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3. Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Mc Cartney, Ann M., Formenti, Giulio, Mouton, Alice, De Panis, Diego, Marins, Luísa S., Leitão, Henrique G., Diedericks, Genevieve, Kirangwa, Joseph, Morselli, Marco, Salces-Ortiz, Judit, Escudero, Nuria, Iannucci, Alessio, Natali, Chiara, Svardal, Hannes, Fernández, Rosa, De Pooter, Tim, Joris, Geert, Strazisar, Mojca, Wood, Jonathan M. D., Herron, Katie E., Seehausen, Ole, Watts, Phillip C., Shaw, Felix, Davey, Robert P., Minotto, Alice, Fernández, José M., Böhne, Astrid, Alegria, Carla, Alioto, Tyler, Alves, Paulo C., Amorim, Isabel R., Aury, Jean-Marc, Backstrom, Niclas, Baldrian, Petr, Baltrunaite, Laima, Barta, Endre, BedHom, Bertrand, Belser, Caroline, Bergsten, Johannes, Bertrand, Laurie, Bilandija, Helena, Binzer-Panchal, Mahesh, Bista, Iliana, Blaxter, Mark, Borges, Paulo A. V., Dias, Guilherme Borges, Bosse, Mirte, Brown, Tom, Bruggmann, Rémy, Buena-Atienza, Elena, Burgin, Josephine, Buzan, Elena, Cariani, Alessia, Casadei, Nicolas, Chiara, Matteo, Chozas, Sergio, Čiampor, Jr., Fedor, Crottini, Angelica, Cruaud, Corinne, Cruz, Fernando, Dalen, Love, De Biase, Alessio, del Campo, Javier, Delic, Teo, Dennis, Alice B., Derks, Martijn F. L., Diroma, Maria Angela, Djan, Mihajla, Duprat, Simone, Eleftheriadi, Klara, Feulner, Philine G. D., Flot, Jean-François, Forni, Giobbe, Fosso, Bruno, Fournier, Pascal, Fournier-Chambrillon, Christine, Gabaldon, Toni, Garg, Shilpa, Gissi, Carmela, Giupponi, Luca, Gomez-Garrido, Jessica, González, Josefa, Grilo, Miguel L., Grüning, Björn, Guerin, Thomas, Guiglielmoni, Nadege, Gut, Marta, Haesler, Marcel P., Hahn, Christoph, Halpern, Balint, Harrison, Peter W., Heintz, Julia, Hindrikson, Maris, Höglund, Jacob, Howe, Kerstin, Hughes, Graham M., Istace, Benjamin, Cock, Mark J., Janžekovič, Franc, Jonsson, Zophonias O., Joye-Dind, Sagane, Koskimäki, Janne J., Krystufek, Boris, Kubacka, Justyna, Kuhl, Heiner, Kusza, Szilvia, Labadie, Karine, Lähteenaro, Meri, Lantz, Henrik, Lavrinienko, Anton, Leclère, Lucas, Lopes, Ricardo Jorge, Madsen, Ole, Magdelenat, Ghislaine, Magoga, Giulia, Manousaki, Tereza, Mappes, Tapio, Marques, Joao Pedro, Redondo, Gemma I. Martinez, Maumus, Florian, McCarthy, Shane A., Megens, Hendrik-Jan, Melo-Ferreira, Jose, Mendes, Sofia L., Montagna, Matteo, Moreno, Joao, Mosbech, Mai-Britt, Moura, Mónica, Musilova, Zuzana, Myers, Eugene, Nash, Will J., Nater, Alexander, Nicholson, Pamela, Niell, Manuel, Nijland, Reindert, Noel, Benjamin, Noren, Karin, Oliveira, Pedro H., Olsen, Remi-Andre, Ometto, Lino, Oomen, Rebekah A., Ossowski, Stephan, Palinauskas, Vaidas, Palsson, Snaebjorn, Panibe, Jerome P., Pauperio, Joana, Pavlek, Martina, Payen, Emilie, Pawlowska, Julia, Pellicer, Jaume, Pesole, Graziano, Pimenta, Joao, Pippel, Martin, Pirttilä, Anna Maria, Poulakakis, Nikos, Rajan, Jeena, M.C. Rego, Rúben, Resendes, Roberto, Resl, Philipp, Riesgo, Ana, Rodin-Morch, Patrik, Soares, Andre E. R., Fernandes, Carlos Rodriguez, Romeiras, Maria M., Roxo, Guilherme, Rüber, Lukas, Ruiz-Lopez, Maria Jose, Saarma, Urmas, da Silva, Luis P., Sim-Sim, Manuela, Soler, Lucile, Sousa, Vitor C., Santos, Carla Sousa, Spada, Alberto, Stefanovic, Milomir, Steger, Viktor, Stiller, Josefin, Stöck, Matthias, Struck, Torsten H., Sudasinghe, Hiranya, Tapanainen, Riikka, Tellgren-Roth, Christian, Trindade, Helena, Tukalenko, Yevhen, Urso, Ilenia, Vacherie, Benoit, Van Belleghem, Steven M., Van Oers, Kees, Vargas-Chavez, Carlos, Velickovic, Nevena, Vella, Noel, Vella, Adriana, Vernesi, Cristiano, Vicente, Sara, Villa, Sara, Pettersson, Olga Vinnere, Volckaert, Filip A. M., Voros, Judit, Wincker, Patrick, Winkler, Sylke, Ciofi, Claudio, Waterhouse, Robert M., and Mazzoni, Camila J.

