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4. The InBIO barcoding initiative database: DNA barcodes of Iberian Trichoptera, documenting biodiversity for freshwater biomonitoring in a Mediterranean hotspot

Author

Paupério, Joana, Martin, Luis, Martínez, Jesús, Gonzalez, Marcos, Martins, Filipa Ms, Veríssimo, Joana, Puppo, Pamela, Pinto, Joana, Chaves, Cátia, Pinho, Catarina J., Grosso-Silva, José Manuel, Quaglietta, Lorenzo, Silva, Teresa Luísa, Sousa, Pedro, Alves, Paulo, Fonseca, Nuno, Beja, Pedro, Ferreira, Sónia, and Pensoft Publishers

Subjects
continental Portugal, continental Spain, Cytochrome c oxidase subunit I (COI), DNA barcode, occurrence records, species distributions, Trichoptera
Published
2023

5. Efficacy and safety of sparsentan versus irbesartan in patients with IgA nephropathy (PROTECT): 2-year results from a randomised, active-controlled, phase 3 trial

Author

Abbasciano, Isabella, Abrantes, Catarina, Accarino, Simone, Adler, Sharon, Adoberg, Annika, Afsari, Rouzbeh, Ahmad, Syeda, Ahmed, Jafar, Ahn, Wooin, Ajayi, Bamidele, Aksamit, Dariusz, Al Chalabi, Saif, Alamartine, Eric, Alchi, Bassam, Ali, Mohammad, Aliotta, Roberta, Almaani, Salem, Almeida, Catarina, Almeida, Edgar, Alvarez, Francisco de la Prada, Alves, Patricia, Annese, Francesca, Appel, Gerald, Arduan, Alberto Ortiz, Arena, Maria, Arevalo, Marta Calvo, Arfaania, Dariush, Arias, Carlos, Aristoy, Emma Calatayud, Asakiene, Egle, Ashley, Sarah, Assefi, Ali, Atenza, Alba, Auerbach, Asta, Augustyniak-Bartosik, Hanna, Avella, Monroy, Ayling-Smith, Jonathan, Ayoub, Isabelle, Ayvazyan, Christine, Baccaro, Rocco, Bailey, Asha, Baker, Bruce, Balamuthusamy, Saravanan, Ballarin, Jose, Barata, Rui, Barbic, Jerko, Barisic, Dunja, Barratt, Jonathan, Barreto, Jose Carlos de Jesus, Barrios, Clara, Belingheri, Mirco, Benesova, Anna, Bernabeu, Ana Avila, Bernhardt, Wanja, Bhadra, Shamik, Biancone, Luigi, Blanchard, Anne, Boaglio, Elena, Bolignano, Davide, Bomback, Andrew, Bonilla, Gustavo Andres Useche, Bordoli, Monica, Bose, Bhadran, Boudville, Neil, Brandon, Donald, Brown, Karen, Broyet, Christian, Bucknall, Thomas, Buffet, Alexandre, Bumblyte', Inga Arune, Burdese, Manuel, Burgos, Natalia Allende, Burguet, Laure, Burtey, Stephane, Busch, Martin, Cakiroglu, Figen, Campbell, Victoria, Canetta, Pietro, Capaccio, Flavia, Carbonell, Juan, Cardoso, Filipa, Carro, Clara Garcia, Carroll, Robert, Carron, Pierre-Louis, Carullo, Nazareno, Cassia, Matthias, Caster, Dawn, Castillo, Belen Vizcaino, Catucci, Davide, Cavalli, Andrea, Chae, Dong-Wan, Chakera, Aron, Chan, Doris, Chan, Gary Chi Wang, Chan, Anthony Ting Pong, Chan, Lai Wan, Chang, Jae Hyun, Chang, Ming-Shan, Chapman, Fiona, Charytan, Chaim, Chaudhry, Asghar, Cheetham, Melissa, Chen, Cheng-Hsu, Chen, Hsin-Yu, Chen, Chien-Liang, Chen, Hung-Yuan, Chen, Hung-Chun, Chenine, Leila, Cheung, Siu Fai, Cheung, Chee Kay, Chiche-Jourde, Noemie, Chiu, Hsien-Fu, Chiu, Yen-Ling, Chiu, Yi-Wen, Chiu, Ian, Choi, Hoon Young, Chou, Kang-Ju, Chowdhury, Paramit, Chowdhury, Pradip, Chrysochou, Constantina, Chukwu, Chukwuma, Chun, Ka Yeong, Chung, Wookyung, Cieniawski, Dominik, Claisse, Guillaume, Clayton, Philip, Cleary, Catalina Martín, Clement, Nisha, Coates, Toby, Cogno, Chiara, Colla, Loredana, Collins, Michael, Colucci, Marco, Combe, Christian, Comi, Nicolino, Comunale, Roderick, Contreras, Gabriel, Cooper, Bruce, Coppock, Gaia, Costa, Ana Cortesão, Costanzi, Stefano, Cozzolino, Mario, Crail, Susan, Cunha, Liliana, Curry, Elizabeth, Dai, Tiane, Daina, Erica, Daneshvari, Sam, Dasgupta, Indranil, DaSilva, Louise, Davidson, Robert, De Bhailis, Aine Maire, de Précigout, Valérie, Decupere, Marc, Delmas, Yahsou, Deodato, Francesca, Dhaun, Neeraj, Dhaygude, Ajay, Dhelaria, Ranjit, Di Maio, Federica, Diezhandino, Maria Angeles Goicoechea, Dika, Zivka, Dinic, Miriana, Dittmer, Ian, Dobre, Mirela, Doctor, Gabriel, Donati, Gabriele, Doubel, Peter, Douthit, Nicole, Draganova, Diliana, Drexler, Yelena, Drinkovic, Martin, Drinovska, Klara, Dudreuilh, Caroline, Dumond, Clement, Durlen, Ivan, Dussol, Bertrand, Encarnacion, Montserrat Diaz, Endre, Zoltan, Enrique, Jorge, Eqbal, Yusuf, Erlich, Jonathan, Esposito, Vittoria, Esposito, Ciro, Fakih, Faisal, Fang, Hua-Chang, Farinha, Ana, Fearday, Aaron, Felgueiras, Joana de Sousa Soares, Felicjanczuk, Elzbieta, Fernandes, João Carlos, Fernandes, Sara, Fernandes, Adriana, Fernandez, Jose Luño, Fernandez, Victor, Fernando, Mangalee, Figueiredo, Ana Carolina, Firre, Eric, Floege, Jürgen, Flossmann, Oliver, Floyd, Lauren, Fonseca, Nuno, Fonseca, Jose Nuno de Almeida Agapito, Foote, Celine, Forbes, Suzanne, Forcen, Angel, Fornoni, Alessia, Fouassier, David, Fraser, Ian, Fung, Ka Shun Samuel, Furlano, Monica, Furtado, Teresa, Gadh, Rajdeep, Gaisset, Roxane, Gallagher, Martin, Gameiro, Joana, Gangadharan, Muralikrishna, Garcia, Fabiola Alonso, Garcia, Olga Gracia, Garg, Gunjan, Garrouste, Cyril, Gautam, Archana, Geara, Abdallah, Geddes, Colin, Gellineo, Lana, Germain, Michael, Gesualdo, Loreto, Ghalli, Farid, Giaroni, Francesco, Giles, Harold, Gillies, Alastair, Gimeno, Ana Vilar, Girardet, Annette, Glaze, Jeffrey, Goh, Tze, Gois, Mario, Goldsmith, Christopher, Goma, Elena, Gomes, Ana Marta, Goncalves, Luis Pedro Falcao, Goncalves, Sara, Gontarek-Kacprzak, Julita, Gonzalez, Carlos, Gopu, Arun, Gowda, Nayan, Gray, Nicholas, Greco, Barbara, Green, Heather, Greze, Clarisse, Griffin, Sian, Guldris, Secundino Cigarran, Guzman, Ursula Verdalles, Ha, Jeffrey Tsun Kit, Hall, Amanda, Hamilton, Patrick, Han, Seung Hyeok, Haws, Robert, Hayat, Ashik, Heath, Lauren, Heinrichs, Sven, Henderson, Andrew, Henderson, Amy, Hendren, Elizabeth, Heng, Anne-Elisabeth, Heres, Salia Virxinia Pol, Herfurth, Johann Konstantin, Herrero, Evangelina Merida, Ho, Tzung-Yo, Hogan, Jonathan, Hohenstein, Bernd, Hollett, Peter, Horvatic, Ivica, Hsu, Bang-Gee, Hsu, Chia-Tien, Hsu, Chih-Yang, Hsu, Shih-Ping, Huang, Chien-Wei, Hudson, Amy, Hung, Chi-Chih, Hwang, Shang-Jyh, Hwang, Daw-Yang, Hyun, Young Youl, Ilmoja, Madis, Irish, Georgina, Jacob, Radu, Jahan, Sadia, Jain, Arunima, Jamar, Sofie, Jander, Anna, Jang, Hye Ryoun, Janko, Catherine, Jardine, Meg, Jaskowski, Piotr, Jeantet, Guillaume, Jelakovic, Bojan, Jeon, Junseok, Jeong, Jong Cheol, Jesudason, Shilpanjali, Jittirat, Arksarapuk, Jo, Sang-Kyung, Jones, Rachel, Joo, Narae, Jorge, Sofia, Julian, Bruce, Jung, JiYong, Jyothinagaram, Praveena, Kadakia, Jigar, Kamal, Fahameedah, Kanigicherla, Durga, Karanovic, Sandra, Karras, Alexandre, Kasimatis, Theodoros, Kassem, Mohamad, Kattamanchi, Siddhartha, Keller, Christopher, Kentric, Dubravka Trajbar, Kettner, Christiane, Khalil, Kassem, Kim, Dana, Kim, Se Joong, Kim, Yeong Hoon, Kim, Yunmi, Kim, Hyung Wook, Kim, Sunggyun, Kim, Jwa-Kyung, Kim, Aejin, Kim, Myung-Gyu, Kimber, Cassandra, Klamm, Kathryn, Koch, Annegret, Koester, Eric, Kolvald, Kulli, Kon, Sui, Kooienga, Laura