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1.  ESICM LIVES 2016: part one 
Bos, L. | Schouten, L. | van Vught, L. | Wiewel, M. | Ong, D. | Cremer, O. | Artigas, A. | Martin-Loeches, I. | Hoogendijk, A. | van der Poll, T. | Horn, J. | Juffermans, N. | Schultz, M. | de Prost, N. | Pham, T. | Carteaux, G. | Dessap, A. Mekontso | Brun-Buisson, C. | Fan, E. | Bellani, G. | Laffey, J. | Mercat, A. | Brochard, L. | Maitre, B. | Howells, P. A. | Thickett, D. R. | Knox, C. | Park, D. P. | Gao, F. | Tucker, O. | Whitehouse, T. | McAuley, D. F. | Perkins, G. D. | Pham, T. | Laffey, J. | Bellani, G. | Fan, E. | Pisani, L. | Roozeman, J. P. | Simonis, F. D. | Giangregorio, A. | Schouten, L. R. | Van der Hoeven, S. M. | Horn, J. | Neto, A. Serpa | Festic, E. | Dondorp, A. M. | Grasso, S. | Bos, L. D. | Schultz, M. J. | Koster-Brouwer, M. | Verboom, D. | Scicluna, B. | van de Groep, K. | Frencken, J. | Schultz, M. | van der Poll, T. | Bonten, M. | Cremer, O. | Ko, J. I. | Kim, K. S. | Suh, G. J. | Kwon, W. Y. | Kim, K. | Shin, J. H. | Ranzani, O. T. | Prina, E. | Menendez, R. | Ceccato, A. | Mendez, R. | Cilloniz, C. | Gabarrus, A. | Ferrer, M. | Torres, A. | Urbano, A. | Zhang, L. A. | Swigon, D. | Pike, F. | Parker, R. S. | Clermont, G. | Scheer, C. | Kuhn, S. O. | Modler, A. | Vollmer, M. | Fuchs, C. | Hahnenkamp, K. | Rehberg, S. | Gründling, M. | Taggu, A. | Darang, N. | Öveges, N. | László, I. | Tánczos, K. | Németh, M. | Lebák, G. | Tudor, B. | Érces, D. | Kaszaki, J. | Huber, W. | Trásy, D. | Molnár, Z. | Ferrara, G. | Edul, V. S. Kanoore | Canales, H. S. | Martins, E. | Canullán, C. | Murias, G. | Pozo, M. O. | Eguillor, J. F. Caminos | Buscetti, M. G. | Ince, C. | Dubin, A. | Aya, H. D. | Rhodes, A. | Fletcher, N. | Grounds, R. M. | Cecconi, M. | Jacquet-Lagrèze, M. | Riche, M. | Schweizer, R. | Portran, P. | Fornier, W. | Lilot, M. | Neidecker, J. | Fellahi, J. L. | Escoresca-Ortega, A. | Gutiérrez-Pizarraya, A. | Charris-Castro, L. | Corcia-Palomo, Y. | Fernandez-Delgado, E. | Garnacho-Montero, J. | Roger, C. | Muller, L. | Elotmani, L. | Lipman, J. | Lefrant, J. Y. | Roberts, J. A. | Muñoz-Bermúdez, R. | Samper, M. | Climent, C. | Vasco, F. | Sara, V. | Luque, S. | Campillo, N. | Cerrato, S. Grau | Masclans, J. R. | Alvarez-Lerma, F. | Brugger, S. Carvalho | Jimenez, G. Jimenez | Torner, M. Miralbés | Cabello, J. Trujillano | Garrido, B. Balsera | Casals, X. Nuvials | Gaite, F. Barcenilla | Vidal, M. Vallverdú | Martínez, M. Palomar | Gusarov, V. | Shilkin, D. | Dementienko, M. | Nesterova, E. | Lashenkova, N. | Kuzovlev, A. | Zamyatin, M. | Demoule, A. | Carreira, S. | Lavault, S. | Palancca, O. | Morawiec, E. | Mayaux, J. | Arnulf, I. | Similowski, T. | Rasmussen, B. S. | Maltesen, R. G. | Hanifa, M. | Pedersen, S. | Kristensen, S. R. | Wimmer, R. | Panigada, M. | Bassi, G. Li | Ranzani, O. T. | Kolobow, T. | Zanella, A. | Cressoni, M. | Berra, L. | Parrini, V. | Kandil, H. | Salati, G. | Livigni, S. | Amatu, A. | Andreotti, A. | Tagliaferri, F. | Moise, G. | Mercurio, G. | Costa, A. | Vezzani, A. | Lindau, S. | Babel, J. | Cavana, M. | Consonni, D. | Pesenti, A. | Gattinoni, L. | Torres, A. | Mansouri, P. | Zand, F. | Zahed, L. | Dehghanrad, F. | Bahrani, M. | Ghorbani, M. | Cambiaghi, B. | Moerer, O. | Mauri, T. | Kunze-Szikszay, N. | Ritter, C. | Pesenti, A. | Quintel, M. | Vilander, L. M. | Kaunisto, M. A. | Vaara, S. T. | Pettilä, V. | Mulier, J. L. G. Haitsma | Rozemeijer, S. | Spoelstra-de Man, A. M. E. | Elbers, P. E. | Tuinman, P. R. | de Waard, M. C. | Oudemans-van Straaten, H. M. | Liberatore, A. M. A. | Souza, R. B. | Martins, A. M. C. R. P. F. | Vieira, J. C. F. | Koh, I. H. J. | Martínez, M. Galindo | Sánchez, R. Jiménez | Gascón, L. Martínez | Mulero, M. D. Rodríguez | Freire, A. Ortín | Muñoz, A. Ojados | Acebes, S. Rebollo | Martínez, Á. Fernández | Aliaga, S. Moreno | Para, L. Herrera | Payá, J. Murcia | Mulero, F. Rodríguez | Guerci, P. | Ince, Y. | Heeman, P. | Ergin, B. | Ince, C. | Uz, Z. | Massey, M. | Ince, Y. | Papatella, R. | Bulent, E. | Guerci, P. | Toraman, F. | Ince, C. | Longbottom, E. R. | Torrance, H. D. | Owen, H. C. | Hinds, C. J. | Pearse, R. M. | O’Dywer, M. J. | Trogrlic, Z. | van der Jagt, M. | Lingsma, H. | Ponssen, H. H. | Schoonderbeek, J. F. | Schreiner, F. | Verbrugge, S. J. | Duran, S. | van Achterberg, T. | Bakker, J. | Gommers, D. A. M. P. J. | Ista, E. | Krajčová, A. | Waldauf, P. | Duška, F. | Shah, A. | Roy, N. | McKechnie, S. | Doree, C. | Fisher, S. | Stanworth, S. J. | Jensen, J. F. | Overgaard, D. | Bestle, M. H. | Christensen, D. F. | Egerod, I. | Pivkina, A. | Gusarov, V. | Zhivotneva, I. | Pasko, N. | Zamyatin, M. | Jensen, J. F. | Egerod, I. | Bestle, M. H. | Christensen, D. F. | Alklit, A. | Hansen, R. L. | Knudsen, H. | Grode, L. B. | Overgaard, D. | Hravnak, M. | Chen, L. | Dubrawski, A. | Clermont, G. | Pinsky, M. R. | Parry, S. M. | Knight, L. D. | Connolly, B. C. | Baldwin, C. E. | Puthucheary, Z. A. | Denehy, L. | Hart, N. | Morris, P. E. | Mortimore, J. | Granger, C. L. | Jensen, H. I. | Piers, R. | Van den Bulcke, B. | Malmgren, J. | Metaxa, V. | Reyners, A. K. | Darmon, M. | Rusinova, K. | Talmor, D. | Meert, A. P. | Cancelliere, L. | Zubek, L. | Maia, P. | Michalsen, A. | Decruyenaere, J. | Kompanje, E. | Vanheule, S. | Azoulay, E. | Vansteelandt, S. | Benoit, D. | Van den