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1. Reductive evolution of virulence repertoire to drive the divergence between community- and hospital-associated methicillin-resistant Staphylococcus aureus of the ST1 lineage

Author

Marina Farrel Côrtes, Ana Maria N. Botelho, Paula Terra Bandeira, William Mouton, Cedric Badiou, Michèle Bes, Nicholas C. B. Lima, André Elias R. Soares, Rangel C. Souza, Luiz G. P. Almeida, Patricia Martins-Simoes, Ana T. R. Vasconcelos, Marisa F. Nicolás, Frédéric Laurent, Paul J. Planet, and Agnes M. S. Figueiredo

Subjects
methicillin-resistant staphylococcus aureus, st1-sccmeciv, comparative genomics, whole genome sequencing, evolution of virulence, evolution of pathogenicity, Infectious and parasitic diseases, RC109-216
Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) of the ST1-SCCmecIV lineage has been associated with community-acquired (CA) infections in North America and Australia. In Brazil, multi-drug resistant ST1-SCCmecIV MRSA has emerged in hospital-associated (HA) diseases in Rio de Janeiro. To understand these epidemiological differences, genomic and phylogenetic analyses were performed. In addition, virulence assays were done for representative CA – and HA-MRSA strains. Despite the conservation of the virulence repertoire, some genes were missing in Brazilian ST1-SCCmecIV including lukSF-PV, fnbB, and several superantigen-encoded genes. Additionally, CA-MRSA lost the splDE while HA-MRSA strains conserved the complete operon. Most of these variable genes were located in mobile genetic elements (MGE). However, conservation and maintenance of MGEs were often observed despite the absence of their associated virulence markers. A Bayesian phylogenetic tree revealed the occurrence of more than one entrance of ST1 strains in Rio de Janeiro. The tree shape and chronology allowed us to infer that the hospital-associated ST1-SCCmecIV from Brazil and the community-acquired USA400 from North America are not closely related and that they might have originated from different MSSA strains that independently acquired SCCmecIV cassettes. As expected, representatives of ST1 strains from Brazil showed lower cytotoxicity and a greater ability to survive inside human host cells. We suggest that Brazilian ST1-SCCmecIV strains have adapted to the hospital setting by reducing virulence and gaining the ability to persist and survive inside host cells. Possibly, these evolutionary strategies may balance the biologic cost of retaining multiple antibiotic resistance genes.

Published
2021
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2. gSeaGen code by KM3NeT: an efficient tool to propagate muons simulated with CORSIKA

Author

Aiello, S., Albert, A., Alhebsi, A. R., Alshamsi, M., Garre, S. Alves, Ambrosone, A., Ameli, F., Andre, M., Androutsou, E., Aphecetche, L., Ardid, M., Ardid, S., Atmani, H., Aublin, J., Badaracco, F., Bailly-Salins, L., Bardačová, Z., Baret, B., Bariego-Quintana, A., Becherini, Y., Bendahman, M., Benfenati, F., Benhassi, M., Bennani, M., Benoit, D. M., Berbee, E., Bertin, V., Beyer, C., Biagi, S., Boettcher, M., Bonanno, D., Bouasla, A. B., Boumaaza, J., Bouta, M., Bouwhuis, M., Bozza, C., Bozza, R. M., Brânzaş, H., Bretaudeau, F., Breuhaus, M., Bruijn, R., Brunner, J., Bruno, R., Buis, E., Buompane, R., Busto, J., Caiffi, B., Calvo, D., Capone, A., Carenini, F., Carretero, V., Cartraud, T., Castaldi, P., Cecchini, V., Celli, S., Cerisy, L., Chabab, M., Chadolias, M., Chen, A., Cherubini, S., Chiarusi, T., Circella, M., Cocimano, R., Coelho, J. A. B., Coleiro, A., Condorelli, A., Coniglione, R., Coyle, P., Creusot, A., Cuttone, G., Dallier, R., Darras, Y., De Benedittis, A., De Martino, B., De Wasseige, G., Decoene, V., Del Rosso, I., Di Mauro, L. S., Di Palma, I., Díaz, A. F., Diego-Tortosa, D., Distefano, C., Domi, A., Donzaud, C., Dornic, D., Drakopoulou, E., Drouhin, D., Ducoin, J. -G., Dvornický, R., Eberl, T., Eckerová, E., Eddymaoui, A., van Eeden, T., Eff, M., van Eijk, D., Bojaddaini, I. El, Hedri, S. El, Ellajosyula, V., Enzenhöfer, A., Ferrara, G., Filipović, M. D., Filippini, F., Franciotti, D., Fusco, L. A., Gagliardini, S., Gal, T., Méndez, J. García, Soto, A. Garcia, Oliver, C. Gatius, Geißelbrecht, N., Genton, E., Ghaddari, H., Gialanella, L., Gibson, B. K., Giorgio, E., Goos, I., Goswami, P., Gozzini, S. R., Gracia, R., Guidi, C., Guillon, B., Gutiérrez, M., Haack, C., van Haren, H., Hassieiev, V., Heijboer, A., Hennig, L., Hernández-Rey, J. J., Ibnsalih, W. Idrissi, Illuminati, G., Joly, D., de Jong, M., de Jong, P., Jung, B. J., Kalaczyński, P., Kistauri, G., Kopper, C., Kouchner, A., Kueviakoe, V., Kulikovskiy, V., Kvatadze, R., Labalme, M., Lahmann, R., Lamoureux, M., Larosa, G., Lastoria, C., Lazo, A., Stum, S. Le, Lehaut, G., Lemaître, V., Leonora, E., Lessing, N., Levi, G., Clark, M. Lindsey, Longhitano, F., Magnani, F., Majumdar, J., Malerba, L., Mamedov, F., Manfreda, A., Marconi, M., Margiotta, A., Marinelli, A., Markou, C., Martin, L., Mastrodicasa, M., Mastroianni, S., Mauro, J., Miele, G., Migliozzi, P., Migneco, E., Mitsou, M. L., Mollo, C. M., Morales-Gallegos, L., Moretti, G., Moussa, A., Mateo, I. Mozun, Muller, R., Musone, M. R., Musumeci, M., Navas, S., Nayerhoda, A., Nicolau, C. A., Nkosi, B., Fearraigh, B. Ó, Oliviero, V., Orlando, A., Oukacha, E., Paesani, D., González, J. Palacios, Papalashvili, G., Parisi, V., Gomez, E. J. Pastor, Păun, A. M., Păvălaş, G. E., Pelegris, I., Martínez, S. Peña, Perrin-Terrin, M., Pestel, V., Pestes, R., Piattelli, P., Poirè, C., Popa, V., Pradier, T., Prado, J., Pulvirenti, S., Quiroz-Rangel, C. A., Rahaman, U., Randazzo, N., Razzaque, S., Rea, I. C., Real, D., Riccobene, G., Robinson, J., Romanov, A., Šaina, A., Greus, F. Salesa, Samtleben, D. F. E., Losa, A. Sánchez, Sanfilippo, S., Sanguineti, M., Santonocito, D., Sapienza, P., Schnabel, J., Schumann, J., Schutte, H. M., Seneca, J., Sennan, N., Setter, B., Sgura, I., Shanidze, R., Sharma, A., Shitov, Y., Šimkovic, F., Simonelli, A., Sinopoulou, A., Spisso, B., Spurio, M., Stavropoulos, D., Štekl, I., Taiuti, M., Tayalati, Y., Thiersen, H., Thoudam, S., de la Torre, P., Melo, I. Tosta e, Tragia, E., Trocmé, B., Tsourapis, V., Tudorache, A., Tzamariudaki, E., Ukleja, A., Vacheret, A., Valsecchi, V., Van Elewyck, V., Vannoye, G., Vasileiadis, G., de Sola, F. Vazquez, Veutro, A., Viola, S., Vivolo, D., van Vliet, A., Warnhofer, H., Weissbrod, S., de Wolf, E., Lhenry-Yvon, I., Zarpapis, G., Zavatarelli, S., Zegarelli, A., Zito, D., Zornoza, J. D., Zúñiga, J., and Zywucka, N.

Subjects
High Energy Physics - Experiment, Astrophysics - Instrumentation and Methods for Astrophysics, Physics - Computational Physics
Abstract

The KM3NeT Collaboration has tackled a common challenge faced by the astroparticle physics community, namely adapting the experiment-specific simulation software to work with the CORSIKA air shower simulation output. The proposed solution is an extension of the open-source code gSeaGen, allowing for the transport of muons generated by CORSIKA to a detector of any size at an arbitrary depth. The gSeaGen code was not only extended in terms of functionalities but also underwent a thorough redesign of the muon propagation routine, resulting in a more accurate and efficient simulation. This paper presents the capabilities of the new gSeaGen code as well as prospects for further developments., Comment: 27 pages, 13 figures

Published
2024

3. Search for quantum decoherence in neutrino oscillations with six detection units of KM3NeT/ORCA

Author

Aiello, S., Albert, A., Alhebsi, A. R., Alshamsi, M., Garre, S. Alves, Ambrosone, A., Ameli, F., Andre, M., Aphecetche, L., Ardid, M., Ardid, S., Atmani, H., Aublin, J., Badaracco, F., Bailly-Salins, L., Bardacova, Z., Baret, B., Bariego-Quintana, A., Becherini, Y., Bendahman, M., Benfenati, F., Benhassi, M., Bennani, M., Benoit, D. M., Berbee, E., Bertin, V., Biagi, S., Boettcher, M., Bonanno, D., Bouasla, A. B., Boumaaza, J., Bouta, M., Bouwhuis, M., Bozza, C., Bozza, R. M., Branzas, H., Bretaudeau, F., Breuhaus, M., Bruijn, R., Brunner, J., Bruno, R., Buis, E., Buompane, R., Busto, J., Caiffi, B., Calvo, D., Capone, A., Carenini, F., Carretero, V., Cartraud, T., Castaldi, P., Cecchini, V., Celli, S., Cerisy, L., Chabab, M., Chen, A., Cherubini, S., Chiarusi, T., Circella, M., Cocimano, R., Coelho, J. A. B., Coleiro, A., Condorelli, A., Coniglione, R., Coyle, P., Creusot, A., Cuttone, G., Dallier, R., De Benedittis, A., De Martino, B., De Wasseige, G., Decoene, V., Del Rosso, I., Di Mauro, L. S., Di Palma, I., Diaz, A. F., Diego-Tortosa, D., Distefano, C., Domi, A., Donzaud, C., Dornic, D., Drakopoulou, E., Drouhin, D., Ducoin, J. -G., Dvornicky, R., Eberl, T., Eckerova, E., Eddymaoui, A., van Eeden, T., Eff, M., van Eijk, D., Bojaddaini, I. El, Hedri, S. El, Ellajosyula, V., Enzenhoefer, A., Ferrara, G., Filipovic, M. D., Filippini, F., Franciotti, D., Fusco, L. A., Gagliardini, S., Gal, T., Mendez, J. Garcia, Soto, A. Garcia, Oliver, C. Gatius, Geißelbrecht, N., Genton, E., Ghaddari, H., Gialanella, L., Gibson, B. K., Giorgio, E., Goos, I., Goswami, P., Gozzini, S. R., Gracia, R., Guidi, C., Guillon, B., Gutierrez, M., Haack, C., van Haren, H., Heijboer, A., Hennig, L., Hernandez-Rey, J. J., Ibnsalih, W. Idrissi, Illuminati, G., Joly, D., de Jong, M., de Jong, P., Jung, B. J., Kistauri, G., Kopper, C., Kouchner, A., Kovalev, Y. Y., Kueviakoe, V., Kulikovskiy, V., Kvatadze, R., Labalme, M., Lahmann, R., Lamoureux, M., Larosa, G., Lastoria, C., Lazo, A., Stum, S. Le, Lehaut, G., Lemaitre, V., Leonora, E., Lessing, N., Levi, G., Clark, M. Lindsey, Longhitano, F., Magnani, F., Majumdar, J., Malerba, L., Mamedov, F., Manczak, J., Manfreda, A., Marconi, M., Margiotta, A., Marinelli, A., Markou, C., Martin, L., Mastrodicasa, M., Mastroianni, S., Mauro, J., Miele, G., Migliozzi, P., Migneco, E., Mitsou, M. L., Mollo, C. M., Morales-Gallegos, L., Moussa, A., Mateo, I. Mozun, Muller, R., Musone, M. R., Musumeci, M., Navas, S., Nayerhoda, A., Nicolau, C. A., Nkosi, B., Fearraigh, B. O., Oliviero, V., Orlando, A., Oukacha, E., Gonzalez, D. Paesaniy J. Palacios, Papalashvili, G., Parisi, V., Gomez, E. J. Pastor, Pastore, C., Paun, A. M., Pavala, G. E., Martinez, S. Pena, Perrin-Terrin, M., Pestel, V., Pestes, R., Piattelli, P., Plavin, A., Poire, C., Popa, V., Pradier, T., Prado, J., Pulvirenti, S., Quiroz-Rangel, C. A., Randazzo, N., Razzaque, S., Rea, I. C., Real, D., Robinson, G. Riccobene. J., Romanov, A., Ros, E., Saina, A., Greus, F. Salesa, Samtleben, D. F. E., Losa, A. Sanchez, Sanfilippo, S., Sanguineti, M., Santonocito, D., Sapienza, P., Schnabel, J., Schumann, J., Schutte, H. M., Seneca, J., Sgura, I., Shanidze, R., Sharma, A., Shitov, Y., Simkovic, F., Simonelli, A., Sinopoulou, A., Spisso, B., Spurio, M., Stavropoulos, D., Stekl, I., Stellacci, S. M., Taiuti, M., Tayalati, Y., Thiersen, H., Thoudam, S., Tosta, I., Melo, e, Trocme, B., Tsourapis, V., Tudorache, A., Tzamariudaki, E., Ukleja, A., Vacheret, A., Valsecchi, V., Van Elewyck, V., Vannoye, G., Vasileiadis, G., de Sola, F. Vazquez, Veutro, A., Viola, S., Vivolo, D., van Vliet, A., de Wolf, E., Lhenry-Yvon, I., Zavatarelli, S., Zegarelli, A., Zito, D., Zornoza, J. D., Zuniga, J., and Zywucka, N.

