-line treatment are infrequent. HIV-1 DNA analysis may thus support the choice of a CCR5 antagonist in treatment switch strategies; however, maraviroc treatment outcome data are required to confirm this option.
doi:10.1093/jac/dkt426
PMCID: PMC3954119  PMID: 24155059
HIV type 1; V3; gp120; genotype interpretation
22.  Association of genetic variation with systolic and diastolic blood pressure among African Americans: the Candidate Gene Association Resource study 
Fox, Ervin R. | Young, J. Hunter | Li, Yali | Dreisbach, Albert W. | Keating, Brendan J. | Musani, Solomon K. | Liu, Kiang | Morrison, Alanna C. | Ganesh, Santhi | Kutlar, Abdullah | Ramachandran, Vasan S. | Polak, Josef F. | Fabsitz, Richard R. | Dries, Daniel L. | Farlow, Deborah N. | Redline, Susan | Adeyemo, Adebowale | Hirschorn, Joel N. | Sun, Yan V. | Wyatt, Sharon B. | Penman, Alan D. | Palmas, Walter | Rotter, Jerome I. | Townsend, Raymond R. | Doumatey, Ayo P. | Tayo, Bamidele O. | Mosley, Thomas H. | Lyon, Helen N. | Kang, Sun J. | Rotimi, Charles N. | Cooper, Richard S. | Franceschini, Nora | Curb, J. David | Martin, Lisa W. | Eaton, Charles B. | Kardia, Sharon L.R. | Taylor, Herman A. | Caulfield, Mark J. | Ehret, Georg B. | Johnson, Toby | Chakravarti, Aravinda | Zhu, Xiaofeng | Levy, Daniel | Munroe, Patricia B. | Rice, Kenneth M. | Bochud, Murielle | Johnson, Andrew D. | Chasman, Daniel I. | Smith, Albert V. | Tobin, Martin D. | Verwoert, Germaine C. | Hwang, Shih-Jen | Pihur, Vasyl | Vollenweider, Peter | O'Reilly, Paul F. | Amin, Najaf | Bragg-Gresham, Jennifer L. | Teumer, Alexander | Glazer, Nicole L. | Launer, Lenore | Zhao, Jing Hua | Aulchenko, Yurii | Heath, Simon | Sõber, Siim | Parsa, Afshin | Luan, Jian'an | Arora, Pankaj | Dehghan, Abbas | Zhang, Feng | Lucas, Gavin | Hicks, Andrew A. | Jackson, Anne U. | Peden, John F. | Tanaka, Toshiko | Wild, Sarah H. | Rudan, Igor | Igl, Wilmar | Milaneschi, Yuri | Parker, Alex N. | Fava, Cristiano | Chambers, John C. | Kumari, Meena | JinGo, Min | van der Harst, Pim | Kao, Wen Hong Linda | Sjögren, Marketa | Vinay, D.G. | Alexander, Myriam | Tabara, Yasuharu | Shaw-Hawkins, Sue | Whincup, Peter H. | Liu, Yongmei | Shi, Gang | Kuusisto, Johanna | Seielstad, Mark | Sim, Xueling | Nguyen, Khanh-Dung Hoang | Lehtimäki, Terho | Matullo, Giuseppe | Wu, Ying | Gaunt, Tom R. | Charlotte Onland-Moret, N. | Cooper, Matthew N. | Platou, Carl G.P. | Org, Elin | Hardy, Rebecca | Dahgam, Santosh | Palmen, Jutta | Vitart, Veronique | Braund, Peter S. | Kuznetsova, Tatiana | Uiterwaal, Cuno S.P.M. | Campbell, Harry | Ludwig, Barbara | Tomaszewski, Maciej | Tzoulaki, Ioanna | Palmer, Nicholette D. | Aspelund, Thor | Garcia, Melissa | Chang, Yen-Pei C. | O'Connell, Jeffrey R. | Steinle, Nanette I. | Grobbee, Diederick E. | Arking, Dan E. | Hernandez, Dena | Najjar, Samer | McArdle, Wendy L. | Hadley, David | Brown, Morris J. | Connell, John M. | Hingorani, Aroon D. | Day, Ian N.M. | Lawlor, Debbie A. | Beilby, John P. | Lawrence, Robert W. | Clarke, Robert | Collins, Rory | Hopewell, Jemma