Ann, Kotwal, Sradha, Krajewska, Magdalena, Kratka, Karolina, Krishnan, Anoushka, Krishnasamy, Rathika, Krueger, Thilo, Kruljac, Ivan, Kulka, Simone, Kunzendorf, Ulrich, Kuo, Mei-Chuan, Kuo, Hung-Tien, Kuo, Sheng, Kwan, Lorraine Pui Yuen, Kwella, Norbert, Kwella, Bogna, Kyaw, Kay, Labat, Aurore, Lafayette, Richard, Lagatta, Mark, Lam, Chi Kwan Darwin, Lambie, Mark, Lanaret, Camille, Latif, Farah, Laute, Margo, Law, Wai Ping, Lawman, Sarah, Lazo, Mercedes Salgueira, Lee, Hajeong, Lee, Moon Hyoung, Lee, Kyu-Beck, Lee, Hyung-seok, Lee, JungEun, Lee, Hyun Hee, Lee, Po-Tsang, Leis, Liisi, Lemahieu, Wim, Leung, Janson, Li, Yan, Lie, Davina Ngoi Wah, Lifland, Howard, Lilienthal, Kadri, Lim, Wai, Limardo, Monica, Livrozet, Marine, Longhi, Selena, Lopes, Daniela, Lopes, Jose Antonio, Lorde, Nathan, Luxton, Grant, Ma, Mingyao, Madhrira, Machaiah, Madonia, Phillip, Maes, Bart, Mahadevan, Kumaradevan, Mahdi, Amar, Mahdi, Eamon, Maillard, Nicolas, Maixnerova, Dita, Majstorovic Barac, Karolina, Malecki, Robert, Malfait, Thomas, Malvica, Silvia, Mandayam, Sreedhar, Manley, Paul, Mansfield, Nick, Marcantoni, Carmelita, Mariat, Christophe, Marin, Tamara Malek, Marin, Lida Maria Rodas, Mark, Patrick, Marques, Joana, Martinez, Eduardo Gutierrez, Martinez, Stacy, Masset, Catherine, Masson, Ingrid, Mather, Amanda, Maung Myint, Thida Maung, Mayet, Valentin, McCafferty, Kieran, McCarthy, Ellen, McDonald, Stephen, McGreal, Kerri, McMahon, Kellyn, McNally, Andrew, McQuarrie, Emily, Medina, Allyson, Meeus, Gert, Mehta, Kshama, Mendoza, Elder, Menezes, Maria, Meng, Jerry, Messa, Piergiorgio, Messias, Ana, Miarka, Przemyslaw, Miglinas, Marius, Mikacic, Ivana, Mikhail, Ashraf, Milicevic, Martina, Minasian, Raffi, Moeller, Marcus, Mohey, Hesham, Mojarrab, Javad, Mok, Maggie Ming Yee, Moncasi, Eduardo Parra, Moonen, Martial, Morales, Wenceslao Adrian Aguilera, Moreno, Eduardo Verde, Moreno, Antolina, Morris, Adam, Moutzouris, Dimitrios, Moya, Mercedes Gonzalez, Mucha, Simon, Musolino, Michela, Napodano, Pietro, Natario, Ana, Negrea, Lavinia, Nelson, Bradley, Neuen, Brendon, Newsome, Britt, Ng, Kit Chung Jack, Nguyen, Thu, Nguyen, Viet, Nicolo, Clementine, Nitschke, Martin, Noble, Euan, Nolasco, Fernando, O'Lone, Emma, Ochoa, Adriana Sierra, Oh, Kook-Hwan, Oh, SeWon, Okoh, Pedro, Ombelet, Sara, O'Shaughnessy, Michelle, Ou, Shih-Hsiang, Packham, David, Padiyar, Aparna, Pai, Mei-Fen, Pamplona, Irene Agraz, Pan, Szu-Yu, Pandya, Bhavna, Papadia, Federica, Pardinhas, Clara, Parikh, Nishita, Parikh, Samir, Park, Hyeong Cheon, Park, Jung Tak, Parreira, Lucia, Passerini, Patrizia, Patak, Ramachandra, Patecki, Margret, Patel, Rajan, Patel, Jusmin, Patel Suthar, Meera, Patella, Gemma, Patrikyan, Artashes, Pavlovic, Drasko, Paxton, William, Peh, Chen, Peleg, Yonatan, Pelicano, Josep Miquel Blasco, Peng, Yu-Sen, Pereira de Vicente, Manuel, Perez, Jonay Pantoja, Perez, Erika, Perez de Jose, Ana, Pérez Gómez, María Vanessa, Perez Lluna, Leticia, Peri, Usha, Perico, Norberto, Philipponnet, Carole, Phua, Elaine, Piel, Julia, Pillai, Unnikrishnan, Pilmore, Helen, Plavljanic, Djuro, Plaza, Mercedes Velo, Pollock, Carol, Ponnusamy, Arvind, Ponti, Serena, Powell, Thomas, Pradhan, Nishigandha, Prado, Raul Fernandez, Prkacin, Ingrid, Pruthi, Rishi, Pugh, Dan, Quinn, Sarah, Quintana, Luis F, Raakesh, Lathika, Rabindranath, Kannaiyan, Radermacher, Luc, Radhakrishnan, Jai, Ragy, Omar Sherin Ibrahim, Raichoudhury, Ritesh, Raimundo, Mario, Randone, Paolo, Razavian, Mona, Reichel, Helmut, Reis, Marina, Remuzzi, Giuseppe, Reynolds, Annie, Ricchiuto, Anna, Rico, Ivon Maritza Bobadilla, Rigothier, Claire, Ritchie, Angus, Rivero, Maria Antonieta Azancot, Rizk, Dana, Ro, Han, Rodriguez, Alfred, Rodriguez Garcia, Eva, Roger, Simon, Rony, Mohammad, Rosenberg, Mai, Roueff, Stephane, Rovin, Brad, Roxburgh, Sarah, Ruiz, Mario, Rusinol, Helena Marco, Rychlik, Ivan, Sá, Helena, Salehi, Tania, Sánchez de la Nieta, Maria Dolores, Sanden, Silja, Santockiene, Lina, Santos, Patricia Valerio, Santos, Iara Da Silva, Sargsyan, Mari, Sarnow, Franziska, Sat, Sebahat, Satora, Ewa, Savuk, Ana, Sayer, Matthew, Schlieper, Georg, Schlosser, Mandy, Schmidt-Guertler, Hans, Schockaert, Olivier, Schulte, Kevin, Schulz, Lisa, Selvaskandan, Haresh, Semple, David, Sen, Shaundeep, Seppet, Elviira, Serrano, Antonio Galan, Serre, Jean-Emmanuel, Sevillano, Angel, Shah, Sapna, Shen, Yvonne, Sheridan, Brittany, Shu, Kai-Hsiang, Sightler, Ford, Silva, Sónia, Silva, Arnold, Sinha, Smeeta, Siriwardana, Amanda, Sitas, Zvonimir, Sivo, Carmen, Sizeland, Peter, Sly, Cathylee, Smith, Priscilla, Snow, Brian, Soares, Elsa Sofia Quadrado, Solazzo, Andrea, Solis, Elena Gutierrez, Solomon, Laurence, Song, Young Rim, Sousa, Helena, Spinowitz, Bruce, Stallworthy, Elizabeth, Stamellou, Eleni, Stanczyk, Malgorzata, Stangenberg, Stefanie, Stankovic, Marija, Stankuviene, Asta, Stea, Emma Diletta, Stompor, Tomasz, Storrar, Joshua, Sullivan, James, Sulowicz, Wladyslaw, Suyumova, Irina, Szeto, Cheuk Chun, Tamarit, Esther, Tan, Eddie, Tan, May, Tang, Sydney Chi Wai, Tang, Hon, Teixeira, Catarina, Telling, Kadri, Terrades, Natalia Ramos, Tesar, Vladimir, Tez, Didem, Thervet, Eric, Thibaudin, Damien, Thomas, Mark, Thyagarajan, Nikhil, Tkaczyk, Marcin, Torreggiani, Massimo, Trillini, Matias, Tsai, Shang-Feng, Tsai, Wan-Chuan, Tsai, Jer-Chia, Tseng, Po-Yu, Tumlin, James, Tung, Kuei-Ting, Turnbull, Angus, Udani, Suneel, Uhlinova, Jana, Unt, Kristin, Urciuolo, Federica, Vanacker, An, Vandewiele, Bert, Vaz, Alvaro, Veermae, Kristi, Viaene, Liesbeth, Vickiene, Alvita, Vigano, Sara, Vila, Maria Antonia Munar, Vilayur, Eswari, Villanueva, Caridad Martinez, Villarroya, Cristina Medrano, Villen, Alejandro Soria, Viramontes, Veronica, Vita, Caterina, Vujcic, Dunja, Wahba, Mona, Wan, Susan, Wang, Chih-Hsien, Warling, Xavier, Waters, Gerald, Waugh, Jane, Weiland, Lea, Weiner, Stefan, Weinreich, Thomas, Werth, Stephan Christian, Wickens, Olivia, Wijeratne, Vidu, Wilder, Karen, Willcocks, Lisa, Williams, Allister, Winiarska, Agata, Wirtz, Nikolaus, Wolf, Lothar, Wolf, Gunter, Wong, Muh Geot, Wong, Yick Hei, Wong, Sze Ho Sunny, Workeneh, Biruh, Wu, Ming-Ju, Wu, Hon-Yen, Wyndham, Roger, Yang, Jihyun, Yang, Ju-Yeh, Yeap, Chii, Yim, Ka Fai, Yong, Kenneth, Yoo, Tae-Hyun, Yoon, Songuk, Yu, Tung-Min, Yue, Tak Tai Andrew, Zakari, Michel, Zakauskiene, Urte, Zaoui, Philippe, Zbrzezniak, Justyna, Zielinska, Dorota, Zizzi, Carlotta Federica, Rovin, Brad H, Heerspink, Hiddo J L, Alpers, Charles E, Bieler, Stewart, Diva, Ulysses A, Inrig, Jula K, Kohan, Donald E, Komers, Radko, Małecki, Robert, Mercer, Alex, Noronha, Irene L, Oh, Se Won, Peh, Chen Au, Praga, Manuel, Preciado, Priscila, Rheault, Michelle N, Rote, William E, Tang, Sydney C W, Trachtman, Howard, Trimarchi, Hernán, Tumlin, James A, and Perkovic, Vlado

