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4. Inferences on the evolution of the ascorbic acid synthesis pathway in insects using Phylogenetic Tree Collapser (PTC), a tool for the automated collapsing of phylogenetic trees using taxonomic information

Author

Glez-Peña Daniel, López-Fernández Hugo, Duque Pedro, Vieira Cristina P., and Vieira Jorge

Subjects
evolutionary biology, phylogenetic trees, sequence analysis, Biotechnology, TP248.13-248.65
Abstract

When inferring the evolution of a gene/gene family, it is advisable to use all available coding sequences (CDS) from as many species genomes as possible in order to infer and date all gene duplications and losses. Nowadays, this means using hundreds or even thousands of CDSs, which makes the inferred phylogenetic trees difficult to visualize and interpret. Therefore, it is useful to have an automated way of collapsing large phylogenetic trees according to a taxonomic term decided by the user (family, class, or order, for instance), in order to highlight the minimal set of sequences that should be used to recapitulate the full history of the gene/gene family being studied at that taxonomic level, that can be refined using additional software. Here we present the Phylogenetic Tree Collapser (PTC) program (https://github.com/pegi3s/phylogenetic-tree-collapser), a flexible tool for automated tree collapsing using taxonomic information, that can be easily used by researchers without a background in informatics, since it only requires the installation of Docker, Podman or Singularity. The utility of PTC is demonstrated by addressing the evolution of the ascorbic acid synthesis pathway in insects. A Docker image is available at Docker Hub (https://hub.docker.com/r/pegi3s/phylogenetic-tree-collapser) with PTC installed and ready-to-run.

Published
2024
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6. Immunoglobulin, glucocorticoid, or combination therapy for multisystem inflammatory syndrome in children: a propensity-weighted cohort study

Author

Channon-Wells, Samuel, Vito, Ortensia, McArdle, Andrew J, Seaby, Eleanor G, Patel, Harsita, Shah, Priyen, Pazukhina, Ekaterina, Wilson, Clare, Broderick, Claire, D'Souza, Giselle, Keren, Ilana, Nijman, Ruud G, Tremoulet, Adriana, Munblit, Daniel, Ulloa-Gutierrez, Rolando, Carter, Michael J, Ramnarayan, Padmanabhan, De, Tisham, Hoggart, Clive, Whittaker, Elizabeth, Herberg, Jethro A, Kaforou, Myrsini, Cunnington, Aubrey J, Blyuss, Oleg, Levin, Michael, consortium, Best Available Treatment Study, Chouli, Mohamed, Hamadouche, Nacera, Ladj, Mohamed Samir, Vázquez, Jorge Agrimbau, Carmona, Rodrigo, Collia, Adrian Gustavo, Ellis, Alejandro, Natta, Diego, Pérez, Laura, Rubiños, Mayra, Veliz, Natalia, Yori, Silvana, Britton, Philip N, Burgner, David P, Carey, Emma, Crawford, Nigel W, Giuliano, Hayley, McMinn, Alissa, Wong, Shirley, Wood, Nicholas, Holter, Wolfgang, Krainz, Matthias, Ulreich, Raphael, Zurl, Christoph, Dehoorne, Joke, Haerynck, Filomeen, Hoste, Levi, Schelstraete, Petra, Vandekerckhove, Kristof, Willems, Jef, Farias, Camila Giuliana Almeida, Almeida, Flávia Jacqueline, Leal, Izabel Alves, da Silva, André Ricardo Araujo, Araujo e Silva, Anna Esther, Barreiro, Sabrina TA, da Silva, Daniella Gregória Bomfim Prado, Cervi, Maria Celia, dos Santos Naja Cardoso, Mirian Viviane, Teixeira, Cristiane Henriques, Jarovsky, Daniel, Araujo, Julienne Martins, Berezin, Eitan Naaman, Sáfadi, Marco Aurélio Palazzi, la Ossa, Rolando Andres Paternina-de, Vieira, Cristina Souza, Dimitrova, Anna, Ganeva, Margarita, Stefanov, Stefan, Telcharova-Mihaylovska, Albena, Biggs, Catherine M, Lopez, Alison, Scuccimarri, Rosie, Tan, Ryan, Wasserman, Sam, Withington, Davinia, Ampuero, Camila, Aravena, Javiera, B, Raul Bustos, Casanova, Daniel, Cruces, Pablo, Diaz, Franco, García-Salum, Tamara, Godoy, Loreto, Medina, Rafael A, Galaz, Gonzalo Valenzuela, Camacho-Moreno, Germán, Avila-Aguero, María L, Brenes-Chacón, Helena, Camacho-Badilla, Kattia, Ivankovich-Escoto, Gabriela, Naranjo-Zuniga, Gabriela, and Soriano-Fallas, Alejandra

