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1. Observation and manipulation of charge carrier distribution at the SiO$_2$/Si interface

Author

Martins, Maria M., Kumar, Piyush, Bathen, Marianne E., Salman, Zaher, Grossner, Ulrike, and Prokscha, Thomas

Subjects
Condensed Matter - Other Condensed Matter, Physics - Applied Physics
Abstract

Using low-energy muons, we map the charge carrier concentration as a function of depth and electric field across the \SiOSi interface up to a depth of \SI{100}{\nano\meter} in Si-based MOS capacitors. The results show that the formation of the anisotropic bond-centered muonium \MuBCz state in Si serves as a direct measure of the local changes in electronic structures. Different band-bending conditions could be distinguished, and the extension of the depletion width was directly extracted using the localized stopping and probing depth of the muons. Furthermore, electron build-up on the Si side of the \SiOO/Si interface, caused by the mirror charge induced by the fixed positive charge in the oxide and the image force effect, was observed. Our work represents a significant extension of the application of the muon spin rotation technique ($\mu$SR) and lays the foundation for further research on direct observation of charge carrier density manipulation at technologically important semiconductor device interfaces.

Published
2024

2. Improving the low-energy muon beam quality of the LEM beamline at PSI: Characterisation of ultra-thin carbon foils

Author

Janka, Gianluca, Martins, Maria Mendes, Ni, Xiaojie, Salman, Zaher, Suter, Andreas, and Prokscha, Thomas

Subjects
Physics - Instrumentation and Detectors
Abstract

The Low-Energy Muon beamline (LEM) at the Paul Scherrer Institute currently stands as the world's only facility providing a continuous beam of low-energy muons with keV energies for conducting muon spin rotation experiments on a nanometer depth scale in heterostructures and near a sample's surface. As such, optimizing the beam quality to reach its full potential is of paramount importance. One of the ongoing efforts is dedicated to improving the already applied technique of single muon tagging through the detection of secondary electrons emerging from an ultra-thin carbon foil. In this work, we present the results from installing a thinner foil with a nominal thickness of 0.5 $\mu g~cm^{-2}$ and compare its performance to that of the previously installed foil with a nominal thickness of 2.0 $\mu g~cm^{-2}$. Our findings indicate improved beam quality, characterized by smaller beam spots, reduced energy loss and straggling of the muons, and enhanced tagging efficiency. Additionally, we introduce a method utilizing blue laser irradiation for cleaning the carbon foil, further improving and maintaining its characteristics

Published
2024

4. Efferocytosis of SARS-CoV-2-infected dying cells impairs macrophage anti-inflammatory functions and clearance of apoptotic cells

Author

Salina, Ana CG, dos-Santos, Douglas, Rodrigues, Tamara S, Fortes-Rocha, Marlon, Freitas-Filho, Edismauro G, Alzamora-Terrel, Daniel L, Castro, Icaro MS, Fraga da Silva, Thais FC, de Lima, Mikhael HF, Nascimento, Daniele C, Silva, Camila M, Toller-Kawahisa, Juliana E, Becerra, Amanda, Oliveira, Samuel, Caetité, Diego B, Almeida, Leticia, Ishimoto, Adriene Y, Lima, Thais M, Martins, Ronaldo B, Veras, Flavio, do Amaral, Natália B, Giannini, Marcela C, Bonjorno, Letícia P, Lopes, Maria IF, Benatti, Maira N, Batah, Sabrina S, Santana, Rodrigo C, Vilar, Fernando C, Martins, Maria A, Assad, Rodrigo L, de Almeida, Sergio CL, de Oliveira, Fabiola R, Arruda Neto, Eurico, Cunha, Thiago M, Alves-Filho, José C, Bonato, Vania LD, Cunha, Fernando Q, Fabro, Alexandre T, Nakaya, Helder I, Zamboni, Dario S, Louzada-Junior, Paulo, Oliveira, Rene DR, and Cunha, Larissa D

Abstract

COVID-19 is a disease of dysfunctional immune responses, but the mechanisms triggering immunopathogenesis are not established. The functional plasticity of macrophages allows this cell type to promote pathogen elimination and inflammation or suppress inflammation and promote tissue remodeling and injury repair. During an infection, the clearance of dead and dying cells, a process named efferocytosis, can modulate the interplay between these contrasting functions. Here, we show that engulfment of SARS-CoV-2-infected apoptotic cells exacerbates inflammatory cytokine production, inhibits the expression of efferocytic receptors, and impairs continual efferocytosis by macrophages. We also provide evidence supporting that lung monocytes and macrophages from severe COVID-19 patients have compromised efferocytic capacity. Our findings reveal that dysfunctional efferocytosis of SARS-CoV-2-infected cell corpses suppresses macrophage anti-inflammation and efficient tissue repair programs and provides mechanistic insights for the excessive production of pro-inflammatory cytokines and accumulation of tissue damage associated with COVID-19 immunopathogenesis.