Published
2024
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4. Building a Portuguese coalition for biodiversity genomics

Author

Marques, João P., Alves, Paulo C., Amorim, Isabel R., Lopes, Ricardo J., Moura, Monica, Myers, Eugene, Sim-sim, Manuela, Sousa-Santos, Carla, Alves, M. Judite, Borges, Paulo A. V., Brown, Thomas, Carneiro, Miguel, Carrapato, Carlos, Ceríaco, Luís M. P., Ciofi, Claúdio, da Silva, Luís P., Diedericks, Genevieve, Diroma, Maria Angela, Farelo, Liliana, Formenti, Giulio, Gil, Fátima, Grilo, Miguel, Iannucci, Alessio, Leitão, Henrique G., Máguas, Cristina, Mc Cartney, Ann M., Mendes, Sofia L., Moreno, João M., Morselli, Marco, Mouton, Alice, Natali, Chiara, Pereira, Fernando, Rego, Rúben M. C., Resendes, Roberto, Roxo, Guilherme, Svardal, Hannes, Trindade, Helena, Vicente, Sara, Winkler, Sylke, Alvarenga, Marcela, Amaral, Andreia J., Antunes, Agostinho, Campos, Paula F., Canário, Adelino V. M., Castilho, Rita, Castro, L. Filipe C., Crottini, Angelica, Cunha, Mónica V., Espregueira Themudo, Gonçalo, Esteves, Pedro J., Faria, Rui, Rodríguez Fernandes, Carlos, Ledoux, Jean-Baptiste, Louro, Bruno, Magalhaes, Sara, Paulo, Octávio S., Pearson, Gareth, Pimenta, João, Pina-Martins, Francisco, Santos, Teresa L., Serrão, Ester, Melo-Ferreira, José, and Sousa, Vítor C.

Published
2024
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5. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Mc Cartney, Ann M., Formenti, Giulio, Mouton, Alice, De Panis, Diego, Marins, Luísa S., Leitão, Henrique G., Diedericks, Genevieve, Kirangwa, Joseph, Morselli, Marco, Salces-Ortiz, Judit, Escudero, Nuria, Iannucci, Alessio, Natali, Chiara, Svardal, Hannes, Fernández, Rosa, De Pooter, Tim, Joris, Geert, Strazisar, Mojca, Wood, Jonathan M. D., Herron, Katie E., Seehausen, Ole, Watts, Phillip C., Shaw, Felix, Davey, Robert P., Minotto, Alice, Fernández, José M., Böhne, Astrid, Alegria, Carla, Alioto, Tyler, Alves, Paulo C., Amorim, Isabel R., Aury, Jean-Marc, Backstrom, Niclas, Baldrian, Petr, Baltrunaite, Laima, Barta, Endre, BedHom, Bertrand, Belser, Caroline, Bergsten, Johannes, Bertrand, Laurie, Bilandija, Helena, Binzer-Panchal, Mahesh, Bista, Iliana, Blaxter, Mark, Borges, Paulo A. V., Dias, Guilherme Borges, Bosse, Mirte, Brown, Tom, Bruggmann, Rémy, Buena-Atienza, Elena, Burgin, Josephine, Buzan, Elena, Cariani, Alessia, Casadei, Nicolas, Chiara, Matteo, Chozas, Sergio, Čiampor, Jr., Fedor, Crottini, Angelica, Cruaud, Corinne, Cruz, Fernando, Dalen, Love, De Biase, Alessio, del Campo, Javier, Delic, Teo, Dennis, Alice B., Derks, Martijn F. L., Diroma, Maria Angela, Djan, Mihajla, Duprat, Simone, Eleftheriadi, Klara, Feulner, Philine G. D., Flot, Jean-François, Forni, Giobbe, Fosso, Bruno, Fournier, Pascal, Fournier-Chambrillon, Christine, Gabaldon, Toni, Garg, Shilpa, Gissi, Carmela, Giupponi, Luca, Gomez-Garrido, Jessica, González, Josefa, Grilo, Miguel L., Grüning, Björn, Guerin, Thomas, Guiglielmoni, Nadege, Gut, Marta, Haesler, Marcel P., Hahn, Christoph, Halpern, Balint, Harrison, Peter W., Heintz, Julia, Hindrikson, Maris, Höglund, Jacob, Howe, Kerstin, Hughes, Graham M., Istace, Benjamin, Cock, Mark J., Janžekovič, Franc, Jonsson, Zophonias O., Joye-Dind, Sagane, Koskimäki, Janne J., Krystufek, Boris, Kubacka, Justyna, Kuhl, Heiner, Kusza, Szilvia, Labadie, Karine, Lähteenaro, Meri, Lantz, Henrik, Lavrinienko, Anton, Leclère, Lucas, Lopes, Ricardo Jorge, Madsen, Ole, Magdelenat, Ghislaine, Magoga, Giulia, Manousaki, Tereza, Mappes, Tapio, Marques, Joao Pedro, Redondo, Gemma I. Martinez, Maumus, Florian, McCarthy, Shane A., Megens, Hendrik-Jan, Melo-Ferreira, Jose, Mendes, Sofia L., Montagna, Matteo, Moreno, Joao, Mosbech, Mai-Britt, Moura, Mónica, Musilova, Zuzana, Myers, Eugene, Nash, Will J., Nater, Alexander, Nicholson, Pamela, Niell, Manuel, Nijland, Reindert, Noel, Benjamin, Noren, Karin, Oliveira, Pedro H., Olsen, Remi-Andre, Ometto, Lino, Oomen, Rebekah A., Ossowski, Stephan, Palinauskas, Vaidas, Palsson, Snaebjorn, Panibe, Jerome P., Pauperio, Joana, Pavlek, Martina, Payen, Emilie, Pawlowska, Julia, Pellicer, Jaume, Pesole, Graziano, Pimenta, Joao, Pippel, Martin, Pirttilä, Anna Maria, Poulakakis, Nikos, Rajan, Jeena, M.C. Rego, Rúben, Resendes, Roberto, Resl, Philipp, Riesgo, Ana, Rodin-Morch, Patrik, Soares, Andre E. R., Fernandes, Carlos Rodriguez, Romeiras, Maria M., Roxo, Guilherme, Rüber, Lukas, Ruiz-Lopez, Maria Jose, Saarma, Urmas, da Silva, Luis P., Sim-Sim, Manuela, Soler, Lucile, Sousa, Vitor C., Santos, Carla Sousa, Spada, Alberto, Stefanovic, Milomir, Steger, Viktor, Stiller, Josefin, Stöck, Matthias, Struck, Torsten H., Sudasinghe, Hiranya, Tapanainen, Riikka, Tellgren-Roth, Christian, Trindade, Helena, Tukalenko, Yevhen, Urso, Ilenia, Vacherie, Benoit, Van Belleghem, Steven M., Van Oers, Kees, Vargas-Chavez, Carlos, Velickovic, Nevena, Vella, Noel, Vella, Adriana, Vernesi, Cristiano, Vicente, Sara, Villa, Sara, Pettersson, Olga Vinnere, Volckaert, Filip A. M., Voros, Judit, Wincker, Patrick, Winkler, Sylke, Ciofi, Claudio, Waterhouse, Robert M., and Mazzoni, Camila J.