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Comparative Effectiveness Research, Clinical Research, 6.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Best Available Treatment Study (BATS) consortium, Clinical sciences
Abstract

BackgroundMultisystem inflammatory syndrome in children (MIS-C), a hyperinflammatory condition associated with SARS-CoV-2 infection, has emerged as a serious illness in children worldwide. Immunoglobulin or glucocorticoids, or both, are currently recommended treatments.MethodsThe Best Available Treatment Study evaluated immunomodulatory treatments for MIS-C in an international observational cohort. Analysis of the first 614 patients was previously reported. In this propensity-weighted cohort study, clinical and outcome data from children with suspected or proven MIS-C were collected onto a web-based Research Electronic Data Capture database. After excluding neonates and incomplete or duplicate records, inverse probability weighting was used to compare primary treatments with intravenous immunoglobulin, intravenous immunoglobulin plus glucocorticoids, or glucocorticoids alone, using intravenous immunoglobulin as the reference treatment. Primary outcomes were a composite of inotropic or ventilator support from the second day after treatment initiation, or death, and time to improvement on an ordinal clinical severity scale. Secondary outcomes included treatment escalation, clinical deterioration, fever, and coronary artery aneurysm occurrence and resolution. This study is registered with the ISRCTN registry, ISRCTN69546370.FindingsWe enrolled 2101 children (aged 0 months to 19 years) with clinically diagnosed MIS-C from 39 countries between June 14, 2020, and April 25, 2022, and, following exclusions, 2009 patients were included for analysis (median age 8·0 years [IQR 4·2-11·4], 1191 [59·3%] male and 818 [40·7%] female, and 825 [41·1%] White). 680 (33·8%) patients received primary treatment with intravenous immunoglobulin, 698 (34·7%) with intravenous immunoglobulin plus glucocorticoids, 487 (24·2%) with glucocorticoids alone; 59 (2·9%) patients received other combinations, including biologicals, and 85 (4·2%) patients received no immunomodulators. There were no significant differences between treatments for primary outcomes for the 1586 patients with complete baseline and outcome data that were considered for primary analysis. Adjusted odds ratios for ventilation, inotropic support, or death were 1·09 (95% CI 0·75-1·58; corrected p value=1·00) for intravenous immunoglobulin plus glucocorticoids and 0·93 (0·58-1·47; corrected p value=1·00) for glucocorticoids alone, versus intravenous immunoglobulin alone. Adjusted average hazard ratios for time to improvement were 1·04 (95% CI 0·91-1·20; corrected p value=1·00) for intravenous immunoglobulin plus glucocorticoids, and 0·84 (0·70-1·00; corrected p value=0·22) for glucocorticoids alone, versus intravenous immunoglobulin alone. Treatment escalation was less frequent for intravenous immunoglobulin plus glucocorticoids (OR 0·15 [95% CI 0·11-0·20]; p

Published
2023

8. Auto-phylo v2 and auto-phylo-pipeliner: building advanced, flexible, and reusable pipelines for phylogenetic inferences, estimation of variability levels and identification of positively selected amino acid sites

Author

López-Fernández Hugo, Pinto Miguel, Vieira Cristina P., Duque Pedro, Reboiro-Jato Miguel, and Vieira Jorge

Subjects
docker, pipeline maker, phylogenetics, gametophytic self-incompatibility, prunus s-rnase, Biotechnology, TP248.13-248.65
Abstract

The vast amount of genome sequence data that is available, and that is predicted to drastically increase in the near future, can only be efficiently dealt with by building automated pipelines. Indeed, the Earth Biogenome Project will produce high-quality reference genome sequences for all 1.8 million named living eukaryote species, providing unprecedented insight into the evolution of genes and gene families, and thus on biological issues. Here, new modules for gene annotation, further BLAST search algorithms, further multiple sequence alignment methods, the adding of reference sequences, further tree rooting methods, the estimation of rates of synonymous and nonsynonymous substitutions, and the identification of positively selected amino acid sites, have been added to auto-phylo (version 2), a recently developed software to address biological problems using phylogenetic inferences. Additionally, we present auto-phylo-pipeliner, a graphical user interface application that further facilitates the creation and running of auto-phylo pipelines. Inferences on S-RNase specificity, are critical for both cross-based breeding and for the establishment of pollination requirements. Therefore, as a test case, we develop an auto-phylo pipeline to identify amino acid sites under positive selection, that are, in principle, those determining S-RNase specificity, starting from both non-annotated Prunus genomes and sequences available in public databases.