Published
2023

8. Consistent patterns of common species across tropical tree communities

Author

Cooper, Declan L. M., Lewis, Simon L., Sullivan, Martin J. P., Prado, Paulo I., ter Steege, Hans, Barbier, Nicolas, Slik, Ferry, Sonké, Bonaventure, Ewango, Corneille E. N., Adu-Bredu, Stephen, Affum-Baffoe, Kofi, de Aguiar, Daniel P. P., Ahuite Reategui, Manuel Augusto, Aiba, Shin-Ichiro, Albuquerque, Bianca Weiss, de Almeida Matos, Francisca Dionízia, Alonso, Alfonso, Amani, Christian A., do Amaral, Dário Dantas, do Amaral, Iêda Leão, Andrade, Ana, de Andrade Miranda, Ires Paula, Angoboy, Ilondea B., Araujo-Murakami, Alejandro, Arboleda, Nicolás Castaño, Arroyo, Luzmila, Ashton, Peter, Aymard C, Gerardo A., Baider, Cláudia, Baker, Timothy R., Balinga, Michael Philippe Bessike, Balslev, Henrik, Banin, Lindsay F., Bánki, Olaf S., Baraloto, Chris, Barbosa, Edelcilio Marques, Barbosa, Flávia Rodrigues, Barlow, Jos, Bastin, Jean-Francois, Beeckman, Hans, Begne, Serge, Bengone, Natacha Nssi, Berenguer, Erika, Berry, Nicholas, Bitariho, Robert, Boeckx, Pascal, Bogaert, Jan, Bonyoma, Bernard, Boundja, Patrick, Bourland, Nils, Boyemba Bosela, Faustin, Brambach, Fabian, Brienen, Roel, Burslem, David F. R. P., Camargo, José Luís, Campelo, Wegliane, Cano, Angela, Cárdenas, Sasha, Cárdenas López, Dairon, de Sá Carpanedo, Rainiellen, Carrero Márquez, Yrma Andreina, Carvalho, Fernanda Antunes, Casas, Luisa Fernanda, Castellanos, Hernán, Castilho, Carolina V., Cerón, Carlos, Chapman, Colin A., Chave, Jerome, Chhang, Phourin, Chutipong, Wanlop, Chuyong, George B., Cintra, Bruno Barçante Ladvocat, Clark, Connie J., Coelho de Souza, Fernanda, Comiskey, James A., Coomes, David A., Cornejo Valverde, Fernando, Correa, Diego F., Costa, Flávia R. C., Costa, Janaina Barbosa Pedrosa, Couteron, Pierre, Culmsee, Heike, Cuni-Sanchez, Aida, Dallmeier, Francisco, Damasco, Gabriel, Dauby, Gilles, Dávila, Nállarett, Dávila Doza, Hilda Paulette, De Alban, Jose Don T., de Assis, Rafael L., De Canniere, Charles, De Haulleville, Thales, de Jesus Veiga Carim, Marcelo, Demarchi, Layon O., Dexter, Kyle G., Di Fiore, Anthony, Din, Hazimah Haji Mohammad, Disney, Mathias I., Djiofack, Brice Yannick, Djuikouo, Marie-Noël K., Do, Tran Van, Doucet, Jean-Louis, Draper, Freddie C., Droissart, Vincent, Duivenvoorden, Joost F., Engel, Julien, Estienne, Vittoria, Farfan-Rios, William, Fauset, Sophie, Feeley, Kenneth J., Feitosa, Yuri Oliveira, Feldpausch, Ted R., Ferreira, Cid, Ferreira, Joice, Ferreira, Leandro Valle, Fletcher, Christine D., Flores, Bernardo Monteiro, Fofanah, Alusine, Foli, Ernest G., Fonty, Émile, Fredriksson, Gabriella M., Fuentes, Alfredo, Galbraith, David, Gallardo Gonzales, George Pepe, Garcia-Cabrera, Karina, García-Villacorta, Roosevelt, Gomes, Vitor H. F., Gómez, Ricardo Zárate, Gonzales, Therany, Gribel, Rogerio, Guedes, Marcelino Carneiro, Guevara, Juan Ernesto, Hakeem, Khalid Rehman, Hall, Jefferson S., Hamer, Keith C., Hamilton, Alan C., Harris, David J., Harrison, Rhett D., Hart, Terese B., Hector, Andy, Henkel, Terry W., Herbohn, John, Hockemba, Mireille B. N., Hoffman, Bruce, Holmgren, Milena, Honorio Coronado, Euridice N., Huamantupa-Chuquimaco, Isau, Hubau, Wannes, Imai, Nobuo, Irume, Mariana Victória, Jansen, Patrick A., Jeffery, Kathryn J., Jimenez, Eliana M., Jucker, Tommaso, Junqueira, André Braga, Kalamandeen, Michelle, Kamdem, Narcisse G., Kartawinata, Kuswata, Kasongo Yakusu, Emmanuel, Katembo, John M., Kearsley, Elizabeth, Kenfack, David, Kessler, Michael, Khaing, Thiri Toe, Killeen, Timothy J., Kitayama, Kanehiro, Klitgaard, Bente, Labrière, Nicolas, Laumonier, Yves, Laurance, Susan G. W., Laurance, William F., Laurent, Félix, Le, Tinh Cong, Le, Trai Trong, Leal, Miguel E., Leão de Moraes Novo, Evlyn Márcia, Levesley, Aurora, Libalah, Moses B., Licona, Juan Carlos, Lima Filho, Diógenes de Andrade, Lindsell, Jeremy A., Lopes, Aline, Lopes, Maria Aparecida, Lovett, Jon C., Lowe, Richard, Lozada, José Rafael, Lu, Xinghui, Luambua, Nestor K., Luize, Bruno Garcia, Maas, Paul, Magalhães, José Leonardo Lima, Magnusson, William E., Mahayani, Ni Putu Diana, Makana, Jean-Remy, Malhi, Yadvinder, Maniguaje Rincón, Lorena, Mansor, Asyraf, Manzatto, Angelo Gilberto, Marimon, Beatriz S., Marimon-Junior, Ben Hur, Marshall, Andrew R, Martins, Maria Pires, Mbayu, Faustin M., de Medeiros, Marcelo Brilhante, Mesones, Italo, Metali, Faizah, Mihindou, Vianet, Millet, Jerome, Milliken, William, Mogollón, Hugo F., Molino, Jean-François, Mohd. Said, Mohd. Nizam, Monteagudo Mendoza, Abel, Montero, Juan Carlos, Moore, Sam, Mostacedo, Bonifacio, Mozombite Pinto, Linder Felipe, Mukul, Sharif Ahmed, Munishi, Pantaleo K. T., Nagamasu, Hidetoshi, Nascimento, Henrique Eduardo Mendonça, Nascimento, Marcelo Trindade, Neill, David, Nilus, Reuben, Noronha, Janaína Costa, Nsenga, Laurent, Núñez Vargas, Percy, Ojo, Lucas, Oliveira, Alexandre A., de Oliveira, Edmar Almeida, Ondo, Fidèle Evouna, Palacios Cuenca, Walter, Pansini, Susamar, Pansonato, Marcelo Petratti, Paredes, Marcos Ríos, Paudel, Ekananda, Pauletto, Daniela, Pearson, Richard G., Pena, José Luis Marcelo, Pennington, R. Toby, Peres, Carlos A., Permana, Andrea, Petronelli, Pascal, Peñuela Mora, Maria Cristina, Phillips, Juan Fernando, Phillips, Oliver L., Pickavance, Georgia, Piedade, Maria Teresa Fernandez, Pitman, Nigel C. A., Ploton, Pierre, Popelier, Andreas, Poulsen, John R., Prieto, Adriana, Primack, Richard B., Priyadi, Hari, Qie, Lan, Quaresma, Adriano Costa, de Queiroz, Helder Lima, Ramirez-Angulo, Hirma, Ramos, José Ferreira, Reis, Neidiane Farias Costa, Reitsma, Jan, Revilla, Juan David Cardenas, Riutta, Terhi, Rivas-Torres, Gonzalo, Robiansyah, Iyan, Rocha, Maira, Rodrigues, Domingos de Jesus, Rodriguez-Ronderos, M. Elizabeth, Rovero, Francesco, Rozak, Andes H., Rudas, Agustín, Rutishauser, Ervan, Sabatier, Daniel, Sagang, Le Bienfaiteur, Sampaio, Adeilza Felipe, Samsoedin, Ismayadi, Satdichanh, Manichanh, Schietti, Juliana, Schöngart, Jochen, Scudeller, Veridiana Vizoni, Seuaturien, Naret, Sheil, Douglas, Sierra, Rodrigo, Silman, Miles R., Silva, Thiago Sanna Freire, da Silva Guimarães, José Renan, Simo-Droissart, Murielle, Simon, Marcelo Fragomeni, Sist, Plinio, Sousa, Thaiane R., de Sousa Farias, Emanuelle, de Souza Coelho, Luiz, Spracklen, Dominick V., Stas, Suzanne M., Steinmetz, Robert, Stevenson, Pablo R., Stropp, Juliana, Sukri, Rahayu S., Sunderland, Terry C. H., Suzuki, Eizi, Swaine, Michael D., Tang, Jianwei, Taplin, James, Taylor, David M., Tello, J. Sebastián, Terborgh, John, Texier, Nicolas, Theilade, Ida, Thomas, Duncan W., Thomas, Raquel, Thomas, Sean C., Tirado, Milton, Toirambe, Benjamin, de Toledo, José Julio, Tomlinson, Kyle W., Torres-Lezama, Armando, Tran, Hieu Dang, Tshibamba Mukendi, John, Tumaneng, Roven D., Umaña, Maria Natalia, Umunay, Peter M., Urrego Giraldo, Ligia Estela, Valderrama Sandoval, Elvis H., Valenzuela Gamarra, Luis, Van Andel, Tinde R., van de Bult, Martin, van de Pol, Jaqueline, van der Heijden, Geertje, Vasquez, Rodolfo, Vela, César I. A., Venticinque, Eduardo Martins, Verbeeck, Hans, Veridiano, Rizza Karen A., Vicentini, Alberto, Vieira, Ima Célia Guimarães, Vilanova Torre, Emilio, Villarroel, Daniel, Villa Zegarra, Boris Eduardo, Vleminckx, Jason, von Hildebrand, Patricio, Vos, Vincent Antoine, Vriesendorp, Corine, Webb, Edward L., White, Lee J. T., Wich, Serge, Wittmann, Florian, Zagt, Roderick, Zang, Runguo, Zartman, Charles Eugene, Zemagho, Lise, Zent, Egleé L., and Zent, Stanford

Published
2024
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9. Control of Meloidogyne javanica in banana by endophytic bacteria

Author

de Souza Gleika Larisse Oliveira Dorásio, Ribeiro Regina Cássia Ferreira, Xavier Adelica Aparecida, Nietsche Silvia, de Castro Moreira Thaís, Martins Maria Josiane, Pimenta Samy, Mizobutsi Edson Hiydu, dos Santos Neto José Augusto, and Santos Isabela Oliveira

Subjects
bacillus spp., screening, biological control, musa sp., root-knot nematode, Agriculture, Agriculture (General), S1-972
Abstract

The aim of this work was to evaluate the effect of 40 endophytic bacteria isolates on the control of Meloidogyne javanica in ‘Prata-Anã’ banana seedlings. Two experiments were carried out in a completely randomized design with eight replicates. In each trial, 20 bacteria isolates and control were evaluated. Bacterial suspensions were applied to substrates during the acclimatization of seedlings at 15 and 30 days. On the 31st day, seedlings were transplanted into pots and soil was infested with M. javanica egg suspension at 8 days. After 90 days, the following variables were evaluated: number of galls, egg masses, eggs per root, reproduction factor (RF), second-stage juveniles, and shoot dry matter. The results of nematological variables were submitted to Principal Components Analysis. In trial I, the variables that most contributed to data variability were as follows: number of eggs and RF. In trial II, RF had greater influence. Of the 40 isolates evaluated, 39 reduced RF, and of the 20 isolates evaluated in the first trial, all reduced the number of eggs per root. Bacillus methylotrophicus EB26, Bacillus cereus EB25, and Bacillus sp. EB37 isolates stood out in the control of nematodes, with RF reduction above 80%.