C. | Ongen, Halit | Bis, Joshua C. | Kähönen, Mika | Viikari, Jorma | Adair, Linda S. | Lee, Nanette R. | Chen, Ming-Huei | Olden, Matthias | Pattaro, Cristian | Hoffman Bolton, Judith A. | Köttgen, Anna | Bergmann, Sven | Mooser, Vincent | Chaturvedi, Nish | Frayling, Timothy M. | Islam, Muhammad | Jafar, Tazeen H. | Erdmann, Jeanette | Kulkarni, Smita R. | Bornstein, Stefan R. | Grässler, Jürgen | Groop, Leif | Voight, Benjamin F. | Kettunen, Johannes | Howard, Philip | Taylor, Andrew | Guarrera, Simonetta | Ricceri, Fulvio | Emilsson, Valur | Plump, Andrew | Barroso, Inês | Khaw, Kay-Tee | Weder, Alan B. | Hunt, Steven C. | Bergman, Richard N. | Collins, Francis S. | Bonnycastle, Lori L. | Scott, Laura J. | Stringham, Heather M. | Peltonen, Leena | Perola, Markus | Vartiainen, Erkki | Brand, Stefan-Martin | Staessen, Jan A. | Wang, Thomas J. | Burton, Paul R. | SolerArtigas, Maria | Dong, Yanbin | Snieder, Harold | Wang, Xiaoling | Zhu, Haidong | Lohman, Kurt K. | Rudock, Megan E. | Heckbert, Susan R. | Smith, Nicholas L. | Wiggins, Kerri L. | Shriner, Daniel | Veldre, Gudrun | Viigimaa, Margus | Kinra, Sanjay | Prabhakaran, Dorairajan | Tripathy, Vikal | Langefeld, Carl D. | Rosengren, Annika | Thelle, Dag S. | MariaCorsi, Anna | Singleton, Andrew | Forrester, Terrence | Hilton, Gina | McKenzie, Colin A. | Salako, Tunde | Iwai, Naoharu | Kita, Yoshikuni | Ogihara, Toshio | Ohkubo, Takayoshi | Okamura, Tomonori | Ueshima, Hirotsugu | Umemura, Satoshi | Eyheramendy, Susana | Meitinger, Thomas | Wichmann, H.-Erich | Cho, Yoon Shin | Kim, Hyung-Lae | Lee, Jong-Young | Scott, James | Sehmi, Joban S. | Zhang, Weihua | Hedblad, Bo | Nilsson, Peter | Smith, George Davey | Wong, Andrew | Narisu, Narisu | Stančáková, Alena | Raffel, Leslie J. | Yao, Jie | Kathiresan, Sekar | O'Donnell, Chris | Schwartz, Steven M. | Arfan Ikram, M. | Longstreth, Will T. | Seshadri, Sudha | Shrine, Nick R.G. | Wain, Louise V. | Morken, Mario A. | Swift, Amy J. | Laitinen, Jaana | Prokopenko, Inga | Zitting, Paavo | Cooper, Jackie A. | Humphries, Steve E. | Danesh, John | Rasheed, Asif | Goel, Anuj | Hamsten, Anders | Watkins, Hugh | Bakker, Stephan J.L. | van Gilst, Wiek H. | Janipalli, Charles S. | Radha Mani, K. | Yajnik, Chittaranjan S. | Hofman, Albert | Mattace-Raso, Francesco U.S. | Oostra, Ben A. | Demirkan, Ayse | Isaacs, Aaron | Rivadeneira, Fernando | Lakatta, Edward G. | Orru, Marco | Scuteri, Angelo | Ala-Korpela, Mika | Kangas, Antti J. | Lyytikäinen, Leo-Pekka | Soininen, Pasi | Tukiainen, Taru | Würz, Peter | Twee-Hee Ong, Rick | Dörr, Marcus | Kroemer, Heyo K. | Völker, Uwe | Völzke, Henry | Galan, Pilar | Hercberg, Serge | Lathrop, Mark | Zelenika, Diana | Deloukas, Panos | Mangino, Massimo | Spector, Tim D. | Zhai, Guangju | Meschia, James F. | Nalls, Michael A. | Sharma, Pankaj | Terzic, Janos | Kranthi Kumar, M.J. | Denniff, Matthew | Zukowska-Szczechowska, Ewa | Wagenknecht, Lynne E. | Fowkes, Gerald R. | Charchar, Fadi J. | Schwarz, Peter E.H. | Hayward, Caroline | Guo, Xiuqing | Bots, Michiel