Subjects
High Energy Physics - Experiment
Abstract

Neutrinos described as an open quantum system may interact with the environment which introduces stochastic perturbations to their quantum phase. This mechanism leads to a loss of coherence along the propagation of the neutrino $-$ a phenomenon commonly referred to as decoherence $-$ and ultimately, to a modification of the oscillation probabilities. Fluctuations in space-time, as envisaged by various theories of quantum gravity, are a potential candidate for a decoherence-inducing environment. Consequently, the search for decoherence provides a rare opportunity to investigate quantum gravitational effects which are usually beyond the reach of current experiments. In this work, quantum decoherence effects are searched for in neutrino data collected by the KM3NeT/ORCA detector from January 2020 to November 2021. The analysis focuses on atmospheric neutrinos within the energy range of a few GeV to $100\,\mathrm{GeV}$. Adopting the open quantum system framework, decoherence is described in a phenomenological manner with the strength of the effect given by the parameters $\Gamma_{21}$ and $\Gamma_{31}$. Following previous studies, a dependence of the type $\Gamma_{ij} \propto (E/E_0)^n$ on the neutrino energy is assumed and the cases $n = -2,-1$ are explored. No significant deviation with respect to the standard oscillation hypothesis is observed. Therefore, $90\,\%$ CL upper limits are estimated as $\Gamma_{21} < 4.6\cdot 10^{-21}\,$GeV and $\Gamma_{31} < 8.4\cdot 10^{-21}\,$GeV for $n = -2$, and $\Gamma_{21} < 1.9\cdot 10^{-22}\,$GeV and $\Gamma_{31} < 2.7\cdot 10^{-22}\,$GeV for $n = -1$, respectively., Comment: 17 pages, 5 figures

Published
2024

4. Measurement of neutrino oscillation parameters with the first six detection units of KM3NeT/ORCA

Author

KM3NeT Collaboration, Aiello, S., Albert, A., Alhebsi, A. R., Alshamsi, M., Garre, S. Alves, Ambrosone, A., Ameli, F., Andre, M., Aphecetche, L., Ardid, M., Ardid, S., Atmani, H., Aublin, J., Badaracco, F., Bailly-Salins, L., Bardačová, Z., Baret, B., Bariego-Quintana, A., Becherini, Y., Bendahman, M., Benfenati, F., Benhassi, M., Bennani, M., Benoit, D. M., Berbee, E., Bertin, V., Biagi, S., Boettcher, M., Bonanno, D., Bouasla, A. B., Boumaaza, J., Bouta, M., Bouwhuis, M., Bozza, C., Bozza, R. M., Brânzaş, H., Bretaudeau, F., Breuhaus, M., Bruijn, R., Brunner, J., Bruno, R., Buis, E., Buompane, R., Busto, J., Caiffi, B., Calvo, D., Capone, A., Carenini, F., Carretero, V., Cartraud, T., Castaldi, P., Cecchini, V., Celli, S., Cerisy, L., Chabab, M., Chen, A., Cherubini, S., Chiarusi, T., Circella, M., Cocimano, R., Coelho, J. A. B., Coleiro, A., Condorelli, A., Coniglione, R., Coyle, P., Creusot, A., Cuttone, G., Dallier, R., De Benedittis, A., De Martino, B., De Wasseige, G., Decoene, V., Del Rosso, I., Di Mauro, L. S., Di Palma, I., Díaz, A. F., Diego-Tortosa, D., Distefano, C., Domi, A., Donzaud, C., Dornic, D., Drakopoulou, E., Drouhin, D., Ducoin, J. -G., Dvornický, R., Eberl, T., Eckerová, E., Eddymaoui, A., van Eeden, T., Eff, M., van Eijk, D., Bojaddaini, I. El, Hedri, S. El, Ellajosyula, V., Enzenhöfer, A., Ferrara, G., Filipović, M. D., Filippini, F., Franciotti, D., Fusco, L. A., Gagliardini, S., Gal, T., Méndez, J. García, Soto, A. Garcia, Oliver, C. Gatius, Geißelbrecht, N., Genton, E., Ghaddari, H., Gialanella, L., Gibson, B. K., Giorgio, E., Goos, I., Goswami, P., Gozzini, S. R., Gracia, R., Guidi, C., Guillon, B., Gutiérrez, M., Haack, C., van Haren, H., Heijboer, A., Hennig, L., Hernández-Rey, J. J., Ibnsalih, W. Idrissi, Illuminati, G., Joly, D., de Jong, M., de Jong, P., Jung, B. J., Kistauri, G., Kopper, C., Kouchner, A., Kovalev, Y. Y., Kueviakoe, V., Kulikovskiy, V., Kvatadze, R., Labalme, M., Lahmann, R., Lamoureux, M., Larosa, G., Lastoria, C., Lazo, A., Stum, S. Le, Lehaut, G., Lemaítre, V., Leonora, E., Lessing, N., Levi, G., Clark, M. Lindsey, Longhitano, F., Magnani, F., Majumdar, J., Malerba, L., Mamedov, F., Mańczak, J., Manfreda, A., Marconi, M., Margiotta, A., Marinelli, A., Markou, C., Martin, L., Mastrodicasa, M., Mastroianni, S., Mauro, J., Miele, G., Migliozzi, P., Migneco, E., Mitsou, M. L., Mollo, C. M., Morales-Gallegos, L., Moussa, A., Mateo, I. Mozun, Muller, R., Musone, M. R., Musumeci, M., Navas, S., Nayerhoda, A., Nicolau, C. A., Nkosi, B., Fearraigh, B. Ó, Oliviero, V., Orlando, A., Oukacha, E., Paesani, D., González, J. Palacios, Papalashvili, G., Parisi, V., Gomez, E. J. Pastor, Păun, A. M., Păvălaş, G. E., Martínez, S. Peña, Perrin-Terrin, M., Pestel, V., Pestes, R., Piattelli, P., Plavin, A., Poirè, C., Popa, V., Pradier, T., Prado, J., Pulvirenti, S., Quiroz-Rangel, C. A., Randazzo, N., Razzaque, S., Rea, I. C., Real, D., Riccobene, G., Robinson, J., Romanov, A., Ros, E., Šaina, A., Greus, F. Salesa, Samtleben, D. F. E., Losa, A. Sánchez, Sanfilippo, S., Sanguineti, M., Santonocito, D., Sapienza, P., Schnabel, J., Schumann, J., Schutte, H. M., Seneca, J., Sgura, I., Shanidze, R., Sharma, A., Shitov, Y., Šimkovic, F., Simonelli, A., Sinopoulou, A., Spisso, B., Spurio, M., Stavropoulos, D., Štekl, I., Stellacci, S. M., Taiuti, M., Tayalati, Y., Thiersen, H., Thoudam, S., Melo, I. Tosta e, Trocmé, B., Tsourapis, V., Tudorache, A., Tzamariudaki, E., Ukleja, A., Vacheret, A., Valsecchi, V., Van Elewyck, V., Vannoye, G., Vasileiadis, G., de Sola, F. Vazquez, Veutro, A., Viola, S., Vivolo, D., van Vliet, A., de Wolf, E., Yvon, I., Zavatarelli, S., Zegarelli, A., Zito, D., Zornoza, J. D., Zúñiga, J., and Zywucka, N.

Subjects
High Energy Physics - Experiment
Abstract

KM3NeT/ORCA is a water Cherenkov neutrino detector under construction and anchored at the bottom of the Mediterranean Sea. The detector is designed to study oscillations of atmospheric neutrinos and determine the neutrino mass ordering. This paper focuses on an initial configuration of ORCA, referred to as ORCA6, which comprises six out of the foreseen 115 detection units of photo-sensors. A high-purity neutrino sample was extracted, corresponding to an exposure of 433 kton-years. The sample of 5828 neutrino candidates is analysed following a binned log-likelihood method in the reconstructed energy and cosine of the zenith angle. The atmospheric oscillation parameters are measured to be $\sin^2\theta_{23}= 0.51^{+0.04}_{-0.05}$, and $ \Delta m^2_{31} = 2.18^{+0.25}_{-0.35}\times 10^{-3}~\mathrm{eV^2} \cup \{-2.25,-1.76\}\times 10^{-3}~\mathrm{eV^2}$ at 68\% CL. The inverted neutrino mass ordering hypothesis is disfavoured with a p-value of 0.25., Comment: 29 pages, 12 figures

Published
2024

5. Search for Neutrino Emission from GRB 221009A using the KM3NeT ARCA and ORCA detectors

Author

Aiello, S., Albert, A., Alshamsi, M., Garre, S. Alves, Ambrosone, A., Ameli, F., Andre, M., Androutsou, E., Anguita, M., Aphecetche, L., Ardid, M., Ardid, S., Atmani, H., Aublin, J., Badaracco, F., Bailly-Salins, L., Bardačová, Z., Baret, B., Bariego-Quintana, A., Pree, S. Basegmez du, Becherini, Y., Bendahman, M., Benfenati, F., Benhassi, M., Benoit, D. M., Berbee, E., Bertin, V., Biagi, S., Boettcher, M., Bonanno, D., Boumaaza, J., Bouta, M., Bouwhuis, M., Bozza, C., Bozza, R. M., Brânzaş, H., Bretaudeau, F., Breuhaus, M., Bruijn, R., Brunner, J., Bruno, R., Buis, E., Buompane, R., Busto, J., Caiffi, B., Calvo, D., Campion, S., Capone, A., Carenini, F., Carretero, V., Cartraud, T., Castaldi, P., Cecchini, V., Celli, S., Cerisy, L., Chabab, M., Chadolias, M., Chen, A., Cherubini, S., Chiarusi, T., Circella, M., Cocimano, R., Coelho, J. A. B., Coleiro, A., Condorelli, A., Coniglione, R., Coyle, P., Creusot, A., Cuttone, G., Dallier, R., Darras, Y., De Benedittis, A., De Martino, B., Decoene, V., Del Burgo, R., Del Rosso, I., Di Mauro, L. S., Di Palma, I., Díaz, A. F., Diaz, C., Diego-Tortosa, D., Distefano, C., Domi, A., Donzaud, C., Dornic, D., Dörr, M., Drakopoulou, E., Drouhin, D., Ducoin, J. G., Dvornický, R., Eberl, T., Eckerová, E., Eddymaoui, A., van Eeden, T., Eff, M., van Eijk, D., Bojaddaini, I. El, Hedri, S. El, Enzenhöfer, A., Ferrara, G., Filipović, M. D., Filippini, F., Franciotti, D., Fusco, L. A., Gagliardini, S., Gal, T., Méndez, J. García, Soto, A. Garcia, Oliver, C. Gatius, Geißelbrecht, N., Ghaddari, H., Gialanella, L., Gibson, B. K., Giorgio, E., Goos, I., Goswami, P., Gozzini, S. R., Gracia, R., Graf, K., Guidi, C., Guillon, B., Gutiérrez, M., Haack, C., van Haren, H., Heijboer, A., Hekalo, A., Hennig, L., Hernández-Rey, J. J., Ibnsalih, W. Idrissi, Illuminati, G., Joly, D., de Jong, M., de Jong, P., Jung, B. J., Kalekin, O., Katz, U. F., Kharkhelauri, L., Kistauri, G., Kopper, C., Kouchner, A., Kueviakoe, V., Kulikovskiy, V., Kvatadze, R., Labalme, M., Lahmann, R., Larosa, G., Lastoria, C., Lazo, A., Stum, S. Le, Lehaut, G., Leonora, E., Lessing, N., Levi, G., Longhitano, F., Magnani, F., Majumdar, J., Malerba, L., Mamedov, F., Mańczak, J., Manfreda, A., Marconi, M., Margiotta, A., Marinelli, A., Markou, C., Martin, L., Marzaioli, F., Mastrodicasa, M., Mastroianni, S., Miccichè, S., Miele, G., Migliozzi, P., Migneco, E., Mitsou, M. L., Mollo, C. M., Morales-Gallegos, L., Moretti, G., Moussa, A., Mateo, I. Mozun, Muller, R., Musone, M. R., Musumeci, M., Navas, S., Nayerhoda, A., Nicolau, C. A., Nkosi, B., Fearraigh, B. Ó, Oliviero, V., Orlando, A., Oukacha, E., Paesani, D., González, J. Palacios, Papalashvili, G., Parisi, V., Gomez, E. J. Pastor, Păun, A. M., Păvălaş, G. E., Pelegris, I., Martínez, S. Pena, Perrin-Terrin, M., Perronnel, J., Pestel, V., Pestes, R., Piattelli, P., Poirè, C., Popa, V., Pradier, T., Prado, J., Pulvirenti, S., Quiroz-Rangel, C. A., Rahaman, U., Randazzo, N., Razzaque, S., Rea, I. C., Real, D., Riccobene, G., Robinson, J., Romanov, A., Šaina, A., Greus, F. Salesa, Samtleben, D. F. E., Losa, A. Sánchez, Sanfilippo, S., Sanguineti, M., Santonastaso, C., Santonocito, D., Sapienza, P., Schnabel, J., Schumann, J., Schutte, H. M., Seneca, J., Sennan, N., Setter, B., Sgura, I., Shanidze, R., Sharma, A., Shitov, Y., Šimkovic, F., Simonelli, A., Sinopoulou, A., Smirnov, M. V., Spisso, B., Spurio, M., Stavropoulos, D., Štekl, I., Taiuti, M., Tangorra-Cascione, R., Tayalati, Y., Thiersen, H., Melo, I. Tosta e, Tragia, E., Trocmé, B., Tsourapis, V., Tudorache, A., Tzamariudaki, E., Ukleja, A., Vacheret, A., Melchor, A. Valer, Valsecchi, V., Van Elewyck, V., Vannoye, G., Vasileiadis, G., de Sola, F. Vazquez, Veutro, A., Viola, S., Vivolo, D., Wilms, J., de Wolf, E., Yepes-Ramirez, H., Yvon, I., Zarpapis, G., Zavatarelli, S., Zegarelli, A., Zito, D., Zornoza, J. D., Zúñiga, J., and Zywucka, N.