Published
2024
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10. Investigation of the SiO2-SiC interface using low energy muon spin rotation spectroscopy

Author

Kumar, Piyush, Martins, Maria Inês Mendes, Bathen, Marianne Etzelmüller, Woerle, Judith, Prokscha, Thomas, and Grossner, Ulrike

Subjects
Condensed Matter - Materials Science
Abstract

Using positive muons as local probes implanted at low energy enables gathering information about the material of interest with nanometer depth resolution (low energy muon spin rotation spectroscopy (LE-$\mu$SR). In this work, we leverage the capabilities of LE-$\mu$SR to perform an investigation of the SiO$_\text{2}$-SiC interface. Thermally oxidized samples are investigated before and after annealing in nitric oxide (NO) and argon (Ar) ambience. Thermal oxidation is found to result in structural changes both in the SiC crystal close to the interface and at the interface itself. Annealing in NO environment is known to passivate the defects leading to a reduction of the density of interface traps (D$_{it}$); LE-$\mu$SR further reveals that the NO annealing results in a thin layer of high carrier concentration in SiC, extending to more than 50 nm depending on the annealing conditions. We also see indications of Si vacancy (V$_{Si}$) formation in SiC after thermal oxidation. Following NO annealing, nitrogen occupies the V$_{Si}$ sites, leading to the reduction in D$_{it}$ and at the same time, creating a charge-carrier-rich region near the interface. By comparing the LE-$\mu$SR data from a sample with known doping density, we perform a high-resolution quantification of the free carrier concentration near the interface after NO annealing and discuss the origin of observed near-surface variations. Finally, the depletion of carriers in a MOS capacitor in the region below the interface is shown using LE-$\mu$SR. The NO annealed sample shows the narrowest depletion region, likely due to the reduced D$_{it}$ and charge-carrier-rich region near the interface. Our findings demonstrate the many benefits of utilizing LE-$\mu$SR to study critical regions of semiconductor devices that have been inaccessible with other techniques while retaining nanoscale depth resolution and a non-destructive approach., Comment: 14 pages, 12 figures

Published
2022

11. The Multi-Disciplinary Approach to an Interdisciplinary Virtual Exchange

Author

Fonseca, Paula, Julian, Kristi, Hulme, Wendi, Martins, Maria De Lurdes, and Brautlacht, Regina

Abstract

New communication technologies are changing the way we work and communicate with people around the world. Given this reality, students in Higher Education (HE) worldwide need to develop knowledge in their area of study as well as attitudes and values that will enable them to be responsible and ethical global citizens in the workforce they will soon enter, regardless of the degree. Different institutional and country-specific requirements are important factors when developing an international Virtual Exchange (VE) program. Digital learning environments such as ProGlobe -- Promoting the Global Exchange of Ideas on Sustainable Goals, Practices, and Cultural Diversity -- offer a platform for collaborating with diverse students around the world to share and reflect on ideas on sustainable practices. Students work together virtually on a joint interdisciplinary project that aims to create knowledge and foster cultural diversity. This project was successfully integrated into each country's course syllabus through a common global theme; sustainability. The focus of this paper is to present multi-disciplinary perspectives on the opportunities and challenges in implementing a VE project in HE. Furthermore, it will present the challenges that country coordinators dealt with when planning and implementing their project. Given the disparity found in each course syllabus, project coordinators uniquely handled the project goal, approach, and assessment for their specific course and program. Not only did the students and faculty gain valuable insight into different aspects of collaboration when working in interdisciplinary HE projects, they also reflected on their own impact on the environment and learned to listen to how people in different countries deal with environmental issues. This approach provided students with meaningful intercultural experiences that helped them link ideas and concepts about a global issue through the lens of their own discipline as well as other disciplines worldwide. [For the complete volume, "Virtual Exchange: Towards Digital Equity in Internationalisation," see ED614868.]

Published
2021

12. Defect Profiling of Oxide-Semiconductor Interfaces Using Low-Energy Muons

Author

Martins, Maria Inês Mendes, Kumar, Piyush, Woerle, Judith, Ni, Xiaojie, Grossner, Ulrike, and Prokscha, Thomas

Subjects
Condensed Matter - Materials Science, Condensed Matter - Other Condensed Matter
Abstract

Muon spin rotation with low-energy muons (LE{\mu}SR) is a powerful nuclear method where electrical and magnetic properties of surface-near regions and thin films can be studied on a length scale of $\approx$\SI{200}{\nano\meter}. In this work, we show the potential of utilizing low-energy muons for a depth-resolved characterization of oxide-semiconductor interfaces, i.e. for silicon (Si) and silicon carbide (4H-SiC). Silicon dioxide (SiO$_2$) grown by plasma-enhanced chemical vapor deposition (PECVD) and by thermal oxidation of the SiO$_2$-semiconductor interface are compared with respect to interface and defect formation. The nanometer depth resolution of {\mu}allows for a clear distinction between the oxide and semiconductor layers, while also quantifying the extension of structural changes caused by the oxidation of both Si and SiC., Comment: The following article has been submitted to Advanced Materials Interfaces

Published
2022

13. Intrinsic magnetism in superconducting infinite-layer nickelates

Author

Fowlie, Jennifer, Hadjimichael, Marios, Martins, Maria M., Li, Danfeng, Osada, Motoki, Wang, Bai Yang, Lee, Kyuho, Lee, Yonghun, Salman, Zaher, Prokscha, Thomas, Triscone, Jean-Marc, Hwang, Harold Y., and Suter, Andreas

Subjects
Condensed Matter - Superconductivity, Condensed Matter - Strongly Correlated Electrons
Abstract

The discovery of superconductivity in Nd$_{0.8}$Sr$_{0.2}$NiO$_2$ [1] introduced a new family of layered nickelate superconductors that has now been extended to include a range of Sr-doping [2, 3], Pr or La in place of Nd [4-6], and the 5-layer Nd$_6$Ni$_5$O$_{12}$ [7]. A number of studies indicate that electron correlations are strong in these materials [8-14], and hence a central question is whether or not magnetism is present as a consequence of these interactions. Here we report muon spin rotation/relaxation studies of a series of superconducting infinite-layer nickelates. In all cases we observe an intrinsic magnetic ground state, regardless of the rare earth ion or doping, arising from local moments on the nickel sublattice. The coexistence of magnetism - which is likely to be antiferromagnetic and short-range ordered - with superconductivity is reminiscent of some iron pnictides [15] and heavy fermion compounds [16], and qualitatively distinct from the doped cuprates [17].

Published
2022
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14. SARS-CoV-2 productively infects primary human immune system cells in vitro and in COVID-19 patients

Author

Pontelli, Marjorie C, Castro, Ítalo A, Martins, Ronaldo B, La Serra, Leonardo, Veras, Flávio P, Nascimento, Daniele C, Silva, Camila M, Cardoso, Ricardo S, Rosales, Roberta, Gomes, Rogério, Lima, Thais M, Souza, Juliano P, Vitti, Brenda C, Caetité, Diego B, de Lima, Mikhael HF, Stumpf, Spencer D, Thompson, Cassandra E, Bloyet, Louis-Marie, Toller-Kawahisa, Juliana E, Giannini, Marcela C, Bonjorno, Letícia P, Lopes, Maria IF, Batah, Sabrina S, Siyuan, Li, Luppino-Assad, Rodrigo, Almeida, Sergio CL, Oliveira, Fabiola R, Benatti, Maíra N, Pontes, Lorena LF, Santana, Rodrigo C, Vilar, Fernando C, Auxiliadora-Martins, Maria, Shi, Pei-Yong, Cunha, Thiago M, Calado, Rodrigo T, Alves-Filho, José C, Zamboni, Dario S, Fabro, Alexandre T, Louzada-Junior, Paulo, Oliveira, Rene DR, Whelan, Sean PJ, Cunha, Fernando Q, and Arruda, Eurico

Abstract

Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is associated with a hyperinflammatory state and lymphocytopenia, a hallmark that appears as both signature and prognosis of disease severity outcome. Although cytokine storm and a sustained inflammatory state are commonly associated with immune cell depletion, it is still unclear whether direct SARS-CoV-2 infection of immune cells could also play a role in this scenario by harboring viral replication. We found that monocytes, as well as both B and T lymphocytes, were susceptible to SARS-CoV-2 infection in vitro, accumulating double-stranded RNA consistent with viral RNA replication and ultimately leading to expressive T cell apoptosis. In addition, flow cytometry and immunofluorescence analysis revealed that SARS-CoV-2 was frequently detected in monocytes and B lymphocytes from coronavirus disease 2019 (COVID-19) patients. The rates of SARS-CoV-2-infected monocytes in peripheral blood mononuclear cells from COVID-19 patients increased over time from symptom onset, with SARS-CoV-2-positive monocytes, B cells, and CD4+ T lymphocytes also detected in postmortem lung tissue. These results indicated that SARS-CoV-2 infection of blood-circulating leukocytes in COVID-19 patients might have important implications for disease pathogenesis and progression, immune dysfunction, and virus spread within the host.