Published
2024
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7. Pre-COVID-19-pandemic RSV epidemiology and clinical burden in pediatric primary care in Italy: a comparative analysis across two regions for the 2019/2020 season

Author

Pandolfi, Elisabetta, Loconsole, Daniela, Chironna, Maria, van Summeren, Jojanneke, Paget, John, Raponi, Massimiliano, Russo, Luisa, Campagna, Ilaria, Croci, Ileana, Concato, Carlo, Perno, Carlo Federico, Tozzi, Alberto Eugenio, Linardos, Giulia, Bartolucci, Veronica, Ciampini, Sara, Muda, Andrea Onetti, De Angelis, Luigi, Ciofi Degli Atti, Marta Luisa, and Rizzo, Caterina

Published
2024
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12. Whole mitochondrial genome sequencing provides new insights into the phylogeography of loggerhead turtles (Caretta caretta) in the Mediterranean Sea

Author

Tolve, Livia, Iannucci, Alessio, Garofalo, Luisa, Ninni, Andrea, Capobianco Dondona, Andrea, Ceciarini, Ilaria, Cocumelli, Cristiano, De Lucia, Alessandra, Falconi, Mattia, Formia, Angela, Iacovelli, Federico, Mancusi, Cecilia, Marchiori, Erica, Marsili, Letizia, Mingozzi, Toni, Nannarelli, Stefano, Natali, Chiara, Terracciano, Giuliana, Zuffi, Marco A. L., Novelletto, Andrea, and Ciofi, Claudio

Published
2024
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14. Accuracy of Pancreatic Stone Protein for diagnosis of sepsis in children admitted to pediatric intensive care or high-dependency care: a pilot study

Author

Bottari, Gabriella, Caruso, Mariangela, Paionni, Emanuel, De Luca, Maia, Romani, Lorenza, Pisani, Mara, Grandin, Annalisa, Gargiullo, Livia, Zampini, Giorgio, Gagliardi, Chiara, Fegatelli, Danilo Alunni, Vestri, Annarita, Lancella, Laura, Porzio, Ottavia, Muda, Andrea Onetti, Villani, Alberto, Atti, Marta Ciofi Degli, Raponi, Massimiliano, and Cecchetti, Corrado

Published
2023
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16. Bitter taste cells in the ventricular walls of the murine brain regulate glucose homeostasis

Author

Yu, Qiang, Gamayun, Igor, Wartenberg, Philipp, Zhang, Qian, Qiao, Sen, Kusumakshi, Soumya, Candlish, Sarah, Götz, Viktoria, Wen, Shuping, Das, Debajyoti, Wyatt, Amanda, Wahl, Vanessa, Ectors, Fabien, Kattler, Kathrin, Yildiz, Daniela, Prevot, Vincent, Schwaninger, Markus, Ternier, Gaetan, Giacobini, Paolo, Ciofi, Philippe, Müller, Timo D., and Boehm, Ulrich

Published
2023
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18. Biomolecular NMR at 1.2 GHz

Author

Banci, Lucia, Barbieri, Letizia, Calderone, Vito, Cantini, Francesca, Cerofolini, Linda, Ciofi-Baffoni, Simone, Felli, Isabella C., Fragai, Marco, Lelli, Moreno, Luchinat, Claudio, Luchinat, Enrico, Parigi, Giacomo, Piccioli, Mario, Pierattelli, Roberta, Ravera, Enrico, Rosato, Antonio, Tenori, Leonardo, and Turano, Paola