Published
2024
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10. Auto-phylo: A Pipeline Maker for Phylogenetic Studies

Author

López-Fenández, Hugo, Pinto, Miguel, Vieira, Cristina P., Duque, Pedro, Reboiro-Jato, Miguel, Vieira, Jorge, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Rocha, Miguel, editor, Fdez-Riverola, Florentino, editor, Mohamad, Mohd Saberi, editor, and Gil-González, Ana Belén, editor

Published
2023
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11. EvoPPI 2: A Web and Local Platform for the Comparison of Protein–Protein Interaction Data from Multiple Sources from the Same and Distinct Species

Author

Reboiro-Jato, Miguel, Vieira, Jorge, Rocha, Sara, Sousa, André D., López-Fernández, Hugo, Vieira, Cristina P., Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Fdez-Riverola, Florentino, editor, Rocha, Miguel, editor, Mohamad, Mohd Saberi, editor, Caraiman, Simona, editor, and Gil-González, Ana Belén, editor

Published
2023
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15. Immunoglobulin, glucocorticoid, or combination therapy for multisystem inflammatory syndrome in children: a propensity-weighted cohort study

Author

Chouli, Mohamed, Hamadouche, Nacera, Ladj, Mohamed Samir, Agrimbau Vázquez, Jorge, Carmona, Rodrigo, Collia, Adrian Gustavo, Ellis, Alejandro, Natta, Diego, Pérez, Laura, Rubiños, Mayra, Veliz, Natalia, Yori, Silvana, Britton, Philip N., Burgner, David P., Carey, Emma, Crawford, Nigel W., Giuliano, Hayley, McMinn, Alissa, Wong, Shirley, Wood, Nicholas, Holter, Wolfgang, Krainz, Matthias, Ulreich, Raphael, Zurl, Christoph, Dehoorne, Joke, Haerynck, Filomeen, Hoste, Levi, Schelstraete, Petra, Vandekerckhove, Kristof, Willems, Jef, Almeida Farias, Camila Giuliana, Almeida, Flávia Jacqueline, Alves Leal, Izabel, Araujo da Silva, André Ricardo, Araujo e Silva, Anna Esther, Barreiro, Sabrina T.A., Bomfim Prado da Silva, Daniella Gregória, Cervi, Maria Celia, dos Santos Naja Cardoso, Mirian Viviane, Henriques Teixeira, Cristiane, Jarovsky, Daniel, Martins Araujo, Julienne, Naaman Berezin, Eitan, Palazzi Sáfadi, Marco Aurélio, Paternina-de la Ossa, Rolando Andres, Souza Vieira, Cristina, Dimitrova, Anna, Ganeva, Margarita, Stefanov, Stefan, Telcharova-Mihaylovska, Albena, Biggs, Catherine M., Lopez, Alison, Scuccimarri, Rosie, Tan, Ryan, Wasserman, Sam, Withington, Davinia, Ampuero, Camila, Aravena, Javiera, Bustos B, Raul, Casanova, Daniel, Cruces, Pablo, Diaz, Franco, García-Salum, Tamara, Godoy, Loreto, Medina, Rafael A., Valenzuela Galaz, Gonzalo, Camacho-Moreno, Germán, Avila-Aguero, María L., Brenes-Chacón, Helena, Camacho-Badilla, Kattia, Ivankovich-Escoto, Gabriela, Naranjo-Zuniga, Gabriela, Soriano-Fallas, Alejandra, Ulloa-Gutierrez, Rolando, Yock-Corrales, Adriana, Amer, Maysa Abbas, Abdelmeguid, Yasmine, Ahmed, Yomna H.H.Z., Badib, Adham, Badreldin, Karim, Elkhashab, Yara, Heshmat, Hassan, Hussein, Amna, Mohamed Hussein, Amna Hussein, Ibrahim, Sandra, Shoman, Walaa, Yakout, Radwa M, Heinonen, Santtu, Angoulvant, François, Belot, Alexandre, Ouldali, Naïm, Beske, Florian, Heep, Axel, Masjosthusmann, Katja, Reiter, Karl, van den Heuvel, Ingeborg, von Both, Ulrich, Agrafiotou, Aikaterini, Antachopoulos, Charalampos, Charisi, Konstantina, Eleftheriou, Irini, Farmaki, Evangelia, Fotis, Lampros, Kafetzis, Dimitrios, Koletsi, Patra, Kourtesi, Katerina, Lampidi, Stavroula, Liakopoulou, Theodota, Maritsi, Despoina, Michailidou, Elisa, Milioudi, Maria, Mparmpounaki, Ioanna, Papadimitriou, Eleni, Papaevangelou, Vassiliki, Roilides, Emmanuel, Tsiatsiou, Olga, Tsolas, Georgios, Tsolia, Maria, Vantsi, Petrina, Banegas