L. | Brand, Eva | Samani, Nilesh J. | Polasek, Ozren | Talmud, Philippa J. | Nyberg, Fredrik | Kuh, Diana | Laan, Maris | Hveem, Kristian | Palmer, Lyle J. | van der Schouw, Yvonne T. | Casas, Juan P. | Mohlke, Karen L. | Vineis, Paolo | Raitakari, Olli | Wong, Tien Y. | Shyong Tai, E. | Laakso, Markku | Rao, Dabeeru C. | Harris, Tamara B. | Morris, Richard W. | Dominiczak, Anna F. | Kivimaki, Mika | Marmot, Michael G. | Miki, Tetsuro | Saleheen, Danish | Chandak, Giriraj R. | Coresh, Josef | Navis, Gerjan | Salomaa, Veikko | Han, Bok-Ghee | Kooner, Jaspal S. | Melander, Olle | Ridker, Paul M. | Bandinelli, Stefania | Gyllensten, Ulf B. | Wright, Alan F. | Wilson, James F. | Ferrucci, Luigi | Farrall, Martin | Tuomilehto, Jaakko | Pramstaller, Peter P. | Elosua, Roberto | Soranzo, Nicole | Sijbrands, Eric J.G. | Altshuler, David | Loos, Ruth J.F. | Shuldiner, Alan R. | Gieger, Christian | Meneton, Pierre | Uitterlinden, Andre G. | Wareham, Nicholas J. | Gudnason, Vilmundur | Rettig, Rainer | Uda, Manuela | Strachan, David P. | Witteman, Jacqueline C.M. | Hartikainen, Anna-Liisa | Beckmann, Jacques S. | Boerwinkle, Eric | Boehnke, Michael | Larson, Martin G. | Järvelin, Marjo-Riitta | Psaty, Bruce M. | Abecasis, Gonçalo R. | Elliott, Paul | van Duijn , Cornelia M. | Newton-Cheh, Christopher
Human Molecular Genetics  2011;20(11):2273-2284.
The prevalence of hypertension in African Americans (AAs) is higher than in other US groups; yet, few have performed genome-wide association studies (GWASs) in AA. Among people of European descent, GWASs have identified genetic variants at 13 loci that are associated with blood pressure. It is unknown if these variants confer susceptibility in people of African ancestry. Here, we examined genome-wide and candidate gene associations with systolic blood pressure (SBP) and diastolic blood pressure (DBP) using the Candidate Gene Association Resource (CARe) consortium consisting of 8591 AAs. Genotypes included genome-wide single-nucleotide polymorphism (SNP) data utilizing the Affymetrix 6.0 array with imputation to 2.5 million HapMap SNPs and candidate gene SNP data utilizing a 50K cardiovascular gene-centric array (ITMAT-Broad-CARe [IBC] array). For Affymetrix data, the strongest signal for DBP was rs10474346 (P= 3.6 × 10−8) located near GPR98 and ARRDC3. For SBP, the strongest signal was rs2258119 in C21orf91 (P= 4.7 × 10−8). The top IBC association for SBP was rs2012318 (P= 6.4 × 10−6) near SLC25A42 and for DBP was rs2523586 (P= 1.3 × 10−6) near HLA-B. None of the top variants replicated in additional AA (n = 11 882) or European-American (n = 69 899) cohorts. We replicated previously reported European-American blood pressure SNPs in our AA samples (SH2B3, P= 0.009; TBX3-TBX5, P= 0.03; and CSK-ULK3, P= 0.0004). These genetic loci represent the best evidence of genetic influences on SBP and DBP in AAs to date. More broadly, this work supports that notion that blood pressure among AAs is a trait with genetic underpinnings but also with significant complexity.