Published
2023
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6. Sound Particles: The sky is not the limit... Recently releasing the world's first spatial audio synthesiser - SkyDust 3D - Sound Particles are catering for both Hollywood's soundtracking juggernauts and creative musicians looking to get more explorative with spatial sound design

Author

Fonseca, Nuno

Subjects
Musicians, Science and technology
Abstract

cm: Hi Nuno, can you give our readers a short overview of SkyDust 3D, what it brings to the table for spatial audio-composers? Nuno Fonseca: 'SkyDust 3D is a modern [...]

Published
2023

7. A user guide for the online exploration and visualization of PCAWG data.

Author

Goldman, Mary J, Zhang, Junjun, Fonseca, Nuno A, Cortés-Ciriano, Isidro, Xiang, Qian, Craft, Brian, Piñeiro-Yáñez, Elena, O'Connor, Brian D, Bazant, Wojciech, Barrera, Elisabet, Muñoz-Pomer, Alfonso, Petryszak, Robert, Füllgrabe, Anja, Al-Shahrour, Fatima, Keays, Maria, Haussler, David, Weinstein, John N, Huber, Wolfgang, Valencia, Alfonso, Park, Peter J, Papatheodorou, Irene, Zhu, Jingchun, Ferretti, Vincent, and Vazquez, Miguel

Subjects
Humans, Neoplasms, Computational Biology, Genomics, Mutation, Genome, Human, Internet, Software, User-Computer Interface, Databases, Genetic, Chromothripsis, Whole Genome Sequencing, Data Analysis, Genome, Human, Databases, Genetic
Abstract

The Pan-Cancer Analysis of Whole Genomes (PCAWG) project generated a vast amount of whole-genome cancer sequencing resource data. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we provide a user's guide to the five publicly available online data exploration and visualization tools introduced in the PCAWG marker paper. These tools are ICGC Data Portal, UCSC Xena, Chromothripsis Explorer, Expression Atlas, and PCAWG-Scout. We detail use cases and analyses for each tool, show how they incorporate outside resources from the larger genomics ecosystem, and demonstrate how the tools can be used together to understand the biology of cancers more deeply. Together, the tools enable researchers to query the complex genomic PCAWG data dynamically and integrate external information, enabling and enhancing interpretation.

Published
2020

8. Genomic basis for RNA alterations in cancer.

Author

PCAWG Transcriptome Core Group, Calabrese, Claudia, Davidson, Natalie R, Demircioğlu, Deniz, Fonseca, Nuno A, He, Yao, Kahles, André, Lehmann, Kjong-Van, Liu, Fenglin, Shiraishi, Yuichi, Soulette, Cameron M, Urban, Lara, Greger, Liliana, Li, Siliang, Liu, Dongbing, Perry, Marc D, Xiang, Qian, Zhang, Fan, Zhang, Junjun, Bailey, Peter, Erkek, Serap, Hoadley, Katherine A, Hou, Yong, Huska, Matthew R, Kilpinen, Helena, Korbel, Jan O, Marin, Maximillian G, Markowski, Julia, Nandi, Tannistha, Pan-Hammarström, Qiang, Pedamallu, Chandra Sekhar, Siebert, Reiner, Stark, Stefan G, Su, Hong, Tan, Patrick, Waszak, Sebastian M, Yung, Christina, Zhu, Shida, Awadalla, Philip, Creighton, Chad J, Meyerson, Matthew, Ouellette, BF Francis, Wu, Kui, Yang, Huanming, PCAWG Transcriptome Working Group, Brazma, Alvis, Brooks, Angela N, Göke, Jonathan, Rätsch, Gunnar, Schwarz, Roland F, Stegle, Oliver, Zhang, Zemin, and PCAWG Consortium

Subjects
PCAWG Transcriptome Core Group, PCAWG Transcriptome Working Group, PCAWG Consortium, Humans, Neoplasms, DNA, Neoplasm, RNA, Genomics, Gene Expression Regulation, Neoplastic, Genome, Human, DNA Copy Number Variations, Transcriptome, DNA, Neoplasm, Gene Expression Regulation, Neoplastic, Genome, Human, General Science & Technology
Abstract

Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)5. Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed 'bridged' fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.