Subjects
Astrophysics - High Energy Astrophysical Phenomena
Abstract

Gamma-ray bursts are promising candidate sources of high-energy astrophysical neutrinos. The recent GRB 221009A event, identified as the brightest gamma-ray burst ever detected, provides a unique opportunity to investigate hadronic emissions involving neutrinos. The KM3NeT undersea neutrino detectors participated in the worldwide follow-up effort triggered by the event, searching for neutrino events. In this letter, we summarize subsequent searches, in a wide energy range from MeV up to a few PeVs. No neutrino events are found in any of the searches performed. Upper limits on the neutrino emission associated with GRB 221009A are computed., Comment: 11 pages, 2 PDF figures. Submitted to JCAP

Published
2024

6. Astronomy potential of KM3NeT/ARCA

Author

Aiello, S., Albert, A., Alshamsi, M., Garre, S. Alves, Aly, Z., Ambrosone, A., Ameli, F., Andre, M., Androutsou, E., Anguita, M., Aphecetche, L., Ardid, M., Ardid, S., Atmani, H., Aublin, J., Badaracco, F., Bailly-Salins, L., Bardacová, Z., Baret, B., Bariego-Quintana, A., Baruzzi, A., Pree, S. Basegmez du, Becherini, Y., Bendahman, M., Benfenati, F., Benhassi, M., Benoit, D. M., Berbee, E., Bertin, V., Biagi, S., Boettcher, M., Bonanno, D., Boumaaza, J., Bouta, M., Bouwhuis, M., Bozza, C., Bozza, R. M., Brânzas, H., Bretaudeau, F., Breuhaus, M., Bruijn, R., Brunner, J., Bruno, R., Buis, E., Buompane, R., Busto, J., Caiffi, B., Calvo, D., Campion, S., Capone, A., Carenini, F., Carretero, V., Cartraud, T., Castaldi, P., Cecchini, V., Celli, S., Cerisy, L., Chabab, M., Chadolias, M., Chen, A., Cherubini, S., Chiarusi, T., Circella, M., Cocimano, R., Coelho, J. A. B., Coleiro, A., Coniglione, R., Coyle, P., Creusot, A., Cuttone, G., Dallier, R., Darras, Y., De Benedittis, A., De Martino, B., Decoene, V., Del Burgo, R., Del Rosso, I., Di Mauro, L. S., Di Palma, I., Díaz, A. F., Diaz, C., Diego-Tortosa, D., Distefano, C., Domi, A., Donzaud, C., Dornic, D., Dörr, M., Drakopoulou, E., Drouhin, D., Ducoin, J. G., Dvornický, R., Eberl, T., Eckerová, E., Eddymaoui, A., van Eeden, T., Eff, M., van Eijk, D., Bojaddaini, I. El, Hedri, S. El, Enzenhöfer, A., Ferrara, G., Filipovic, M. D., Filippini, F., Franciotti, D., Fusco, L. A., Gabriel, J., Gagliardini, S., Gal, T., Méndez, J. García, Soto, A. Garcia, Oliver, C. Gatius, Geißelbrecht, N., Ghaddari, H., Gialanella, L., Gibson, B. K., Giorgio, E., Goos, I., Goswami, P., Goupilliere, D., Gozzini, S. R., Gracia, R., Graf, K., Guidi, C., Guillon, B., Gutiérrez, M., van Haren, H., Heijboer, A., Hekalo, A., Hennig, L., Hernández-Rey, J. J., Ibnsalih, W. Idrissi, Illuminati, G., de Jong, M., de Jong, P., Jung, B. J., Kalaczynski, P., Kalekin, O., Katz, U. F., Kistauri, G., Kopper, C., Kouchner, A., Kueviakoe, V., Kulikovskiy, V., Kvatadze, R., Labalme, M., Lahmann, R., Larosa, G., Lastoria, C., Lazo, A., Stum, S. Le, Lehaut, G., Leonora, E., Lessing, N., Levi, G., Clark, M. Lindsey, Longhitano, F., Magnani, F., Majumdar, J., Malerba, L., Mamedov, F., Manczak, J., Manfreda, A., Marconi, M., Margiotta, A., Marinelli, A., Markou, C., Martin, L., Martínez-Mora, J. A., Marzaioli, F., Mastrodicasa, M., Mastroianni, S., Miccichè, S., Miele, G., Migliozzi, P., Migneco, E., Mitsou, M. L., Mollo, C. M., Morales-Gallegos, L., Morga, M., Moussa, A., Mateo, I. Mozun, Muller, R., Musone, M. R., Musumeci, M., Navas, S., Nayerhoda, A., Nicolau, C. A., Nkosi, B., Fearraigh, B. Ó, Oliviero, V., Orlando, A., Oukacha, E., Paesani, D., González, J. Palacios, Papalashvili, G., Parisi, V., Gomez, E. J. Pastor, Paun, A. M., Pavalas, G. E., Pelegris, I., Martínez, S. Peña, Perrin-Terrin, M., Perronnel, J., Pestel, V., Pestes, R., Piattelli, P., Poirè, C., Popa, V., Pradier, T., Prado, J., Pulvirenti, S., Quiroz-Rangel, C. A., Rahaman, U., Randazzo, N., Randriatoamanana, R., Razzaque, S., Rea, I. C., Real, D., Riccobene, G., Robinson, J., Romanov, A., Šaina, A., Greus, F. Salesa, Samtleben, D. F. E., Losa, A. Sánchez, Sanfilippo, S., Sanguineti, M., Santonastaso, C., Santonocito, D., Sapienza, P., Schnabel, J., Schumann, J., Schutte, H. M., Seneca, J., Sennan, N., Setter, B., Sgura, I., Shanidze, R., Sharma, A., Shitov, Y., Šimkovic, F., Simonelli, A., Sinopoulou, A., Smirnov, M. V., Spisso, B., Spurio, M., Stavropoulos, D., Štekl, I., Taiuti, M., Tayalati, Y., Thiersen, H., Melo, I. Tosta e, Tragia, E., Trocmé, B., Tsourapis, V., Tudorache, A., Tzamariudaki, E., Vacheret, A., Melchor, A. Valer, Valsecchi, V., Van Elewyck, V., Vannoye, G., Vasileiadis, G., de Sola, F. Vazquez, Verilhac, C., Veutro, A., Viola, S., Vivolo, D., Wilms, J., de Wolf, E., Yepes-Ramirez, H., Zarpapis, G., Zavatarelli, S., Zegarelli, A., Zito, D., Zornoza, J. D., Zúñiga, J., and Zywucka, N.

Subjects
Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

The KM3NeT/ARCA neutrino detector is currently under construction at 3500 m depth offshore Capo Passero, Sicily, in the Mediterranean Sea. The main science objectives are the detection of high-energy cosmic neutrinos and the discovery of their sources. Simulations were conducted for the full KM3NeT/ARCA detector, instrumenting a volume of 1 km$^3$, to estimate the sensitivity and discovery potential to point-like neutrino sources and an all-sky diffuse neutrino flux. This paper covers the reconstruction of track- and shower-like signatures, as well as the criteria employed for neutrino event selection. By leveraging both the track and shower observation channels, the KM3NeT/ARCA detector demonstrates the capability to detect the diffuse astrophysical neutrino flux within half a year of operation, achieving a 5$\sigma$ statistical significance. With an angular resolution below 0.1$^\circ$ for tracks and under 2$^\circ$ for showers, the sensitivity to point-like neutrino sources surpasses existing observed limits across the entire sky., Comment: 20 pages, 30 figures, Published by EPJ-C

Published
2024
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7. Searches for neutrino counterparts of gravitational waves from the LIGO/Virgo third observing run with KM3NeT

Author

KM3NeT Collaboration, Aiello, S., Albert, A., Garre, S. Alves, Aly, Z., Ambrosone, A., Ameli, F., Andre, M., Androutsou, E., Anguita, M., Aphecetche, L., Ardid, M., Ardid, S., Atmani, H., Aublin, J., Bailly-Salins, L., Bardačová, Z., Baret, B., Bariego-Quintana, A., Pree, S. Basegmez du, Becherini, Y., Bendahman, M., Benfenati, F., Benhassi, M., Benoit, D. M., Berbee, E., Bertin, V., Biagi, S., Boettcher, M., Bonanno, D., Boumaaza, J., Bouta, M., Bouwhuis, M., Bozza, C., Bozza, R. M., Brânzaş, H., Bretaudeau, F., Bruijn, R., Brunner, J., Bruno, R., Buis, E., Buompane, R., Busto, J., Caiffi, B., Calvo, D., Campion, S., Capone, A., Carenini, F., Carretero, V., Cartraud, T., Castaldi, P., Cecchini, V., Celli, S., Cerisy, L., Chabab, M., Chadolias, M., Chen, A., Cherubini, S., Chiarusi, T., Circella, M., Cocimano, R., Coelho, J. A. B., Coleiro, A., Coniglione, R., Coyle, P., Creusot, A., Cuttone, G., Dallier, R., Darras, Y., De Benedittis, A., De Martino, B., De Wasseige, G., Decoene, V., Del Burgo, R., Del Rosso, I., Di Cerbo, U. M., Di Mauro, L. S., Di Palma, I., Díaz, A. F., Diaz, C., Diego-Tortosa, D., Distefano, C., Domi, A., Donzaud, C., Dornic, D., Dörr, M., Drakopoulou, E., Drouhin, D., Dvornický, R., Eberl, T., Eckerová, E., Eddymaoui, A., van Eeden, T., Eff, M., van Eijk, D., Bojaddaini, I. El, Hedri, S. El, Enzenhöfer, A., Ferrara, G., Filipović, M. D., Filippini, F., Franciotti, D., Fusco, L. A., Gabriel, J., Gagliardini, S., Gal, T., Méndez, J. García, Soto, A. Garcia, Oliver, C. Gatius, Geißelbrecht, N., Ghaddari, H., Gialanella, L., Gibson, B. K., Giorgio, E., Goos, I., Goswami, P., Goupilliere, D., Gozzini, S. R., Gracia, R., Graf, K., Guidi, C., Guillon, B., Gutiérrez, M., van Haren, H., Heijboer, A., Hekalo, A., Hennig, L., Hernández-Rey, J. J., Ibnsalih, W. Idrissi, Illuminati, G., de Jong, M., de Jong, P., Jung, B. J., Kalaczyński, P., Kalekin, O., Katz, U. F., Khatun, A., Kistauri, G., Kopper, C., Kouchner, A., Kueviakoe, V., Kulikovskiy, V., Kvatadze, R., Labalme, M., Lahmann, R., Lamoureux, M., Larosa, G., Lastoria, C., Lazo, A., Stum, S. Le, Lehaut, G., Leonora, E., Lessing, N., Levi, G., Clark, M. Lindsey, Longhitano, F., Majumdar, J., Malerba, L., Mamedov, F., Mańczak, J., Manfreda, A., Marconi, M., Margiotta, A., Marinelli, A., Markou, C., Martin, L., Martínez-Mora, J. A., Marzaioli, F., Mastrodicasa, M., Mastroianni, S., Miccichè, S., Miele, G., Migliozzi, P., Migneco, E., Mitsou, M. L., Mollo, C. M., Morales-Gallegos, L., Morga, M., Moussa, A., Mateo, I. Mozun, Muller, R., Musone, M. R., Musumeci, M., Navas, S., Nayerhoda, A., Nicolau, C. A., Nkosi, B., Fearraigh, B. Ó, Oliviero, V., Orlando, A., Oukacha, E., Paesani, D., González, J. Palacios, Papalashvili, G., Parisi, V., Gomez, E. J. Pastor, Păun, A. M., Păvălaş, G. E., Martínez, S. Peña, Perrin-Terrin, M., Perronnel, J., Pestel, V., Pestes, R., Piattelli, P., Poirè, C., Popa, V., Pradier, T., Prado, J., Pulvirenti, S., Quéméner, G., Quiroz-Rangel, C. A., Rahaman, U., Randazzo, N., Randriatoamanana, R., Razzaque, S., Rea, I. C., Real, D., Riccobene, G., Robinson, J., Romanov, A., Šaina, A., Greus, F. Salesa, Samtleben, D. F. E., Losa, A. Sánchez, Sanfilippo, S., Sanguineti, M., Santonastaso, C., Santonocito, D., Sapienza, P., Schnabel, J., Schumann, J., Schutte, H. M., Seneca, J., Sennan, N., Setter, B., Sgura, I., Shanidze, R., Sharma, A., Shitov, Y., Šimkovic, F., Simonelli, A., Sinopoulou, A., Smirnov, M. V., Spisso, B., Spurio, M., Stavropoulos, D., Štekl, I., Taiuti, M., Tayalati, Y., Thiersen, H., Melo, I. Tosta e, Tragia, E., Trocmé, B., Tsourapis, V., Tzamariudaki, E., Vacheret, A., Melchor, A. Valer, Valsecchi, V., Van Elewyck, V., Vannoye, G., Vasileiadis, G., de Sola, F. Vazquez, Verilhac, C., Veutro, A., Viola, S., Vivolo, D., Wilms, J., de Wolf, E., Yepes-Ramirez, H., Zarpapis, G., Zavatarelli, S., Zegarelli, A., Zito, D., Zornoza, J. D., Zúñiga, J., and Zywucka, N.

Subjects
Astrophysics - High Energy Astrophysical Phenomena, General Relativity and Quantum Cosmology
Abstract

The KM3NeT neutrino telescope is currently being deployed at two different sites in the Mediterranean Sea. First searches for astrophysical neutrinos have been performed using data taken with the partial detector configuration already in operation. The paper presents the results of two independent searches for neutrinos from compact binary mergers detected during the third observing run of the LIGO and Virgo gravitational wave interferometers. The first search looks for a global increase in the detector counting rates that could be associated with inverse beta decay events generated by MeV-scale electron anti-neutrinos. The second one focuses on upgoing track-like events mainly induced by muon (anti-)neutrinos in the GeV--TeV energy range. Both searches yield no significant excess for the sources in the gravitational wave catalogs. For each source, upper limits on the neutrino flux and on the total energy emitted in neutrinos in the respective energy ranges have been set. Stacking analyses of binary black hole mergers and neutron star-black hole mergers have also been performed to constrain the characteristic neutrino emission from these categories., Comment: 19 pages, 11 figures

Published
2023
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8. Measurement of neutrino oscillation parameters with the first six detection units of KM3NeT/ORCA