Bulcke, B. | Piers, R. | Jensen, H. I. | Malmgren, J. | Metaxa, V. | Reyners, A. K. | Darmon, M. | Rusinova, K. | Talmor, D. | Meert, A. P. | Cancelliere, L. | Zubek, L. | Maia, P. | Michalsen, A. | Decruyenaere, J. | Kompanje, E. | Vanheule, S. | Azoulay, E. | Vansteelandt, S. | Benoit, D. | Ryan, C. | Dawson, D. | Ball, J. | Noone, K. | Aisling, B. | Prudden, S. | Ntantana, A. | Matamis, D. | Savvidou, S. | Giannakou, M. | Gouva, M. | Nakos, G. | Koulouras, V. | Aron, J. | Lumley, G. | Milliken, D. | Dhadwal, K. | McGrath, B. A. | Lynch, S. J. | Bovento, B. | Sharpe, G. | Grainger, E. | Pieri-Davies, S. | Wallace, S. | McGrath, B. | Lynch, S. J. | Bovento, B. | Grainger, E. | Pieri-Davies, S. | Sharpe, G. | Wallace, S. | Jung, M. | Cho, J. | Park, H. | Suh, G. | Kousha, O. | Paddle, J. | Gripenberg, L. Gamrin | Rehal, M. Sundström | Wernerman, J. | Rooyackers, O. | de Grooth, H. J. | Choo, W. P. | Spoelstra-de Man, A. M. | Swart, E. L. | Oudemans-van Straaten, H. M. | Talan, L. | Güven, G. | Altıntas, N. D. | Padar, M. | Uusvel, G. | Starkopf, L. | Starkopf, J. | Blaser, A. Reintam | Kalaiselvan, M. S. | Arunkumar, A. S. | Renuka, M. K. | Shivkumar, R. L. | Volbeda, M. | ten Kate, D. | Hoekstra, M. | van der Maaten, J. M. | Nijsten, M. W. | Komaromi, A. | Rooyackers, O. | Wernerman, J. | Norberg, Å. | Smedberg, M. | Mori, M. | Pettersson, L. | Norberg, Å. | Rooyackers, O. | Wernerman, J. | Theodorakopoulou, M. | Christodoulopoulou, T. | Diamantakis, A. | Frantzeskaki, F. | Kontogiorgi, M. | Chrysanthopoulou, E. | Lygnos, M. | Diakaki, C. | Armaganidis, A. | Gundogan, K. | Dogan, E. | Coskun, R. | Muhtaroglu, S. | Sungur, M. | Ziegler, T. | Guven, M. | Kleyman, A. | Khaliq, W. | Andreas, D. | Singer, M. | Meierhans, R. | Schuepbach, R. | De Brito-Ashurst, I. | Zand, F. | Sabetian, G. | Nikandish, R. | Hagar, F. | Masjedi, M. | Maghsudi, B. | Vazin, A. | Ghorbani, M. | Asadpour, E. | Kao, K. C. | Chiu, L. C. | Hung, C. Y. | Chang, C. H. | Li, S. H. | Hu, H. C. | El Maraghi, S. | Ali, M. | Rageb, D. | Helmy, M. | Marin-Corral, J. | Vilà, C. | Masclans, J. R. | Vàzquez, A. | Martín-Loeches, I. | Díaz, E. | Yébenes, J. C. | Rodriguez, A. | Álvarez-Lerma, F. | Varga, N. | Cortina-Gutiérrez, A. | Dono, L. | Martínez-Martínez, M. | Maldonado, C. | Papiol, E. | Pérez-Carrasco, M. | Ferrer, R. | Nweze, K. | Morton, B. | Welters, I. | Houard, M. | Voisin, B. | Ledoux, G. | Six, S. | Jaillette, E. | Nseir, S. | Romdhani, S. | Bouneb, R. | Loghmari, D. | Aicha, N. Ben | Ayachi, J. | Meddeb, K. | Chouchène, I. | Khedher, A. | Boussarsar, M. | Chan, K. S. | Yu, W. L. | Marin-Corral, J. | Vilà, C. | Masclans, J. R. | Nolla, J. | Vidaur, L. | Bonastre, J. | Suberbiola, B. | Guerrero, J. E. | Rodriguez, A. | Coll, N. Ramon | Jiménez, G. Jiménez | Brugger, S. Carvalho | Calero, J. Codina | Garrido, B. Balsera | García, M. | Martínez, M. Palomar | Vidal, M. Vallverdú | de la Torre, M. C. | Vendrell, E. | Palomera, E. | Güell, E. | Yébenes, J. C. | Serra-Prat, M. | Bermejo-Martín, J. F. | Almirall, J. | Tomas, E. | Escoval, A. | Froe, F. | Pereira, M. H. Vitoria | Velez, N. | Viegas, E. | Filipe, E. | Groves, C. | Reay, M. | Chiu, L. C. | Hu, H. C. | Hung, C. Y. | Chang, C. H. | Li, S. H. | Kao, K. C. | Ballin, A. | Facchin, F. | Sartori, G. | Zarantonello, F. | Campello, E. | Radu, C. M. | Rossi, S. | Ori, C. | Simioni, P. | Umei, N. | Shingo, I. | Santos, A. C. | Candeias, C. | Moniz, I. | Marçal, R. | e Silva, Z. Costa | Ribeiro, J. M. | Georger, J. F. | Ponthus, J. P. | Tchir, M. | Amilien, V. | Ayoub, M. | Barsam, E. | Martucci, G. | Panarello, G. | Tuzzolino, F. | Capitanio, G. | Ferrazza, V. | Carollo, T. | Giovanni, L. | Arcadipane, A. | Sánchez, M. López | González-Gay, M. A. | Díaz, F. J. Llorca | López, M. I. Rubio | Zogheib, E. | Villeret, L. | Nader, J. | Bernasinski, M. | Besserve, P. | Caus, T. | Dupont, H. | Morimont, P. | Habran, S. | Hubert, R. | Desaive, T. | Blaffart, F. | Janssen, N. | Guiot, J. | Pironet, A. | Dauby, P. | Lambermont, B. | Zarantonello, F. | Ballin, A. | Facchin, F. | Sartori, G. | Campello, E. | Pettenuzzo, T. | Citton, G. | Rossi, S. | Simioni, P. | Ori, C. | Kirakli, C. | Ediboglu, O. | Ataman, S. | Yarici, M. | Tuksavul, F. | Keating, S. | Gibson, A. | Gilles, M. | Dunn, M. | Price, G. | Young, N. | Remeta, P. | Bishop, P. | Zamora, M. D. Fernández | Muñoz-Bono, J. | Curiel-Balsera, E. | Aguilar-Alonso, E. | Hinojosa, R. | Gordillo-Brenes, A. | Arboleda-Sánchez, J. A. | Skorniakov, I. | Vikulova, D. | Whiteley, C. | Shaikh, O. | Jones, A. | Ostermann, M. | Forni, L. | Scott, M. | Sahatjian, J. | Linde-Zwirble, W. | Hansell, D. | Laoveeravat, P. | Srisawat, N. | Kongwibulwut, M. | Peerapornrattana, S. | Suwachittanont, N. | Wirotwan, T. O. | Chatkaew, P. | Saeyub, P. | Latthaprecha, K. | Tiranathanagul, K. | Eiam-ong, S. | Kellum, J. A. | Berthelsen, R. E. | Perner, A. | Jensen, A. E. K. | Jensen, J. U. | Bestle, M. H. | Gebhard, D. J. | Price, J. | Kennedy, C. E. | Akcan-Arikan, A. | Liberatore, A. M. A. | Souza, R. B. | Martins, A. M. C. R. P. F. | Vieira, J. C. F. | Kang, Y. R. | Nakamae, M. N. | Koh, I. H. J. | Hamed, K. | Khaled, M. M. | Soliman, R. Aly | Mokhtar, M. Sherif | Seller-Pérez, G. | Arias-Verdú, D. | Llopar-Valdor, E. | De-Diós-Chacón, I. | Quesada-García, G. | Herrera-Gutierrez, M. E. | Hafes, R. | Carroll, G. | Doherty, P. | Wright, C. | Vera, I. G. Guerra | Ralston, M. | Gemmell, M. L. | MacKay, A. | Black, E. | Wright, C. | Docking, R. I. | Appleton, R. | Ralston, M. R. | Gemmell, L. | Appleton, R. | Wright, C. | Docking, R. I. | Black, E. | Mackay, A. | Rozemeijer, S. | Mulier, J. L. G. Haitsma | Röttgering, J. G. | Elbers, P. W. G. | Spoelstra-de Man, A. M. E. | Tuinman, P. R. | de Waard, M. C. | Oudemans-van Straaten, H. M. | Mejeni, N. | Nsiala, J. | Kilembe, A. | Akilimali, P. | Thomas, G. | Egerod, I. | Andersson, A. E. | Fagerdahl, A. M. | Knudsen, V. | Meddeb, K. | Cheikh, A. Ben | Hamdaoui, Y. | Ayachi, J. | Guiga, A. | Fraj, N. | Romdhani, S. | Sma, N. | Bouneb, R. | Chouchene, I. | Khedher, A. | Bouafia, N. | Boussarsar, M. | Amirian, A. | Ziaian, B. | Masjedi, M. | Fleischmann, C. | Thomas-Rueddel, D. O. | Schettler, A. | Schwarzkopf, D. | Stacke, A. | Reinhart, K. | Filipe, E. | Escoval, A. | Martins, A. | Sousa, P. | Velez, N. | Viegas, E. | Tomas, E. | Snell, G. | Matsa, R. | Paary, T. T. S. | Kalaiselvan, M. S. | Cavalheiro, A. M. | Rocha, L. L. | Vallone, C. S. | Tonilo, A. | Lobato, M. D. S. | Malheiro, D. T. | Sussumo, G. | Lucino, N. M. | Zand, F. | Rosenthal, V. D. | Masjedi, M. | Sabetian, G. | Maghsudi, B. | Ghorbani, M. | Dashti, A. Sanaei | Yousefipour, A. | Goodall, J. R. | Williamson, M. | Tant, E. | Thomas, N. | Balci, C. | Gonen, C. | Haftacı, E. | Gurarda, H. | Karaca, E. | Paldusová, B. | Zýková, I. | Šímová, D. | Houston, S. | D’Antona, L. | Lloyd, J. | Garnelo-Rey, V. | Sosic, M. | Sotosek-Tokmazic, V. | Kuharic, J. | Antoncic, I. | Dunatov, S. | Sustic, A. | Chong, C. T. | Sim, M. | Lyovarin, T. | Díaz, F. M. Acosta | Galdó, S. Narbona | Garach, M. Muñoz | Romero, O. Moreno | Bailón, A. M. Pérez | Pinel, A. Carranza | Colmenero, M. | Gritsan, A. | Gazenkampf, A. | Korchagin, E. | Dovbish, N. | Lee, R. M. | Lim, M. P. P. | Chong, C. T. | Lim, B. C. L. | See, J. J. | Assis, R. | Filipe, F. | Lopes, N. | Pessoa, L. | Pereira, T. | Catorze, N. | Aydogan, M. S. | Aldasoro, C. | Marchio, P. | Jorda, A. | Mauricio, M. D. | Guerra-Ojeda, S. | Gimeno-Raga, M. | Colque-Cano, M. | Bertomeu-Artecero, A. | Aldasoro, M. | Valles, S. L. | Tonon, D. | Triglia, T. | Martin, J. C. | Alessi, M. 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doi:10.1186/s40635-016-0098-x
PMCID: PMC5042924
2.  ESICM LIVES 2016: part two 
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doi:10.1186/s40635-016-0099-9
PMCID: PMC5042923
3.  ESICM LIVES 2016: part three 
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Pedraza | Pham, T. | Beduneau, G. | Schortgen, F. | Piquilloud, L. | Zogheib, E. | Jonas, M. | Grelon, F. | Runge, I. | Terzi, N. | Grangé, S. | Barberet, G. | Guitard, P. G. | Frat, J. P. | Constan, A. | Chrétien, J. M. | Mancebo, J. | Mercat, A. | Richard, J. C. M. | Brochard, L. | Soilemezi, E. | Koco, E. | Savvidou, S. | Nouris, C. | Matamis, D. | Di Mussi, R. | Spadaro, S. | Volta, C. A. | Mariani, M. | Colaprico, A. | Antonio, C. | Bruno, F. | Grasso, S. | Rodriguez, A. | Martín-Loeches, I. | Díaz, E. | Masclans, J. R. | Gordo, F. | Solé-Violán, J. | Bodí, M. | Avilés-Jurado, F. X. | Trefler, S. | Magret, M. | Reyes, L. F. | Marín-Corral, J. | Yebenes, J. C. | Esteban, A. | Anzueto, A. | Aliberti, S. | Restrepo, M. I. | Larsson, J. Skytte | Redfors, B. | Ricksten, S. E. | Haines, R. | Powell-Tuck, J. | Leonard, H. | Ostermann, M. | Berthelsen, R. E. | Itenov, T. S. | Perner, A. | Jensen, J. U. | Ibsen, M. | Jensen, A. E. K. | Bestle, M. H. | Bucknall, T. | Dixon, J. | Boa, F. | MacPhee, I. | Philips, B. J. | Doyle, J. | Saadat, F. | Samuels, T. | Huddart, S. | McCormick, B. | DeBrunnar, R. | Preece, J. | Swart, M. | Peden, C. | Richardson, S. | Forni, L. | Kalfon, P. | Baumstarck, K. | Estagnasie, P. | Geantot, M. A. | Berric, A. | Simon, G. | Floccard, B. | Signouret, T. | Boucekine, M. | Fromentin, M. | Nyunga, M. | Sossou, A. | Venot, M. | Robert, R. | Follin, A. | Renault, A. | Garrouste, M. | Collange, O. | Levrat, Q. | Villard, I. | Thévenin, D. | Pottecher, J. | Patrigeon, R. G. | Revel, N. | Vigne, C. | Mimoz, O. | Auquier, P. | Pawar, S. | Jacques, T. | Deshpande, K. | Pusapati, R. | Wood, B. | Pulham, R. A. | Wray, J. | Brown, K. | Pierce, C. | Nadel, S. | Ramnarayan, P. | Azevedo, J. R. | Montenegro, W. S. | Rodrigues, D. P. | Sousa, S. C. | Araujo, V. F. | Leitao, A. L. | Prazeres, P. H. | Mendonca, A. V. | Paula, M. P. | Das Neves, A. | Loudet, C. I. | Busico, M. | Vazquez, D. | Villalba, D. | Lischinsky, A. | Veronesi, M. | Emmerich, M. | Descotte, E. | Juliarena, A. | Bisso, M. Carboni | Grando, M. | Tapia, A. | Camargo, M. | Ulla, D. Villani | Corzo, L. | dos Santos, H. Placido | Ramos, A. | Doglia, J. A. | Estenssoro, E. | Carbonara, M. | Magnoni, S. | Donald, C. L. Mac | Shimony, J. S. | Conte, V. | Triulzi, F. | Stretti, F. | Macrì, M. | Snyder, A. Z. | Stocchetti, N. | Brody, D. L. | Podlepich, V. | Shimanskiy, V. | Savin, I. | Lapteva, K. | Chumaev, A. | Tjepkema-Cloostermans, M. C. | Hofmeijer, J. | Beishuizen, A. | Hom, H. | Blans, M. J. | van Putten, M. J. A. M. | Longhi, L. | Frigeni, B. | Curinga, M. | Mingone, D. | Beretta, S. | Patruno, A. | Gandini, L. | Vargiolu, A. | Ferri, F. | Ceriani, R. | Rottoli, M. R. | Lorini, L. | Citerio, G. | Pifferi, S. | Battistini, M. | Cordolcini, V. | Agarossi, A. | Di Rosso, R. | Ortolano, F. | Stocchetti, N. | Lourido, C. Mora | Cabrera, J. L. Santana | Santana, J. D. Martín | Alzola, L. Melián | del Rosario, C. García | Pérez, H. Rodríguez | Torrent, R. Lorenzo | Eslami, S. | Dalhuisen, A. | Fiks, T. | Schultz, M. J. | Hanna, A. Abu | Spronk, P. E. | Wood, M. | Maslove, D. | Muscedere, J. | Scott, S. H.