Published
2020

9. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Author

Rheinbay, Esther, Nielsen, Morten Muhlig, Abascal, Federico, Wala, Jeremiah A, Shapira, Ofer, Tiao, Grace, Hornshøj, Henrik, Hess, Julian M, Juul, Randi Istrup, Lin, Ziao, Feuerbach, Lars, Sabarinathan, Radhakrishnan, Madsen, Tobias, Kim, Jaegil, Mularoni, Loris, Shuai, Shimin, Lanzós, Andrés, Herrmann, Carl, Maruvka, Yosef E, Shen, Ciyue, Amin, Samirkumar B, Bandopadhayay, Pratiti, Bertl, Johanna, Boroevich, Keith A, Busanovich, John, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Craft, David, Dhingra, Priyanka, Diamanti, Klev, Fonseca, Nuno A, Gonzalez-Perez, Abel, Guo, Qianyun, Hamilton, Mark P, Haradhvala, Nicholas J, Hong, Chen, Isaev, Keren, Johnson, Todd A, Juul, Malene, Kahles, Andre, Kahraman, Abdullah, Kim, Youngwook, Komorowski, Jan, Kumar, Kiran, Kumar, Sushant, Lee, Donghoon, Lehmann, Kjong-Van, Li, Yilong, Liu, Eric Minwei, Lochovsky, Lucas, Park, Keunchil, Pich, Oriol, Roberts, Nicola D, Saksena, Gordon, Schumacher, Steven E, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stewart, Chip, Tamborero, David, Tubio, Jose MC, Umer, Husen M, Uusküla-Reimand, Liis, Wadelius, Claes, Wadi, Lina, Yao, Xiaotong, Zhang, Cheng-Zhong, Zhang, Jing, Haber, James E, Hobolth, Asger, Imielinski, Marcin, Kellis, Manolis, Lawrence, Michael S, von Mering, Christian, Nakagawa, Hidewaki, Raphael, Benjamin J, Rubin, Mark A, Sander, Chris, Stein, Lincoln D, Stuart, Joshua M, Tsunoda, Tatsuhiko, Wheeler, David A, Johnson, Rory, Reimand, Jüri, Gerstein, Mark, Khurana, Ekta, Campbell, Peter J, López-Bigas, Núria, PCAWG Drivers and Functional Interpretation Working Group, PCAWG Structural Variation Working Group, Weischenfeldt, Joachim, Beroukhim, Rameen, Martincorena, Iñigo, Pedersen, Jakob Skou, Getz, Gad, and PCAWG Consortium

Subjects
PCAWG Drivers and Functional Interpretation Working Group, PCAWG Structural Variation Working Group, PCAWG Consortium, Humans, Neoplasms, Gene Expression Regulation, Neoplastic, Mutation, Genome, Human, Databases, Genetic, DNA Breaks, INDEL Mutation, Genome-Wide Association Study, Gene Expression Regulation, Neoplastic, Genome, Human, Databases, Genetic, General Science & Technology
Abstract

The discovery of drivers of cancer has traditionally focused on protein-coding genes1-4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5' region of TP53, in the 3' untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.

Published
2020

10. High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.

Author

Zhang, Yiqun, Chen, Fengju, Fonseca, Nuno A, He, Yao, Fujita, Masashi, Nakagawa, Hidewaki, Zhang, Zemin, Brazma, Alvis, PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, Creighton, Chad J, and PCAWG Consortium

Subjects
PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, PCAWG Consortium, Humans, Neoplasms, DNA Methylation, Gene Expression Regulation, Neoplastic, Regulatory Sequences, Nucleic Acid, Genes, Tumor Suppressor, Oncogenes, Databases, Genetic, Enhancer Elements, Genetic, Genomic Structural Variation, Whole Genome Sequencing, Gene Expression Regulation, Neoplastic, Regulatory Sequences, Nucleic Acid, Genes, Tumor Suppressor, Databases, Genetic, Enhancer Elements
Abstract

The impact of somatic structural variants (SVs) on gene expression in cancer is largely unknown. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole-genome sequencing data and RNA sequencing from a common set of 1220 cancer cases, we report hundreds of genes for which the presence within 100 kb of an SV breakpoint associates with altered expression. For the majority of these genes, expression increases rather than decreases with corresponding breakpoint events. Up-regulated cancer-associated genes impacted by this phenomenon include TERT, MDM2, CDK4, ERBB2, CD274, PDCD1LG2, and IGF2. TERT-associated breakpoints involve ~3% of cases, most frequently in liver biliary, melanoma, sarcoma, stomach, and kidney cancers. SVs associated with up-regulation of PD1 and PDL1 genes involve ~1% of non-amplified cases. For many genes, SVs are significantly associated with increased numbers or greater proximity of enhancer regulatory elements near the gene. DNA methylation near the promoter is often increased with nearby SV breakpoint, which may involve inactivation of repressor elements.

Published
2020

12. Sparsentan in patients with IgA nephropathy: a prespecified interim analysis from a randomised, double-blind, active-controlled clinical trial