Pineda, Linda Yajeira, Borjas Aguilar, Karla Leversia, Cantillano Quintero, Edwin Mauricio, Ip, Patrick, Kwan, Mike Yat Wah, Kwok, Janette, Lau, Yu Lung, To, Kelvin, Wong, Joshua Sung Chih, David, Mate, Farkas, David, Kalcakosz, Szofia, Szekeres, Klaudia, Zsigmond, Borbala, Aslam, Nadeem, Luder, Anthony, Andreozzi, Laura, Bianco, Francesco, Bucciarelli, Valentina, Buonsenso, Danilo, Cimaz, Rolando, De Luca, Maia, Dellepiane, Rosa Maria, Fabi, Marianna, Filice, Emanuele, Lanari, Marcello, Lo Vecchio, Andrea, Mastrolia, Maria Vincenza, Mauro, Angela, Mazza, Angelo, Papa, Mario Virgilio, Romani, Lorenza, Scarano, Sara Maria, Simonini, Gabriele, Tipo, Vincenzo, Verdoni, Lucio, Macharia, Anne-Marie, Musiime, Grace, Reel, Bhupi, Wangai, Frederick, Pace, David, Torpiano, Paul, Anaya-Enriquez, Nancy, Carreon-Guerrero, Juan Manuel, Chacon-Cruz, Enrique, Cheung López, Mariana, Faugier Fuentes, Enrique, Fonseca Flores, Marisol, García-Domínguez, Miguel, Giron Vargas, Ana Luisa, Lopez-Delgado, Ivan, Lopez Hernández, Liliana, Menchaca Aguayo, Hector F., Montaño-Duron, Jesus Gilberto, Pérez-Gaxiola, Giordano, Ramos Tiñini, Pamela, Tostado-Morales, Edgardo, Valadez, Julio, Inchley, Christopher, Klevberg, Sjur, Knudsen, Per Kristian, Måseide, Per Helge, Carrera, Jose Manuel, Castaño, Elizabeth, Daza Timana, Carlos Alberto, De Leon, Tirza, Estripeaut, Dora, Levy, Jacqueline, Norero, Ximena, Record, Javier, Rojas-Bonilla, Magda, Wong, Mayra, Iramain, Ricardo, Hernandez, Roger, Huamán, Gian, Munaico, Manuel, Peralta, Carlos, Seminario, Diego, Zapata Yarlequé, Elmer Hans, Gadzinska, Justyna, Ludwikowska, Kamila, Mandziuk, Joanna, Okarska-Napierała, Magdalena, Alacheva, Zalina A., Alexeeva, Ekaterina, Ananin, Petr V., Antsupova, Margarita, Bakradze, Maya D., Berbenyuk, Anna, Bobkova, Polina, Borzakova, Svetlana, Chashchina, Irina L., El-Taravi, Yasmin, Fisenko, Andrey P., Gautier, Marina S., Glazyrina, Anastasia, Gorlenko, Cyrill, Grosheva, Mariia, Kiselev, Herman, Kondrikova, Elena, Korobyants, Evgeniya, Korsunskiy, Anatoliy A., Kovygina, Karina, Krasnaya, Ekaterina, Kurbanova, Seda, Kurdup, Maria K., Mamutova, Anna V., Mazankova, Lyudmila, Mitushin, Ilya L., Munblit, Daniel, Nargizyan, Anzhelika, Orlova, Yanina O., Osmanov, Ismail M., Polyakova, Anastasia S., Pushkareva, Anna, Romanova, Olga, Samitova, Elmira, Shvedova, Anastasia, Sologub, Anna, Iakovleva, Ekaterina, Tepaev, Rustem F., Tkacheva, Anna A., Yegiyan, Margarita, Yusupova, Valeriya, Zholobova, Elena, Grasa, Carlos Daniel, Epalza, Cristina, Lopez Segura, Nuria, Martinon-Torres, Federico, Melendo, Susana, Mendez-Echevarria, Ana, Mesa Guzmán, Juan Miguel, Palacios Argueta, Jorge Roberto, Rivero-Calle, Irene, Rivière, Jacques, Rodríguez-González, Moisés, Rojo, Pablo, Sanchez Manubens, Judith, Soler-Palacin, Pere, Soriano-Arandes, Antoni, Tagarro, Alfredo, Villaverde, Serena, Altman, Maria, Brodin, Petter, Horne, AnnaCarin, Palmblad, Karin, Brotschi, Barbara, Meyer Sauteur, Patrick, Pachlopnik Schmid, Jana, Prader, Seraina, Relly, Christa, Schlapbach, Luregn J., Seiler, Michelle, Strasser, Sophie, Trück, Johannes, Weber, Kathrin, Wütz, Daniela, Hamdan, Alaa, Melhem, Ibrahim, Moussa, Ahmed, Dunk, Joke, Ketharanathan, Naomi, Vermont, Clementien, Akyüz