Author

Aiello, S., Albert, A., Alhebsi, A. R., Alshamsi, M., Alves Garre, S., Ambrosone, A., Ameli, F., Andre, M., Aphecetche, L., Ardid, M., Ardid, S., Atmani, H., Aublin, J., Badaracco, F., Bailly-Salins, L., Bardačová, Z., Baret, B., Bariego-Quintana, A., Becherini, Y., Bendahman, M., Benfenati, F., Benhassi, M., Bennani, M., Benoit, D. M., Berbee, E., Bertin, V., Biagi, S., Boettcher, M., Bonanno, D., Bouasla, A. B., Boumaaza, J., Bouta, M., Bouwhuis, M., Bozza, C., Bozza, R. M., Brânzaş, H., Bretaudeau, F., Breuhaus, M., Bruijn, R., Brunner, J., Bruno, R., Buis, E., Buompane, R., Busto, J., Caiffi, B., Calvo, D., Capone, A., Carenini, F., Carretero, V., Cartraud, T., Castaldi, P., Cecchini, V., Celli, S., Cerisy, L., Chabab, M., Chen, A., Cherubini, S., Chiarusi, T., Circella, M., Cocimano, R., Coelho, J. A. B., Coleiro, A., Condorelli, A., Coniglione, R., Coyle, P., Creusot, A., Cuttone, G., Dallier, R., De Benedittis, A., De Martino, B., De Wasseige, G., Decoene, V., Del Rosso, I., Di Mauro, L. S., Di Palma, I., Díaz, A. F., Diego-Tortosa, D., Distefano, C., Domi, A., Donzaud, C., Dornic, D., Drakopoulou, E., Drouhin, D., Ducoin, J.-G., Dvornický, R., Eberl, T., Eckerová, E., Eddymaoui, A., van Eeden, T., Eff, M., van Eijk, D., El Bojaddaini, I., El Hedri, S., Ellajosyula, V., Enzenhöfer, A., Ferrara, G., Filipović, M. D., Filippini, F., Franciotti, D., Fusco, L. A., Gagliardini, S., Gal, T., García Méndez, J., Garcia Soto, A., Gatius Oliver, C., Geißelbrecht, N., Genton, E., Ghaddari, H., Gialanella, L., Gibson, B. K., Giorgio, E., Goos, I., Goswami, P., Gozzini, S. R., Gracia, R., Guidi, C., Guillon, B., Gutiérrez, M., Haack, C., van Haren, H., Heijboer, A., Hennig, L., Hernández-Rey, J. J., Idrissi Ibnsalih, W., Illuminati, G., Joly, D., de Jong, M., de Jong, P., Jung, B. J., Kistauri, G., Kopper, C., Kouchner, A., Kovalev, Y. Y., Kueviakoe, V., Kulikovskiy, V., Kvatadze, R., Labalme, M., Lahmann, R., Lamoureux, M., Larosa, G., Lastoria, C., Lazo, A., Le Stum, S., Lehaut, G., Lemaître, V., Leonora, E., Lessing, N., Levi, G., Lindsey Clark, M., Longhitano, F., Magnani, F., Majumdar, J., Malerba, L., Mamedov, F., Mańczak, J., Manfreda, A., Marconi, M., Margiotta, A., Marinelli, A., Markou, C., Martin, L., Mastrodicasa, M., Mastroianni, S., Mauro, J., Miele, G., Migliozzi, P., Migneco, E., Mitsou, M. L., Mollo, C. M., Morales-Gallegos, L., Moussa, A., Mozun Mateo, I., Muller, R., Musone, M. R., Musumeci, M., Navas, S., Nayerhoda, A., Nicolau, C. A., Nkosi, B., Fearraigh, B. Ó, Oliviero, V., Orlando, A., Oukacha, E., Paesani, D., Palacios González, J., Papalashvili, G., Parisi, V., Pastor Gomez, E. J., Păun, A. M., Păvălaş, G. E., Peña Martínez, S., Perrin-Terrin, M., Pestel, V., Pestes, R., Piattelli, P., Plavin, A., Poirè, C., Popa, V., Pradier, T., Prado, J., Pulvirenti, S., Quiroz-Rangel, C. A., Randazzo, N., Razzaque, S., Rea, I. C., Real, D., Riccobene, G., Robinson, J., Romanov, A., Ros, E., Šaina, A., Salesa Greus, F., Samtleben, D. F. E., Sánchez Losa, A., Sanfilippo, S., Sanguineti, M., Santonocito, D., Sapienza, P., Schnabel, J., Schumann, J., Schutte, H. M., Seneca, J., Sgura, I., Shanidze, R., Sharma, A., Shitov, Y., Šimkovic, F., Simonelli, A., Sinopoulou, A., Spisso, B., Spurio, M., Stavropoulos, D., Štekl, I., Stellacci, S. M., Taiuti, M., Tayalati, Y., Thiersen, H., Thoudam, S., Tosta e Melo, I., Trocmé, B., Tsourapis, V., Tudorache, A., Tzamariudaki, E., Ukleja, A., Vacheret, A., Valsecchi, V., Van Elewyck, V., Vannoye, G., Vasileiadis, G., Vazquez de Sola, F., Veutro, A., Viola, S., Vivolo, D., van Vliet, A., de Wolf, E., Lhenry-Yvon, I., Zavatarelli, S., Zegarelli, A., Zito, D., Zornoza, J. D., Zúñiga, J., and Zywucka, N.

Published
2024
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9. Comparative Genomic Analysis of a Clinical Isolate of Klebsiella quasipneumoniae subsp. similipneumoniae, a KPC-2 and OKP-B-6 Beta-Lactamases Producer Harboring Two Drug-Resistance Plasmids from Southeast Brazil

Author

Marisa F. Nicolás, Pablo Ivan Pereira Ramos, Fabíola Marques de Carvalho, Dhian R. A. Camargo, Carlene de Fátima Morais Alves, Guilherme Loss de Morais, Luiz G. P. Almeida, Rangel C. Souza, Luciane P. Ciapina, Ana C. P. Vicente, Roney S. Coimbra, and Ana T. Ribeiro de Vasconcelos

Subjects
Klebsiella quasipneumoniae subsp similipneumoniae, KPC-2, OKP-B-6, silver resistance, nosocomial infection, complete genome sequence, Microbiology, QR1-502
Abstract

The aim of this study was to unravel the genetic determinants responsible for multidrug (including carbapenems) resistance and virulence in a clinical isolate of Klebsiella quasipneumoniae subsp. similipneumoniae by whole-genome sequencing and comparative analyses. Eighty-three clinical isolates initially identified as carbapenem-resistant K. pneumoniae were collected from nosocomial infections in southeast Brazil. After RAPD screening, the KPC-142 isolate, showing the most divergent DNA pattern, was selected for complete genome sequencing in an Illumina HiSeq 2500 instrument. Reads were assembled into scaffolds, gaps between scaffolds were resolved by in silico gap filling and extensive bioinformatics analyses were performed, using multiple comparative analysis tools and databases. Genome sequencing allowed to correct the classification of the KPC-142 isolate as K. quasipneumoniae subsp. similipneumoniae. To the best of our knowledge this is the first complete genome reported to date of a clinical isolate of this subspecies harboring both class A beta-lactamases KPC-2 and OKP-B-6 from South America. KPC-142 has one 5.2 Mbp chromosome (57.8% G+C) and two plasmids: 190 Kbp pKQPS142a (50.7% G+C) and 11 Kbp pKQPS142b (57.3% G+C). The 3 Kbp region in pKQPS142b containing the blaKPC−2 was found highly similar to that of pKp13d of K. pneumoniae Kp13 isolated in Southern Brazil in 2009, suggesting the horizontal transfer of this resistance gene between different species of Klebsiella. KPC-142 additionally harbors an integrative conjugative element ICEPm1 that could be involved in the mobilization of pKQPS142b and determinants of resistance to other classes of antimicrobials, including aminoglycoside and silver. We present the completely assembled genome sequence of a clinical isolate of K. quasipneumoniae subsp. similipneumoniae, a KPC-2 and OKP-B-6 beta-lactamases producer and discuss the most relevant genomic features of this important resistant pathogen in comparison to several strains belonging to K. quasipneumoniae subsp. similipneumoniae (phylogroup II-B), K. quasipneumoniae subsp. quasipneumoniae (phylogroup II-A), K. pneumoniae (phylogroup I), and K. variicola (phylogroup III). Our study contributes to the description of the characteristics of a novel K. quasipneumoniae subsp. similipneumoniae strain circulating in South America that currently represent a serious potential risk for nosocomial settings.

Published
2018
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10. Atmospheric muons measured with the KM3NeT detectors in comparison with updated numeric predictions

Author

Aiello, S., Albert, A., Alshamsi, M., Alves Garre, S., Ambrosone, A., Ameli, F., Andre, M., Androutsou, E., Anguita, M., Aphecetche, L., Ardid, M., Ardid, S., Arsenic, A., Atmani, H., Aublin, J., Badaracco, F., Bailly-Salins, L., Bardačová, Z., Baret, B., Bariego-Quintana, A., Pree, S. Basegmez du, Becherini, Y., Bendahman, M., Benfenati, F., Benhassi, M., Benoit, D. M., Berbee, E., Bertin, V., Biagi, S., Boettcher, M., Bonanno, D., Boumaaza, J., Bouta, M., Bouwhuis, M., Bozza, C., Bozza, R. M., Brânzaş, H., Bretaudeau, F., Breuhaus, M., Bruijn, R., Brunner, J., Bruno, R., Buis, E., Buompane, R., Busto, J., Caiffi, B., Calvo, D., Campion, S., Capone, A., Carenini, F., Carretero, V., Cartraud, T., Castaldi, P., Cecchini, V., Celli, S., Cerisy, L., Chabab, M., Chadolias, M., Chen, A., Cherubini, S., Chiarusi, T., Circella, M., Cocimano, R., Coelho, J. A. B., Coleiro, A., Condorelli, A., Coniglione, R., Coyle, P., Creusot, A., Cuttone, G., Dallier, R., Darras, Y., De Benedittis, A., De Martino, B., Decoene, V., Del Burgo, R., Del Rosso, I., Mauro, L. S. Di, Di Palma, I., Díaz, A. F., Diaz, C., Diego-Tortosa, D., Distefano, C., Domi, A., Donzaud, C., Dornic, D., Dörr, M., Drakopoulou, E., Drouhin, D., Ducoin, J.-G., Dvornický, R., Eberl, T., Eckerová, E., Eddymaoui, A., van Eeden, T., Eff, M., van Eijk, D., El Bojaddaini, I., El Hedri, S., Enzenhöfer, A., Ferrara, G., Filipović, M. D., Filippini, F., Franciotti, D., Fusco, L. A., Gagliardini, S., Gal, T., Méndez, J. García, Soto, A. Garcia, Oliver, C. Gatius, Geißelbrecht, N., Ghaddari, H., Gialanella, L., Gibson, B. K., Giorgio, E., Goos, I., Goswami, P., Gozzini, S. R., Gracia, R., Graf, K., Guidi, C., Guillon, B., Gutiérrez, M., Haack, C., van Haren, H., Heijboer, A., Hekalo, A., Hennig, L., Hernández-Rey, J. J., Ibnsalih, W. Idrissi, Illuminati, G., Joly, D., de Jong, M., de Jong, P., Jung, B. J., Kalaczyński, P., Kalekin, O., Katz, U. F., Khatun, A., Kistauri, G., Kopper, C., Kouchner, A., Kueviakoe, V., Kulikovskiy, V., Kvatadze, R., Labalme, M., Lahmann, R., Larosa, G., Lastoria, C., Lazo, A., Le Stum, S., Lehaut, G., Leonora, E., Lessing, N., Levi, G., Longhitano, F., Magnani, F., Majumdar, J., Malerba, L., Mamedov, F., Mańczak, J., Manfreda, A., Marconi, M., Margiotta, A., Marinelli, A., Markou, C., Martin, L., Marzaioli, F., Mastrodicasa, M., Mastroianni, S., Miccichè, S., Miele, G., Migliozzi, P., Migneco, E., Mitsou, M. L., Mollo, C. M., Morales-Gallegos, L., Moretti, G., Moussa, A., Mateo, I. Mozun, Muller, R., Musone, M. R., Musumeci, M., Navas, S., Nayerhoda, A., Nicolau, C. A., Nkosi, B., Fearraigh, B. Ó., Oliviero, V., Orlando, A., Oukacha, E., Paesani, D., González, J. Palacios, Papalashvili, G., Parisi, V., Pastor Gomez, E. J., Păun, A. M., Păvălaş, G. E., Pelegris, I., Peña Martínez, S., Perrin-Terrin, M., Perronnel, J., Pestel, V., Pestes, R., Piattelli, P., Poirè, C., Popa, V., Pradier, T., Prado, J., Pulvirenti, S., Quiroz-Rangel, C. A., Rahaman, U., Randazzo, N., Razzaque, S., Rea, I. C., Real, D., Riccobene, G., Robinson, J., Romanov, A., Šaina, A., Greus, F. Salesa, Samtleben, D. F. E., Losa, A. Sánchez, Sanfilippo, S., Sanguineti, M., Santonastaso, C., Santonocito, D., Sapienza, P., Schnabel, J., Schumann, J., Schutte, H. M., Seneca, J., Sennan, N., Setter, B., Sgura, I., Shanidze, R., Sharma, A., Shitov, Y., Šimkovic, F., Simonelli, A., Sinopoulou, A., Smirnov, M. V., Spisso, B., Spurio, M., Stavropoulos, D., Štekl, I., Taiuti, M., Tayalati, Y., Thiersen, H., Melo, I. Tosta e, Tragia, E., Trocmé, B., Tsourapis, V., Tudorache, A., Tzamariudaki, E., Vacheret, A., Melchor, A. Valer, Valsecchi, V., Elewyck, V. Van, Vannoye, G., Vasileiadis, G., de Sola, F. Vazquez, Veutro, A., Viola, S., Vivolo, D., Wilms, J., de Wolf, E., Yepes-Ramirez, H., Yvon, I., Zarpapis, G., Zavatarelli, S., Zegarelli, A., Zito, D., Zornoza, J. D., Zúñiga, J., and Zywucka, N.

Published
2024
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11. Xylella fastidiosa comparative genomic database is an information resource to explore the annotation, genomic features, and biology of different strains

Author

Alessandro M. Varani, Claudia B. Monteiro-Vitorello, Luiz G.P. de Almeida, Rangel C. Souza, Oberdan L. Cunha, Wanessa C. Lima, Edwin Civerolo, Marie-Anne Van Sluys, and Ana T.R. Vasconcelos

Subjects
genome annotation and assembly, comparative genomics, mobile genetic elements, Genetics, QH426-470
Abstract

The Xylella fastidiosa comparative genomic database is a scientific resource with the aim to provide a user-friendly interface for accessing high-quality manually curated genomic annotation and comparative sequence analysis, as well as for identifying and mapping prophage-like elements, a marked feature of Xylella genomes. Here we describe a database and tools for exploring the biology of this important plant pathogen. The hallmarks of this database are the high quality genomic annotation, the functional and comparative genomic analysis and the identification and mapping of prophage-like elements. It is available from web site http://www.xylella.lncc.br.

Published
2012

13. AEGIS-X: Deep Chandra imaging of the Central Groth Strip

Author

Nandra, K., Laird, E. S., Aird, J. A., Salvato, M., Georgakakis, A., Barro, G., Gonzalez, P. G. Perez, Barmby, P., Chary, R. -R., Coil, A., Cooper, M. C., Davis, M., Dickinson, M., Faber, S. M., Fazio, G. G., Guhathakurta, P., Gwyn, S., Hsu, L. -T., Huang, J. -S., Ivison, R. J., Koo, D. C., Newman, J. A., Rangel, C., Yamada, T., and Willmer, C.