doi:10.1186/s40635-016-0100-7
PMCID: PMC5042925
4.  Dynamic sinking behaviour in marine phytoplankton: rapid changes in buoyancy may aid in nutrient uptake 
Phytoplankton sinking is an important property that can determine community composition in the photic zone and material loss to the deep ocean. To date, studies of diatom suspension have relied on bulk measurements with assumptions that bulk rates adequately capture the essential characteristics of diatom sinking. However, recent work has illustrated that individual diatom sinking rates vary considerably from the mean bulk rate. In this study, we apply high-resolution optical techniques, individual-based observations of diatom sinking and a recently developed method of flow visualization around freely sinking cells. The results show that in both field samples and laboratory cultures, some large species of centric diatoms are capable of a novel behaviour, whereby cells undergo bursts of rapid sinking that alternate with near-zero sinking rates on the timescales of seconds. We also demonstrate that this behaviour is under direct metabolic control of the cell. We discuss these results in the context of implications for nutrient flux to the cell surface. While nutrient flux in large diatoms increases during fast sinking, current mass transport models cannot incorporate the unsteady sinking behaviour observed in this study. However, large diatoms appear capable of benefiting from the enhanced nutrient flux to their surface during rapid sinking even during brief intervening periods of near-zero sinking rates.
doi:10.1098/rspb.2016.1126
PMCID: PMC5069504  PMID: 27708154
diatom; sinking; nutrient flux; phytoplankton
5.  Partial malrotation of the bowel in an adult patient presenting with abdominal pain 
BMJ Case Reports  2015;2015:bcr2015211591.
doi:10.1136/bcr-2015-211591
PMCID: PMC4551017  PMID: 26294361
6.  Introduction of a male-harming mitochondrial haplotype via ‘Trojan Females’ achieves population suppression in fruit flies 
eLife  null;6:e23551.
Pests are a global threat to biodiversity, ecosystem function, and human health. Pest control approaches are thus numerous, but their implementation costly, damaging to non-target species, and ineffective at low population densities. The Trojan Female Technique (TFT) is a prospective self-perpetuating control technique that is species-specific and predicted to be effective at low densities. The goal of the TFT is to harness naturally occurring mutations in the mitochondrial genome that impair male fertility while having no effect on females. Here, we provide proof-of-concept for the TFT, by showing that introduction of a male fertility-impairing mtDNA haplotype into replicated populations of Drosophila melanogaster causes numerical population suppression, with the magnitude of effect positively correlated with its frequency at trial inception. Further development of the TFT could lead to establishing a control strategy that overcomes limitations of conventional approaches, with broad applicability to invertebrate and vertebrate species, to control environmental and economic pests.
DOI: http://dx.doi.org/10.7554/eLife.23551.001
eLife digest
Insect and other animal pests pose some of the greatest challenges to biodiversity, global economies and human health. The environmental and agricultural losses caused by pests have been estimated at 120 billion US dollars a year in the US alone. Many pests also spread diseases, such as dengue fever and malaria. A variety of different strategies are used to control pests, but their effects are generally short-lived and they are often ineffective when pest numbers are low. Furthermore, many of these strategies are harmful to other wildlife, such as bees.
Most of the DNA within an animal cell is contained within a structure called the nucleus. However, some DNA is also found within other compartments called mitochondria. The Trojan Female technique has been proposed as a new strategy to control insect pests that harnesses naturally-occurring changes (known as mutations) in this mitochondrial DNA (or mtDNA for short). Introducing mutations that lower the fertility of males, but have no effects on females, into a pest population should, in theory, lead to a long-lasting decline in the size of the population, even if it is relatively small to begin with.
Wolff et al. tested this theory in fruit flies, which are often used as models of insects and other animals in research projects. Adding female fruit flies carrying a mutation in mtDNA that lowers male fertility (known as “Trojan Females”) into populations of fruit flies reduced the size of the population over several generations. The mutation was maintained in the population for at least ten generations, and no “rescue” mutations evolved in the nuclear DNA to compensate for the mtDNA mutation. This indicates that the Trojan Female technique could be effective at controlling pests, without the need for Trojan Females to be repeatedly released into the populations.