Özkan, Esra, Cetin, Benhur Sirvan, Erdeniz, Emine Hafize, Şahin, Irfan Oğuz, Borisova, Galina, Boyarchuk, Oksana, Boychenko, Lidiya, Boyko, Yaryna, Diudenko, Nadiia, Dyvonyak, Olha, Kasiyan, Olexandr, Katerynych, Kostiantyn, Kostyuchenko, Larysa, Mamenko, Marina, Melnyk, Kateryna, Miagka, Nelia, Nazarenko, Liliya, Nezgoda, Iryna, Rykova, Stanislava, Svyst, Olga, Teslenko, Maria, Trykosh, Mykola, Vasilenko, Nataliya, Volokha, Alla, Adams, Charlotte, Akomolafe, Toju, Al-Abadi, Eslam, Alders, Nele, Alifieraki, Styliani, Ansumanu, Hareef, Aston, Emily, Avram, Paula, Bamford, Alasdair, Banks, Millie, Basu Roy, Robin, Beattie, Thomas, Boleti, Olga, Bracken, Abbey, Broad, Jonathan, Cai, James, Carrol, Enitan D., Carter, Michael, Chandran, Anchit, Charlesworth, James, Chawla, Jaya, Cooper, Hannah, Cooray, Samantha, Davies, Patrick, Davis, Francesca, Drysdale, Simon B., Dzora, Ella, Emonts, Marieke, Evans, Ceri, Fidler, Katy, Foster, Caroline, Gong, Chen, Gongrun, Berin, Gonzalez, Carmen, Gorgun, Berin, Grandjean, Louis, Grant, Karlie, Guo, Jonathan, Hacohen, Yael, Hall, Jack, Hamid, Hytham K.S., Hassell, Jane, Hesketh, Christine, Hewlett, Jessica, Hnieno, Ahmad, Holt-Davis, Hannah, Hossain, Aleena, Hu, Shiying, Hudson, Lee D., Jheeta, Sharon, Johnson, Mae, Johnson, Sarah, Jyothish, Deepthi, Kampmann, Beate, Kavirayani, Akhila, Kelly, Deborah, Kirubakaran, Arangan, Kucera, Filip, Langer, Daniel, Lawson, George, Lees, Emily A, Lenihan, Rebecca, Lillie, Jon, Longbottom, Katherine, Lyall, Hermione, Mackdermott, Niamh, Maltby, Sarah, Mclelland, Thomas, McMahon, Anne-Marie, Miller, Danielle, Miranda, Mariana, Mirza, Luwaiza, Morrison, Zoe, Moshal, Karyn, Muller, Jennifer, Musuka, Phoebe, Myttaraki, Evangelia, Nadel, Simon, Nair, Sreedevi, Nuttall, Luke, Oremakinde, Oyinkansola, Osaghae, Daniella, Osman, Fatima, Ostrzewska, Anna, Paccagnella, Davide, Panthula, Mrinalini, Papachatzi, Eleni, Papadopoulou, Charalampia, Patel, Fahim, Patel, Harsita, Payne, Helen, Penner, Justin, Polandi, Shervin, Prendergast, Andrew J., Ramnarayan, Padmanabhan, Ranasinghe, Lasith, Ravichandran, Muthukumaran, Rhys-Evans, Sophie, Riordan, Andrew, Rodrigues, Charlene M.C., Roe, Lauren, Romaine, Sam, Schobi, Nina, Seddon, James, Shingadia, Delane, Sikdar, Oishi, Srivastava, Anand, Struik, Siske, Sun, Thomas, Tan, Rachel Wei, Taylor, Alice, Taylor, Amanda, Taylor, Andrew, Tran, Steven, Tsagkaris, Stavros, Tudor-Williams, Gareth, van den Berg, Sarah, van der Velden, Fabian, Ventilacion, Lyn, Wellman, Paul A., Withers Green, Joseph, Yanney, Michael P., Yeung, Shunmay, Badheka, Aditya, Badran, Sarah, Bailey, Dwight M., Burch, Anna Kathryn, Burns, Jane C., Cichon, Catherine, Cirks, Blake, Dallman, Michael D., Delany, Dennis R., Fairchok, Mary, Friedman, Samantha, Geracht, Jennifer, Langs-Barlow, Allison, Mann, Kelly, Padhye, Amruta, Quade, Alexis, Ramirez, Kacy Alyne, Rockett, John, Sayed, Imran Ali, Santos, Roberto P., Shahin, Amr A., Tremoulet, Adriana, Umaru, Samuel, Widener, Rebecca, Mujuru, Hilda Angela, Kandawasvika, Gwendoline, Channon-Wells, Samuel, Vito, Ortensia, McArdle, Andrew J, Seaby, Eleanor G, Shah, Priyen, Pazukhina, Ekaterina, Wilson, Clare, Broderick, Claire, D'Souza, Giselle, Keren, Ilana, Nijman, Ruud G, Carter, Michael J, De, Tisham, Hoggart, Clive, Whittaker, Elizabeth, Herberg, Jethro A, Kaforou, Myrsini, Cunnington, Aubrey J, Blyuss, Oleg, and Levin, Michael