doi:10.1093/hmg/ddr092
PMCID: PMC3090190  PMID: 21378095
23.  Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution 
Pope, Welkin H. | Jacobs-Sera, Deborah | Russell, Daniel A. | Peebles, Craig L. | Al-Atrache, Zein | Alcoser, Turi A. | Alexander, Lisa M. | Alfano, Matthew B. | Alford, Samantha T. | Amy, Nichols E. | Anderson, Marie D. | Anderson, Alexander G. | Ang, Andrew A. S. | Ares, Manuel | Barber, Amanda J. | Barker, Lucia P. | Barrett, Jonathan M. | Barshop, William D. | Bauerle, Cynthia M. | Bayles, Ian M. | Belfield, Katherine L. | Best, Aaron A. | Borjon, Agustin | Bowman, Charles A. | Boyer, Christine A. | Bradley, Kevin W. | Bradley, Victoria A. | Broadway, Lauren N. | Budwal, Keshav | Busby, Kayla N. | Campbell, Ian W. | Campbell, Anne M. | Carey, Alyssa | Caruso, Steven M. | Chew, Rebekah D. | Cockburn, Chelsea L. | Cohen, Lianne B. | Corajod, Jeffrey M. | Cresawn, Steven G. | Davis, Kimberly R. | Deng, Lisa | Denver, Dee R. | Dixon, Breyon R. | Ekram, Sahrish | Elgin, Sarah C. R. | Engelsen, Angela E. | English, Belle E. V. | Erb, Marcella L. | Estrada, Crystal | Filliger, Laura Z. | Findley, Ann M. | Forbes, Lauren | Forsyth, Mark H. | Fox, Tyler M. | Fritz, Melissa J. | Garcia, Roberto | George, Zindzi D. | Georges, Anne E. | Gissendanner, Christopher R. | Goff, Shannon | Goldstein, Rebecca | Gordon, Kobie C. | Green, Russell D. | Guerra, Stephanie L. | Guiney-Olsen, Krysta R. | Guiza, Bridget G. | Haghighat, Leila | Hagopian, Garrett V. | Harmon, Catherine J. | Harmson, Jeremy S. | Hartzog, Grant A. | Harvey, Samuel E. | He, Siping | He, Kevin J. | Healy, Kaitlin E. | Higinbotham, Ellen R. | Hildebrandt, Erin N. | Ho, Jason H. | Hogan, Gina M. | Hohenstein, Victoria G. | Holz, Nathan A. | Huang, Vincent J. | Hufford, Ericka L. | Hynes, Peter M. | Jackson, Arrykka S. | Jansen, Erica C. | Jarvik, Jonathan | Jasinto, Paul G. | Jordan, Tuajuanda C. | Kasza, Tomas | Katelyn, Murray A. | Kelsey, Jessica S. | Kerrigan, Larisa A. | Khaw, Daryl | Kim, Junghee | Knutter, Justin Z. | Ko, Ching-Chung | Larkin, Gail V. | Laroche, Jennifer R. | Latif, Asma | Leuba, Kohana D. | Leuba, Sequoia I. | Lewis, Lynn O. | Loesser-Casey, Kathryn E. | Long, Courtney A. | Lopez, A. Javier | Lowery, Nicholas | Lu, Tina Q. | Mac, Victor | Masters, Isaac R. | McCloud, Jazmyn J. | McDonough, Molly J. | Medenbach, Andrew J. | Menon, Anjali | Miller, Rachel | Morgan, Brandon K. | Ng, Patrick C. | Nguyen, Elvis | Nguyen, Katrina T. | Nguyen, Emilie T. | Nicholson, Kaylee M. | Parnell, Lindsay A. | Peirce, Caitlin E. | Perz, Allison M. | Peterson, Luke J. | Pferdehirt, Rachel E. | Philip, Seegren V. | Pogliano, Kit | Pogliano, Joe | Polley, Tamsen | Puopolo, Erica J. | Rabinowitz, Hannah S. |