Subjects
Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Astrophysics of Galaxies
Abstract

We present the results of deep \chandra\ imaging of the central region of the Extended Groth Strip, the AEGIS-X Deep (AEGIS-XD) survey. When combined with previous \chandra\ observations of a wider area of the strip, AEGIS-X Wide (AEGIS-XW; Laird et~al. 2009), these provide data to a nominal exposure depth of 800ks in the three central ACIS-I fields, a region of approximately $0.29$~deg$^{2}$. This is currently the third deepest X-ray survey in existence, a factor $\sim 2-3$ shallower than the Chandra Deep Fields (CDFs) but over an area $\sim 3$ times greater than each CDF. We present a catalogue of 937 point sources detected in the deep \chandra\ observations. We present identifications of our X-ray sources from deep ground-based, Spitzer, GALEX and HST imaging. Using a likelihood ratio analysis, we associate multi band counterparts for 929/937 of our X-ray sources, with an estimated 95~\% reliability, making the identification completeness approximately 94~\% in a statistical sense. Reliable spectroscopic redshifts for 353 of our X-ray sources are provided predominantly from Keck (DEEP2/3) and MMT Hectospec, so the current spectroscopic completeness is $\sim 38$~per cent. For the remainder of the X-ray sources, we compute photometric redshifts based on multi-band photometry in up to 35 bands from the UV to mid-IR. Particular attention is given to the fact that the vast majority the X-ray sources are AGN and require hybrid templates. Our photometric redshifts have mean accuracy of $\sigma=0.04$ and an outlier fraction of approximately 5\%, reaching $\sigma=0.03$ with less than 4\% outliers in the area covered by CANDELS . The X-ray, multi-wavelength photometry and redshift catalogues are made publicly available., Comment: 35 pages, 15 figures, accepted for publication in ApJS

Published
2015
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14. Complete genome sequence of community-associated methicillin-resistant Staphylococcus aureus (strain USA400-0051), a prototype of the USA400 clone

Author

Marina Farrel Côrtes, Maiana OC Costa, Nicholas CB Lima, Rangel C Souza, Luiz GP Almeida, Luciane Prioli Ciapina Guedes, Ana TR Vasconcelos, Marisa F Nicolás, and Agnes MS Figueiredo

Subjects
methicillin-resistant Staphylococcus aureus, whole genome, USA400, ST1-SCCmecIV, Microbiology, QR1-502, Infectious and parasitic diseases, RC109-216
Abstract

Staphylococcus aureus subsp. aureus, commonly referred as S. aureus, is an important bacterial pathogen frequently involved in hospital- and community-acquired infections in humans, ranging from skin infections to more severe diseases such as pneumonia, bacteraemia, endocarditis, osteomyelitis, and disseminated infections. Here, we report the complete closed genome sequence of a community-acquired methicillin-resistant S. aureus strain, USA400-0051, which is a prototype of the USA400 clone.

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16. X-ray spectral modelling of the AGN obscuring region in the CDFS: Bayesian model selection and catalogue

Author

Buchner, J., Georgakakis, A., Nandra, K., Hsu, L., Rangel, C., Brightman, M., Merloni, A., Salvato, M., Donley, J., and Kocevski, D.

Subjects
Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

AGN are known to have complex X-ray spectra that depend on both the properties of the accreting SMBH (e.g. mass, accretion rate) and the distribution of obscuring material in its vicinity ("torus"). Often however, simple and even unphysical models are adopted to represent the X-ray spectra of AGN. In the case of blank field surveys in particular, this should have an impact on e.g. the determination of the AGN luminosity function, the inferred accretion history of the Universe and also on our understanding of the relation between AGN and their host galaxies. We develop a Bayesian framework for model comparison and parameter estimation of X-ray spectra. We take into account uncertainties associated with X-ray data and photometric redshifts. We also demonstrate how Bayesian model comparison can be used to select among ten different physically motivated X-ray spectral models the one that provides a better representation of the observations. Despite the use of low-count spectra, our methodology is able to draw strong inferences on the geometry of the torus. For a sample of 350 AGN in the 4 Ms Chandra Deep Field South field, our analysis identifies four components needed to represent the diversity of the observed X-ray spectra: (abridged). Simpler models are ruled out with decisive evidence in favour of a geometrically extended structure with significant Compton scattering. Regarding the geometry of the obscurer, there is strong evidence against both a completely closed or entirely open toroidal geometry, in favour of an intermediate case. The additional Compton reflection required by data over that predicted by toroidal geometry models, may be a sign of a density gradient in the torus or reflection off the accretion disk. Finally, we release a catalogue with estimated parameters such as the accretion luminosity in the 2-10 keV band and the column density, $N_{H}$, of the obscurer., Comment: 28 pages, 18 figures, catalogue available from https://www.mpe.mpg.de/~jbuchner/agn_torus/analysis/cdfs4Ms_cat/, software available from https://github.com/JohannesBuchner/BXA

Published
2014
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17. AEGIS-X: DEEP CHANDRA IMAGING OF THE CENTRAL GROTH STRIP

Author

Nandra, K, Laird, ES, Aird, JA, Salvato, M, Georgakakis, A, Barro, G, Perez-Gonzalez, PG, Barmby, P, Chary, R-R, Coil, A, Cooper, MC, Davis, M, Dickinson, M, Faber, SM, Fazio, GG, Guhathakurta, P, Gwyn, S, Hsu, L-T, Huang, J-S, Ivison, RJ, Koo, DC, Newman, JA, Rangel, C, Yamada, T, and Willmer, C

Subjects
galaxies: active, galaxies: nuclei, surveys, astro-ph.HE, astro-ph.GA, Astronomical and Space Sciences, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Physical Chemistry (incl. Structural), Astronomy & Astrophysics
Abstract

We present the results of deep Chandra imaging of the central region of the Extended Groth Strip, the AEGIS-X Deep (AEGIS-XD) survey. When combined with previous Chandra observations of a wider area of the strip, AEGIS-X Wide (AEGIS-XW), these provide data to a nominal exposure depth of 800 ks in the three central ACIS-I fields, a region of approximately 0.29 deg2. This is currently the third deepest X-ray survey in existence; a factor shallower than the Chandra Deep Fields (CDFs), but over an area ∼3 times greater than each CDF. We present a catalog of 937 point sources detected in the deep Chandra observations, along with identifications of our X-ray sources from deep ground-based, Spitzer, GALEX, and Hubble Space Telescope imaging. Using a likelihood ratio analysis, we associate multiband counterparts for 929/937 of our X-ray sources, with an estimated 95% reliability, making the identification completeness approximately 94% in a statistical sense. Reliable spectroscopic redshifts for 353 of our X-ray sources are available predominantly from Keck (DEEP2/3) and MMT Hectospec, so the current spectroscopic completeness is ∼38%. For the remainder of the X-ray sources, we compute photometric redshifts based on multiband photometry in up to 35 bands from the UV to mid-IR. Particular attention is given to the fact that the vast majority the X-ray sources are active galactic nuclei and require hybrid templates. Our photometric redshifts have mean accuracy of and an outlier fraction of approximately 5%, reaching with less than 4% outliers in the area covered by CANDELS . The X-ray, multiwavelength photometry, and redshift catalogs are made publicly available.

Published
2015

18. Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis

Author

Teixeira, Marcus M, de Almeida, Luiz GP, Kubitschek-Barreira, Paula, Alves, Fernanda L, Kioshima, Érika S, Abadio, Ana KR, Fernandes, Larissa, Derengowski, Lorena S, Ferreira, Karen S, Souza, Rangel C, Ruiz, Jeronimo C, de Andrade, Nathalia C, Paes, Hugo C, Nicola, André M, Albuquerque, Patrícia, Gerber, Alexandra L, Martins, Vicente P, Peconick, Luisa DF, Neto, Alan Viggiano, Chaucanez, Claudia B, Silva, Patrícia A, Cunha, Oberdan L, de Oliveira, Fabiana FM, dos Santos, Tayná C, Barros, Amanda LN, Soares, Marco A, de Oliveira, Luciana M, Marini, Marjorie M, Villalobos-Duno, Héctor, Cunha, Marcel ML, de Hoog, Sybren, da Silveira, José F, Henrissat, Bernard, Niño-Vega, Gustavo A, Cisalpino, Patrícia S, Mora-Montes, Héctor M, Almeida, Sandro R, Stajich, Jason E, Lopes-Bezerra, Leila M, Vasconcelos, Ana TR, and Felipe, Maria SS

Subjects
Human Genome, Biotechnology, Infectious Diseases, Genetics, Emerging Infectious Diseases, 2.2 Factors relating to the physical environment, 2.1 Biological and endogenous factors, Aetiology, Infection, Adaptation, Biological, Animals, Cat Diseases, Cats, Evolution, Molecular, Fungal Proteins, Genetic Speciation, Genome, Mitochondrial, Humans, Phylogeny, Sporothrix, Sporotrichosis, Virulence Factors, Sporothrix schenckii, Sporothrix brasiliensis, Comparative genomics, Fungal evolution, Biological Sciences, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics
Abstract

BackgroundThe fungal genus Sporothrix includes at least four human pathogenic species. One of these species, S. brasiliensis, is the causal agent of a major ongoing zoonotic outbreak of sporotrichosis in Brazil. Elsewhere, sapronoses are caused by S. schenckii and S. globosa. The major aims on this comparative genomic study are: 1) to explore the presence of virulence factors in S. schenckii and S. brasiliensis; 2) to compare S. brasiliensis, which is cat-transmitted and infects both humans and cats with S. schenckii, mainly a human pathogen; 3) to compare these two species to other human pathogens (Onygenales) with similar thermo-dimorphic behavior and to other plant-associated Sordariomycetes.ResultsThe genomes of S. schenckii and S. brasiliensis were pyrosequenced to 17x and 20x coverage comprising a total of 32.3 Mb and 33.2 Mb, respectively. Pair-wise genome alignments revealed that the two species are highly syntenic showing 97.5% average sequence identity. Phylogenomic analysis reveals that both species diverged about 3.8-4.9 MYA suggesting a recent event of speciation. Transposable elements comprise respectively 0.34% and 0.62% of the S. schenckii and S. brasiliensis genomes and expansions of Gypsy-like elements was observed reflecting the accumulation of repetitive elements in the S. brasiliensis genome. Mitochondrial genomic comparisons showed the presence of group-I intron encoding homing endonucleases (HE's) exclusively in S. brasiliensis. Analysis of protein family expansions and contractions in the Sporothrix lineage revealed expansion of LysM domain-containing proteins, small GTPases, PKS type1 and leucin-rich proteins. In contrast, a lack of polysaccharide lyase genes that are associated with decay of plants was observed when compared to other Sordariomycetes and dimorphic fungal pathogens, suggesting evolutionary adaptations from a plant pathogenic or saprobic to an animal pathogenic life style.ConclusionsComparative genomic data suggest a unique ecological shift in the Sporothrix lineage from plant-association to mammalian parasitism, which contributes to the understanding of how environmental interactions may shape fungal virulence. . Moreover, the striking differences found in comparison with other dimorphic fungi revealed that dimorphism in these close relatives of plant-associated Sordariomycetes is a case of convergent evolution, stressing the importance of this morphogenetic change in fungal pathogenesis.

Published
2014

19. X-ray selected AGN Hosts are Similar to Inactive Galaxies out to z=3: Results from CANDELS/CDF-S

Author

Rosario, D. J., Mozena, M., Wuyts, S., Nandra, K., Koekemoer, A., McGrath, E., Hathi, N., Dekel, A., Donley, J., Dunlop, J. S., Faber, S. M., Ferguson, H., Giavalisco, M., Grogin, N., Guo, Y., Newman, J., Kocevski, D. D., Koo, D. C., Laird, E., Rangel, C., and Somerville, R.

Subjects
Astrophysics - Cosmology and Extragalactic Astrophysics
Abstract

We use multi-band spatially resolved photometry from the Cosmic Assembly Near-IR Deep Legacy Survey (CANDELS) in the 4 MSec Chandra Deep Field-South (CDF-S) to explore the nuclear and extended colors, color gradients and stellar populations of X-ray selected AGN host galaxies out to z=3. Based on a study of their central light, we develop X-ray based criteria to exclude objects with strong AGN contamination. We use stellar masses from the FIREWORKS database to understand and account for stellar mass selection effects, and carefully study, for the first time, the resolved host galaxy properties of AGNs at z~2 in their rest-frame optical light without substantial nuclear contamination. AGN hosts span a sizable range of stellar masses, colors and color gradients at these redshifts. Their colors, color gradients and stellar population properties are very similar to inactive galaxies of the same stellar mass. At z~1, we find a slightly narrower range in host colors compared to inactive galaxies, as well as hints of more recent star-formation. These differences are weaker or non-existent among AGN hosts at z~2. We discuss the importance of AGN driven feedback in the quenching of galaxies at z>~1 and speculate on possible evolution in the relationship between black hole accretion and the host galaxy towards high redshifts., Comment: 20 pages, 14 figures

Published
2011
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20. Preliminary study of the application of thermal mortar in 3D printed concrete walls

Author

Pessoa, S., Jesus, M., Rangel, C., Guimarães, A.S., Lucas, S.S., Simões, N., Pessoa, S., Jesus, M., Rangel, C., Guimarães, A.S., Lucas, S.S., and Simões, N.

Abstract

3D printing (3DP), as an emerging technology in the construction industry, has the potential to solve the sector's labour shortages and low efficiency, as well as helping to reduce its negative environmental impact. On the investigative path towards new construction solutions, the thermal performance of buildings must not be compromised. In additively manufactured buildings to date, walls have been printed with cavities that are subsequently manually filled or projected with conventional thermal insulation materials, such as polyurethane and vermiculite. To bridge the gap between conventional building construction and 3DP, it is important to present feasible and effective thermal solutions that can be applied using an automatic mode. This paper explores the viability of applying a commercial thermal mortar as an insulation in 3D printed concrete walls. Therefore, a preliminary experimental campaign was carried out to assess the behaviour of the thermal mortar during and after its application. It was found that concrete walls constrain the drying process of the thermal mortar, generating stresses that lead to the occurrence of cracks. To avoid their formation, some strategies were tested, namely by adding superplasticizer to the mixture, opening joints, drilling holes or opting for an incomplete filling of the cavities.