Published
2023
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16. The pegi3s Bioinformatics Docker Images Project

Author

López-Fernández, Hugo, Ferreira, Pedro, Reboiro-Jato, Miguel, Vieira, Cristina P., Vieira, Jorge, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Rocha, Miguel, editor, Fdez-Riverola, Florentino, editor, Mohamad, Mohd Saberi, editor, and Casado-Vara, Roberto, editor

Published
2022
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17. Adolescents' and Parents' Perceptions about Core Values to Individual and Family Life: A Cross-Sectional Study Involving Seven European Countries

Author

Vieira, Cristina C., Gonçalves, Luis, Jochl, Anja, Van Essche, Marianne, Stavrianos, Athanasios, Brie, Laura, Pustovrh, Matija, and Summermatter, Ayfer

Abstract

Family, community and school are privileged contexts to acquire and consolidate fundamental values for governing individual life and interpersonal relations across lifespan, and such learning is more effective if there is congruence in the messages learned, and if children and adolescents are stimulated to develop critical thinking competences to deal with information. Involving a convenience sample of 889 subjects, 446 adolescents and 443 parents from seven European countries to whom a self-administered questionnaire was applied, this paper presents the main results of cross-comparisons between and within countries about the perceived importance of values for family. Participants were also asked to do a self-evaluation of themselves as models of citizenship for others. Overall, mothers tend to consider that values are more promoted in families than fathers, but there are no differences in the opinions of adolescent boys and girls. When males and females are compared with no distinction of generations, the latter agreed more with the significance of values for the family than the former. There are some specific differences between and within countries and sample groups in the evaluation of values and self-perceptions of citizenship performance. Despite the limited number of participants in each country, the discussion of results highlights the importance of debating the values that guide personal and societal principles inside and outside the family, in an effort to construct a world free of prejudice and discrimination and where every person, regardless of cultural, religious or ethnical identities, is invited to contribute to the common well-being. [This article was written in collaboration with: Harald Seeber, Elisabeth Brueggl, Aziza Majri, Diane Licoppe, Christos Kolozof, Cristina Costa, Isabel Cristina Borges, Isabel Pratas, Laura Cruceat, Jana Mlakar, and Köksal Sezgin.]

Published
2016

27. Inferences on Mycobacterium Leprae Host Immune Response Escape and Antibiotic Resistance Using Genomic Data and GenomeFastScreen

Author

López-Fernández, Hugo, Vieira, Cristina P., Fdez-Riverola, Florentino, Reboiro-Jato, Miguel, Vieira, Jorge, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Panuccio, Gabriella, editor, Rocha, Miguel, editor, Fdez-Riverola, Florentino, editor, Mohamad, Mohd Saberi, editor, and Casado-Vara, Roberto, editor

Published
2021
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29. Inferring Positive Selection in Large Viral Datasets

Author

López-Fernández, Hugo, Duque, Pedro, Vázquez, Noé, Fdez-Riverola, Florentino, Reboiro-Jato, Miguel, Vieira, Cristina P., Vieira, Jorge, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Fdez-Riverola, Florentino, editor, Rocha, Miguel, editor, Mohamad, Mohd Saberi, editor, Zaki, Nazar, editor, and Castellanos-Garzón, José A., editor

Published
2020
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30. COLABORAR PARA INOVAR

Author

Fresca, Fabio, primary, Aras Neto, José Soares Ferreira, additional, Baptista Filho, Sílvio Neves, additional, Catafesta, Claudia, additional, Santos, Claudio Camargo dos, additional, Vieira, Cristina de Albuquerque, additional, Ramajo, Carmen Lúcia Rodrigues, additional, and Ballalai, Luciana Assad Luppi, additional

Published
2022
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31. Dialogando sobre Juventudes

Author

Oliveira, Victor Hugo Nedel, primary, Vieira, Cristina Pereira, additional, Severo, Ricardo, additional, Lacerda, Miriam Pires Corrêa de, additional, Oliveira, Adelson Dias de, additional, Adad, Shara Jane Holanda Costa, additional, Pinheiro, Leandro R., additional, Pimenta, Melissa de Mattos, additional, Vommaro, Pablo, additional, Gutierrez, Martha Lucía Bonilla, additional, and Aguilera, Óscar, additional

Published
2022
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35. Post-traumatic stress disorder as a risk factor for major adverse cardiovascular events: A cohort study of a South African medical insurance scheme

Author

Circulatory Health, Global Public Health & Bioethics, Mesa-Vieira, Cristina, Didden, Christiane, Schomaker, Michael, Mouton, Johannes P., Folb, Naomi, Van Den Heuvel, Leigh L., Gastaldon, Chiara, Cornell, Morna, Tlali, Mpho, Kassanjee, Reshma, Franco, Oscar H., Seedat, Soraya, Haas, Andreas D., Circulatory Health, Global Public Health & Bioethics, Mesa-Vieira, Cristina, Didden, Christiane, Schomaker, Michael, Mouton, Johannes P., Folb, Naomi, Van Den Heuvel, Leigh L., Gastaldon, Chiara, Cornell, Morna, Tlali, Mpho, Kassanjee, Reshma, Franco, Oscar H., Seedat, Soraya, and Haas, Andreas D.