Published
2022

17. Mapping density, diversity and species-richness of the Amazon tree flora

Author

ter Steege, Hans, Pitman, Nigel C. A., do Amaral, Iêda Leão, de Souza Coelho, Luiz, de Almeida Matos, Francisca Dionízia, de Andrade Lima Filho, Diógenes, Salomão, Rafael P., Wittmann, Florian, Castilho, Carolina V., Guevara, Juan Ernesto, Veiga Carim, Marcelo de Jesus, Phillips, Oliver L., Magnusson, William E., Sabatier, Daniel, Revilla, Juan David Cardenas, Molino, Jean-François, Irume, Mariana Victória, Martins, Maria Pires, da Silva Guimarães, José Renan, Ramos, José Ferreira, Bánki, Olaf S., Piedade, Maria Teresa Fernandez, Cárdenas López, Dairon, Rodrigues, Domingos de Jesus, Demarchi, Layon O., Schöngart, Jochen, Almeida, Everton José, Barbosa, Luciane Ferreira, Cavalheiro, Larissa, dos Santos, Márcia Cléia Vilela, Luize, Bruno Garcia, de Leão Novo, Evlyn Márcia Moraes, Vargas, Percy Núñez, Silva, Thiago Sanna Freire, Venticinque, Eduardo Martins, Manzatto, Angelo Gilberto, Reis, Neidiane Farias Costa, Terborgh, John, Casula, Katia Regina, Honorio Coronado, Euridice N., Monteagudo Mendoza, Abel, Montero, Juan Carlos, Costa, Flávia R. C., Feldpausch, Ted R., Quaresma, Adriano Costa, Castaño Arboleda, Nicolás, Zartman, Charles Eugene, Killeen, Timothy J., Marimon, Beatriz S., Marimon-Junior, Ben Hur, Vasquez, Rodolfo, Mostacedo, Bonifacio, Assis, Rafael L., Baraloto, Chris, do Amaral, Dário Dantas, Engel, Julien, Petronelli, Pascal, Castellanos, Hernán, de Medeiros, Marcelo Brilhante, Simon, Marcelo Fragomeni, Andrade, Ana, Camargo, José Luís, Laurance, William F., Laurance, Susan G. W., Maniguaje Rincón, Lorena, Schietti, Juliana, Sousa, Thaiane R., de Sousa Farias, Emanuelle, Lopes, Maria Aparecida, Magalhães, José Leonardo Lima, Nascimento, Henrique Eduardo Mendonça, de Queiroz, Helder Lima, Aymard C., Gerardo A., Brienen, Roel, Stevenson, Pablo R., Araujo-Murakami, Alejandro, Baker, Tim R., Cintra, Bruno Barçante Ladvocat, Feitosa, Yuri Oliveira, Mogollón, Hugo F., Duivenvoorden, Joost F., Peres, Carlos A., Silman, Miles R., Ferreira, Leandro Valle, Lozada, José Rafael, Comiskey, James A., Draper, Freddie C., de Toledo, José Julio, Damasco, Gabriel, García-Villacorta, Roosevelt, Lopes, Aline, Vicentini, Alberto, Cornejo Valverde, Fernando, Alonso, Alfonso, Arroyo, Luzmila, Dallmeier, Francisco, Gomes, Vitor H. F., Jimenez, Eliana M., Neill, David, Peñuela Mora, Maria Cristina, Noronha, Janaína Costa, de Aguiar, Daniel P. P., Barbosa, Flávia Rodrigues, Bredin, Yennie K., de Sá Carpanedo, Rainiellen, Carvalho, Fernanda Antunes, de Souza, Fernanda Coelho, Feeley, Kenneth J., Gribel, Rogerio, Haugaasen, Torbjørn, Hawes, Joseph E., Pansonato, Marcelo Petratti, Ríos Paredes, Marcos, Barlow, Jos, Berenguer, Erika, da Silva, Izaias Brasil, Ferreira, Maria Julia, Ferreira, Joice, Fine, Paul V. A., Guedes, Marcelino Carneiro, Levis, Carolina, Licona, Juan Carlos, Villa Zegarra, Boris Eduardo, Vos, Vincent Antoine, Cerón, Carlos, Durgante, Flávia Machado, Fonty, Émile, Henkel, Terry W., Householder, John Ethan, Huamantupa-Chuquimaco, Isau, Pos, Edwin, Silveira, Marcos, Stropp, Juliana, Thomas, Raquel, Daly, Doug, Dexter, Kyle G., Milliken, William, Molina, Guido Pardo, Pennington, Toby, Vieira, Ima Célia Guimarães, Weiss Albuquerque, Bianca, Campelo, Wegliane, Fuentes, Alfredo, Klitgaard, Bente, Pena, José Luis Marcelo, Tello, J. Sebastián, Vriesendorp, Corine, Chave, Jerome, Di Fiore, Anthony, Hilário, Renato Richard, de Oliveira Pereira, Luciana, Phillips, Juan Fernando, Rivas-Torres, Gonzalo, van Andel, Tinde R., von Hildebrand, Patricio, Balee, William, Barbosa, Edelcilio Marques, de Matos Bonates, Luiz Carlos, Dávila Doza, Hilda Paulette, Zárate Gómez, Ricardo, Gonzales, Therany, Gallardo Gonzales, George Pepe, Hoffman, Bruce, Junqueira, André Braga, Malhi, Yadvinder, de Andrade Miranda, Ires Paula, Pinto, Linder Felipe Mozombite, Prieto, Adriana, Rudas, Agustín, Ruschel, Ademir R., Silva, Natalino, Vela, César I. A., Zent, Egleé L., Zent, Stanford, Cano, Angela, Carrero Márquez, Yrma Andreina, Correa, Diego F., Costa, Janaina Barbosa Pedrosa, Flores, Bernardo Monteiro, Galbraith, David, Holmgren, Milena, Kalamandeen, Michelle, Lobo, Guilherme, Torres Montenegro, Luis, Nascimento, Marcelo Trindade, Oliveira, Alexandre A., Pombo, Maihyra Marina, Ramirez-Angulo, Hirma, Rocha, Maira, Scudeller, Veridiana Vizoni, Sierra, Rodrigo, Tirado, Milton, Umaña, Maria Natalia, van der Heijden, Geertje, Vilanova Torre, Emilio, Reategui, Manuel Augusto Ahuite, Baider, Cláudia, Balslev, Henrik, Cárdenas, Sasha, Casas, Luisa Fernanda, Endara, María José, Farfan-Rios, William, Ferreira, Cid, Linares-Palomino, Reynaldo, Mendoza, Casimiro, Mesones, Italo, Parada, Germaine Alexander, Torres-Lezama, Armando, Urrego Giraldo, Ligia Estela, Villarroel, Daniel, Zagt, Roderick, Alexiades, Miguel N., de Oliveira, Edmar Almeida, Garcia-Cabrera, Karina, Hernandez, Lionel, Cuenca, Walter Palacios, Pansini, Susamar, Pauletto, Daniela, Ramirez Arevalo, Freddy, Sampaio, Adeilza Felipe, Valderrama Sandoval, Elvis H., Gamarra, Luis Valenzuela, Levesley, Aurora, Pickavance, Georgia, and Melgaço, Karina

Published
2023
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18. Unraveling Amazon tree community assembly using Maximum Information Entropy: a quantitative analysis of tropical forest ecology