Published
2023

21. The Power Board of the KM3NeT Digital Optical Module: design, upgrade, and production

Author

Aiello, S., Albert, A., Garre, S. Alves, Aly, Z., Ambrosone, A., Ameli, F., Andre, M., Androutsou, E., Anguita, M., Aphecetche, L., Ardid, M., Ardid, S., Atmani, H., Aublin, J., Badaracco, F., Bailly-Salins, L., Bardacova, Z., Baret, B., Quintana, A. Bariego, Pree, S. Basegmez du, Becherini, Y., Bendahman, M., Benfenati, F., Benhassi, M., Benoit, D. M., Berbee, E., Bertin, V., van Beveren, V., Biagi, S., Boettcher, M., Bonanno, D., Boumaaza, J., Bouta, M., Bouwhuis, M., Bozza, C., Bozza, R. M., Branzas, H., Bretaudeau, F., Bruijn, R., Brunner, J., Bruno, R., Buis, E., Buompane, R., Busto, J., Caiffi, B., Calvo, D., Campion, S., Capone, A., Careniniu, F., Carretero, V., Cartraud, T., Castaldi, P., Cecchini, V., Celli, S., Cerisy, L., Chabab, M., Chadolias, M., Champion, C., Chena, A., Cherubini, S., Chiarusi, T., Circella, M., Cocimano, R., Coelho, J. A. B., Coleiro, A., Colonges, S., Coniglione, R., Coyle, P., Creusot, A., Cuttone, G., Dallier, R., Darras, Y., De Benedittis, A., De Martino, B., Decoene, V., Del Burgo, R., Del Rosso, I., Di Cerbo, U. M., Di Mauro, L. S., Di Palma, I., Díaz, A. F., Diaz, C., Diego-Tortosa, D., Distefano, C., Domia, A., Donzaud, C., Dornic, D., Dorra, M., Drakopoulou, E., Drouhin, D., Dvornicky, R., Eberla, T., Eckerova, E., Eddymaoui, A., van Eeden, T., Eff, M., van Eijk, D., Bojaddaini, I. El, Hedri, S. El, Enzenhofer, A., Ferrara, G., Filipovica, M. D., Filippini, F., Franciotti, D., Fusco, L. A., Gabellaa, O., Gabriela, J., Gagliardini, S., Gal, T., Mendez, J. Garcıa, Soto, A. Garcia, Oliver, C. Gatius, Geißelbrecht, N., Ghaddari, H., Gialanella, L., Gibson, B. K., Giorgio, E., Goos, I., Goswami, P., Goupilliere, D., Gozzini, S. R., Gracia, R., Grafa, K., Guidi, C., Guillon, B., Gutierrez, M., van Haren, H., Heijboer, A., Hekalo, A., Henniga, L., Hernandez-Rey, J. J., Ibnsalih, W. Idrissi, Illuminati, G., Jansweijer, P., de Jonga, M., de Jonga, P., Jung, B. J., Kalaczynski, P., Kalekin, O., Katz, U. F., Khatun, A., Kistauri, G., Kopper, C., Kouchner, A., Kueviakoe, V., Kulikovskiy, V., Kvatadze, R., Labalme, M., Lahmann, R., Larosa, G., Lastoria, C., Lazo, A., Stum, S. Le, Lehaut, G., Leonora, E., Lessing, N., Levi, G., Clark, M. Lindsey, Litrico, P., Longhitano, F., Majumdar, J., Malerba, L., Mamedov, F., Manczak, J., Manfredae, A., Marconi, M., Margiotta, A., Marinelli, A., Markou, C., Martin, L., Martınez-Mora, J. A., Marzaioli, F., Mastrodicasa, M., Mastroianni, S., Miccich, S., Miele, G., Migliozzi, P., Migneco, E., Minutoli, S., Mitsou, M. L., Mollo, C. M., Morales-Gallegos, L., Morga, M., Moussa, A., Mateo, I. Mozun, Muller, R., Musico, P., Musone, M. R., Musumeci, M., Navas, S., Nayerhoda, A., Nicolau, C. A., Nkosi, B., Fearraigh, B. O., Oliviero, V., Orlando, A., Oukacha, E., Paesani, D., Gonzalez, J. Palacios, Papalashvili, G., Parisi, V., Gomez, E. J. Pastor, Pauna, A. M., Pavalas, G. E., Pellegrini, G., Martinez, S. Peñaa, Perrin-Terrin, M., Perronnel, J., Pestel, V., Pestes, R., Piattelli, P., Poirre, C., Popa, V., Pradier, T., Prado, J., Pulvirenti, S., Quemener, G., Quiroz-Rangel, C. A., Rahaman, U., Randazzo, N., Randriatoamana, R., Razzaque, S., Rea, I. C., Real, D., Riccobene, G., Robinson, J., Romanov, A., Saina, A., Greus, F. Salesa, Samtleben, D. F. E., Losa, A. Sanchez, Sanfilippo, S., Sanguineti, M., Santonastaso, C., Santonocito, D., Sapienza, P., Schmelling, J., Schnabel, J., Schumann, J., Schutt, H. M., Seneca, J., Sennan, N., Setter, B., Sgura, I., Shanidze, R., Sharma, A., Shitov, Y., Simkovic, F., Simonelli, A., Sinopoulou, A., Smirnov, M. V., Spisso, B., Spurio, M., Stavropoulos, D., Stekl, I., Taiuti, M., Tayalati, Y., Thiersen, H., Melo, I. Tosta e, Tragi, E., Trocme, B., Tsourapis, V., Tzamariudaki, E., Vacheret, A., Melchor, A. Valer, Valsecchi, V., Van Elewyck, V., Vannoye, G., Vasileiadis, G., de Sola, F. Vazquez, Verilhac, C., Veutro, A., Viola, S., Vivolo, D., Wilms, J., de Wolf, E., Ramirez, H. Yepes, Zarpapis, G., Zavatarelli, S., Zegarelli, A., Zito, D., Zornoza, J. D., Zuniga, J., Zywuck, N., Aiello, S., Albert, A., Garre, S. Alves, Aly, Z., Ambrosone, A., Ameli, F., Andre, M., Androutsou, E., Anguita, M., Aphecetche, L., Ardid, M., Ardid, S., Atmani, H., Aublin, J., Badaracco, F., Bailly-Salins, L., Bardacova, Z., Baret, B., Quintana, A. Bariego, Pree, S. Basegmez du, Becherini, Y., Bendahman, M., Benfenati, F., Benhassi, M., Benoit, D. M., Berbee, E., Bertin, V., van Beveren, V., Biagi, S., Boettcher, M., Bonanno, D., Boumaaza, J., Bouta, M., Bouwhuis, M., Bozza, C., Bozza, R. M., Branzas, H., Bretaudeau, F., Bruijn, R., Brunner, J., Bruno, R., Buis, E., Buompane, R., Busto, J., Caiffi, B., Calvo, D., Campion, S., Capone, A., Careniniu, F., Carretero, V., Cartraud, T., Castaldi, P., Cecchini, V., Celli, S., Cerisy, L., Chabab, M., Chadolias, M., Champion, C., Chena, A., Cherubini, S., Chiarusi, T., Circella, M., Cocimano, R., Coelho, J. A. B., Coleiro, A., Colonges, S., Coniglione, R., Coyle, P., Creusot, A., Cuttone, G., Dallier, R., Darras, Y., De Benedittis, A., De Martino, B., Decoene, V., Del Burgo, R., Del Rosso, I., Di Cerbo, U. M., Di Mauro, L. S., Di Palma, I., Díaz, A. F., Diaz, C., Diego-Tortosa, D., Distefano, C., Domia, A., Donzaud, C., Dornic, D., Dorra, M., Drakopoulou, E., Drouhin, D., Dvornicky, R., Eberla, T., Eckerova, E., Eddymaoui, A., van Eeden, T., Eff, M., van Eijk, D., Bojaddaini, I. El, Hedri, S. El, Enzenhofer, A., Ferrara, G., Filipovica, M. D., Filippini, F., Franciotti, D., Fusco, L. A., Gabellaa, O., Gabriela, J., Gagliardini, S., Gal, T., Mendez, J. Garcıa, Soto, A. Garcia, Oliver, C. Gatius, Geißelbrecht, N., Ghaddari, H., Gialanella, L., Gibson, B. K., Giorgio, E., Goos, I., Goswami, P., Goupilliere, D., Gozzini, S. R., Gracia, R., Grafa, K., Guidi, C., Guillon, B., Gutierrez, M., van Haren, H., Heijboer, A., Hekalo, A., Henniga, L., Hernandez-Rey, J. J., Ibnsalih, W. Idrissi, Illuminati, G., Jansweijer, P., de Jonga, M., de Jonga, P., Jung, B. J., Kalaczynski, P., Kalekin, O., Katz, U. F., Khatun, A., Kistauri, G., Kopper, C., Kouchner, A., Kueviakoe, V., Kulikovskiy, V., Kvatadze, R., Labalme, M., Lahmann, R., Larosa, G., Lastoria, C., Lazo, A., Stum, S. Le, Lehaut, G., Leonora, E., Lessing, N., Levi, G., Clark, M. Lindsey, Litrico, P., Longhitano, F., Majumdar, J., Malerba, L., Mamedov, F., Manczak, J., Manfredae, A., Marconi, M., Margiotta, A., Marinelli, A., Markou, C., Martin, L., Martınez-Mora, J. A., Marzaioli, F., Mastrodicasa, M., Mastroianni, S., Miccich, S., Miele, G., Migliozzi, P., Migneco, E., Minutoli, S., Mitsou, M. L., Mollo, C. M., Morales-Gallegos, L., Morga, M., Moussa, A., Mateo, I. Mozun, Muller, R., Musico, P., Musone, M. R., Musumeci, M., Navas, S., Nayerhoda, A., Nicolau, C. A., Nkosi, B., Fearraigh, B. O., Oliviero, V., Orlando, A., Oukacha, E., Paesani, D., Gonzalez, J. Palacios, Papalashvili, G., Parisi, V., Gomez, E. J. Pastor, Pauna, A. M., Pavalas, G. E., Pellegrini, G., Martinez, S. Peñaa, Perrin-Terrin, M., Perronnel, J., Pestel, V., Pestes, R., Piattelli, P., Poirre, C., Popa, V., Pradier, T., Prado, J., Pulvirenti, S., Quemener, G., Quiroz-Rangel, C. A., Rahaman, U., Randazzo, N., Randriatoamana, R., Razzaque, S., Rea, I. C., Real, D., Riccobene, G., Robinson, J., Romanov, A., Saina, A., Greus, F. Salesa, Samtleben, D. F. E., Losa, A. Sanchez, Sanfilippo, S., Sanguineti, M., Santonastaso, C., Santonocito, D., Sapienza, P., Schmelling, J., Schnabel, J., Schumann, J., Schutt, H. M., Seneca, J., Sennan, N., Setter, B., Sgura, I., Shanidze, R., Sharma, A., Shitov, Y., Simkovic, F., Simonelli, A., Sinopoulou, A., Smirnov, M. V., Spisso, B., Spurio, M., Stavropoulos, D., Stekl, I., Taiuti, M., Tayalati, Y., Thiersen, H., Melo, I. Tosta e, Tragi, E., Trocme, B., Tsourapis, V., Tzamariudaki, E., Vacheret, A., Melchor, A. Valer, Valsecchi, V., Van Elewyck, V., Vannoye, G., Vasileiadis, G., de Sola, F. Vazquez, Verilhac, C., Veutro, A., Viola, S., Vivolo, D., Wilms, J., de Wolf, E., Ramirez, H. Yepes, Zarpapis, G., Zavatarelli, S., Zegarelli, A., Zito, D., Zornoza, J. D., Zuniga, J., and Zywuck, N.

Abstract

The KM3NeT Collaboration is building an underwater neutrino observatory at the bottom of the Mediterranean Sea consisting of two neutrino telescopes, both composed of a three-dimensional array of light detectors, known as digital optical modules. Each digital optical module contains a set of 31 three inch photomultiplier tubes distributed over the surface of a 0.44 m diameter pressure-resistant glass sphere. The module includes also calibration instruments and electronics for power, readout and data acquisition. The power board was developed to supply power to all the elements of the digital optical module. The design of the power board began in 2013, and several prototypes were produced and tested. After an exhaustive validation process in various laboratories within the KM3NeT Collaboration, a mass production batch began, resulting in the construction of over 1200 power boards so far. These boards were integrated in the digital optical modules that have already been produced and deployed, 828 until October 2023. In 2017, an upgrade of the power board, to increase reliability and efficiency, was initiated. After the validation of a pre-production series, a production batch of 800 upgraded boards is currently underway. This paper describes the design, architecture, upgrade, validation, and production of the power board, including the reliability studies and tests conducted to ensure the safe operation at the bottom of the Mediterranean Sea throughout the observatory's lifespan

Published
2023

22. Multiuser Cooperative OFDMA Uplink With Nonlinear Power Amplifiers: Theoretical Characterization and Resource Allocation

Author

C. Alexandre R. Fernandes, Livia Christinie S. Teles, and Syllas Rangel C. Magalhaes

Subjects
Computer science, Orthogonal frequency-division multiple access, ComputerSystemsOrganization_COMPUTER-COMMUNICATIONNETWORKS, Data_CODINGANDINFORMATIONTHEORY, Subcarrier, law.invention, Antenna array, Base station, Relay, law, Nonlinear distortion, Telecommunications link, Computer Science::Networking and Internet Architecture, Electronic engineering, Resource allocation, Electrical and Electronic Engineering, Computer Science::Information Theory
Abstract

In this work, a resource allocation problem is investigated for a relay-based multiuser cooperative orthogonal frequency division multiple access (OFDMA) uplink system, considering a very large antenna array at the base station and nonlinear power amplifiers (PAs) in both user and relay nodes. Firstly, a theoretical characterization of the considered scenario is performed. Then, some analytical expressions for the nonlinear distortion (NLD) variance and the PA constant of a third-order polynomial PA are derived, as well as the instantaneous signal-to-noise ratio (SNR) of the considered system is calculated. Then, a low-complexity suboptimal relay selection and subcarrier allocation technique is proposed for the considered scenario based on the developed expressions. Numerical simulation results are presented to validate the derived expressions and to evaluate the performance of the proposed technique.

Published
2021

24. Study of the degradation of Nafion modified membranes

Author

Teixeira, Fatima, Teixeira, António P. S., and Rangel, C. M.