The next steps following on from this work are to test this approach in economically important pest species, and to find out whether the approach is effective in various environments outside the laboratory. If these findings do indeed translate into these pests, then the Trojan Female technique may have the potential to be used to control a wide variety of different pest species from mosquitos through to rats.
DOI: http://dx.doi.org/10.7554/eLife.23551.002
doi:10.7554/eLife.23551
PMCID: PMC5441865  PMID: 28467301
mitochondria; mitonuclear; fertility control; bio control; male-harming mutations; mtDNA; D. melanogaster
7.  Cryptic female choice enhances fertilization success and embryo survival in chinook salmon 
In this study, we investigated two potentially important intersexual postcopulatory gametic interactions in a population of chinook salmon (Oncorhynchus tshawytscha): (i) the effect of female ovarian fluid (OF) on the behaviour of spermatozoa during fertilization and (ii) the effects of multilocus heterozygosity (MLH) (as an index of male quality) and female–male genetic relatedness on sperm behaviour and male fertilization success when there is sperm competition in the presence of that OF. To do this, we conducted a series of in vitro competitive fertilization experiments and found that, when ejaculates from two males are competing for access to a single female's unfertilized eggs, fertilization success was significantly biased towards the male whose sperm swam fastest in the female's OF. Embryo survival—a measure of fitness—was also positively correlated with both sperm swimming speed in OF and male MLH, providing novel evidence that cryptic female choice is adaptive for the female, enhancing the early survival of her offspring and potentially influencing her fitness.
doi:10.1098/rspb.2016.0001
PMCID: PMC4822462  PMID: 27009221
cryptic female choice; sperm competition; ovarian fluid; sexual selection; embryo survival; salmon
8.  SmartMom Text Messaging for Prenatal Education: A Qualitative Focus Group Study to Explore Canadian Women’s Perceptions 
Background
We engaged Canadian women in the development of a prenatal education program delivered via one-way text messaging called SmartMom. SmartMom is the first peer-reviewed, evidence-based mHealth program for prenatal education in Canada and the first to be endorsed by the Society of Obstetricians and Gynaecologists of Canada.
Objective
To explore women’s preferences for a prenatal education program by text messaging.
Methods
We conducted a qualitative focus group study in three Canadian communities in the Northern Health Authority. Women completed a demographic questionnaire, participated in a guided discussion about their pregnancy information-seeking behavior, reviewed a printed copy of the SmartMom text messages, and then engaged in a moderated discussion about their perceptions of the usability of the SmartMom program. Open-ended questions explored women’s perceptions regarding the message content, acceptability of receiving information by text message, positive health behaviors they might engage in after receiving a message, modifiable program factors, and intention to use the program. Thematic analysis of transcribed audio recordings was undertaken and modifications were made to the SmartMom program based on these findings.
Results
A total of 40 women participated in seven focus groups in three rural northern communities. The vast majority had a mobile phone (39/40, 98%), used text messages “all the time” (28/40, 70%), and surfed the Internet on their phone (37/40, 93%). Participants perceived SmartMom to be highly acceptable and relevant. The text message modality reflected how participants currently sought pregnancy-related information and provided them with local information tailored to their gestational age, which they had not received through other pregnancy resources. Women recommended adding the opportunity to receive supplemental streams of messages tailored to their individual needs, for example, depression, pregnancy after previous cesarean, >35 years of age, new immigrants, and harm reduction for smoking and alcohol.
Conclusions
This formative qualitative evaluation provides evidence that a prenatal education program by text messaging, SmartMom, is acceptable to the end users. These findings support the usability of the SmartMom program at a population level and the development of an evaluation program exploring the effects of the text messages on adoption of health-promoting behaviors and maternal-child health outcomes.
doi:10.2196/publichealth.6949
PMCID: PMC5320393  PMID: 28174149
pregnancy; text messaging; prenatal education; health behavior
9.  Microsatellite polymorphisms associated with human behavioural and psychological phenotypes including a gene-environment interaction 
BMC Medical Genetics  2017;18:12.
Background
The genetic and environmental influences on human personality and behaviour are a complex matter of ongoing debate. Accumulating evidence indicates that short tandem repeats (STRs) in regulatory regions are good candidates to explain heritability not accessed by genome-wide association studies.
Methods
We tested for associations between the genotypes of four selected repeats and 18 traits relating to personality, behaviour, cognitive ability and mental health in a well-studied longitudinal birth cohort (n = 458-589) using one way analysis of variance. The repeats were a highly conserved poly-AC microsatellite in the upstream promoter region of the T-box brain 1 (TBR1) gene and three previously studied STRs in the activating enhancer-binding protein 2-beta (AP2-β) and androgen receptor (AR) genes. Where significance was found we used multiple regression to assess the influence of confounding factors.
Results
Carriers of the shorter, most common, allele of the AR gene’s GGN microsatellite polymorphism had fewer anxiety-related symptoms, which was consistent with previous studies, but in our study this was not significant following Bonferroni correction. No associations with two repeats in the AP2-β gene withstood this correction. A novel finding was that carriers of the minor allele of the TBR1 AC microsatellite were at higher risk of conduct problems in childhood at age 7-9 (p = 0.0007, which did pass Bonferroni correction). Including maternal smoking during pregnancy (MSDP) in models controlling for potentially confounding influences showed that an interaction between TBR1 genotype and MSDP was a significant predictor of conduct problems in childhood and adolescence (p < 0.001), and of self-reported criminal behaviour up to age 25 years (p ≤ 0.02). This interaction remained significant after controlling for possible confounders including maternal age at birth, socio-economic status and education, and offspring birth weight.
Conclusions
The potential functional importance of the TBR1 gene’s promoter microsatellite deserves further investigation. Our results suggest that it participates in a gene-environment interaction with MDSP and antisocial behaviour. However, previous evidence that mothers who smoke during pregnancy carry genes for antisocial behaviour suggests that epistasis may influence the interaction.
Electronic supplementary material
The online version of this article (doi:10.1186/s12881-017-0374-y) contains supplementary material, which is available to authorized users.
doi:10.1186/s12881-017-0374-y
PMCID: PMC5291968  PMID: 28158988
TBR1; Androgen receptor; AP2-β; Microsatellite; STR; Antisocial; Behaviour; Pregnancy; Smoking; Gene-environment interaction
10.  Toxocariasis as a cause of multiple pulmonary nodules in a paediatric patient 
BMJ Case Reports  2015;2015:bcr2014207073.
doi:10.1136/bcr-2014-207073
PMCID: PMC4289785  PMID: 25564589
11.  A Comparison of Singlet Oxygen Explicit Dosimetry (SOED) and Singlet Oxygen Luminescence Dosimetry (SOLD) for Photofrin-Mediated Photodynamic Therapy 
Cancers  2016;8(12):109.