Author

Pos, Edwin, de Souza Coelho, Luiz, de Andrade Lima Filho, Diogenes, Salomão, Rafael P., Amaral, Iêda Leão, de Almeida Matos, Francisca Dionízia, Castilho, Carolina V., Phillips, Oliver L., Guevara, Juan Ernesto, de Jesus Veiga Carim, Marcelo, López, Dairon Cárdenas, Magnusson, William E., Wittmann, Florian, Irume, Mariana Victória, Martins, Maria Pires, Sabatier, Daniel, da Silva Guimarães, José Renan, Molino, Jean-François, Bánki, Olaf S., Piedade, Maria Teresa Fernandez, Pitman, Nigel C. A., Mendoza, Abel Monteagudo, Ramos, José Ferreira, Hawes, Joseph E., Almeida, Everton José, Barbosa, Luciane Ferreira, Cavalheiro, Larissa, dos Santos, Márcia Cléia Vilela, Luize, Bruno Garcia, de Leão Novo, Evlyn Márcia Moraes, Vargas, Percy Núñez, Silva, Thiago Sanna Freire, Venticinque, Eduardo Martins, Manzatto, Angelo Gilberto, Reis, Neidiane Farias Costa, Terborgh, John, Casula, Katia Regina, Coronado, Euridice N. Honorio, Montero, Juan Carlos, Marimon, Beatriz S., Marimon-Junior, Ben Hur, Feldpausch, Ted R., Duque, Alvaro, Baraloto, Chris, Arboleda, Nicolás Castaño, Engel, Julien, Petronelli, Pascal, Zartman, Charles Eugene, Killeen, Timothy J., Vasquez, Rodolfo, Mostacedo, Bonifacio, Assis, Rafael L., Schöngart, Jochen, Castellanos, Hernán, de Medeiros, Marcelo Brilhante, Simon, Marcelo Fragomeni, Andrade, Ana, Camargo, José Luís, Demarchi, Layon O., Laurance, William F., Laurance, Susan G. W., de Sousa Farias, Emanuelle, Lopes, Maria Aparecida, Magalhães, José Leonardo Lima, Nascimento, Henrique Eduardo Mendonça, de Queiroz, Helder Lima, Aymard, Gerardo A. C., Brienen, Roel, Revilla, Juan David Cardenas, Costa, Flávia R. C., Quaresma, Adriano, Vieira, Ima Célia Guimarães, Cintra, Bruno Barçante Ladvocat, Stevenson, Pablo R., Feitosa, Yuri Oliveira, Duivenvoorden, Joost F., Mogollón, Hugo F., Ferreira, Leandro Valle, Comiskey, James A., Draper, Freddie, de Toledo, José Julio, Damasco, Gabriel, Dávila, Nállarett, García-Villacorta, Roosevelt, Lopes, Aline, Vicentini, Alberto, Noronha, Janaína Costa, Barbosa, Flávia Rodrigues, de Sá Carpanedo, Rainiellen, Emilio, Thaise, Levis, Carolina, de Jesus Rodrigues, Domingos, Schietti, Juliana, Souza, Priscila, Alonso, Alfonso, Dallmeier, Francisco, Gomes, Vitor H. F., Lloyd, Jon, Neill, David, de Aguiar, Daniel Praia Portela, Araujo-Murakami, Alejandro, Arroyo, Luzmila, Carvalho, Fernanda Antunes, de Souza, Fernanda Coelho, do Amaral, Dário Dantas, Feeley, Kenneth J., Gribel, Rogerio, Pansonato, Marcelo Petratti, Barlow, Jos, Berenguer, Erika, Ferreira, Joice, Fine, Paul V. A., Guedes, Marcelino Carneiro, Jimenez, Eliana M., Licona, Juan Carlos, Mora, Maria Cristina Peñuela, Peres, Carlos A., Zegarra, Boris Eduardo Villa, Cerón, Carlos, Henkel, Terry W., Maas, Paul, Silveira, Marcos, Stropp, Juliana, Thomas-Caesar, Raquel, Baker, Tim R., Daly, Doug, Dexter, Kyle G., Householder, John Ethan, Huamantupa-Chuquimaco, Isau, Pennington, Toby, Paredes, Marcos Ríos, Fuentes, Alfredo, Pena, José Luis Marcelo, Silman, Miles R., Tello, J. Sebastián, Chave, Jerome, Valverde, Fernando Cornejo, Di Fiore, Anthony, Hilário, Renato Richard, Phillips, Juan Fernando, Rivas-Torres, Gonzalo, van Andel, Tinde R., von Hildebrand, Patricio, Barbosa, Edelcilio Marques, de Matos Bonates, Luiz Carlos, Doza, Hilda Paulette Dávila, Fonty, Émile, Gómez, Ricardo Zárate, Gonzales, Therany, Gonzales, George Pepe Gallardo, Guillaumet, Jean-Louis, Hoffman, Bruce, Junqueira, André Braga, Malhi, Yadvinder, de Andrade Miranda, Ires Paula, Pinto, Linder Felipe Mozombite, Prieto, Adriana, Rudas, Agustín, Ruschel, Ademir R., Silva, Natalino, Vela, César I. A., Vos, Vincent Antoine, Zent, Egleé L., Zent, Stanford, Albuquerque, Bianca Weiss, Cano, Angela, Correa, Diego F., Costa, Janaina Barbosa Pedrosa, Flores, Bernardo Monteiro, Holmgren, Milena, Nascimento, Marcelo Trindade, Oliveira, Alexandre A., Ramirez-Angulo, Hirma, Rocha, Maira, Scudeller, Veridiana Vizoni, Sierra, Rodrigo, Tirado, Milton, Umaña, Maria Natalia, van der Heijden, Geertje, Torre, Emilio Vilanova, Vriesendorp, Corine, Wang, Ophelia, Young, Kenneth R., Reategui, Manuel Augusto Ahuite, Baider, Cláudia, Balslev, Henrik, Cárdenas, Sasha, Casas, Luisa Fernanda, Farfan-Rios, William, Ferreira, Cid, Linares-Palomino, Reynaldo, Mendoza, Casimiro, Mesones, Italo, Torres-Lezama, Armando, Giraldo, Ligia Estela Urrego, Villarroel, Daniel, Zagt, Roderick, Alexiades, Miguel N., Garcia-Cabrera, Karina, Hernandez, Lionel, Milliken, William, Cuenca, Walter Palacios, Pansini, Susamar, Pauletto, Daniela, Arevalo, Freddy Ramirez, Sampaio, Adeilza Felipe, Sandoval, Elvis H. Valderrama, Gamarra, Luis Valenzuela, Boenisch, Gerhard, Kattge, Jens, Kraft, Nathan, Levesley, Aurora, Melgaço, Karina, Pickavance, Georgia, Poorter, Lourens, and ter Steege, Hans

Published
2023
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19. Inflammasomes are activated in response to SARS-CoV-2 infection and are associated with COVID-19 severity in patients

Author

Rodrigues, Tamara S, de Sá, Keyla SG, Ishimoto, Adriene Y, Becerra, Amanda, Oliveira, Samuel, Almeida, Leticia, Gonçalves, Augusto V, Perucello, Debora B, Andrade, Warrison A, Castro, Ricardo, Veras, Flavio P, Toller-Kawahisa, Juliana E, Nascimento, Daniele C, de Lima, Mikhael HF, Silva, Camila MS, Caetite, Diego B, Martins, Ronaldo B, Castro, Italo A, Pontelli, Marjorie C, de Barros, Fabio C, do Amaral, Natália B, Giannini, Marcela C, Bonjorno, Letícia P, Lopes, Maria Isabel F, Santana, Rodrigo C, Vilar, Fernando C, Auxiliadora-Martins, Maria, Luppino-Assad, Rodrigo, de Almeida, Sergio CL, de Oliveira, Fabiola R, Batah, Sabrina S, Siyuan, Li, Benatti, Maira N, Cunha, Thiago M, Alves-Filho, José C, Cunha, Fernando Q, Cunha, Larissa D, Frantz, Fabiani G, Kohlsdorf, Tiana, Fabro, Alexandre T, Arruda, Eurico, de Oliveira, Renê DR, Louzada-Junior, Paulo, and Zamboni, Dario S

Abstract

Severe cases of COVID-19 are characterized by a strong inflammatory process that may ultimately lead to organ failure and patient death. The NLRP3 inflammasome is a molecular platform that promotes inflammation via cleavage and activation of key inflammatory molecules including active caspase-1 (Casp1p20), IL-1β, and IL-18. Although participation of the inflammasome in COVID-19 has been highly speculated, the inflammasome activation and participation in the outcome of the disease are unknown. Here we demonstrate that the NLRP3 inflammasome is activated in response to SARS-CoV-2 infection and is active in COVID-19 patients. Studying moderate and severe COVID-19 patients, we found active NLRP3 inflammasome in PBMCs and tissues of postmortem patients upon autopsy. Inflammasome-derived products such as Casp1p20 and IL-18 in the sera correlated with the markers of COVID-19 severity, including IL-6 and LDH. Moreover, higher levels of IL-18 and Casp1p20 are associated with disease severity and poor clinical outcome. Our results suggest that inflammasomes participate in the pathophysiology of the disease, indicating that these platforms might be a marker of disease severity and a potential therapeutic target for COVID-19.

Published
2021

20. Description, distribution and ecology of living Reophax pyriformis n. sp. (Campos Basin, South Atlantic Ocean)

Author

Yamashita, Cintia, Sousa, Silvia Helena de Mello e, Kaminski, Michael A., Martins, Maria Virgínia Alves, Elmadjian, Carlos Eduardo Leão, Nagai, Renata Hanae, Yamamoto, Naira Tiemi, Koutsoukos, Eduardo Apostolos Machado, and Figueira, Rubens Cesar Lopes

Subjects
Quantitative Biology - Populations and Evolution
Abstract

The distribution of living (rose Bengal stained) Reophax pyriformis Yamashita, Sousa and Kaminski, n. sp., an agglutinated benthic foraminiferal species, was analyzed in the area of the Campos Basin (southeastern Brazilian continental margin). The study is based on 34 oceanographic stations (54 samples), located between 400 m and 3,000 m water depth. The distribution of living Reophax pyriformis n.sp. density is compared to sedimentological parameters, such as total organic carbon, total nitrogen, calcium carbonate, phytopigment, lipids biomarkers (sterols, fatty acids and n-alcohols), total lipids, and bacterial biomass, as well as the particulate organic matter flux to the seafloor. This species was found in the range of 1,000--1,200 m water depth, with an average living depth of 1.52 cm in the sediment. The distribution of this species seems to be related to lipid biomarkers (allochthone and/or continental derivative, zooplankton and/or fauna, phytoplankton or primary producers) and total organic carbon under the influence of Intermediate Western Boundary Current conditions.