Published
2024

36. Attitudes and Behaviors towards Vaccination in Portuguese Nursing Students

Author

Alves Marques-Vieira, Cristina Maria, Dias Domingues, Tiago, Dutra Tholl, Adriana, Gonçalves Nitschke, Rosane, Pérez Rivas, Francisco Javier, Ajejas Bazán, María Julia, Roquette Viana, Maria Clara, Alves Marques-Vieira, Cristina Maria, Dias Domingues, Tiago, Dutra Tholl, Adriana, Gonçalves Nitschke, Rosane, Pérez Rivas, Francisco Javier, Ajejas Bazán, María Julia, and Roquette Viana, Maria Clara

Abstract

Knowing the attitudes and behaviors of nursing students in relation to vaccination is important because they will soon be determinant for the health literacy of the population. Vaccination remains the most effective response in the fight against communicable diseases, including COVID-19 and influenza. The objective of this study is to analyze the attitudes and behaviors of Portuguese nursing students with regard to vaccination. A cross-sectional study was carried out, with data collection from nursing students at a university in Lisbon, Portugal. A sample of 216 nursing students was obtained, representing 67.1% of the students enrolled in this university. What stands out from the results of the questionnaire “Attitudes and Behaviors in Relation to Vaccination among Students of Health Sciences” is that for the majority of students the answers were positive; in addition, 84.7% had a completed vaccination schedule for COVID-19. Being a nursing student, being in the final years of the course and being a woman are the factors that most influence the positive attitude of the students. The results obtained are motivating, because these students will be the future health professionals most likely to integrate health promotion programs through vaccination., Foundation for Science and Technology (FCT), Depto. de Enfermería, Fac. de Enfermería, Fisioterapia y Podología, TRUE, pub

Published
2024

38. The Transformative Potential of Gender Equality Plans to Expand Women's, Gender, and Feminist Studies in Higher Education: Grounds for Vigilant Optimism.

Author

Lopes, Mónica, Santos, Caynnã, Ferreira, Virgínia, Monteiro, Rosa, and Vieira, Cristina C.

Subjects
GENDER inequality, WOMEN'S studies, HIGHER education, INTERNET surveys, SEMI-structured interviews
Abstract

The introduction of women's, gender, and feminist studies (WGFS) into higher education (HE) curricula has primarily been driven by individual efforts rather than institutional objectives. This article employs a multimethod approach to comprehensively understand the potential contribution of gender equality plans (GEPs) to strengthening the integration of WGFS in HE curricula and pedagogical practices. The study's documentary corpus includes data from GEPs in implementation, semi-structured interviews with 27 WGFS lecturers, and a web survey of 118 lecturers who teach courses related to or integrating gender aspects. This approach reveals divergent perspectives on the role of GEPs in HEIs, summarized into three categories: cautious optimism, skepticism, and simplistic views. The tensions and constraints associated with the contributions of the GEPs, as perceived by many involved in incorporating gender issues into teaching, outline a vigilant optimism for the future implementation of these mechanisms. Nonetheless, given the historically limited role of institutional initiatives in consolidating WGFS in Portuguese higher education, we argue that the potential contribution of GEPs to this field should not be underestimated, as integrating WGFS into institutional planning can legitimize, support, and leverage efforts that have predominantly been individual. [ABSTRACT FROM AUTHOR]

Published
2024
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39. EvoPPI: A Web Application to Compare Protein-Protein Interactions (PPIs) from Different Databases and Species

Author

Vázquez, Noé, Rocha, Sara, López-Fernández, Hugo, Torres, André, Camacho, Rui, Fdez-Riverola, Florentino, Vieira, Jorge, Vieira, Cristina P., Reboiro-Jato, Miguel, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Fdez-Riverola, Florentino, editor, Mohamad, Mohd Saberi, editor, Rocha, Miguel, editor, De Paz, Juan F., editor, and González, Pascual, editor

Published
2019
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40. A Bioinformatics Protocol for Quickly Creating Large-Scale Phylogenetic Trees