Accurate photodynamic therapy (PDT) dosimetry is critical for the use of PDT in the treatment of malignant and nonmalignant localized diseases. A singlet oxygen explicit dosimetry (SOED) model has been developed for in vivo purposes. It involves the measurement of the key components in PDT—light fluence (rate), photosensitizer concentration, and ground-state oxygen concentration ([3O2])—to calculate the amount of reacted singlet oxygen ([1O2]rx), the main cytotoxic component in type II PDT. Experiments were performed in phantoms with the photosensitizer Photofrin and in solution using phosphorescence-based singlet oxygen luminescence dosimetry (SOLD) to validate the SOED model. Oxygen concentration and photosensitizer photobleaching versus time were measured during PDT, along with direct SOLD measurements of singlet oxygen and triplet state lifetime (τΔ and τt), for various photosensitizer concentrations to determine necessary photophysical parameters. SOLD-determined cumulative [1O2]rx was compared to SOED-calculated [1O2]rx for various photosensitizer concentrations to show a clear correlation between the two methods. This illustrates that explicit dosimetry can be used when phosphorescence-based dosimetry is not feasible. Using SOED modeling, we have also shown evidence that SOLD-measured [1O2]rx using a 523 nm pulsed laser can be used to correlate to singlet oxygen generated by a 630 nm laser during a clinical malignant pleural mesothelioma (MPM) PDT protocol by using a conversion formula.
doi:10.3390/cancers8120109
PMCID: PMC5187507  PMID: 27929427
photodynamic therapy; singlet oxygen explicit dosimetry (SOED); singlet oxygen luminescence dosimetry (SOLD); Photofrin; oxygen
12.  Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies 
Microbiome  2016;4:61.
Background
Sequencing-based analysis has become a well-established approach to deciphering the composition of the gut microbiota. However, due to the complexity of accessing sufficient material from colonoscopic biopsy samples, most studies have focused on faecal microbiota analysis, even though it is recognised that differences exist between the microbial composition of colonic biopsies and faecal samples. We determined the suitability of colonic lavage samples to see if it had comparable microbial diversity composition to colonic biopsies as they are without the limitations associated with sample size. We collected paired colonic biopsies and lavage samples from subjects who were attending for colorectal cancer screening colonoscopy.
Results
Next-generation sequencing and qPCR validation were performed with multiple bioinformatics analyses to determine the composition and predict function of the microbiota. Colonic lavage samples contained significantly higher numbers of operational taxonomic units (OTUs) compared to corresponding biopsy samples, however, diversity and evenness between lavage and biopsy samples were similar. The differences seen were driven by the presence of 12 OTUs which were in higher relative abundance in biopsies and were either not present or in low relative abundance in lavage samples, whilst a further 3 OTUs were present in higher amounts in the lavage samples compared to biopsy samples. However, predicted functional community profiling based on 16S ribosomal ribonucleic acid (rRNA) data indicated minimal differences between sample types.
Conclusions
We propose that colonic lavage samples provide a relatively accurate representation of biopsy microbiota composition and should be considered where biopsy size is an issue.
Electronic supplementary material
The online version of this article (doi:10.1186/s40168-016-0207-9) contains supplementary material, which is available to authorized users.
doi:10.1186/s40168-016-0207-9
PMCID: PMC5123352  PMID: 27884202
Colonic lavage; Colonic biopsies; Microbiome analysis; Next-generation sequencing
13.  Recommendations for standards of monitoring during anaesthesia and recovery 2015 : Association of Anaesthetists of Great Britain and Ireland[Link]  
Anaesthesia  2015;71(1):85-93.
Summary
This guideline updates and replaces the 4th edition of the AAGBI Standards of Monitoring published in 2007. The aim of this document is to provide guidance on the minimum standards for physiological monitoring of any patient undergoing anaesthesia or sedation under the care of an anaesthetist. The recommendations are primarily aimed at anaesthetists practising in the United Kingdom and Ireland. Minimum standards for monitoring patients during anaesthesia and in the recovery phase are included. There is also guidance on monitoring patients undergoing sedation and also during transfer of anaesthetised or sedated patients. There are new sections discussing the role of monitoring depth of anaesthesia, neuromuscular blockade and cardiac output. The indications for end‐tidal carbon dioxide monitoring have been updated.
doi:10.1111/anae.13316
PMCID: PMC5063182  PMID: 26582586
14.  Dynamic criteria of plankton jumping out of water 
Journal of the Royal Society Interface  2015;12(111):20150582.
In nature, jumping out of water is a behaviour commonly observed in aquatic species to either escape from predators or hunt prey. However, not all aquatic species are capable of jumping out, especially small organisms whose length scales are comparable to the capillary length (approx. 2.7 mm for water). Some aquatic animals smaller than the capillary length are able to jump out while others are not, as observed in some marine copepods. To understand the dynamics of jumping out of the water–air interface, we perform physical experiments by shooting a spherical particle towards the liquid–air interface from below. Experimental results show that the particle either penetrates or bounces back from the interface, depending on the particle and fluid properties, and the impact velocity. The transition from bouncing to penetration regimes, which is theoretically predicted based on a particle force balance, is in good agreement with both physical experiments and plankton behavioural data.
doi:10.1098/rsif.2015.0582
PMCID: PMC4614495  PMID: 26468066
copepod; jumping out of water; surface tension
15.  Kinetics of Epstein-Barr Virus (EBV) Neutralizing and Virus-Specific Antibodies after Primary Infection with EBV 
Prospective studies of antibodies to multiple Epstein-Barr virus (EBV) proteins and EBV neutralizing antibodies in the same individuals before, during, and after primary EBV infection have not been reported. We studied antibody responses to EBV in college students who acquired primary EBV infection during prospective surveillance and correlated the kinetics of antibody response with the severity of disease. Neutralizing antibodies and enzyme-linked immunosorbent assay (ELISA) antibodies to gp350, the major target of neutralizing antibody, reached peak levels at medians of 179 and 333 days after the onset of symptoms of infectious mononucleosis, respectively. No clear correlation was found between the severity of the symptoms of infectious mononucleosis and the peak levels of antibody to individual viral proteins or to neutralizing antibody. In summary, we found that titers of neutralizing antibody and antibodies to multiple EBV proteins increase over many months after primary infection with EBV.
doi:10.1128/CVI.00674-15
PMCID: PMC4820504  PMID: 26888186
16.  A tale of the ciliate tail: investigation into the adaptive significance of this sub-cellular structure 
Ciliates can form an important link between the microbial loop and higher trophic levels primarily through consumption by copepods. This high predation pressure has resulted in a number of ciliate species developing rapid escape swimming behaviour. Several species of these escaping ciliates also possess a long contractile tail for which the functionality remains unresolved. We use high-speed video, specialized optics and novel fluid visualization tools to evaluate the role of this contractile appendage in two free-swimming ciliates, Pseudotontonia sp. and Tontonia sp., and compare the performance to escape swimming behaviour of a non-tailed species, Strobilidium sp. Here, we show that ‘tailed’ species respond to hydrodynamic disturbances with extremely short response latencies (less than or equal to 0.89 ms) by rapidly contracting the tail which carries the cell body 2–4 cell diameters within a few milliseconds. This provides an advantage over non-tailed species during the critical first 10–30 ms of an escape. Two small, short-lived vortex rings are created during contraction of the tail. The flow imposed by the ciliate jumping can be described as two well-separated impulsive Stokeslets and the overall flow attenuates spatially as r−3. The high initial velocities and spatio-temporal arrangement of vortices created by tail contractions appear to provide a means for rapid escape as well as hydrodynamic ‘camouflage’ against fast striking, mechanoreceptive predators such as copepods.
doi:10.1098/rspb.2015.0770
PMCID: PMC4528511  PMID: 26180066
escape; low Reynolds number; hydrodynamic camouflage; propulsion; protozoan
17.  Mitonuclear interactions, mtDNA-mediated thermal plasticity, and implications for the Trojan Female Technique for pest control 
Scientific Reports  2016;6:30016.