Published
2019

21. Rarity of monodominance in hyperdiverse Amazonian forests.

Author

Ter Steege, Hans, Henkel, Terry W, Helal, Nora, Marimon, Beatriz S, Marimon-Junior, Ben Hur, Huth, Andreas, Groeneveld, Jürgen, Sabatier, Daniel, Coelho, Luiz de Souza, Filho, Diogenes de Andrade Lima, Salomão, Rafael P, Amaral, Iêda Leão, Matos, Francisca Dionízia de Almeida, Castilho, Carolina V, Phillips, Oliver L, Guevara, Juan Ernesto, Carim, Marcelo de Jesus Veiga, Cárdenas López, Dairon, Magnusson, William E, Wittmann, Florian, Irume, Mariana Victória, Martins, Maria Pires, Guimarães, José Renan da Silva, Molino, Jean-François, Bánki, Olaf S, Piedade, Maria Teresa Fernandez, Pitman, Nigel CA, Mendoza, Abel Monteagudo, Ramos, José Ferreira, Luize, Bruno Garcia, Moraes de Leão Novo, Evlyn Márcia, Núñez Vargas, Percy, Silva, Thiago Sanna Freire, Venticinque, Eduardo Martins, Manzatto, Angelo Gilberto, Reis, Neidiane Farias Costa, Terborgh, John, Casula, Katia Regina, Honorio Coronado, Euridice N, Montero, Juan Carlos, Feldpausch, Ted R, Duque, Alvaro, Costa, Flávia RC, Arboleda, Nicolás Castaño, Schöngart, Jochen, Killeen, Timothy J, Vasquez, Rodolfo, Mostacedo, Bonifacio, Demarchi, Layon O, Assis, Rafael L, Baraloto, Chris, Engel, Julien, Petronelli, Pascal, Castellanos, Hernán, de Medeiros, Marcelo Brilhante, Quaresma, Adriano, Simon, Marcelo Fragomeni, Andrade, Ana, Camargo, José Luís, Laurance, Susan GW, Laurance, William F, Rincón, Lorena M, Schietti, Juliana, Sousa, Thaiane R, de Sousa Farias, Emanuelle, Lopes, Maria Aparecida, Magalhães, José Leonardo Lima, Mendonça Nascimento, Henrique Eduardo, Lima de Queiroz, Helder, Aymard C, Gerardo A, Brienen, Roel, Revilla, Juan David Cardenas, Vieira, Ima Célia Guimarães, Cintra, Bruno Barçante Ladvocat, Stevenson, Pablo R, Feitosa, Yuri Oliveira, Duivenvoorden, Joost F, Mogollón, Hugo F, Araujo-Murakami, Alejandro, Ferreira, Leandro Valle, Lozada, José Rafael, Comiskey, James A, de Toledo, José Julio, Damasco, Gabriel, Dávila, Nállarett, Draper, Freddie, García-Villacorta, Roosevelt, Lopes, Aline, Vicentini, Alberto, Alonso, Alfonso, Dallmeier, Francisco, Gomes, Vitor HF, Lloyd, Jon, Neill, David, de Aguiar, Daniel Praia Portela, Arroyo, Luzmila, Carvalho, Fernanda Antunes, de Souza, Fernanda Coelho, do Amaral, Dário Dantas, and Feeley, Kenneth J

Abstract

Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such "monodominant" forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors.

Published
2019

22. Aurora kinase A drives the evolution of resistance to third-generation EGFR inhibitors in lung cancer

Author

Shah, Khyati N, Bhatt, Roma, Rotow, Julia, Rohrberg, Julia, Olivas, Victor, Wang, Victoria E, Hemmati, Golzar, Martins, Maria M, Maynard, Ashley, Kuhn, Jonathan, Galeas, Jacqueline, Donnella, Hayley J, Kaushik, Swati, Ku, Angel, Dumont, Sophie, Krings, Gregor, Haringsma, Henry J, Robillard, Liliane, Simmons, Andrew D, Harding, Thomas C, McCormick, Frank, Goga, Andrei, Blakely, Collin M, Bivona, Trever G, and Bandyopadhyay, Sourav

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Rare Diseases, Lung, Cancer, Lung Cancer, 5.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Development of treatments and therapeutic interventions, 6.1 Pharmaceuticals, Good Health and Well Being, Animals, Apoptosis, Aurora Kinase A, Cell Count, Cell Cycle Proteins, Cell Line, Tumor, Drug Resistance, Neoplasm, ErbB Receptors, Humans, Lung Neoplasms, Mice, Microtubule-Associated Proteins, Mutation, Neoplasm, Residual, Nuclear Proteins, Phosphorylation, Protein Kinase Inhibitors, Medical and Health Sciences, Immunology, Biomedical and clinical sciences, Health sciences
Abstract

Although targeted therapies often elicit profound initial patient responses, these effects are transient due to residual disease leading to acquired resistance. How tumors transition between drug responsiveness, tolerance and resistance, especially in the absence of preexisting subclones, remains unclear. In epidermal growth factor receptor (EGFR)-mutant lung adenocarcinoma cells, we demonstrate that residual disease and acquired resistance in response to EGFR inhibitors requires Aurora kinase A (AURKA) activity. Nongenetic resistance through the activation of AURKA by its coactivator TPX2 emerges in response to chronic EGFR inhibition where it mitigates drug-induced apoptosis. Aurora kinase inhibitors suppress this adaptive survival program, increasing the magnitude and duration of EGFR inhibitor response in preclinical models. Treatment-induced activation of AURKA is associated with resistance to EGFR inhibitors in vitro, in vivo and in most individuals with EGFR-mutant lung adenocarcinoma. These findings delineate a molecular path whereby drug resistance emerges from drug-tolerant cells and unveils a synthetic lethal strategy for enhancing responses to EGFR inhibitors by suppressing AURKA-driven residual disease and acquired resistance.

Published
2019

25. Implementation of a text messaging intervention to patients on warfarin therapy in Brazilian primary care units: a quasi-experimental study

Author

Souza-Silva, Maira Viana Rego, Domingues, Mara Luiza de Paiva, Chagas, Victor Schulthais, Pereira, Daniella Nunes, de Sá, Laura Caetano, Almeida, Mychelle Stefany Santos, Sales, Thaís Lorenna Souza, Raposo, Magda César, Guimarães, Nathalia Sernizon, Oliveira, João Antônio de Queiroz, Ribeiro, Antonio Luiz Pinho, Cardoso, Clareci Silva, Martins, Maria Auxiliadora Parreiras, Enes, Thais Bueno, Soares, Thiago Barbabela de Castro, Baldoni, André Oliveira, and Marcolino, Milena Soriano

Published
2022
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27. Peculiar enhancement in the neutral K and Na layers observed during atypical E-region event in the South American magnetic anomaly (SAMA) region.

Author

Andrioli, Vania F., Xu, Jiyao, Batista, Paulo P., Resende, Laysa C. A., Silva, Ligia A. Da, Pimenta, Alexandre A., Martins, Maria P. P., Santos, Angela M., Moro, Juliano, Vieira, Luis, Chen, Sony S., Yang, Guotao, Wang, Chi, and Liu, Zhengkuan

Subjects
MAGNETIC anomalies, SODIUM, LATITUDE, ELECTRONS, METALS
Abstract

The sudden enhancement in the mesospheric neutral metal layers (Ns) has been studied in different latitudes for decades. Specifically, at 23°S, Sodium Ns layers have been analyzed since their first observation at the end of the seventies. Several studies have reported Sodium Ns during events of energetic particle precipitation (EPP) and the formation of auroral-type sporadic E (Esa) layers at high-latitude stations. The Esa layers are also observed in the Brazilian low-latitude sector during the EPP events due to the South American Magnetic Anomaly (SAMA). However, despite extensive studies on the SAMA region, no reports exist about the co-occurrence of the Ns layer and the Esa layer. Therefore, in the present work, for the first time, we observed on 26 April 2023 a peculiar Ns layer event synchronously occurring with the development of the Esa layer in the SAMA region. [ABSTRACT FROM AUTHOR]

Published
2024
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30. Systemic Immunity Is Required for Effective Cancer Immunotherapy

Author

Spitzer, Matthew H, Carmi, Yaron, Reticker-Flynn, Nathan E, Kwek, Serena S, Madhireddy, Deepthi, Martins, Maria M, Gherardini, Pier Federico, Prestwood, Tyler R, Chabon, Jonathan, Bendall, Sean C, Fong, Lawrence, Nolan, Garry P, and Engleman, Edgar G

Subjects
Vaccine Related, Cancer, Bioengineering, Immunization, Rare Diseases, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, Inflammatory and immune system, Animals, B7-H1 Antigen, Bone Marrow, Cell Proliferation, Disease Models, Animal, Female, Humans, Immune Tolerance, Immunotherapy, Killer Cells, Natural, Lymphocyte Activation, Lymphoid Tissue, Male, Melanoma, Mice, Inbred BALB C, Mice, Inbred C57BL, Neoplasms, T-Lymphocyte Subsets, Triple Negative Breast Neoplasms, Tumor Microenvironment, cancer immunotherapy, immune responses, immunotherapy, mass cytometry, secondary lymphoid organs, single-cell analysis, systems immunology, tumor immunology, tumor microenvironment, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Immune responses involve coordination across cell types and tissues. However, studies in cancer immunotherapy have focused heavily on local immune responses in the tumor microenvironment. To investigate immune activity more broadly, we performed an organism-wide study in genetically engineered cancer models using mass cytometry. We analyzed immune responses in several tissues after immunotherapy by developing intuitive models for visualizing single-cell data with statistical inference. Immune activation was evident in the tumor and systemically shortly after effective therapy was administered. However, during tumor rejection, only peripheral immune cells sustained their proliferation. This systemic response was coordinated across tissues and required for tumor eradication in several immunotherapy models. An emergent population of peripheral CD4 T cells conferred protection against new tumors and was significantly expanded in patients responding to immunotherapy. These studies demonstrate the critical impact of systemic immune responses that drive tumor rejection.