Subjects
Physics - Chemical Physics, Physics - Biological Physics
Abstract

The development of new superconducting ceramic materials, which maintain the superconductivity at very intense magnetic fields, has prompted the development of a new generation of highly homogeneous high field magnets that has trespassed the magnetic field attainable with the previous generation of instruments. But how can biomolecular NMR benefit from this? In this work, we review a few of the notable applications that, we expect, will be blooming thanks to this newly available technology., Comment: 17 pages, 13 figures

Published
2019

19. Global phylogeography of ridley sea turtles (Lepidochelys spp.): evolution, demography, connectivity, and conservation

Author

Vilaça, Sibelle Torres, Hahn, Anelise Torres, Naro-Maciel, Eugenia, Abreu-Grobois, F. Alberto, Bowen, Brian W., Castilhos, Jaqueline C., Ciofi, Claudio, FitzSimmons, Nancy N., Jensen, Michael P., Formia, Angela, Limpus, Colin J., Natali, Chiara, Soares, Luciano S., de Thoisy, Benoit, Whiting, Scott D., and Bonatto, Sandro L.

Published
2022
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20. Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards

Author

Lind, Abigail L, Lai, Yvonne YY, Mostovoy, Yulia, Holloway, Alisha K, Iannucci, Alessio, Mak, Angel CY, Fondi, Marco, Orlandini, Valerio, Eckalbar, Walter L, Milan, Massimo, Rovatsos, Michail, Kichigin, Ilya G, Makunin, Alex I, Johnson Pokorná, Martina, Altmanová, Marie, Trifonov, Vladimir A, Schijlen, Elio, Kratochvíl, Lukáš, Fani, Renato, Velenský, Petr, Rehák, Ivan, Patarnello, Tomaso, Jessop, Tim S, Hicks, James W, Ryder, Oliver A, Mendelson, Joseph R, Ciofi, Claudio, Kwok, Pui-Yan, Pollard, Katherine S, and Bruneau, Benoit G

Subjects
Climate Change Impacts and Adaptation, Biological Sciences, Environmental Sciences, Genetics, Cardiovascular, Human Genome, Acclimatization, Animals, Cardiovascular System, Chromosomes, Lizards, Ecology, Evolutionary biology, Environmental management
Abstract

Monitor lizards are unique among ectothermic reptiles in that they have high aerobic capacity and distinctive cardiovascular physiology resembling that of endothermic mammals. Here, we sequence the genome of the Komodo dragon Varanus komodoensis, the largest extant monitor lizard, and generate a high-resolution de novo chromosome-assigned genome assembly for V. komodoensis using a hybrid approach of long-range sequencing and single-molecule optical mapping. Comparing the genome of V. komodoensis with those of related species, we find evidence of positive selection in pathways related to energy metabolism, cardiovascular homoeostasis, and haemostasis. We also show species-specific expansions of a chemoreceptor gene family related to pheromone and kairomone sensing in V. komodoensis and other lizard lineages. Together, these evolutionary signatures of adaptation reveal the genetic underpinnings of the unique Komodo dragon sensory and cardiovascular systems, and suggest that selective pressure altered haemostasis genes to help Komodo dragons evade the anticoagulant effects of their own saliva. The Komodo dragon genome is an important resource for understanding the biology of monitor lizards and reptiles worldwide.

Published
2019

21. Comprehensive Modeling of Graphene Resistivity

Author

Contino, Antonino, Ciofi, Ivan, Wu, Xiangyu, Asselberghs, Inge, Wilson, Christopher J., Tokei, Zsolt, Groeseneken, Guido, and Soree, Bart

Subjects
Physics - Applied Physics, Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

Since the first graphene layer was fabricated in the early 2000's, graphene properties have been studied extensively both experimentally and theoretically. However, when comparing the many resistivity models reported in literature, several discrepancies can be found, as well as a number of inconsistencies between formulas. In this paper, we revise the main scattering mechanisms in graphene, based on theory and goodness of fit to in-house experimental data. In particular, a step-by-step evaluation of the interaction between electrons and optical phonons is carried out, where we demonstrate that the process of optical phonon emission scattering is completely suppressed for all low-field applications and all temperatures in the range of interest, as opposed to what is often reported in literature. Finally, we identify the best scattering models based on the goodness of fit to experimental data., Comment: 7 pages, 5 figures, to be submitted to Journal of Applied Physics

Published
2017

22. In-medium nucleon dynamics at short range: ground-state energy,radii, momentum distribution and spectral functions of few-nucleon systems and complex nuclei

Author

Atti, Claudio Ciofi degli and Morita, Hiko

Subjects
Nuclear Theory
Abstract

Talk given at the "International Workshop on (e,e'p) Processes", July 2-6, 2017, Bled, Slovenia. Various many-body calculations are compared and the results provided by the Normalization Conserving Linked Cluster Expansion with realistic NN interactions are reviewed and analyzed in detail, as far as ground state energies, momentum distributions and spectral functions of few-nucleon system and complex nuclei are concerned., Comment: Corrected typos, renewed references, and added Journal reference

Published
2017

23. Universality of many-body two-nucleon momentum distributions: the correlated nucleon spectral function of complex nuclei revisited