Author

López-Fernández, Hugo, Duque, Pedro, Henriques, Sílvia, Vázquez, Noé, Fdez-Riverola, Florentino, Vieira, Cristina P., Reboiro-Jato, Miguel, Vieira, Jorge, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Fdez-Riverola, Florentino, editor, Mohamad, Mohd Saberi, editor, Rocha, Miguel, editor, De Paz, Juan F., editor, and González, Pascual, editor

Published
2019
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42. Association between multidrug-resistant bacteria and outcomes in intensive care unit patients: a non-interventional study

Author

Martins, Alessandro Pacheco Silveira, primary, da Mata, Camila Pacheco Silveira Martins, additional, dos Santos, Uener Ribeiro, additional, de Araújo, César Augusto, additional, Leite, Edna Marilea Meireiles, additional, de Carvalho, Luciana Debortoli, additional, Vidigal, Pedro Guatimosim, additional, Vieira, Cristina Dutra, additional, and dos Santos-Key, Simone Gonçalves, additional

Published
2024
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44. Post-traumatic stress disorder as a risk factor for major adverse cardiovascular events: a cohort study of a South African medical insurance scheme

Author

Mesa-Vieira, Cristina, primary, Didden, Christiane, additional, Schomaker, Michael, additional, Mouton, Johannes P., additional, Folb, Naomi, additional, van den Heuvel, Leigh L., additional, Gastaldon, Chiara, additional, Cornell, Morna, additional, Tlali, Mpho, additional, Kassanjee, Reshma, additional, Franco, Oscar H., additional, Seedat, Soraya, additional, and Haas, Andreas D., additional

Published
2024
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47. A comprehensive evolutionary scenario for the origin and neofunctionalization of the Drosophila speciation gene Odysseus (OdsH)

Author

Nunes, William Vilas Boas, primary, Oliveira, Daniel Siqueira, additional, Dias, Guilherme de Rezende, additional, Carvalho, Antonio Bernardo, additional, Caruso, Ícaro Putinhon, additional, Biselli, Joice Matos, additional, Guegen, Nathalie, additional, Akkouche, Abdou, additional, Burlet, Nelly, additional, Vieira, Cristina, additional, and Carareto, Claudia M A, additional

Published
2023
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48. PLENATITUDE Teacher Education for Effectiveness and Well-Being with Neuro-Linguistic Programming

Author

Vieira, Cristina Rocha and Gaspar, Maria Filomena

Abstract

The role and functioning of schools are changing as well as what is expected of teachers (who face growing and diversified challenges); consequentially, well-being at the schools is endangered. As teachers and teachers' educators concern is: How to improve schools' and teachers' effectiveness and promote well-being. Believing that the path to effectiveness is through evidence-based practice, according to research results (meta-analysis and effect-sizes), the authors analyzed which factors have more impact on schools effectiveness; teachers arise as a significant factor, accounting for about 30% of the variance on pupils' achievement. So, the authors have searched for factors that have significant impact on teachers' effectiveness. Evidence shows that, among other factors, giving/receiving feedback, beliefs and expectations, self-efficacy, establishing clear goals, effective interpersonal communication, and classroom climate are determinant. In face of these findings, the authors have explored how NLP (neuro-linguistic programming) can contribute to improving teachers' effectiveness, through professional training. (Contains 2 tables, 8 figures, and 15 footnotes.)

Published
2013

49. On the identification of potential novel therapeutic targets for spinocerebellar ataxia type 1 (SCA1) neurodegenerative disease using EvoPPI3

Author

Sousa André, Rocha Sara, Vieira Jorge, Reboiro-Jato Miguel, López-Fernández Hugo, and Vieira Cristina P.

Subjects
ataxin-1, comparative analyses, polyq diseases, protein-protein interaction, Biotechnology, TP248.13-248.65
Abstract

EvoPPI (http://evoppi.i3s.up.pt), a meta-database for protein-protein interactions (PPI), has been upgraded (EvoPPI3) to accept new types of data, namely, PPI from patients, cell lines, and animal models, as well as data from gene modifier experiments, for nine neurodegenerative polyglutamine (polyQ) diseases caused by an abnormal expansion of the polyQ tract. The integration of the different types of data allows users to easily compare them, as here shown for Ataxin-1, the polyQ protein involved in spinocerebellar ataxia type 1 (SCA1) disease. Using all available datasets and the data here obtained for Drosophila melanogaster wt and exp Ataxin-1 mutants (also available at EvoPPI3), we show that, in humans, the Ataxin-1 network is much larger than previously thought (380 interactors), with at least 909 interactors. The functional profiling of the newly identified interactors is similar to the ones already reported in the main PPI databases. 16 out of 909 interactors are putative novel SCA1 therapeutic targets, and all but one are already being studied in the context of this disease. The 16 proteins are mainly involved in binding and catalytic activity (mainly kinase activity), functional features already thought to be important in the SCA1 disease.

Published
2023
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