Author

Alarmartine, Eric, Barratt, Jonathan, Chae, Dong Wan, Del Vecchio, Lucia, Floege, Jurgen, Hwang, Shang-Jyh, Jelakovic, Bojan, Maes, Bart, Malecki, Robert, Miglinas, Marius, Nolasco, Fernando Eduardo Barbosa, Praga, Manual, Rabindranath, Kannaiyan, Rosenberg, Mai, Rovin, Brad, Tang, Sydney Chi Wai, Tesar, Vladmir, Wong, Muh Geot, Bose, Bhadran, Gangadharan, Muralikrishna, McDonald, Stephen, Peh, Chen, Jahan, Sadia, Yeap, Chii, Clayton, Philip, Irish, Georgina, Thyagarajan, Nikhil, Hollett, Peter, Krishnasamy, Rathika, Carroll, Robert, Jesudason, Shilpanjali, Crail, Susan, Coates, Toby, Waugh, Jane, Noble, Euan, Mahadevan, Kumaradevan, Campbell, Victoria, Salehi, Tania, Lim, Wai, Boudville, Neil, Chakera, Aron, Chan, Doris, Krishnan, Anoushka, Eqbal, Yusuf, Gillies, Alastair, Vilayur, Eswari, Maung Myint, Thida Maung, Gray, Nicholas, Cheetham, Melissa, Pollock, Carol, Cooper, Bruce, Mather, Amanda, Roxburgh, Sarah, Shen, Yvonne, Stangenberg, Stefanie, Siriwardana, Amanda, O'Lone, Emma, Wan, Susan, Neuen, Brendon, Tsun Kit Ha, Jeffrey, Kim, Dana, Heath, Lauren, Jain, Arunima, Phua, Elaine, Li, Yan, Gallagher, Martin, Jardine, Meg, Ritchie, Angus, Razavian, Mona, Foote, Celine, Wyndham, Roger, Sen, Shaundeep, Endre, Zoltan, Erlich, Jonathan, Fernando, Mangalee, Yong, Kenneth, Luxton, Grant, Kotwal, Sradha, Roger, Simon, Wijeratne, Vidu, Packham, David, Fraser, Ian, Vandewiele, Bert, Laute, Margo, Lemahieu, Wim, Jamar, Sofie, Ombelet, Sara, Meeus, Gert, Decupere, Marc, Schockaert, Olivier, Doubel, Peter, Viaene, Liesbeth, Radermacher, Luc, Masset, Catherine, Moonen, Martial, Firre, Eric, Milicevic, Martina, Warling, Xavier, Vanacker, An, Malfait, Thomas, Durlen, Ivan, Horvatic, Ivica, Savuk, Ana, Gellineo, Lana, Karanovic, Sandra, Dika, Zivka, Plavljanic, Djuro, Mikacic, Ivana, Trajbar Kentric, Dubravka, Barisic, Dunja, Stankovic, Marija, Majstorovic Barac, Karolina, Kruljac, Ivan, Pavlovic, Drasko, Drinkovic, Martin, Prkacin, Ingrid, Barbic, Jerko, Sitas, Zvonimir, Vujcic, Dunja, Rychlik, Ivan, Benesova, Anna, Drinovska, Klara, Kratka, Karolina, Maixnerova, Dita, Ilmoja, Madis, Unt, Kristin, Lilienthal, Kadri, Auerbach, Asta, Leis, Liisi, Piel, Julia, Adoberg, Annika, Kolvald, Kulli, Veermae, Kristi, Telling, Kadri, Seppet, Elviira, Uhlinova, Jana, Zaoui, Philippe, Carron, Pierre-Louis, Masson, Ingrid, Dinic, Miriana, Thibaudin, Damien, Broyet, Christian, Maillard, Nicolas, Mohey, Hesham, Mariat, Christophe, Claisse, Guillaume, Alamartine, Eric, Dussol, Bertrand, Burtey, Stephane, Chiche-Jourde, Noemie, Serre, Jean-Emmanuel, Jeantet, Guillaume, Chenine, Leila, Blanchard, Anne, Roueff, Stephane, Thervet, Eric, Fouassier, David, Buffet, Alexandre, Livrozet, Marine, Gaisset, Roxane, Karras, Alexandre, Heng, Anne-Elisabeth, Garrouste, Cyril, Philipponnet, Carole, Nicolo, Clementine, Atenza, Alba, Lanaret, Camille, Greze, Clarisse, Mayet, Valentin, Dumond, Clement, Delmas, Yahsou, Combe, Christian, Rigothier, Claire, Burguet, Laure, Labat, Aurore, Mucha, Simon, de Précigout, Valérie, Weinreich, Thomas, Reichel, Helmut, Draganova, Diliana, Wolf, Lothar, Hohenstein, Bernd, Heinrichs, Sven, Kulka, Simone, Sat, Sebahat, Weiland, Lea, Krueger, Thilo, Wolf, Gunter, Kettner, Christiane, Schlosser, Mandy, Herfurth, Johann Konstantin, Koch, Annegret, Busch, Martin, Werth, Stephan Christian, Nitschke, Martin, Cakiroglu, Figen, Sarnow, Franziska, Schulz, Lisa, Weiner, Stefan, Wirtz, Nikolaus, Koester, Eric, Moeller, Marcus, Stamellou, Eleni, Sanden, Silja, Schmidt-Guertler, Hans, Bernhardt, Wanja, Patecki, Margret, Schlieper, Georg, Schulte, Kevin, Girardet, Annette, Kunzendorf, Ulrich, Kwan, Lorraine Pui Yuen, Mok, Maggie Ming Yee, Chan, Gary Chi Wang, Ma, Mingyao, Lie, Davina Ngoi Wah, Chan, Anthony Ting Pong, Szeto, Cheuk Chun, Ng, Kit Chung Jack, Cheung, Siu Fai, Yue, Tak Tai Andrew, Fung, Ka Shun Samuel, Tang, Hon, Yim, Ka Fai, Law, Wai Ping, Wong, Yick Hei, Lam, Chi Kwan Darwin, Wong, Sze Ho Sunny, Marcantoni, Carmelita, Aliotta, Roberta, Deodato, Francesca, Patella, Gemma, Comi, Nicolino, Vita, Caterina, Carullo, Nazareno, Bolignano, Davide, Musolino, Michela, Trillini, Matias, Perico, Norberto, Remuzzi, Giuseppe, Daina, Erica, Biancone, Luigi, Colla, Loredana, Burdese, Manuel, Cogno, Chiara, Boaglio, Elena, Abbasciano, Isabella, Zizzi, Carlotta Federica, Randone, Paolo, Napodano, Pietro, Ricchiuto, Anna, Cassia, Matthias, Accarino, Simone, Cozzolino, Mario, Baccaro, Rocco, Costanzi, Stefano, Di Maio, Federica, Arena, Maria, Urciuolo, Federica, Vigano, Sara, Cavalli, Andrea, Limardo, Monica, Bordoli, Monica, Ponti, Serena, Longhi, Selena, Solazzo, Andrea, Giaroni, Francesco, Donati, Gabriele, Torreggiani, Massimo, Catucci, Davide, Colucci, Marco, Esposito, Vittoria, Esposito, Ciro, Gesualdo, Loreto, Capaccio, Flavia, Diletta Stea, Emma, Sivo, Carmen, Annese, Francesca, Papadia, Federica, Messa, Piergiorgio, Belingheri, Mirco, Passerini, Patrizia, Malvica, Silvia, Vickiene, Alvita, Zakauskiene, Urte, Asakiene, Egle, Bumblyte', Inga Arune, Stankuviene, Asta, Santockiene, Lina, Hayat, Ashik, Williams, Allister, Sizeland, Peter, Tan, Eddie, Waters, Gerald, Chan, Lai Wan, Henderson, Andrew, Turnbull, Angus, McNally, Andrew, Reynolds, Annie, Pilmore, Helen, Dittmer, Ian, Manley, Paul, Stallworthy, Elizabeth, Goh, Tze, Semple, David, Collins, Michael, Curry, Elizabeth, Ahmed, Jafar, Nguyen, Thu, Winiarska, Agata, Zbrzezniak, Justyna, Stompor, Tomasz, Krajewska, Magdalena, Augustyniak-Bartosik, Hanna, Zielinska, Dorota, Jander, Anna, Stanczyk, Malgorzata, Tkaczyk, Marcin, Miarka, Przemyslaw, Aksamit, Dariusz, Jaskowski, Piotr, Sulowicz, Wladyslaw, Cieniawski, Dominik, Gontarek-Kacprzak, Julita, Felicjanczuk, Elzbieta, Kwella, Norbert, Kwella, Bogna, Satora, Ewa, Fernandes, João Carlos, Gomes, Ana Marta, Reis, Marina, Lopes, Daniela, Almeida, Catarina, Sá, Helena, Figueiredo, Ana Carolina, Pardinhas, Clara, Almeida, Edgar, Raimundo, Mario, Cortesão Costa, Ana, Falcao Goncalves, Luis Pedro, Fernandes, Sara, Silva, Sónia, Teixeira, Catarina, Fernandes, Adriana, Nolasco, Fernando, Alves, Patricia, Gois, Mario, Fonseca, Nuno, Messias, Ana, Menezes, Maria, Cardoso, Filipa, Sousa, Helena, Marques, Joana, Barata, Rui, Lopes, Jose Antonio, Jorge, Sofia, Gameiro, Joana, de Almeida Agapito Fonseca, Jose Nuno, Goncalves, Sara, Farinha, Ana, Valerio Santos, Patricia, Natario, Ana, de