Author

Atti, Claudio Ciofi degli and Morita, Hiko

Subjects
Nuclear Theory
Abstract

Realistic NN interactions and many-body approaches have been used to calculate ground-state properties of nuclei with A=3, 4, 12, 16, 40, with particular emphasis on various kinds of momentum distributions. It is shown that at proper values of the relative (rel) and center-of-mass (c.m.) momenta, the two-nucleon momentum distribution n_A^{N_1N_2} (k_{rel}, K_{c.m.}, \theta) exhibits the property of factorization, namely n_A^{N_1N_2} (k_{rel}, K_{c.m.}, \theta) \simeq n_{rel}(k_{rel}) n_(c.m.)( K{c.m.}). The factorization of the momentum distributions , bearing a universal character, results from a general property of realistic nuclear wave functions, namely their factorization at short inter-nucleon separations. The factorization of the two-nucleon momentum distribution allows one to develop the correlated part of the nucleon spectral function P(k,E) in terms of a convolution integral involving the product of the many-body, parameter-free relative and c.m. momentum distributions of a given nucleus. It is shown that: (i) the obtained spectral function perfectly satisfies the momentum sum rule, i.e. when it is integrated over the removal energy E, it fully reproduces the momentum distributions obtained from realistic many-body wave functions , (ii) in order to saturate the momentum sum rule at high values of the momentum (k \simeq 5 fm^{-1}) the spectral function has to be integrate up to E \simeq 400 MeV. To sum up a realistic, parameter-free many-body Spectral function has been developed such that : i) a phenomenological convolution spectral function developed in the past is fully justified from a many-body point of view , and (ii) the model dependence which might be present in calculations of inclusive electroweak processes could be reduced by the use of the convolution spectral function developed here., Comment: 42 pages, 15 figures

Published
2017
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24. Tagged EMC Measurements on Light Nuclei

Author

Armstrong, Whitney, Arrington, John, Cloet, Ian, Hafidi, Kawtar, Hattawy, Mohammad, Potteveld, David, Reimer, Paul, Riordan, Seamus, Yi, Z., Ball, Jacques, Defurne, Maxime, Garcon, Michel, Moutarde, Herve, Procureur, Sebastien, Sabatie, Franck, Cosyn, Wim, Mazouz, Malek, Accardi, Alberto, Bettane, Julien, Charles, Gabriel, Dupre, Raphael, Guidal, Michel, Marchand, Dominique, Munoz, Carlos, Niccolai, Silvia, Voutier, Eric, Adhikari, Krishna, Dunne, James, Dutta, Dipangkar, Fassi, Lamiaa El, Ye, Li, Amarian, Moskov, Dodge, Gail, Guzey, Vadim, Baltzell, Nathan, Girod, Francois-Xavier, Keppel, Cynthia, Stepanyan, Stepan, Duran, Burcu, Joosten, Sylvester, Meziani, Zein-Eddine, Paolone, Michael, Rehfuss, Melanie, Sparveris, Nikos, Cao, F., Joo, Kyungseon, Kim, Andrei, Markov, N., Atti, Claudio Ciofi degli, Scopetta, Sergio, Brooks, William, El-Alaoui, Ahmed, and Liuti, Simonetta

Subjects
Nuclear Experiment
Abstract

We propose to measure tagged deep inelastic scattering from light nuclei (deuterium and $^4$He) by detecting the low energy nuclear spectator recoil (p, $^3$H and $^3$He) in addition to the scattered electron. The proposed experiment will provide stringent tests leading to clear differentiation between the many models describing the EMC effect, by accessing the bound nucleon virtuality through its initial momentum at the point of interaction. Indeed, conventional nuclear physics explanations of the EMC effect mainly based on Fermi motion and binding effects yield very different predictions than more exotic scenarios, where bound nucleons basically loose their identity when embedded in the nuclear medium. By distinguishing events where the interacting nucleon was slow, as described by a mean field scenario, or fast, very likely belonging to a correlated pair, will clearly indicate which phenomenon is relevant to explain the EMC effect. An important challenge for such measurements using nuclear spectators is the control of the theoretical framework and, in particular, final state interactions. This experiment will directly provide the necessary data needed to test our understanding of spectator tagging and final state interactions in $^2$H and $^4$He and their impact on the semi-inclusive measurements of the EMC effect described above.

Published
2017

26. Giant tortoise genomes provide insights into longevity and age-related disease

Author

Quesada, Víctor, Freitas-Rodríguez, Sandra, Miller, Joshua, Pérez-Silva, José G, Jiang, Zi-Feng, Tapia, Washington, Santiago-Fernández, Olaya, Campos-Iglesias, Diana, Kuderna, Lukas FK, Quinzin, Maud, Álvarez, Miguel G, Carrero, Dido, Beheregaray, Luciano B, Gibbs, James P, Chiari, Ylenia, Glaberman, Scott, Ciofi, Claudio, Araujo-Voces, Miguel, Mayoral, Pablo, Arango, Javier R, Tamargo-Gómez, Isaac, Roiz-Valle, David, Pascual-Torner, María, Evans, Benjamin R, Edwards, Danielle L, Garrick, Ryan C, Russello, Michael A, Poulakakis, Nikos, Gaughran, Stephen J, Rueda, Danny O, Bretones, Gabriel, Marquès-Bonet, Tomàs, White, Kevin P, Caccone, Adalgisa, and López-Otín, Carlos

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Aging, Biotechnology, Generic health relevance, Animals, DNA Repair, Evolution, Molecular, Genome, HEK293 Cells, Humans, Inflammation Mediators, Male, Neoplasms, Phylogeny, Population Density, Turtles, Ecology, Evolutionary biology, Environmental management
Abstract

Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George-the iconic last member of Chelonoidis abingdonii-and the Aldabra giant tortoise (Aldabrachelys gigantea). Comparison of these genomes with those of related species, using both unsupervised and supervised analyses, led us to detect lineage-specific variants affecting DNA repair genes, inflammatory mediators and genes related to cancer development. Our study also hints at specific evolutionary strategies linked to increased lifespan, and expands our understanding of the genomic determinants of ageing. These new genome sequences also provide important resources to help the efforts for restoration of giant tortoise populations.