Pest species pose major challenges to global economies, ecosystems, and health. Unfortunately, most conventional approaches to pest control remain costly, and temporary in effect. As such, a heritable variant of the Sterile Insect Technique (SIT) was proposed, based on the introduction of mitochondrial DNA mutations into pest populations, which impair male fertility but have no effects on females. Evidence for this “Trojan Female Technique” (TFT) was recently provided, in the form of a mutation in the mitochondrial cytochrome b gene (mt:Cyt-b) of Drosophila melanogaster which reduces male fertility across diverse nuclear backgrounds. However, recent studies have shown that the magnitude of mitochondrial genetic effects on the phenotype can vary greatly across environments, with mtDNA polymorphisms commonly entwined in genotype-by-environment (G × E) interactions. Here we test whether the male-sterilizing effects previously associated with the mt:Cyt-b mutation are consistent across three thermal and three nuclear genomic contexts. The effects of this mutation were indeed moderated by the nuclear background and thermal environment, but crucially the fertility of males carrying the mutation was invariably reduced relative to controls. This mutation thus constitutes a promising candidate for the further development of the TFT.
doi:10.1038/srep30016
PMCID: PMC4956753  PMID: 27443488
18.  Control of vortex rings for manoeuvrability 
Journal of the Royal Society Interface  2015;12(108):20150389.
Manoeuvrability is critical to the success of many species. Selective forces acting over millions of years have resulted in a range of capabilities currently unmatched by machines. Thus, understanding animal control of fluids for manoeuvring has both biological and engineering applications. Within inertial fluid regimes, propulsion involves the formation and interaction of vortices to generate thrust. We use both volumetric and planar imaging techniques to quantify how jellyfish (Aurelia aurita) modulate vortex rings during turning behaviour. Our results show that these animals distort individual vortex rings during turns to alter the force balance across the animal, primarily through kinematic modulation of the bell margin. We find that only a portion of the vortex ring separates from the body during turns, which may increase torque. Using a fluorescent actin staining method, we demonstrate the presence of radial muscle fibres lining the bell along the margin. The presence of radial muscles provides a mechanistic explanation for the ability of scyphomedusae to alter their bell kinematics to generate non-symmetric thrust for manoeuvring. These results illustrate the advantage of combining imaging methods and provide new insights into the modulation and control of vorticity for low-speed animal manoeuvring.
doi:10.1098/rsif.2015.0389
PMCID: PMC4528605  PMID: 26136226
manoeuvrability; vortex ring; position control; swimming; jellyfish
19.  A tale of two haplotype groups: Evaluating the New World Junonia ring species hypothesis using the distribution of divergent COI haplotypes 
Systematic entomology  2015;40(3):532-546.
The New World Junonia butterflies are a possible ring species with a circum-Caribbean distribution. Previous reports suggest a steady transition between North and South American forms in Mesoamerica, but in Cuba the forms were thought to co-exist without interbreeding representing the overlapping ends of the ring. Three criteria establish the existence of a ring species: a ring-shaped geographic distribution, gene flow among intervening forms, and genetic isolation in the region of range overlap. We evaluated mitochondrial cytochrome oxidase I haplotypes in Junonia from 9 species in the Western Hemisphere to test the Junonia ring species hypothesis. Junonia species are generally not monophyletic with respect to COI haplotypes, which are shared across species. However, two major COI haplotype groups exist. Group A predominates in South America, and Group B predominates in North and Central America. Therefore, COI haplotypes can be used to assess the degree of genetic influence a population receives from each continent. Junonia shows a ring-shaped distribution around the Caribbean, and evidence is consistent with gene flow among forms of Junonia, including those from Mesoamerica. However, we detected no discontinuity in gene flow in Cuba or elsewhere in the Caribbean consistent with genetic isolation in the region of overlap. Though sampling is still very limited in the critical region, the only remaining possiblity for a circum-Caribbean discontinuity in gene flow is at the Isthmus of Panama, where there may be a transition from 98% Group B haplotypes in Costa Rica to 85–100% Group A haplotypes in South America.
doi:10.1111/syen.12120
PMCID: PMC4532355  PMID: 26279602
Junonia; ring species; adaptive radiation; cytochrome oxidase I; phylogeography
20.  Rabbit-specific computational modelling of ventricular cell electrophysiology: Using populations of models to explore variability in the response to ischemia 
Computational modelling, combined with experimental investigations, is a powerful method for investigating complex cardiac electrophysiological behaviour. The use of rabbit-specific models, due to the similarities of cardiac electrophysiology in this species with human, is especially prevalent. In this paper, we first briefly review rabbit-specific computational modelling of ventricular cell electrophysiology, multi-cellular simulations including cellular heterogeneity, and acute ischemia. This mini-review is followed by an original computational investigation of variability in the electrophysiological response of two experimentally-calibrated populations of rabbit-specific ventricular myocyte action potential models to acute ischemia. We performed a systematic exploration of the response of the model populations to varying degrees of ischemia and individual ischemic parameters, to investigate their individual and combined effects on action potential duration and refractoriness. This revealed complex interactions between model population variability and ischemic factors, which combined to enhance variability during ischemia. This represents an important step towards an improved understanding of the role that physiological variability may play in electrophysiological alterations during acute ischemia.
doi:10.1016/j.pbiomolbio.2016.06.003
PMCID: PMC5405055  PMID: 27320382
Cardiac cell electrophysiology; Computational modelling; Ischemia; Populations of models; Rabbit; Variability
21.  Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved 
PLoS Computational Biology  2016;12(6):e1004964.
About 8% of the human genome is made up of endogenous retroviruses (ERVs). Though most human endogenous retroviruses (HERVs) are thought to be irrelevant to our biology notable exceptions include members of the HERV-H family that are necessary for the correct functioning of stem cells. ERVs are commonly found in two forms, the full-length proviral form, and the more numerous solo-LTR form, thought to result from homologous recombination events. Here we introduce a phylogenetic framework to study ERV insertion and solo-LTR formation. We then apply the framework to site patterns sampled from a set of long alignments covering six primate genomes. Studying six categories of ERVs we quantitatively recapitulate patterns of insertional activity that are usually described in qualitative terms in the literature. A slowdown in most ERV groups is observed but we suggest that HERV-K activity may have increased in humans since they diverged from chimpanzees. We find that the rate of solo-LTR formation decreases rapidly as a function of ERV age and that an age dependent model of solo-LTR formation describes the history of ERVs more accurately than the commonly used exponential decay model. We also demonstrate that HERV-H loci are markedly less likely to form solo-LTRs than ERVs from other families. We conclude that the slower dynamics of HERV-H suggest a host role for the internal regions of these exapted elements and posit that in future it will be possible to use the relationship between full-length proviruses and solo-LTRs to help identify large scale co-options in distant vertebrate genomes.