Published
2017

32. Online Role-Plays: Combining Situational and Interactional Authenticity in Foreign Language Learning

Author

Correia Martins, Maria de Lurdes, Moreira, Gillian, and Moreira, António

Abstract

Role-plays have been almost ubiquitous in foreign language classes and their potential has been widely recognised. In the last decade, the dissemination of Web 2.0 has created a wide range of possibilities for this type of activity, including conducting online role-plays between institutions, the opportunity to combine synchronous and asynchronous communication tools and also articulate online with face-to-face interactions. Online role-plays are first and foremost a social process in which knowledge is emergent resulting from interactions between participants. It is also an activity that mirrors contextualised everyday situations and students are faced with new information, promoting research and reflection, thus enhancing autonomy. Within a dialogical and dialectical perspective of English language learning, the following research question was developed: how can online role-plays in English language learning in higher education be integrated in order to enhance the development of communicative competence? In order to answer the research question, an action research project was carried out, according to the model proposed by Stringer (2007), and an online role-play was implemented over six weeks in the English II course unit from the degree in Tourism at the Polytechnic Institute of Viseu, Portugal. [For full proceedings, see ED565044.]

Published
2013

34. Promising self-emulsifying drug delivery system loaded with lycopene from red guava (Psidium guajava L.): in vivo toxicity, biodistribution and cytotoxicity on DU-145 prostate cancer cells

Author

Vasconcelos, Andreanne G., Barros, Ana Luisa A. N., Cabral, Wanessa F., Moreira, Daniel C., da Silva, Ingrid Gracielle M., Silva-Carvalho, Amandda É., de Almeida, Miguel P., Albuquerque, Lucas F. F., dos Santos, Raimunda C., S. Brito, Ana Karolinne, Saldanha-Araújo, Felipe, Arcanjo, Daniel D. R., C. Martins, Maria do Carmo, dos S. Borges, Tatiana K., Báo, Sônia N., Plácido, Alexandra, Eaton, Peter, Kuckelhaus, Selma A. S., and Leite, José Roberto S. A.

Published
2021
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36. Direct tissue-sensing reprograms TLR4+ Tfh-like cells inflammatory profile in the joints of rheumatoid arthritis patients

Author

Amaral-Silva, Daniela, Gonçalves, Rute, Torrão, Rita C., Torres, Rita, Falcão, Sandra, Gonçalves, Maria João, Araújo, Maria Paula, Martins, Maria José, Lopes, Carina, Neto, Agna, Marona, José, Costa, Tiago, Castelão, Walter, Silva, Ana Bento, Silva, Inês, Lourenço, Maria Helena, Mateus, Margarida, Gonçalves, Nuno Pina, Manica, Santiago, Costa, Manuela, Pimentel-Santos, Fernando M., Mourão, Ana Filipa, Branco, Jaime C., and Soares, Helena

Published
2021
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40. Web 2.0 and Authentic Foreign Language Learning at Higher Education Level

Author

Martins, Maria de Lurdes Correia, Moreira, Gillian, and Moreira, António

Abstract

Web 2.0 has afforded a number of opportunities for foreign language learning due to its open, participatory and social nature. A crucial aspect is authenticity--both situational and interactional--since students become involved in meaningful tasks, interacting in the target language with an authentic audience. In this paper we will reflect upon the potential of Web 2.0 tools, namely social networks, wikis and podcasts in enhancing foreign language learning opportunities at higher education level under the Bologna process. An action research project was carried out with undergraduate tourism students from Portugal. During two semesters, interactional tasks using Web 2.0 applications and involving the construction of collaborative outputs were designed and implemented, with the main goal of promoting and developing interactive communication skills in English amongst students with low levels of motivation and prior learning. Data was collected at different stages of the project aided by different data collection tools, namely questionnaires, focus group interviews, individual interviews, written reflections and corpus analyses, and a combination of quantitative and qualitative approaches was used. Results point towards impacts on students' language awareness, which has contributed to the creation of opportunities for language self-development, enhancing autonomous learning. In addition, it increased motivation for language learning by providing more opportunities for authentic input, social interaction and collaboration through the target language. Finally, the development of meta-competences such as metacognition and meta-learning can be highlighted. [For the complete volume, see ED574893.]

Published
2012

42. Linking Tumor Mutations to Drug Responses via a Quantitative Chemical–Genetic Interaction Map

Author

Martins, Maria M, Zhou, Alicia Y, Corella, Alexandra, Horiuchi, Dai, Yau, Christina, Rakhshandehroo, Taha, Gordan, John D, Levin, Rebecca S, Johnson, Jeff, Jascur, John, Shales, Mike, Sorrentino, Antonio, Cheah, Jaime, Clemons, Paul A, Shamji, Alykhan F, Schreiber, Stuart L, Krogan, Nevan J, Shokat, Kevan M, McCormick, Frank, Goga, Andrei, and Bandyopadhyay, Sourav

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Oncology and Carcinogenesis, Cancer, Health Disparities, Human Genome, Women's Health, Cancer Genomics, Biotechnology, Precision Medicine, Breast Cancer, Aetiology, Development of treatments and therapeutic interventions, 5.1 Pharmaceuticals, 2.1 Biological and endogenous factors, Generic health relevance, Good Health and Well Being, Animals, Breast Neoplasms, Cell Line, Tumor, Drug Resistance, Neoplasm, Drug Screening Assays, Antitumor, Female, Genomics, High-Throughput Screening Assays, Humans, Mice, Mice, Inbred BALB C, Mice, Nude, Mutation, Random Allocation, Signal Transduction, Xenograft Model Antitumor Assays, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

UnlabelledThere is an urgent need in oncology to link molecular aberrations in tumors with therapeutics that can be administered in a personalized fashion. One approach identifies synthetic-lethal genetic interactions or dependencies that cancer cells acquire in the presence of specific mutations. Using engineered isogenic cells, we generated a systematic and quantitative chemical-genetic interaction map that charts the influence of 51 aberrant cancer genes on 90 drug responses. The dataset strongly predicts drug responses found in cancer cell line collections, indicating that isogenic cells can model complex cellular contexts. Applying this dataset to triple-negative breast cancer, we report clinically actionable interactions with the MYC oncogene, including resistance to AKT-PI3K pathway inhibitors and an unexpected sensitivity to dasatinib through LYN inhibition in a synthetic lethal manner, providing new drug and biomarker pairs for clinical investigation. This scalable approach enables the prediction of drug responses from patient data and can accelerate the development of new genotype-directed therapies.SignificanceDetermining how the plethora of genomic abnormalities that exist within a given tumor cell affects drug responses remains a major challenge in oncology. Here, we develop a new mapping approach to connect cancer genotypes to drug responses using engineered isogenic cell lines and demonstrate how the resulting dataset can guide clinical interrogation.

Published
2015

43. Quantum Information, Thermofield Dynamics and Thermalized Bosonic Oscillator

Author

Trindade, Marco A. S., Filho, Lourival M. Silva, Santos, Leandro C., Martins, Maria Graças R., and Vianna, José David M.

Subjects
Quantum Physics
Abstract

We show through Thermofield Dynamics approach that the action of the thermalized quantum logic gate on the thermalized state is equivalent to thermalization of the state that arise from the application of the non-thermalized quantum logic gate. In particular, we study the effect of temperature on a mixed state associated to a system capable of implementing a CNOT quantum logic gate. According to a proposal in the literature, a way of implementing such a logic gate is by using a representation of the qubit states as elements of the Fock space of a bosonic system. We consider such a proposal and use the Thermofield Dynamics to determine the thermalized qubit states. The temperature acts as a quantum noise on pure states, making them a statistical mixture. In this context we analyze the fidelity as a function of the temperature and using the Mandel parameter, we determine temperature ranges for which the statistics of the system becomes subpoissonian, poissonian and superpoissonian. Finally, we calculate the Wigner function, allowing an analysis of the thermal state in phase space, and we obtain that the increase of temperature decreases non-classical properties of the system. The temperature range where one has a subpoissonian statistics and high fidelity is determined.

Published
2012
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44. Mapping the molecular determinants of BRAF oncogene dependence in human lung cancer

Author

Lin, Luping, Asthana, Saurabh, Chan, Elton, Bandyopadhyay, Sourav, Martins, Maria M, Olivas, Victor, Yan, Jenny Jiacheng, Pham, Luu, Wang, Mingxue Michelle, Bollag, Gideon, Solit, David B, Collisson, Eric A, Rudin, Charles M, Taylor, Barry S, and Bivona, Trever G

Subjects
Genetics, Lung Cancer, Cancer, Lung, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, Autocrine Communication, Base Sequence, Carcinoma, Non-Small-Cell Lung, Drug Resistance, Neoplasm, ErbB Receptors, Humans, Immunohistochemistry, Molecular Sequence Data, Mutation, Missense, Oncogene Protein v-akt, Phosphorylation, Proto-Oncogene Proteins B-raf, Sequence Analysis, RNA, targeted therapy, combination therapy
Abstract

Oncogenic mutations in the BRAF kinase occur in 6-8% of nonsmall cell lung cancers (NSCLCs), accounting for more than 90,000 deaths annually worldwide. The biological and clinical relevance of these BRAF mutations in NSCLC is incompletely understood. Here we demonstrate that human NSCLC cells with BRAF(V600E), but not other BRAF mutations, initially are sensitive to BRAF-inhibitor treatment. However, these BRAF(V600E) NSCLC cells rapidly acquire resistance to BRAF inhibition through at least one of two discrete molecular mechanisms: (i) loss of full-length BRAF(V600E) coupled with expression of an aberrant form of BRAF(V600E) that retains RAF pathway dependence or (ii) constitutive autocrine EGF receptor (EGFR) signaling driven by c-Jun-mediated EGFR ligand expression. BRAF(V600E) cells with EGFR-driven resistance are characterized by hyperphosphorylated protein kinase AKT, a biomarker we validated in BRAF inhibitor-resistant NSCLC clinical specimens. These data reveal the multifaceted molecular mechanisms by which NSCLCs establish and regulate BRAF oncogene dependence, provide insights into BRAF-EGFR signaling crosstalk, and uncover mechanism-based strategies to optimize clinical responses to BRAF oncogene inhibition.