Published
2019

27. Theory, practice, and conservation in the age of genomics: The Galápagos giant tortoise as a case study

Author

Gaughran, Stephen J, Quinzin, Maud C, Miller, Joshua M, Garrick, Ryan C, Edwards, Danielle L, Russello, Michael A, Poulakakis, Nikos, Ciofi, Claudio, Beheregaray, Luciano B, and Caccone, Adalgisa

Subjects
Human Genome, Genetics, Generic health relevance, Life on Land, Chelonoidis, conservation, genomics, population structure, sampling design, single nucleotide polymorphism, Medicinal and Biomolecular Chemistry, Evolutionary Biology
Abstract

High-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in nonmodel species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few individuals are sampled. Still, sampling design can have a strong impact on such inferences. Here, we use simulations and empirical SNP data to investigate the impacts of sampling design on estimating genetic differentiation among populations that represent three species of Galápagos giant tortoises (Chelonoidis spp.). Though microsatellite and mitochondrial DNA analyses have supported the distinctiveness of these species, a recent study called into question how well these markers matched with data from genomic SNPs, thereby questioning decades of studies in nonmodel organisms. Using >20,000 genomewide SNPs from 30 individuals from three Galápagos giant tortoise species, we find distinct structure that matches the relationships described by the traditional genetic markers. Furthermore, we confirm that accurate estimates of genetic differentiation in highly structured natural populations can be obtained using thousands of SNPs and 2-5 individuals, or hundreds of SNPs and 10 individuals, but only if the units of analysis are delineated in a way that is consistent with evolutionary history. We show that the lack of structure in the recent SNP-based study was likely due to unnatural grouping of individuals and erroneous genotype filtering. Our study demonstrates that genomic data enable patterns of genetic differentiation among populations to be elucidated even with few samples per population, and underscores the importance of sampling design. These results have specific implications for studies of population structure in endangered species and subsequent management decisions.

Published
2018

28. Author Correction: Identification of Genetically Important Individuals of the Rediscovered Floreana Galápagos Giant Tortoise (Chelonoidis elephantopus) Provides Founders for Species Restoration Program.

Author

Miller, Joshua M, Quinzin, Maud C, Poulakakis, Nikos, Gibbs, James P, Beheregaray, Luciano B, Garrick, Ryan C, Russello, Michael A, Ciofi, Claudio, Edwards, Danielle L, Hunter, Elizabeth A, Tapia, Washington, Rueda, Danny, Carrión, Jorge, Valdivieso, Andrés A, and Caccone, Adalgisa

Subjects
Biochemistry and Cell Biology, Other Physical Sciences
Abstract

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Published
2018

36. A microscopic nucleon spectral function for finite nuclei featuring two- and trhee-nucleon short-range correlations: I. The model vs. ab-initio calculations for the three-nucleon systems

Author

Atti, Claudio Ciofi degli, Mezzetti, Chiara Benedetta, and Morita, Hiko

Subjects
Nuclear Theory
Abstract

The main features of the convolution model which, in the region of two-nucleon (2N) and three-nucleon (3N) short-range correlations (SRC), describes the one-nucleon momentum distribution n(k_1) and the spectral function P(k_1,E) in terms of a convolution integral involving the relative n_{rel}(k_{rel}) and the center-of-mass n_{c.m.}(K_{c.m.}) momentum distributions of a nucleon-nucleon pair, are illustrated in detail. It is stressed that the model, which stems from the universal property of factorization exhibited by the nuclear wave function at short inter-nucleon distances, is only applicable in a well-defined region of k_{rel} and K_{c.m.}; it is shown, in particular, that the requirement of factorization introduces a severe constraint on the values of k_{rel} and K_{c.m.} that appear in the convolution integral. Using ab-initio relative and c.m. momentum distributions for ^3He, the validity of the convolution model is investigated by comparing the model spectral function and momentum distributions with the ones resulting from ab-initio calculations performed with realistic local NN interaction of the Argonne family. It is shown that when the constraint on the value of k_{rel} and K_{c.m.} are correctly taken into account and only 2N SRC are taken into account, the convolution model is in good agreement with the ab-initio spectral function in the region of the peak exhibited by the latter, whereas far from the peak, particularly at high values of the removal energy, the model spectral function can be qualitatively reconciled with the ab-initio spectral function only by considering the effects of 3N SRC. As for the nucleon momentum distribution, the effects of 3N SRC appears to be very small., Comment: 25 pages, 8 figures

Published
2017
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37. GnRH neurons recruit astrocytes in infancy to facilitate network integration and sexual maturation

Author

Pellegrino, Giuliana, Martin, Marion, Allet, Cécile, Lhomme, Tori, Geller, Sarah, Franssen, Delphine, Mansuy, Virginie, Manfredi-Lozano, Maria, Coutteau-Robles, Adrian, Delli, Virginia, Rasika, S., Mazur, Danièle, Loyens, Anne, Tena-Sempere, Manuel, Siepmann, Juergen, Pralong, François P., Ciofi, Philippe, Corfas, Gabriel, Parent, Anne-Simone, Ojeda, Sergio R., Sharif, Ariane, and Prevot, Vincent