Author Summary
Animal genomes contain ancient pathogens known as endogenous retroviruses (ERVs). Though the widespread abundance of ERVs is due to their ability to self replicate, some ERVs are known to have become important to host processes including placentation, and in the case of HERV-H, the functioning of human stem cells. In our study we place the insertion and deletion activity of primate ERV families in direct quantitative comparison. In particular, we show that ERV deletion is an age dependent process, so that as an ERV ages it becomes less likely to be deleted at any given instant. We also find that ERVs from the HERV-H family are unusually slowly deleted, an interesting result that suggests that the exaptation of HERV-H may have involved internal regions of the virus and not just its terminal promoters. Assuming the behaviour of primate ERVs is not unusual, our study suggests that future bioinformatics screening for ERVs with slow deletion dynamics could help identify large-scale exaptations in distant species. Furthermore, as we demonstrate that ERVs are deleted rapidly, we think that such screening could be performed using ratios of conserved to deleted elements and could therefore be applied to single genomes.
doi:10.1371/journal.pcbi.1004964
PMCID: PMC4905674  PMID: 27295277
22.  Measurement of the centrality dependence of the charged-particle pseudorapidity distribution in proton–lead collisions at \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sqrt{s_{_\text {NN}}} = 5.02$$\end{document}sNN=5.02 TeV with the ATLAS detector 
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The centrality dependence of the mean charged-particle multiplicity as a function of pseudorapidity is measured in approximately 1 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\upmu $$\end{document}μb\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{-1}$$\end{document}-1 of proton–lead collisions at a nucleon–nucleon centre-of-mass energy of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sqrt{s_{_\text {NN}}} = 5.02$$\end{document}sNN=5.02 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\text {TeV}$$\end{document}TeV using the ATLAS detector at the Large Hadron Collider. Charged particles with absolute pseudorapidity less than 2.7 are reconstructed using the ATLAS pixel detector. The collision centrality is characterised by the total transverse energy measured in the Pb-going direction of the forward calorimeter. The charged-particle pseudorapidity distributions are found to vary strongly with centrality, with an increasing asymmetry between the proton-going and Pb-going directions as the collisions become more central. Three different estimations of the number of nucleons participating in the collision have been carried out using the Glauber model as well as two Glauber–Gribov inspired extensions to the Glauber model. Charged-particle multiplicities per participant pair are found to vary differently for these three models, highlighting the importance of including colour fluctuations in nucleon–nucleon collisions in the modelling of the initial state of collisions.
doi:10.1140/epjc/s10052-016-4002-3
PMCID: PMC5312138
23.  A feasibility study of singlet oxygen explicit dosmietry (SOED) of PDT by intercomparison with a singlet oxygen luminescence dosimetry (SOLD) system 
An explicit dosimetry model has been developed to calculate the apparent reacted 1O2 concentration ([1O2]rx) in an in-vivo model. In the model, a macroscopic quantity, g, is introduced to account for oxygen perfusion to the medium during PDT. In this study, the SOED model is extended for PDT treatment in phantom conditions where vasculature is not present; the oxygen perfusion is achieved through the air-phantom interface instead. The solution of the SOED model is obtained by solving the coupled photochemical rate equations incorporating oxygen perfusion through the air-liquid interface. Experiments were performed for two photosensitizers (PS), Rose Bengal (RB) and Photofrin (PH), in solution, using SOED and SOLD measurements to determine both the instantaneous [1O2] as well as cumulative [1O2]rx concentrations, where [1O2]rx = (1/τΔ) · ∫[1O2]dt. The PS concentrations varied between 10 and 100 mM for RB and ~200 mM for Photofrin. The resulting magnitudes of [1O2] were compared between SOED and SOLD.
doi:10.1117/12.2213236
PMCID: PMC4823004  PMID: 27064489
photodynamic therapy; PDT; singlet oxygen; SOLD; SOED; explicit PDT dosimetry
24.  Uncovering the pathways underlying whole body regeneration in a chordate model, Botrylloides leachi using de novo transcriptome analysis 
BMC Genomics  2016;17:114.
Background
Regenerative capacity differs greatly between animals. In vertebrates regenerative abilities are highly limited and tissue or organ specific. However the closest related chordate to the vertebrate clade, Botrylloides leachi, can undergo whole body regeneration (WBR). Therefore, research on WBR in B. leachi has focused on pathways known to be important for regeneration in vertebrates. To obtain a comprehensive vision of this unique process we have carried out the first de novo transcriptome sequencing for multiple stages of WBR occurring in B. leachi. The identified changes in gene expression during B. leachi WBR offer novel insights into this remarkable ability to regenerate.
Results
The transcriptome of B. leachi tissue undergoing WBR were analysed using differential gene expression, gene ontology and pathway analyses. We observed up-regulation in the expression of genes involved in wound healing and known developmental pathways including WNT, TGF-β and Notch, during the earliest stages of WBR. Later in WBR, the expression patterns in several pathways required for protein synthesis, biogenesis and the organisation of cellular components were up-regulated.
Conclusions
While the genes expressed early on are characteristic of a necessary wound healing response to an otherwise lethal injury, the subsequent vast increase in protein synthesis conceivably sustains the reestablishment of the tissue complexity and body axis polarity within the regenerating zooid. We have, for the first time, provided a global overview of the genes and their corresponding pathways that are modulated during WBR in B. leachi.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-016-2435-6) contains supplementary material, which is available to authorized users.
doi:10.1186/s12864-016-2435-6
PMCID: PMC4755014  PMID: 26879048
Whole body regeneration; Botrylloides leachi; Transcriptome
25.  Evolutionary Footprints of Short Tandem Repeats in Avian Promoters 
Scientific Reports  2016;6:19421.
Short tandem repeats (STRs) or microsatellites are well-known sequence elements that may change the spacing between transcription factor binding sites (TFBSs) in promoter regions by expansion or contraction of repetitive units. Some of these mutations have the potential to contribute to phenotypic diversity by altering patterns of gene expression. To explore how repetitive sequence motifs within promoters have evolved in avian lineages under mutation-selection balance, more than 400 evolutionary conserved STRs (ecSTRs) were identified in this study by comparing the 2 kb upstream promoter sequences of chicken against those of other birds (turkey, duck, zebra finch, and flycatcher). The rate of conservation was significantly higher in AG dinucleotide repeats than in AC or AT repeats, with the expansion of AG motifs being noticeably constrained in passerines. Analysis of the relative distance between ecSTRs and TFBSs revealed a significantly higher rate of conserved TFBSs in the vicinity of ecSTRs in both chicken-duck and chicken-passerine comparisons. Our comparative study provides a novel insight into which intrinsic factors have influenced the degree of constraint on repeat expansion/contraction during avian promoter evolution.
doi:10.1038/srep19421
PMCID: PMC4725869  PMID: 26766026

Results 1-25 (196)