Published
2014

45. Long-term eutrophication and contamination of the central area of Sepetiba Bay (SW Brazil)

Author

Castelo, Wellen Fernanda Louzada, Martins, Maria Virgínia Alves, de Lima Ferreira, Paulo Alves, Figueira, Rubens, da Costa, Carolina Ferreira, da Fonseca, Lauren Brito, Bergamashi, Sérgio, Pereira, Egberto, Terroso, Denise, Pinto, Anita Fernandes Souza, Simon, Maurício Bulhões, Socorro, Orangel Antonio Aguilera, Frontalini, Fabrizio, da Silva, Layla Cristine, Rocha, Fernando, Geraldes, Mauro, and Guerra, Josefa Varela

Published
2021
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46. Hochschild Cohomology of skew group rings and invariants

Author

Marcos, Eduardo do Nascimento, Martinez-Villa, Roberto, and Martins, Maria Izabel Ramalho

Subjects
Mathematics - Representation Theory, 16E40, 16D20, 16S37
Abstract

Let $A$ be a $k$-algebra and $G$ be a group acting on $A$. We show that $G$ also acts on the Hochschild cohomology algebra $HH^{\bullet}(A)$ and that there is a monomorphism of rings $HH^{\bullet}(A)^G \hookrightarrow HH^{\bullet}(A[G])$. That allows us to show the existence of a monomorphism from $HH^{\bullet}(\widetilde{A})^G$ into $HH^{\bullet}(A)$, where $\widetilde{A}$ is a Galois covering with group $G$.

Published
2003

48. Biased-corrected richness estimates for the Amazonian tree flora

Author

ter Steege, Hans, Prado, Paulo I., Lima, Renato A. F. de, Pos, Edwin, de Souza Coelho, Luiz, de Andrade Lima Filho, Diogenes, Salomão, Rafael P., Amaral, Iêda Leão, de Almeida Matos, Francisca Dionízia, Castilho, Carolina V., Phillips, Oliver L., Guevara, Juan Ernesto, de Jesus Veiga Carim, Marcelo, Cárdenas López, Dairon, Magnusson, William E., Wittmann, Florian, Martins, Maria Pires, Sabatier, Daniel, Irume, Mariana Victória, da Silva Guimarães, José Renan, Molino, Jean-François, Bánki, Olaf S., Piedade, Maria Teresa Fernandez, Pitman, Nigel C. A., Ramos, José Ferreira, Monteagudo Mendoza, Abel, Venticinque, Eduardo Martins, Luize, Bruno Garcia, Núñez Vargas, Percy, Silva, Thiago Sanna Freire, de Leão Novo, Evlyn Márcia Moraes, Reis, Neidiane Farias Costa, Terborgh, John, Manzatto, Angelo Gilberto, Casula, Katia Regina, Honorio Coronado, Euridice N., Montero, Juan Carlos, Duque, Alvaro, Costa, Flávia R. C., Castaño Arboleda, Nicolás, Schöngart, Jochen, Zartman, Charles Eugene, Killeen, Timothy J., Marimon, Beatriz S., Marimon-Junior, Ben Hur, Vasquez, Rodolfo, Mostacedo, Bonifacio, Demarchi, Layon O., Feldpausch, Ted R., Engel, Julien, Petronelli, Pascal, Baraloto, Chris, Assis, Rafael L., Castellanos, Hernán, Simon, Marcelo Fragomeni, de Medeiros, Marcelo Brilhante, Quaresma, Adriano, Laurance, Susan G. W., Rincón, Lorena M., Andrade, Ana, Sousa, Thaiane R., Camargo, José Luís, Schietti, Juliana, Laurance, William F., de Queiroz, Helder Lima, Nascimento, Henrique Eduardo Mendonça, Lopes, Maria Aparecida, de Sousa Farias, Emanuelle, Magalhães, José Leonardo Lima, Brienen, Roel, Aymard C., Gerardo A., Revilla, Juan David Cardenas, Vieira, Ima Célia Guimarães, Cintra, Bruno Barçante Ladvocat, Stevenson, Pablo R., Feitosa, Yuri Oliveira, Duivenvoorden, Joost F., Mogollón, Hugo F., Araujo-Murakami, Alejandro, Ferreira, Leandro Valle, Lozada, José Rafael, Comiskey, James A., de Toledo, José Julio, Damasco, Gabriel, Dávila, Nállarett, Lopes, Aline, García-Villacorta, Roosevelt, Draper, Freddie, Vicentini, Alberto, Cornejo Valverde, Fernando, Lloyd, Jon, Gomes, Vitor H. F., Neill, David, Alonso, Alfonso, Dallmeier, Francisco, de Souza, Fernanda Coelho, Gribel, Rogerio, Arroyo, Luzmila, Carvalho, Fernanda Antunes, de Aguiar, Daniel Praia Portela, do Amaral, Dário Dantas, Pansonato, Marcelo Petratti, Feeley, Kenneth J., Berenguer, Erika, Fine, Paul V. A., Guedes, Marcelino Carneiro, Barlow, Jos, Ferreira, Joice, Villa, Boris, Peñuela Mora, Maria Cristina, Jimenez, Eliana M., Licona, Juan Carlos, Cerón, Carlos, Thomas, Raquel, Maas, Paul, Silveira, Marcos, Henkel, Terry W., Stropp, Juliana, Paredes, Marcos Ríos, Dexter, Kyle G., Daly, Doug, Baker, Tim R., Huamantupa-Chuquimaco, Isau, Milliken, William, Pennington, Toby, Tello, J. Sebastián, Pena, José Luis Marcelo, Peres, Carlos A., Klitgaard, Bente, Fuentes, Alfredo, Silman, Miles R., Di Fiore, Anthony, von Hildebrand, Patricio, Chave, Jerome, van Andel, Tinde R., Hilário, Renato Richard, Phillips, Juan Fernando, Rivas-Torres, Gonzalo, Noronha, Janaína Costa, Prieto, Adriana, Gonzales, Therany, de Sá Carpanedo, Rainiellene, Gonzales, George Pepe Gallardo, Gómez, Ricardo Zárate, de Jesus Rodrigues, Domingos, Zent, Egleé L., Ruschel, Ademir R., Vos, Vincent Antoine, Fonty, Émile, Junqueira, André Braga, Doza, Hilda Paulette Dávila, Hoffman, Bruce, Zent, Stanford, Barbosa, Edelcilio Marques, Malhi, Yadvinder, de Matos Bonates, Luiz Carlos, de Andrade Miranda, Ires Paula, Silva, Natalino, Barbosa, Flávia Rodrigues, Vela, César I. A., Pinto, Linder Felipe Mozombite, Rudas, Agustín, Albuquerque, Bianca Weiss, Umaña, Maria Natalia, Carrero Márquez, Yrma Andreina, van der Heijden, Geertje, Young, Kenneth R., Tirado, Milton, Correa, Diego F., Sierra, Rodrigo, Costa, Janaina Barbosa Pedrosa, Rocha, Maira, Vilanova Torre, Emilio, Wang, Ophelia, Oliveira, Alexandre A., Kalamandeen, Michelle, Vriesendorp, Corine, Ramirez-Angulo, Hirma, Holmgren, Milena, Nascimento, Marcelo Trindade, Galbraith, David, Flores, Bernardo Monteiro, Scudeller, Veridiana Vizoni, Cano, Angela, Ahuite Reategui, Manuel Augusto, Mesones, Italo, Baider, Cláudia, Mendoza, Casimiro, Zagt, Roderick, Urrego Giraldo, Ligia Estela, Ferreira, Cid, Villarroel, Daniel, Linares-Palomino, Reynaldo, Farfan-Rios, William, Farfan-Rios, William, Casas, Luisa Fernanda, Cárdenas, Sasha, Balslev, Henrik, Torres-Lezama, Armando, Alexiades, Miguel N., Garcia-Cabrera, Karina, Valenzuela Gamarra, Luis, Valderrama Sandoval, Elvis H., Ramirez Arevalo, Freddy, Hernandez, Lionel, Sampaio, Adeilza Felipe, Pansini, Susamar, Palacios Cuenca, Walter, de Oliveira, Edmar Almeida, Pauletto, Daniela, Levesley, Aurora, Melgaço, Karina, and Pickavance, Georgia

Published
2020
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