Jesus Barreto, Jose Carlos, Abrantes, Catarina, Quadrado Soares, Elsa Sofia, Soares Felgueiras, Joana de Sousa, Cunha, Liliana, Parreira, Lucia, Furtado, Teresa, Vaz, Alvaro, Oh, Kook-Hwan, Lee, Hajeong, Joong Kim, Se, Jeong, Jong Cheol, Hoon Kim, Yeong, Kim, Yunmi, Park, Hyeong Cheon, Choi, Hoon Young, Wook Kim, Hyung, Lee, Moon Hyoung, Yoon, Songuk, Lee, Kyu-Beck, Hyun, YoungYoul, Yoo, Tae-Hyun, Han, Seung Hyeok, Park, Jung Tak, Kim, Sunggyun, Song, Young Rim, Kim, Jwa-Kyung, Lee, Hyung-seok, Joo, Narae, Lee, JungEun, Ryoun Jang, Hye, Jeon, Junseok, Chung, Wookyung, Lee, HyunHee, Chang, Jae Hyun, Chun, Ka Yeong, Jung, Ji Yong, Ro, Han, Kim, Aejin, Jo, Sang-Kyung, Yang, Jihyun, Kim, Myung-Gyu, Oh, SeWon, Martinez Villanueva, Caridad, Gimeno, Ana Vilar, Andres Useche Bonilla, Gustavo, Tamarit, Esther, Galan Serrano, Antonio, Verde Moreno, Eduardo, Fernandez, Jose Luño, Goicoechea Diezhandino, Maria Angeles, Verdalles Guzman, Ursula, de Jose, Ana Perez, Ortiz Arduan, Alberto, Pérez Gómez, María Vanessa, Martín Cleary, Catalina, Prado, Raul Fernandez, Goma, Elena, Ballarin, Jose, Encarnacion, Montserrat Diaz, Da Silva Santos, Iara, Marco Rusinol, Helena, Furlano, Monica, Arias, Carlos, Barrios, Clara, Garcia, Eva Rodriguez, Sierra Ochoa, Adriana, Vizcaino Castillo, Belen, Pantoja Perez, Jonay, Gonzalez Moya, Mercedes, Sargsyan, Mari, Calatayud Aristoy, Emma, Bernabeu, Ana Avila, Perez Lluna, Leticia, Malek Marin, Tamara, Antonia Munar Vila, Maria, Bobadilla Rico, Ivon Maritza, Allende Burgos, Natalia, Gutierrez Martinez, Eduardo, Gutierrez Solis, Elena, Sevillano, Angel, Merida Herrero, Evangelina, Miquel Blasco Pelicano, Josep, Rodas Marin, Lida Maria, Quintana, Luis F, Antonieta Azancot Rivero, Maria, Ramos Terrades, Natalia, Garcia Carro, Clara, Agraz Pamplona, Irene, Salgueira Lazo, Mercedes, de la Prada Alvarez, Francisco, Alonso Garcia, Fabiola, Adrian Aguilera Morales, Wenceslao, Virxinia Pol Heres, Salia, Forcen, Angel, Parra Moncasi, Eduardo, Medrano Villarroya, Cristina, Soria Villen, Alejandro, Gracia Garcia, Olga, Velo Plaza, Mercedes, Sánchez de la Nieta, Maria Dolores, Calvo Arevalo, Marta, Moreno, Antolina, Cigarran Guldris, Secundino, de Vicente, Manuel Pereira, Munar Vila, Maria Antonia, Hsu, Bang-Gee, Wang, Chih-Hsien, Chen, Cheng-Hsu, Yu, Tung-Min, Wu, Ming-Ju, Tsai, Shang-Feng, Hsu, Chia-Tien, Chiu, Hsien-Fu, Chou, Kang-Ju, Fang, Hua-Chang, Lee, Po-Tsang, Chen, Hsin-Yu, Chen, Chien-Liang, Huang, Chien-Wei, Ou, Shih-Hsiang, Ho, Tzung-Yo, Hsu, Chih-Yang, Chang, Ming-Shan, Chiu, Yen-Ling, Peng, Yu-Sen, Shu, Kai-Hsiang, Pan, Szu-Yu, Hsu, Shih-Ping, Yang, Ju-Yeh, Pai, Mei-Fen, Tseng, Po-Yu, Wu, Hon-Yen, Tsai, Wan-Chuan, Tung, Kuei-Ting, Chen, Hung-Yuan, Chen, Hung-Chun, Kuo, Mei-Chuan, Hwang, Daw-Yang, Chiu, Yi-Wen, Hung, Chi-Chih, Kuo, Hung-Tien, Tsai, Jer-Chia, McCafferty, Kieran, Forbes, Suzanne, Dasgupta, Indranil, Thomas, Mark, Mahdi, Amar, Ajayi, Bamidele, Chowdhury, Paramit, Kasimatis, Theodoros, Moutzouris, Dimitrios, Dudreuilh, Caroline, Pruthi, Rishi, Mansfield, Nick, Doctor, Gabriel, Shah, Sapna, Kon, Sui, Smith, Priscilla, Hamilton, Patrick, Kanigicherla, Durga, Ibrahim Ragy, Omar Sherin, Alchi, Bassam, Flossmann, Oliver, Ghalli, Farid, Lawman, Sarah, Sinha, Smeeta, Chrysochou, Constantina, Chukwu, Chukwuma, Maire De Bhailis, Aine, Al Chalabi, Saif, Hudson, Amy, Gopu, Arun, Wickens, Olivia, Storrar, Joshua, Wahba, Mona, Lorde, Nathan, Rony, Mohammad, Griffin, Sian, Latif, Farah, Ali, Mohammad, DaSilva, Louise, Ayling-Smith, Jonathan, Mahdi, Eamon, Willcocks, Lisa, Jones, Rachel, Cheung, Chee Kay, Selvaskandan, Haresh, Pugh, Dan, Sayer, Matthew, Dhaun, Neeraj, Chapman, Fiona, Mark, Patrick, Geddes, Colin, McQuarrie, Emily, Patel, Rajan, Solomon, Laurence, Ponnusamy, Arvind, Morris, Adam, Okoh, Pedro, Floyd, Lauren, Dhaygude, Ajay, Leung, Janson, Goldsmith, Christopher, Pandya, Bhavna, Tez, Didem, Mikhail, Ashraf, Brown, Karen, Bucknall, Thomas, Lambie, Mark, Comunale, Roderick, Brandon, Donald, Martinez, Stacy, Hall, Amanda, Henderson, Amy, Fearday, Aaron, Douthit, Nicole, Snow, Brian, Silva, Arnold, Sly, Cathylee, Keller, Christopher, Davidson, Robert, Meng, Jerry, Haws, Robert, Kattamanchi, Siddhartha, Mojarrab, Javad, Pillai, Unnikrishnan, Lafayette, Richard, O'Shaughnessy, Michelle, Kamal, Fahameedah, Mehta, Kshama, Baker, Bruce, Ruiz, Mario, Jyothinagaram, Praveena, Peri, Usha, Paxton, William, Tumlin, James, McGreal, Kerri, McCarthy, Ellen, Kimber, Cassandra, Gautam, Archana, Khalil, Kassem, Nguyen, Viet, Minasian, Raffi, Arfaania, Dariush, Daneshvari, Sam, Zakari, Michel, Patrikyan, Artashes, Afsari, Rouzbeh, Ayvazyan, Christine, Fakih, Faisal, Lagatta, Mark, Rodriguez, Alfred, Avella, Jorge Enrique Monroy, Patak, Ramachandra, Kadakia, Jigar, Radhakrishnan, Jai, Appel, Gerald, Ahn, Wooin, Nelson, Bradley, Medina, Allyson, Ahmad, Syeda, Peleg, Yonatan, Clement, Nisha, Chiu, Ian, Hendren, Elizabeth, Bomback, Andrew, Canetta, Pietro, Spinowitz, Bruce, Charytan, Chaim, Parikh, Nishita, Kuo, Sheng, Raichoudhury, Ritesh, Dobre, Mirela, Negrea, Lavinia, Padiyar, Aparna, Jittirat, Arksarapuk, Pradhan, Nishigandha, Dhelaria, Ranjit, Balamuthusamy, Saravanan, Madhrira, Machaiah, Powell, Thomas, Lifland, Howard, Bailey, Asha, Ford Sightler, Sarah Ashley, Suthar, Meera Patel, Green, Heather, Parikh, Samir, Ayoub, Isabelle, Almaani, Salem, Contreras, Gabriel, Fornoni, Alessia, Drexler, Yelena, Geara, Abdallah, Sheridan, Brittany, Coppock, Gaia, Hogan, Jonathan, Gonzalez, Carlos, Bhadra, Shamik, Chowdhury, Pradip, Kyaw, Kay, Tan, May, Raakesh, Lathika, Mendoza, Elder, Viramontes, Veronica, Chaudhry, Asghar, Carbonell, Juan, Gadh, Rajdeep, Fernandez, Victor, Kassem, Mohamad, Jacob, Radu, Wilder, Karen, Newsome, Britt, Klamm, Kathryn, Suyumova, Irina, Kooienga, Laura Ann, Janko, Catherine, Rizk, Dana, Julian, Bruce, Caster, Dawn, Perez, Erika, Garg, Gunjan, Gowda, Nayan, Udani, Suneel, Mandayam, Sreedhar, Workeneh, Biruh, Assefi, Ali, Greco, Barbara, Germain, Michael, Patel, Jusmin, Quinn, Sarah, Sullivan, James, Glaze, Jeffrey, Madonia, Phillip, McMahon, Kellyn, Giles, Harold, Adler, Sharon, Dai, Tiane, Heerspink, Hiddo J L, Alpers, Charles E, Bieler, Stewart, Diva, Ulysses, Inrig, Jula, Komers, Radko, Mercer, Alex, Noronha, Irene L, Rheault, Michelle N, Rote, William, Trachtman, Howard, Trimarchi, Hernán, and Perkovic, Vlado