Published
2021
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38. Universality of nucleon-nucleon short-range correlations: the factorization property of the nuclear wave function, the relative and center-of-mass momentum distributions, and the nuclear contacts

Author

Alvioli, Massimiliano, Atti, Claudio Ciofi degli, and Morita, Hiko

Subjects
Nuclear Theory, Nuclear Experiment
Abstract

The two-nucleon momentum distributions have been calculated for nuclei up to A=40 and various values of the relative and center-of-mass momenta and angle between them. For complex nuclei a parameter-free linked-cluster expansion, based upon a realistic local two-nucleon interaction of the Argonne family and variational wave function featuring central, tensor, spin and iso-spin correlations, has been used. The obtained results show that: 1) independently of the mass number A, at values of the relative momentum k_rel> 2 fm^{-1} the proton-neutron momentum distributions for back-to-back (BB) nucleons (K_cm=0) exhibit the factorization property n_A^{pn}(k_rel,K_cm=0)=C_A^{pn} n_D(k_rel) n_{cm}^{pn}(K_cm=0), where n_D is the deuteron momentum distribution, n_{cm}^{pn}(K_{cm}=0) the momentum distribution of the c.m. motion of the pair and C_A^{pn} the nuclear contact measuring the number of BB pn pairs with deuteron-like momenta; 2) the values of the proton-neutron nuclear contact C_A^{pn} are obtained in a model-independent way from the ratio n_A^{pn}(k_rel,K_cm=0)/n_D(k_rel) n_{cm}^{pn}(K_cm=0); 3) also the K_cm-integrated pn momentum distributions divided by the deuteron momentum distribution exhibits a constant behavior equal to C_A^{pn}, but only at very high values of k_{rel}> 3.5fm^{-1}, where the relative momentum distribution is entirely governed by BB short-range correlated nucleons; 4) the absolute value of the number of pn and pp short-range correlated pairs is calculated, illustrating that the high values (K_cm>1 fm^{-1}) of the pair c.m. momentum appreciably reduce the dominance of the pn over pp pairs produced by the tensor force when K_cm=0; 5) calculations are in good agreement with the VMC calculations for light nuclei and with available experimental on the processes A(e,e'pn)X and A(e,e'pp)X., Comment: 22 pages, 17 figures, 4 tables

Published
2016
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40. Identification of Genetically Important Individuals of the Rediscovered Floreana Galápagos Giant Tortoise (Chelonoidis elephantopus) Provide Founders for Species Restoration Program.

Author

Miller, Joshua M, Quinzin, Maud C, Poulakakis, Nikos, Gibbs, James P, Beheregaray, Luciano B, Garrick, Ryan C, Russello, Michael A, Ciofi, Claudio, Edwards, Danielle L, Hunter, Elizabeth A, Tapia, Washington, Rueda, Danny, Carrión, Jorge, Valdivieso, Andrés A, and Caccone, Adalgisa

Subjects
Animals, Humans, Turtles, DNA, Mitochondrial, Cluster Analysis, Breeding, Microsatellite Repeats, Founder Effect, Genotype, Genetic Variation, DNA, Mitochondrial, Biochemistry and Cell Biology, Other Physical Sciences
Abstract

Species are being lost at an unprecedented rate due to human-driven environmental changes. The cases in which species declared extinct can be revived are rare. However, here we report that a remote volcano in the Galápagos Islands hosts many giant tortoises with high ancestry from a species previously declared as extinct: Chelonoidis elephantopus or the Floreana tortoise. Of 150 individuals with distinctive morphology sampled from the volcano, genetic analyses revealed that 65 had C. elephantopus ancestry and thirty-two were translocated from the volcano's slopes to a captive breeding center. A genetically informed captive breeding program now being initiated will, over the next decades, return C. elephantopus tortoises to Floreana Island to serve as engineers of the island's ecosystems. Ironically, it was the haphazard translocations by mariners killing tortoises for food centuries ago that created the unique opportunity to revive this "lost" species today.

Published
2017

41. Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.

Author

Nuttle, Xander, Giannuzzi, Giuliana, Duyzend, Michael H, Schraiber, Joshua G, Narvaiza, Iñigo, Sudmant, Peter H, Penn, Osnat, Chiatante, Giorgia, Malig, Maika, Huddleston, John, Benner, Chris, Camponeschi, Francesca, Ciofi-Baffoni, Simone, Stessman, Holly AF, Marchetto, Maria CN, Denman, Laura, Harshman, Lana, Baker, Carl, Raja, Archana, Penewit, Kelsi, Janke, Nicolette, Tang, W Joyce, Ventura, Mario, Banci, Lucia, Antonacci, Francesca, Akey, Joshua M, Amemiya, Chris T, Gage, Fred H, Reymond, Alexandre, and Eichler, Evan E

Subjects
Chromosomes, Human, Pair 16, Animals, Humans, Pan troglodytes, Chromosome Breakage, Genetic Predisposition to Disease, Iron, Proteins, Autistic Disorder, Evolution, Molecular, Species Specificity, Gene Duplication, Recombination, Genetic, Homeostasis, Time Factors, DNA Copy Number Variations, Pongo, Human Genome, Genetics, Biotechnology, General Science & Technology
Abstract