Subjects
Proton exchange membrane, Nafion, Fuel cells
Abstract

The development of new proton exchange membranes for PEM technology in fuel cells and electrolysers with increased durability is paramount to system´s lifetime and scalability. In this work, new modified Nafion membranes are proposed with increased resilience to chemical degradation by H2O2 /Fe2+, mimicking ex-situ radical attack to membrane structure. N/A

Published
2022

25. Reductive evolution of virulence repertoire to drive the divergence between community- and hospital-associated methicillin-resistant Staphylococcus aureus of the ST1 lineage

Author

Ana Tereza Ribeiro de Vasconcelos, Marisa Fabiana Nicolás, Patricia Martins-Simoes, Nicholas Costa Barroso Lima, William Mouton, Paul J. Planet, Rangel C. Souza, Marina Farrel Côrtes, Michèle Bes, Ana Maria Nunes Botelho, André E. R. Soares, Agnes Marie Sá Figueiredo, Paula Terra Bandeira, Luiz Gonzaga Paula de Almeida, Frédéric Laurent, and Cédric Badiou

Subjects
Microbiology (medical), Methicillin-Resistant Staphylococcus aureus, Lineage (genetic), Genotype, Virulence Factors, Immunology, Virulence, evolution of pathogenicity, Infectious and parasitic diseases, RC109-216, comparative genomics, Biology, medicine.disease_cause, Microbiology, Divergence, Evolution, Molecular, 03 medical and health sciences, medicine, Humans, Phylogeny, 030304 developmental biology, Comparative genomics, Genetics, Whole genome sequencing, 0303 health sciences, whole genome sequencing, Cross Infection, 030306 microbiology, Repertoire, Bayes Theorem, Genomics, biochemical phenomena, metabolism, and nutrition, Staphylococcal Infections, bacterial infections and mycoses, Methicillin-resistant Staphylococcus aureus, Community-Acquired Infections, Infectious Diseases, Staphylococcus aureus, ST1-SCCmecIV, Parasitology, Genome, Bacterial, Research Article, Research Paper, evolution of virulence
Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) of the ST1-SCCmecIV lineage has been associated with community-acquired (CA) infections in North America and Australia. In Brazil, multi-drug resistant ST1-SCCmecIV MRSA has emerged in hospital-associated (HA) diseases in Rio de Janeiro. To understand these epidemiological differences, genomic and phylogenetic analyses were performed. In addition, virulence assays were done for representative CA – and HA-MRSA strains. Despite the conservation of the virulence repertoire, some genes were missing in Brazilian ST1-SCCmecIV including lukSF-PV, fnbB, and several superantigen-encoded genes. Additionally, CA-MRSA lost the splDE while HA-MRSA strains conserved the complete operon. Most of these variable genes were located in mobile genetic elements (MGE). However, conservation and maintenance of MGEs were often observed despite the absence of their associated virulence markers. A Bayesian phylogenetic tree revealed the occurrence of more than one entrance of ST1 strains in Rio de Janeiro. The tree shape and chronology allowed us to infer that the hospital-associated ST1-SCCmecIV from Brazil and the community-acquired USA400 from North America are not closely related and that they might have originated from different MSSA strains that independently acquired SCCmecIV cassettes. As expected, representatives of ST1 strains from Brazil showed lower cytotoxicity and a greater ability to survive inside human host cells. We suggest that Brazilian ST1-SCCmecIV strains have adapted to the hospital setting by reducing virulence and gaining the ability to persist and survive inside host cells. Possibly, these evolutionary strategies may balance the biologic cost of retaining multiple antibiotic resistance genes.

Published
2021

27. Position Paper - Production

Author

Aricò, A. S., Popov, J., Moreno, A., Vladikova, D., Basile, F., Borchiellini, R., Amorim, V., Calnan, S., Castro, Á, Fleischhacker, N., Tal-Gutelmacher, E., Rangel, C. M., and Hočevar, S.

Subjects
green hydrogen, production, agenda process, strategic research and innovation agenda
Abstract

On 1st December 2020, the Council conclusion of the European Union has invited the Commission and interested Member States to carry out an agenda process for a green hydrogen R&I ERA pilot action in 2021, while ensuring consistency with other related EU initiatives. In this context, green hydrogen production represents, undoubtedly a field in which significant research and innovation efforts are needed. This position paper was prepared by the expert group forproduction and identifies the most relevant research needs in this area.

Published
2022
Full Text
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28. EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes

Author

Rangel C. Souza, Yasmmin Côrtes Martins, Ana Tereza Ribeiro de Vasconcelos, and Cristina dos Santos Ferreira

Subjects
Bioinformatics, SARS-CoV-2, General Neuroscience, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Immunoinformatic approaches, COVID-19, Genomics, General Medicine, Computational biology, Biology, Computational Science, General Biochemistry, Genetics and Molecular Biology, Epitope, EpiCurator, Workflow, Virology, HLA alleles binding affinity, Medicine, Epitopes prediction, General Agricultural and Biological Sciences
Abstract

The ongoing coronavirus 2019 (COVID-19) pandemic, triggered by the emerging SARS-CoV-2 virus, represents a global public health challenge. Therefore, the development of effective vaccines is an urgent need to prevent and control virus spread. One of the vaccine production strategies uses thein silicoepitope prediction from the virus genome by immunoinformatic approaches, which assist in selecting candidate epitopes forin vitroand clinical trials research. This study introduces the EpiCurator workflow to predict and prioritize epitopes from SARS-CoV-2 genomes by combining a series of computational filtering tools. To validate the workflow effectiveness, SARS-CoV-2 genomes retrieved from the GISAID database were analyzed. We identified 11 epitopes in the receptor-binding domain (RBD) of Spike glycoprotein, an important antigenic determinant, not previously described in the literature or published on the Immune Epitope Database (IEDB). Interestingly, these epitopes have a combination of important properties: recognized in sequences of the current variants of concern, present high antigenicity, conservancy, and broad population coverage. The RBD epitopes were the source for a multi-epitope design toin silicovalidation of their immunogenic potential. The multi-epitope overall quality was computationally validated, endorsing its efficiency to trigger an effective immune response since it has stability, high antigenicity and strong interactions with Toll-Like Receptors (TLR). Taken together, the findings in the current study demonstrated the efficacy of the workflow for epitopes discovery, providing target candidates for immunogen development.

Published
2021

29. Metal hydride-based hydrogen production and storage system for stationary applications powered by renewable sources

Author

Rangel, C. M., Fernandes, Vitor, and Gano, António

Subjects
Green chemistry, Renewable Energy, Sustainability and the Environment, Renewable energies, Hydrogen production, Metallic hydrides, Fuel cells, Renewable energy sources
Abstract

In this work, a compact and low-cost electrochemical laboratory prototype for the storage and production of hydrogen, based on metallic hydrides, with high reversibility in the charge/discharge process is demonstrated, using electricity either from the grid or by direct coupling to renewable energies as power source. The reactor is a 316 L stainless steel vessel with a capacity up to 15 bar internal pressure. It includes working electrodes of alloy LaNi4.3Co0.4Al0.3 and counter-electrodes of Ni foam in an electrolyte solution of 35% KOH. The reactor uses unicellular/multicellular configurations, so that the overall capacity of the system can be extended by increasing the number of working electrodes, resulting in a highly modular system. Results show excellent linearity, reversibility, and stability under cycling at room temperature and pressure, demonstrated either when powered by the grid or by off-grid renewable energy. Furthermore, criteria were established for the quantification of the state of full charge and full discharge. The system was integrated with a custom electronic system, developed inhouse for monitoring and control the reactor and to optimize the performance and energy efficiency of the hydrogen storage and discharge processes. info:eu-repo/semantics/publishedVersion

Published
2021

30. Community-acquired methicillin-resistant Staphylococcus aureus from ST1 lineage harboring a new SCCmec IV subtype (SCCmec IVm) containing the tetK gene

Author

Marina Farrel Côrtes, Agnes Marie Sá Figueiredo, Luiz Gonzaga Paula de Almeida, Oberdan de Lima Cunha, Ana Tereza Ribeiro de Vasconcelos, Ana Maria Nunes Botelho, Rangel C. Souza, and Marisa Fabiana Nicolás

Subjects
0301 basic medicine, Pharmacology, Genetics, Doxycycline, Tetracycline, SCCmec, 030106 microbiology, Virulence, biochemical phenomena, metabolism, and nutrition, Biology, bacterial infections and mycoses, medicine.disease_cause, Methicillin-resistant Staphylococcus aureus, 03 medical and health sciences, Infectious Diseases, Plasmid, Staphylococcus aureus, medicine, Pharmacology (medical), Gene, medicine.drug
Abstract

A pivotal event in the evolutionary path of methicillin-resistant Staphylococcus aureus (MRSA) is the acquisition of the staphylococcal cassette chromosome mec (SCCmec) element carrying the mecA gene, the determinant of methicillin resistance. Community-acquired (CA) MRSA is commonly associated with skin/soft tissue infections, and doxycycline is one of the drug choices for this purpose. Doxycycline resistance is associated with the acquisition of the tetK gene carried by the S. aureus plasmid pT181, which may also be integrated into SCCmec III and V. The aim of this study was to describe a novel SCCmec IV subtype (IVm) carrying tetK and reveal the genetic context of this element. The SCCmec sequence was obtained by whole-genome sequencing of the MRSA strain 2288 (ST1 CA-MRSA) and genomic analysis performed using different bioinformatics tools. A copy of pT181 was found to be integrated in the new SCCmec IVm of the strain 2288. The SCCmec IVm has high nucleotide identity (99%) with SCCmec IVa of the strain MW2, except for the J3 region, where the pT181 - carrying tetK gene - is inserted. Inverted repeats (IRs) flanking pT181 were found in this region, suggesting the occurrence of recombination events. The strain 2288 (spa type t125) shares most of the virulence attributes with MW2 (spa type t128), which is recognized in the past as a cause of severe infections in children in USA. The pattern of branching in the phylogenetic tree depicts a recent common ancestor shared by the 2228 strain and other MRSA from USA, including ERS410852, TCH70, CIG1835, CO-41, MW2, and USA400-0051, but none of them carried pT181. This study also showed that the tetK carried by SCCmec IVm is functional, determining resistance to doxycycline and tetracycline. The potential dissemination of the tetK and mecA genes in the same genetic event by the acquisition of this new SCCmec subtype is of concern for community infections.

Published
2018

34. Reductive evolution of virulence repertoire to drive the divergence between community- and hospital-associated methicillin-resistant Staphylococcus aureus of the ST1 lineage

Author

Côrtes, Marina Farrel, primary, Botelho, Ana Maria N., additional, Bandeira, Paula Terra, additional, Mouton, William, additional, Badiou, Cedric, additional, Bes, Michèle, additional, Lima, Nicholas C. B., additional, Soares, André Elias R., additional, Souza, Rangel C., additional, Almeida, Luiz G. P., additional, Martins-Simoes, Patricia, additional, Vasconcelos, Ana T. R., additional, Nicolás, Marisa F., additional, Laurent, Frédéric, additional, Planet, Paul J., additional, and Figueiredo, Agnes M. S., additional

Published
2021
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35. Smart Materials for Hydrogen Energy

Author

Titus, Elby, Gil, João Campos, Chaudhari, Ajay, and Rangel, C. M.

Subjects
Clean energy, Materials, Hydrogen
Abstract

Hydrogen has come out as a dominant part of clean energy component. Despite being the most abundant element in universe, passing the milestones of renewable hydrogen economy, from production to application is challenging. Great effort is required to extract the embedded hydrogen gas from other compounds, store and transport the same. Hydrogen found in organic compounds (hydrocarbons) can be separated by thermal processing known as reforming and it is the most commonly used method today. Electrolysis is a promising technology that uses electric current to split water into oxygen and hydrogen. Renewable energy sources like sun and wind can be used as clean energy source to produce hydrogen by water splitting. In future hydrogen could also be used as electricity, being an important energy carrier. AEM2018, the 3rd International conference on advanced energy materials held at the University of Surrey, England, gathered eminent researchers, from over 50 countries to discuss the latest technologies that can be employed in advanced renewable energy projects. The special issue of AEM2018 is a collection of selected papers on topic hydrogen energy, presented at AEM2018. The highlights were hydrogen production, storage, transportation, photovoltaics, fuel cells and electrochemical systems. info:eu-repo/semantics/publishedVersion

Published
2020

36. New analytical potential energy surface for the F([super 2]P) C[H.sub.4] hydrogen abstraction reaction: Kinetics and dynamics

Author

Espinosa-Garcia, J., Bravo, J.L., and Rangel, C.

Subjects
Chemical reaction, Rate of -- Analysis, Adiabatic processes (Thermodynamics) -- Analysis, Carbon compounds -- Chemical properties, Carbon compounds -- Thermal properties, Chemicals, plastics and rubber industries
Abstract

A new potential energy surface is described for the gas-phase F([super 2]P) C[H.sub.4] and its deuterated analogues and its kinetics and dynamics are analyzed. The kinetic and dynamic results have indicated that a single, adiabatic potential energy surface is sufficient for describing this reaction.

Published
2007

37. Origin of photocatalytic activity enhancement in Pd/Pt-deposited anatase N-TiO2 – experimental insights and DFT study of the (001) surface

Author

Batalovic, K., Radakovic, J., Bundaleski, N., Rakocevic, Z., Pasti, I, Skorodumova, Natalia V., Rangel, C. M., Batalovic, K., Radakovic, J., Bundaleski, N., Rakocevic, Z., Pasti, I, Skorodumova, Natalia V., and Rangel, C. M.

Abstract

In pursuit of the ideal photocatalyst, cheap and stable semiconductor TiO(2)is considered to be a good choice if one is able to reduce its band gap and decrease the recombination rate of charge carriers. The approach that offers such improvements for energy conversion applications is the modification of TiO(2)with nitrogen and noble metals. However, the origin of these improvements and possibilities for further design of single-atom catalysts are not always straightforward. To shed light on the atomic-scale picture, we modeled the nitrogen-doped (001) anatase TiO(2)surface as a support for palladium and platinum single-atom deposition. The thermodynamics of various synthesis routes for Pd/Pt deposition and nitrogen doping is considered based on density functional theory (DFT)-calculated energies, highlighting the effect of nitrogen doping on metal dimer formation and metal-support interaction. XPS analysis of the valence band of the modified TiO(2)nanocrystals, and the calculated charge transfer and electronic structure of single-atom catalysts supported on the (001) anatase TiO(2)surface provide an insight into modifications occurring in the valence zone of TiO(2)due to nitrogen doping and Pd/Pt deposition at the surface. DFT results also show that substitutional nitrogen doping significantly increases metal-support interaction, while interstitial nitrogen doping promotes only Pt-support interaction.