Published
2023
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13. A Study on Burrows-Wheeler Aligner’s Performance Optimization for Ancient DNA Mapping

Author

Sarmento, Cindy, Guimarães, Sílvia, Kılınç, Gülşah Merve, Götherström, Anders, Pires, Ana Elisabete, Ginja, Catarina, Fonseca, Nuno A., 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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14. Nucleolin expression has prognostic value in neuroblastoma patients

Author

Cangelosi, Davide, Brignole, Chiara, Bensa, Veronica, Tamma, Roberto, Malaguti, Fabiana, Carlini, Barbara, Giusto, Elena, Calarco, Enzo, Perri, Patrizia, Ribatti, Domenico, Fonseca, Nuno André, Moreira, Joao Nuno, Eva, Alessandra, Amoroso, Loredana, Conte, Massimo, Garaventa, Alberto, Sementa, Angela Rita, Corrias, Maria Valeria, Ponzoni, Mirco, and Pastorino, Fabio

Published
2022
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19. Author Correction: Tumour gene expression signature in primary melanoma predicts long-term outcomes

Author

Garg, Manik, Couturier, Dominique-Laurent, Nsengimana, Jérémie, Fonseca, Nuno A., Wongchenko, Matthew, Yan, Yibing, Lauss, Martin, Jönsson, Göran B., Newton-Bishop, Julia, Parkinson, Christine, Middleton, Mark R., Bishop, D. Timothy, McDonald, Sarah, Stefanos, Nikki, Tadross, John, Vergara, Ismael A., Lo, Serigne, Newell, Felicity, Wilmott, James S., Thompson, John F., Long, Georgina V., Scolyer, Richard A., Corrie, Pippa, Adams, David J., Brazma, Alvis, and Rabbie, Roy

Published
2022
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22. Smartphone Recommendation System to Prevent Potential Injuries in Young Athletes

Author

Matos, Paulo, Rocha, João, Gonçalves, Ramiro, Santos, Filipe, Marreiros, Goreti, Mota, Daniel, Fonseca, Nuno, Martins, Constantino, Magjarevic, Ratko, Series Editor, Ładyżyński, Piotr, Associate Editor, Ibrahim, Fatimah, Associate Editor, Lackovic, Igor, Associate Editor, Rock, Emilio Sacristan, Associate Editor, Henriques, Jorge, editor, Neves, Nuno, editor, and de Carvalho, Paulo, editor

Published
2020
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23. Mobile Application to Support Children with Anxiety Disorders

Author

Fonseca, Nuno, Almeida, Ana, Moreno, Maria, de Almeida, Raquel Simões, Faria, Luiz, Marques, António, Matos, Paulo, Rocha, Pedro, Martins, Constantino, Magjarevic, Ratko, Series Editor, Ładyżyński, Piotr, Associate Editor, Ibrahim, Fatimah, Associate Editor, Lackovic, Igor, Associate Editor, Rock, Emilio Sacristan, Associate Editor, Henriques, Jorge, editor, Neves, Nuno, editor, and de Carvalho, Paulo, editor

Published
2020
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24. Hydrodynamic Responses and Loads of a Model Floating Hydrocarbon Storage Tank System for Concept Validation and Numerical Verification

Author

Zhang, Chi, Magee, Allan R., Fonseca, Nuno, Hellan, Øyvind, Ang, Kok Keng, di Prisco, Marco, Series Editor, Chen, Sheng-Hong, Series Editor, Vayas, Ioannis, Series Editor, Kumar Shukla, Sanjay, Series Editor, Sharma, Anuj, Series Editor, Kumar, Nagesh, Series Editor, Wang, Chien Ming, Series Editor, Lim, Soon Heng, editor, and Tay, Zhi Yung, editor

Published
2020
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26. GMP-grade nanoparticle targeted to nucleolin downregulates tumor molecular signature, blocking growth and invasion, at low systemic exposure

Author

Fonseca, Nuno A., Gregório, Ana C., Mendes, Vera M., Lopes, Rui, Abreu, Teresa, Gonçalves, Nélio, Manadas, Bruno, Lacerda, Manuela, Figueiredo, Paulo, Pereira, Marta, Gaspar, Manuela, Colelli, Fabiana, Pesce, Daniela, Signorino, Giacomo, Focareta, Laura, Fucci, Alessandra, Cardile, Francesco, Pisano, Claudio, Cruz, Tony, Almeida, Luís, Moura, Vera, Simões, Sérgio, and Moreira, João N.

Published
2021
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27. A Wave Drift Force Model for Semi-Submersible Types of Floating Wind Turbines in Large Waves and Current.

Author

Fonseca, Nuno and Dadmarzi, Fatemeh H.

Subjects
WIND turbines, WAVE forces, TRANSFER functions, HEURISTIC, DATA modeling
Abstract

The correct prediction of slowly varying wave drift loads is important for the mooring analysis of floating wind turbines (FWTs). However, present design analysis tools fail to correctly predict these loads in conditions with current and moderate and large waves. This paper presents a semi-empirical method to correct zero-current potential-flow quadratic transfer functions (QTFs) of horizontal wave drift loads in conditions with current and moderate and large waves. The method is applicable to column-stabilized types of substructures or semi-submersibles. In the first step, the potential-flow QTF is corrected for potential-flow wave–current effects by applying a heuristic method. Second, the generalized Exwave formula corrects for viscous drift effects. Viscous drift effects become important for moderate and large waves. Conditions with current in the same direction as the waves increase the viscous drift contribution further. The method is validated by comparing QTF predictions with empirical QTFs identified from model test data for the INO Windmoor semi. While potential-flow QTFs agree well with the empirical data for small seastates without current, they underestimate the wave drift loads for moderate and large seastates. Conditions with current increase the underestimation. The semi-empirical correction method significantly improves predictions. [ABSTRACT FROM AUTHOR]

Published
2024
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28. Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

Author

Rheinbay, Esther, Nielsen, Morten Muhlig, Abascal, Federico, Wala, Jeremiah A., Shapira, Ofer, Tiao, Grace, Hornshøj, Henrik, Hess, Julian M., Juul, Randi Istrup, Lin, Ziao, Feuerbach, Lars, Sabarinathan, Radhakrishnan, Madsen, Tobias, Kim, Jaegil, Mularoni, Loris, Shuai, Shimin, Lanzós, Andrés, Herrmann, Carl, Maruvka, Yosef E., Shen, Ciyue, Amin, Samirkumar B., Bandopadhayay, Pratiti, Bertl, Johanna, Boroevich, Keith A., Busanovich, John, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Craft, David, Dhingra, Priyanka, Diamanti, Klev, Fonseca, Nuno A., Gonzalez-Perez, Abel, Guo, Qianyun, Hamilton, Mark P., Haradhvala, Nicholas J., Hong, Chen, Isaev, Keren, Johnson, Todd A., Juul, Malene, Kahles, Andre, Kahraman, Abdullah, Kim, Youngwook, Komorowski, Jan, Kumar, Kiran, Kumar, Sushant, Lee, Donghoon, Lehmann, Kjong-Van, Li, Yilong, Liu, Eric Minwei, Lochovsky, Lucas, Park, Keunchil, Pich, Oriol, Roberts, Nicola D., Saksena, Gordon, Schumacher, Steven E., Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stewart, Chip, Tamborero, David, Tubio, Jose M. C., Umer, Husen M., Uusküla-Reimand, Liis, Wadelius, Claes, Wadi, Lina, Yao, Xiaotong, Zhang, Cheng-Zhong, Zhang, Jing, Haber, James E., Hobolth, Asger, Imielinski, Marcin, Kellis, Manolis, Lawrence, Michael S., von Mering, Christian, Nakagawa, Hidewaki, Raphael, Benjamin J., Rubin, Mark A., Sander, Chris, Stein, Lincoln D., Stuart, Joshua M., Tsunoda, Tatsuhiko, Wheeler, David A., Johnson, Rory, Reimand, Jüri, Gerstein, Mark, Khurana, Ekta, Campbell, Peter J., López-Bigas, Núria, Weischenfeldt, Joachim, Beroukhim, Rameen, Martincorena, Iñigo, Pedersen, Jakob Skou, and Getz, Gad

Published
2023
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29. Author Correction: Genomic basis for RNA alterations in cancer

Author

Calabrese, Claudia, Davidson, Natalie R., Demircioğlu, Deniz, Fonseca, Nuno A., He, Yao, Kahles, André, Lehmann, Kjong-Van, Liu, Fenglin, Shiraishi, Yuichi, Soulette, Cameron M., Urban, Lara, Greger, Liliana, Li, Siliang, Liu, Dongbing, Perry, Marc D., Xiang, Qian, Zhang, Fan, Zhang, Junjun, Bailey, Peter, Erkek, Serap, Hoadley, Katherine A., Hou, Yong, Huska, Matthew R., Kilpinen, Helena, Korbel, Jan O., Marin, Maximillian G., Markowski, Julia, Nandi, Tannistha, Pan-Hammarström, Qiang, Pedamallu, Chandra Sekhar, Siebert, Reiner, Stark, Stefan G., Su, Hong, Tan, Patrick, Waszak, Sebastian M., Yung, Christina, Zhu, Shida, Awadalla, Philip, Creighton, Chad J., Meyerson, Matthew, Ouellette, B. F. Francis, Wu, Kui, Yang, Huanming, Brazma, Alvis, Brooks, Angela N., Göke, Jonathan, Rätsch, Gunnar, Schwarz, Roland F., Stegle, Oliver, and Zhang, Zemin