Genetic differences that specify unique aspects of human evolution have typically been identified by comparative analyses between the genomes of humans and closely related primates, including more recently the genomes of archaic hominins. Not all regions of the genome, however, are equally amenable to such study. Recurrent copy number variation (CNV) at chromosome 16p11.2 accounts for approximately 1% of cases of autism and is mediated by a complex set of segmental duplications, many of which arose recently during human evolution. Here we reconstruct the evolutionary history of the locus and identify bolA family member 2 (BOLA2) as a gene duplicated exclusively in Homo sapiens. We estimate that a 95-kilobase-pair segment containing BOLA2 duplicated across the critical region approximately 282 thousand years ago (ka), one of the latest among a series of genomic changes that dramatically restructured the locus during hominid evolution. All humans examined carried one or more copies of the duplication, which nearly fixed early in the human lineage--a pattern unlikely to have arisen so rapidly in the absence of selection (P

Published
2016

45. Universality of nucleon-nucleon short-range correlations and nucleon momentum distributions

Author

Alvioli, Massimiliano, Atti, Claudio Ciofi degli, Kaptari, Leonid P., Mezzetti, Chiara Benedetta, and Morita, Hiko

Subjects
Nuclear Theory, High Energy Physics - Phenomenology, Nuclear Experiment
Abstract

By analyzing recent microscopic many-body calculations of few-nucleon systems and complex nuclei performed by different groups in terms of realistic nucleon-nucleon (NN) interactions, it is shown that NN short-range correlations (SRCs) have a universal character, in that the correlation hole that they produce in nuclei appears to be almost A-independent and similar to the correlation hole in the deuteron. The correlation hole creates high-momentum components, missing in a mean-field (MF) description and exhibiting several scaling properties and a peculiar spin-isospin structure. In particular, the momentum distribution of a pair of nucleons in spin-isospin state $(ST)=(10)$, depending upon the pair relative ($k_{rel}$) and center-of-mass (c.m.) ($K_{c.m.}$) momenta, as well as upon the angle $\Theta$ between them, exhibits a remarkable property: in the region $k_{rel}\gtrsim 2\,fm^{-1}$ and $K_{c.m.}\lesssim 1\,fm^{-1} $, the relative and c.m. motions are decoupled and the two-nucleon momentum distribution factorizes into the deuteron momentum distribution and an A-dependent momentum distribution describing the c.m. motion of the pair in the medium. The impact of these and other properties of one- and two-nucleon momentum distributions on various nuclear phenomena, on ab initio calculations in terms of low-momentum interactions, as well as on ongoing experimental investigations of SRCs, are briefly commented., Comment: 32 pages, 19 figures, Review paper to appear in Int. Journal of Mod. Phys. E

Published
2013
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49. Prevention of recurrent respiratory infections: Inter-society Consensus

Author

Chiappini, Elena, Santamaria, Francesca, Marseglia, Gian Luigi, Marchisio, Paola, Galli, Luisa, Cutrera, Renato, de Martino, Maurizio, Antonini, Sara, Becherucci, Paolo, Biasci, Paolo, Bortone, Barbara, Bottero, Sergio, Caldarelli, Valeria, Cardinale, Fabio, Gattinara, Guido Castelli, Ciarcià, Martina, Ciofi, Daniele, D’Elios, Sofia, Di Mauro, Giuseppe, Doria, Mattia, Indinnimeo, Luciana, Lo Vecchio, Andrea, Macrì, Francesco, Mattina, Roberto, Miniello, Vito Leonardo, del Giudice, Michele Miraglia, Morbin, Guido, Motisi, Marco Antonio, Novelli, Andrea, Palamara, Anna Teresa, Panatta, Maria Laura, Pasinato, Angela, Peroni, Diego, Perruccio, Katia, Piacentini, Giorgio, Pifferi, Massimo, Pignataro, Lorenzo, Sitzia, Emanuela, Tersigni, Chiara, Torretta, Sara, Trambusti, Irene, Trippella, Giulia, Valentini, Diletta, Valentini, Sandro, Varricchio, Attilio, Verga, Maria Carmen, Vicini, Claudio, Zecca, Marco, and Villani, Alberto

Published
2021
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50. Italian consensus on the therapeutic management of uncomplicated acute hematogenous osteomyelitis in children

Author

Krzysztofiak, Andrzej, Chiappini, Elena, Venturini, Elisabetta, Gargiullo, Livia, Roversi, Marco, Montagnani, Carlotta, Bozzola, Elena, Chiurchiu, Sara, Vecchio, Davide, Castagnola, Elio, Tomà, Paolo, Rossolini, Gian Maria, Toniolo, Renato Maria, Esposito, Susanna, Cirillo, Marco, Cardinale, Fabio, Novelli, Andrea, Beltrami, Giovanni, Tagliabue, Claudia, Boero, Silvio, Deriu, Daniele, Bianchini, Sonia, Grandin, Annalisa, Bosis, Samantha, Ciarcià, Martina, Ciofi, Daniele, Tersigni, Chiara, Bortone, Barbara, Trippella, Giulia, Nicolini, Giangiacomo, Lo Vecchio, Andrea, Giannattasio, Antonietta, Musso, Paola, Serrano, Elena, Marchisio, Paola, Donà, Daniele, Garazzino, Silvia, Pierantoni, Luca, Mazzone, Teresa, Bernaschi, Paola, Ferrari, Alessandra, Gattinara, Guido Castelli, Galli, Luisa, and Villani, Alberto

Published
2021
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