Published
2020
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38. Swine and poultry pathogens: the complete genome sequences of two strains of Mycoplasma hyopneumoniae and a strain of Mycoplasma synoviae

Author

Vasconcelos, Ana Tereza R., Ferreira, Henrique B., Bizarro, Cristiano V., Bonatto, Sandro L., Carvalho, Marcos O., Pinto, Paulo M., Almeida, Darcy F., Almeida, Luiz G.P., Almeida, Rosana, Alves-Filho, Leonardo, Assuncao, Enedina N., Azevedo, Vasco A.C., Bogo, Mauricio R., Brigido, Marcelo M., Brocchi, Marcelo, Burity, Helio A., Camargo, Anamaria A., Camargo, Sandro S., Carepo, Marta S., Carraro, Dirce M., de Mattos Cascardo, Julio C., Castro, Luiza A., Cavalcanti, Gisele, Chemale, Gustavo, Collevatti, Rosane G., Cunha, Cristina W., Dallagiovanna, Bruno, Dambros, Bibiana P., Dellagostin, Odir A., Falcao, Clarissa, Fantinatti-Garboggini, Fabiana, Felipe, Maria S.S., Fiorentin, Laurimar, Franco, Gloria R., Freitas, Nara S.A., Frias, Diego, Grangeiro, Thalles B., Grisard, Edmundo C., Guimaraes, Claudia T., Hungria, Mariangela, Jardim, Silvia N., Krieger, Marco A., Laurino, Jomar P., Lima, Lucymara F.A., Lopes, Maryellen I., Loreto, Elgion L.S., Madeira, Humberto M.F., Manfio, Gilson P., Maranhao, Andrea Q., Martinkovics, Christyanne T., Medeiros, Silvia R.B., Moreira, Miguel A.M., Neiva, Marcia, Ramalho-Neto, Cicero E., Nicolas, Marisa F., Oliveira, Sergio C., Paixao, Roger F.C., Pedrosa, Fabio O., Pena, Sergio D.J., Pereira, Maristela, Pereira-Ferrari, Lilian, Piffer, Itamar, Pinto, Luciano S., Potrich, Deise P., Salim, Anna C.M., Santos, Fabricio R., Schmitt, Renata, Schneider, Maria P.C., Schrank, Augusto, Schrank, Irene S., Schuck, Adriana F., Seuanez, Hector N., Silva, Denise W., Silva, Rosane, Silva, Sergio C., Soares, Celia M.A., Souza, Kelly R.L., Souza, Rangel C., Staats, Charley C., Steffens, Maria B.R., Teixeira, Santuza M.R., Urmenyi, Turan P., Vainstein, Marilene H., Zuccherato, Luciana W., Simpson, Andrew J.G., and Zaha, Arnaldo

Subjects
Pathogenic microorganisms -- Research, Nucleotide sequence -- Research, Mycoplasma -- Genetic aspects, Swine -- Genetic aspects, Biological sciences
Abstract

This work reports the results of analyses of three complete mycoplasma genomes, a pathogenic (7448) and a nonpathogenic (J) strain of the swine pathogen Mycoplasma hyopneumoniae and a strain of the avian pathogen Mycoplasma synoviae; the genome sizes of the three strains were 920,079 bp, 897,405 bp, and 799,476 bp, respectively. These genomes were compared with other sequenced mycoplasma genomes reported in the literature to examine several aspects of mycoplasma evolution. Strain-specific regions, including integrative and conjugal elements, and genome rearrangements and alterations in adhesin sequences were observed in the M. hyopneumoniae strains, and all of these were potentially related to pathogenicity. Genomic comparisons revealed that reduction in genome size implied loss of redundant metabolic pathways, with maintenance of alternative routes in different species. Horizontal gene transfer was consistently observed between M. synoviae and Mycoplasma gallisepticum. Our analyses indicated a likely transfer event of hemagglutinin-coding DNA sequences from M. gallisepticum to M. synoviae.

Published
2005

39. Local Diversification of Methicillin- Resistant Staphylococcus aureus ST239 in South America After Its Rapid Worldwide Dissemination

Author

Ana Tereza Ribeiro de Vasconcelos, Paula Terra Bandeira, Agnes Marie Sá Figueiredo, Deborah Nascimento dos Santos Silva, Paul J. Planet, Chanelle Ryan, Rangel C. Souza, Luiz Gonzaga Paula de Almeida, Bruno de Souza Scramignon Costa, Ahmed M Moustafa, Kelsey O’Brien, Nicholas Costa Barroso Lima, Fabienne Antunes Ferreira, Maiana O. C. Costa, Marina Farrel Côrtes, Ana Maria Nunes Botelho, Apurva Narechania, Marisa Fabiana Nicolás, Sergios-Orestis Kolokotronis, and Cristiana Ossaille Beltrame

Subjects
Microbiology (medical), Lineage (genetic), lcsh:QR1-502, Allopatric speciation, Brazilian/Hungarian clone, Context (language use), comparative genomics, Biology, methicillin-resistant Staphylococcus aureus, medicine.disease_cause, Genome, Microbiology, Brazilian epidemic clone, lcsh:Microbiology, 03 medical and health sciences, ST239-SCCmecIII, Genotype, medicine, Clade, 030304 developmental biology, Original Research, Comparative genomics, 0303 health sciences, 030306 microbiology, Methicillin-resistant Staphylococcus aureus, 3. Good health, Evolutionary biology
Abstract

The global spread of specific clones of methicillin-resistant Staphylococcus aureus (MRSA) has become a major public health problem, and understanding the dynamics of geographical spread requires worldwide surveillance. Over the past 20 years, the ST239 lineage of MRSA has been recognized as an emerging clone across the globe, with detailed studies focusing on isolates from Europe and Asia. Less is known about this lineage in South America, and, particularly, Brazil where it was the predominant lineage of MRSA in the early 1990s to 2000s. To gain a better understanding about the introduction and spread of ST239 MRSA in Brazil we undertook a comparative phylogenomic analysis of ST239 genomes, adding seven completed, closed Brazilian genomes. Brazilian ST239 isolates grouped in a subtree with those from South American, and Western, romance-language-speaking, European countries, here designated the South American clade. After an initial worldwide radiation in the 1960s and 1970s, we estimate that ST239 began to spread in South America and Brazil in approximately 1988. This clone demonstrates specific genomic changes that are suggestive of local divergence and adaptational change including agrC single-nucleotide polymorphisms variants, and a distinct pattern of virulence-associated genes (mainly the presence of the chp and the absence of sea and sasX). A survey of a geographically and chronologically diverse set of 100 Brazilian ST239 isolates identified this virulence genotype as the predominant pattern in Brazil, and uncovered an unexpectedly high prevalence of agr-dysfunction (30%). ST239 isolates from Brazil also appear to have undergone transposon (IS256) insertions in or near global regulatory genes (agr and mgr) that likely led to rapid reprogramming of bacterial traits. In general, the overall pattern observed in phylogenomic analyses of ST239 is of a rapid initial global radiation, with subsequent local spread and adaptation in multiple different geographic locations. Most ST239 isolates harbor the ardA gene, which we show here to have in vivo anti-restriction activity. We hypothesize that this gene may have improved the ability of this lineage to acquire multiple resistance genes and distinct virulence-associated genes in each local context. The allopatric divergence pattern of ST239 also may suggest strong selective pressures for specific traits in different geographical locations.

Published
2019

40. Pressurized electrochemical process for syngas production [Resumo]

Author

Messias, Sofia, Sousa, Miguel M., Rangel, C. M., Pardal, T., Ponte, Manuel Nunes, and Machado, Ana

Subjects
Electrolytes, Electrochemical reduction, Carbon dioxide, Green chemistry, Energy conversion
Abstract

Carbon Capture and Utilisation (CCU) comprise technologies that capture carbon dioxide and convert it into chemical products, such as fuels, chemicals and building materials that can replace the same products derived from fossil resources. These technologies can thus contribute to reach the ambitious 2030 targets set by the European Union for decarbonisation of the economy of 40% CO2 reduction, introduction of 27% renewable energies in the energy mix and 27% energy efficiency. CCU technologies are at different stages of maturity and some are already commercially deployed. One of these commercial technologies is the production of methanol by CO2 hydrogenation at high temperature using hydrogen produced by water electrolysis. Another CCU technology that is still at laboratory stage is electrochemical CO2 reduction. In this process carbon dioxide is co-electrolyzed with water near room temperature. Hydrogen is produced in situ. Depending on process conditions and catalysts CO2 reduction originates a series of products, such as CO, formic acid, hydrocarbons, alcohols etc. at the cathode. Oxygen is produced at the anode resulting from water oxidation reaction. Figure 1 illustrates the process. Electrochemical CO2 reduction presents several technological challenges that have not been surpassed yet, such as low CO2 conversions, poor stability of electrodes and low energy efficiencies. This work reports not yet published results of the development of a pressurized electrochemical process for producing syngas (CO + H2) by electrochemical reduction of carbon dioxide. Green syngas produced using renewable energy can be an important platform for introducing renewable energy in the chemical industry. The development of a process that works at pressures higher then atmospheric pressure seems promising to circumvent the aforementioned challenges, namely low conversions and low energy efficiencies. N/A

Published
2019

42. Hydrogen production from sodium borohydride: the role of Ni-Ru supported catalysts

Author

Nunes, H. X., Rangel, C. M., and Pinto, A. M. F. R.

Subjects
Green chemistry, Catalysts, Hydrolysis, Hydrogen production, Sodium borohydride
Abstract

Nowadays, the concerns about greenhouse-gas emissions from fossil fuel sources are generating a demand for clean and abundant energy. Since early 2000’s the chemical hydrides, in particular sodium borohydride (NaBH4), hydrolysis reaction attracted much attention as a hydrogen carrier due to its high hydrogen storage capacity, safe handling and fast kinetics of hydrogen release. Although, during the last decades, several studies have been focused on sodium borohydride hydrolysis improvement, the reaction kinetics is not fully understood. Thus, the performance of nickel-ruthenium supported catalysts was studied both in alkaline hydrolysis (x = 16) and alkali-free hydrolysis (x = 2) reactions. The results present high hydrogen generation rates, at uncontrolled room temperature, that compete directly with the rates previously obtained with a nickel-ruthenium unsupported catalyst, which are advantages for an on demand low/medium power NaBH4-H2-PEMFC system. N/A

Published
2019

43. Electrochemical CO2 reduction at room temperature and mild pressures

Author

Messias, Sofia, Sousa, Miguel M., Ponte, Manuel Nunes, Rangel, C. M., Pardal, T., and Machado, Ana

Subjects
Electrochemical reduction, Carbon dioxide, Sustainable energy storage, Green chemistry
Abstract

Carbon capture and utilization technologies (CCU) and electrolytic hydrogen production are closely interconnected technologies and necessary for a sustainable energy system. This work describes the development of a process for room temperature co-electrolysis of CO2 and water to produce syngas, at mild pressures. The influence of several parameters in the performance of the process is reported. N/A

Published
2019

44. Doped ferrites and their role on the production of hydrogen through thermochemical redox cycles [Resumo]

Author

Furtado, Olívia and Rangel, C. M.

Subjects
Thermochemical cycle, Energy storage, Solar energy, Green chemistry, Hydrogen production
Abstract

The thermochemical storage of solar energy is a method to store high energy densities in the form of chemical bonds, requiring only small amounts of material to store large amounts of energy. Metal oxides are promising materials to produce hydrogen from thermochemical cycles, being an environmentally friendly and sustainable option. N/A

Published
2019

45. Low load Pt catalyst with surface functionalised carbon supports for PEM fuel cells: half and full cell asssessments

Author

Capelo, Anabela, González, L., Sá, A.I. De, and Rangel, C. M.

Subjects
Electrochemical properties, Electrocatalyst, Fuel cells, Materials, Platinum-group metals
Abstract

Current US DOE 2020 targets for electrocatalysts aim for a total platinum group metals (PGM) loading of 0.125 mgcm-2 on membrane-electrode assemblies. The catalysts are expected to endure an elevated number of load cycles in order to comply with the expected 5000 h stack lifetime. At the stated PGM low loading attributes of performance, power and durability, as well as costs, are simultaneously required. The present paper deals with performance assessment of new catalyst using Pt nanoparticles and a surface functionalized carbon support. Due to its relevance to fuel cell operation, the stability and durability were assessed in half cell mode, through the application of demanding aging cycling protocols (30000 cycles). Full fuel cell assessments were also conducted entailing power density curves and cell electrochemical impedance. Results denote significant improvements in cell performance as well as in catalyst stability, regarding a commercial catalyst tested in the same conditions, at Pt loadings of 0.1 mgcm-2. N/A

Published
2019

46. Photocatalytic hydrogen production using noble and transition metals surface modified titania [Resumo]

Author

Capelo, Anabela, Esteves, M. Alexandra, Fernandes, Vitor, and Rangel, C. M.

Subjects
Titania, Photo-catalytic materials, Hydrogen production
Abstract

A large number of photocatalytic materials have been studied for water splitting since the seminal work of Fujishima and Honda1, showing great potential for solar energy conversion, including H2 production. The irradiation of a suspension of semiconductor oxides, as is the case of TiO2, presents attracting features but also stringent requirements regarding materials properties, including the tailoring of the electronic structure. Furthermore, efficient charge transport is necessary, as well as effective charge separation and prevention of electron-hole pair recombination, before the redox reactions can proceed2,3. In this work, the catalytic activity under UV excitation of TiO2-Au photocatalyst for H2 production was undertaken using glycerol and ethanol as sacrificial agents. Furthermore, substitution of Au by transition metal Cu was attempted with good results. Comparison is made with results obtained using TiO2-rGO-Pt catalyst under analogous loading conditions. N/A

Published
2019

47. Photocatalytic hydrogen production using ethanol as sacrificial agent from gas and liquid phases on reduced graphene oxide-TiO2- Pt nanocomposites

Author

Esteves, M. Alexandra, Fresno, F., Fernandes, Vitor, O'Shea, V. A. de la Peña, and Rangel, C. M.

Subjects
Ethanol, Hydrogen production, Photocatalytic, TiO2 nanoparticles, Nanocomposites
Abstract

Various strategies such as heterostructuring, crystal/textural modifications and band gap engineering, have been applied to the improvement of the photocatalytic activity of Titania for hydrogen production from water splitting. In this work deposited Pt on TiO2 is used as electron trap to suppress charge recombination. To reinforce this effect, composites with graphene oxide (GO) have been prepared, exhibiting promising photocatalytic performance for both hydrogen generation and the degradation of ethanol added as hole scavenger. Photocatalytic reactions were conducted in gas and liquid phases. N/A

Published
2019

49. Hydrogen production and storage from hydrolysis of sodium borohydride: study of the recyclability of the by-product of reaction [Resumo]

Author

Silva, D., Nunes, H. X., Rangel, C. M., and Pinto, A. M. F. R.

Subjects
Green chemistry, Hydrolysis, Hydrogen production, Clean energy, Sodium borohydride
Abstract

Hydrogen is one of the most valuable alternatives to fossil fuels to produce energy. However, although it is abundant in the universe and has the highest gravimetric density, it is difficult to obtain and store in its molecular form and in safe conditions. One alternative to the conventional hydrogen storage is to use the high hydrogen content (10.66 wt. %) of sodium borohydride to, simultaneously, produce and store it. N/A

Published
2019

50. New proton conductive heteroaromatic bisphosphonic acid-Nafion membranes for PEMFC [Resumo]

Author

Teixeira, Fatima, Sá, A.I. De, Teixeira, António P. S., and Rangel, C. M.

Subjects
Proton exchange membrane, Green chemistry, PEM, Fuel cells
Abstract

The integration of new cleaner, renewable and environment-friendly sources and energy vectors for sustainable energy systems are a key challenge for 21st century society. Fuel cells are among the clean energy conversion technologies with vast applications and scope, introducing hydrogen as a flexible and storage energy vector and presenting a viable alternative to fossil fuels. Proton exchange membrane fuel cells (PEMFCs) are considered promising power sources, but their performance depends crucially on the properties of their proton exchange membranes (PEM). N/A

Published
2019

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