Published
2023
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35. Genomic basis for RNA alterations in cancer

Author

Calabrese, Claudia, Davidson, Natalie R., Demircioglu, Deniz, Fonseca, Nuno A., He, Yao, Kahles, André, and Lehmann, Kjong-Van

Subjects
Nucleotide sequencing -- Identification and classification, Gene expression -- Identification and classification, DNA sequencing -- Identification and classification, RNA -- Health aspects, Cancer -- Genetic aspects -- Identification and classification, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Transcript alterations often result from somatic changes in cancer genomes.sup.1. Various forms of RNA alterations have been described in cancer, including overexpression.sup.2, altered splicing.sup.3 and gene fusions.sup.4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA).sup.5. Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed 'bridged' fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer. Integrative analyses of transcriptome and whole-genome sequencing data for 1,188 tumours across 27 types of cancer are used to provide a comprehensive catalogue of RNA-level alterations in cancer., Author(s): Claudia Calabrese [sup.2] , Natalie R. Davidson [sup.3] [sup.4] [sup.5] [sup.6] [sup.7] , Deniz Demircioglu [sup.8] [sup.9] , Nuno A. Fonseca [sup.2] , Yao He [sup.10] , André Kahles [...]

Published
2020
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36. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Author

Bradnam, Keith R., Fass, Joseph N., Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, İnanç, Boisvert, Sébastien, Chapman, Jarrod A., Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T. Roderick, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A., Ganapathy, Ganeshkumar, Gibbs, Richard A., Gnerre, Sante, Godzaridis, Élénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B., Ho, Isaac Y., Howard, Jason, Hunt, Martin, Jackman, Shaun D., Jaffe, David B, Jarvis, Erich, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J., Kitzman, Jacob O., Knight, James R., Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, MacCallum, Iain, MacManes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Vieira, Bruno Miguel, Naquin, Delphine, Ning, Zemin, Otto, Thomas D., Paten, Benedict, Paulo, Octávio S., Phillippy, Adam M., Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S., Ruby, J. Graham, Scalabrin, Simone, Schatz, Michael C., Schwartz, David C., Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I., Shendure, Jay, Shi, Yujian, Simpson, Jared T., Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Wang, Jun, Worley, Kim C., Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, and Korf, Ian F.

Subjects
Quantitative Biology - Genomics
Abstract

Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results - In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions - Many current genome assemblers produced useful assemblies, containing a significant representation of their genes, regulatory sequences, and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another., Comment: Additional files available at http://korflab.ucdavis.edu/Datasets/Assemblathon/Assemblathon2/Additional_files/ Major changes 1. Accessions for the 3 read data sets have now been included 2. New file: spreadsheet containing details of all Study, Sample, Run, & Experiment identifiers 3. Made miscellaneous changes to address reviewers comments. DOIs added to GigaDB datasets

Published
2013
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38. Cell surface Nucleolin represents a novel cellular target for neuroblastoma therapy

Author

Brignole, Chiara, Bensa, Veronica, Fonseca, Nuno A., Del Zotto, Genny, Bruno, Silvia, Cruz, Ana F., Malaguti, Fabiana, Carlini, Barbara, Morandi, Fabio, Calarco, Enzo, Perri, Patrizia, Moura, Vera, Emionite, Laura, Cilli, Michele, De Leonardis, Francesco, Tondo, Annalisa, Amoroso, Loredana, Conte, Massimo, Garaventa, Alberto, Sementa, Angela R., Corrias, Maria V., Ponzoni, Mirco, Moreira, Joao N., and Pastorino, Fabio

Published
2021
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39. Tumour gene expression signature in primary melanoma predicts long-term outcomes

Author

Garg, Manik, Couturier, Dominique-Laurent, Nsengimana, Jérémie, Fonseca, Nuno A., Wongchenko, Matthew, Yan, Yibing, Lauss, Martin, Jönsson, Göran B., Newton-Bishop, Julia, Parkinson, Christine, Middleton, Mark R., Bishop, D. Timothy, McDonald, Sarah, Stefanos, Nikki, Tadross, John, Vergara, Ismael A., Lo, Serigne, Newell, Felicity, Wilmott, James S., Thompson, John F., Long, Georgina V., Scolyer, Richard A., Corrie, Pippa, Adams, David J., Brazma, Alvis, and Rabbie, Roy

Published
2021
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44. Efficacy and safety of sparsentan versus irbesartan in patients with IgA nephropathy (PROTECT): 2-year results from a randomised, active-controlled, phase 3 trial

Author

Rovin, Brad H, primary, Barratt, Jonathan, additional, Heerspink, Hiddo J L, additional, Alpers, Charles E, additional, Bieler, Stewart, additional, Chae, Dong-Wan, additional, Diva, Ulysses A, additional, Floege, Jürgen, additional, Gesualdo, Loreto, additional, Inrig, Jula K, additional, Kohan, Donald E, additional, Komers, Radko, additional, Kooienga, Laura Ann, additional, Lafayette, Richard, additional, Maes, Bart, additional, Małecki, Robert, additional, Mercer, Alex, additional, Noronha, Irene L, additional, Oh, Se Won, additional, Peh, Chen Au, additional, Praga, Manuel, additional, Preciado, Priscila, additional, Radhakrishnan, Jai, additional, Rheault, Michelle N, additional, Rote, William E, additional, Tang, Sydney C W, additional, Tesar, Vladimir, additional, Trachtman, Howard, additional, Trimarchi, Hernán, additional, Tumlin, James A, additional, Wong, Muh Geot, additional, Perkovic, Vlado, additional, Abbasciano, Isabella, additional, Abrantes, Catarina, additional, Accarino, Simone, additional, Adler, Sharon, additional, Adoberg, Annika, additional, Afsari, Rouzbeh, additional, Ahmad, Syeda, additional, Ahmed, Jafar, additional, Ahn, Wooin, additional, Ajayi, Bamidele, additional, Aksamit, Dariusz, additional, Al Chalabi, Saif, additional, Alamartine, Eric, additional, Alchi, Bassam, additional, Ali, Mohammad, additional, Aliotta, Roberta, additional, Almaani, Salem, additional, Almeida, Catarina, additional, Almeida, Edgar, additional, Alvarez, Francisco de la Prada, additional, Alves, Patricia, additional, Annese, Francesca, additional, Appel, Gerald, additional, Arduan, Alberto Ortiz, additional, Arena, Maria, additional, Arevalo, Marta Calvo, additional, Arfaania, Dariush, additional, Arias, Carlos, additional, Aristoy, Emma Calatayud, additional, Asakiene, Egle, additional, Ashley, Sarah, additional, Assefi, Ali, additional, Atenza, Alba, additional, Auerbach, Asta, additional, Augustyniak-Bartosik, Hanna, additional, Avella, Monroy, additional, Ayling-Smith, Jonathan, additional, Ayoub, Isabelle, additional, Ayvazyan, Christine, additional, Baccaro, Rocco, additional, Bailey, Asha, additional, Baker, Bruce, additional, Balamuthusamy, Saravanan, additional, Ballarin, Jose, additional, Barata, Rui, additional, Barbic, Jerko, additional, Barisic, Dunja, additional, Barreto, Jose Carlos de Jesus, additional, Barrios, Clara, additional, Belingheri, Mirco, additional, Benesova, Anna, additional, Bernabeu, Ana Avila, additional, Bernhardt, Wanja, additional, Bhadra, Shamik, additional, Biancone, Luigi, additional, Blanchard, Anne, additional, Boaglio, Elena, additional, Bolignano, Davide, additional, Bomback, Andrew, additional, Bonilla, Gustavo Andres Useche, additional, Bordoli, Monica, additional, Bose, Bhadran, additional, Boudville, Neil, additional, Brandon, Donald, additional, Brown, Karen, additional, Broyet, Christian, additional, Bucknall, Thomas, additional, Buffet, Alexandre, additional, Bumblyte', Inga Arune, additional, Burdese, Manuel, additional, Burgos, Natalia Allende, additional, Burguet, Laure, additional, Burtey, Stephane, additional, Busch, Martin, additional, Cakiroglu, Figen, additional, Campbell, Victoria, additional, Canetta, Pietro, additional, Capaccio, Flavia, additional, Carbonell, Juan, additional, Cardoso, Filipa, additional, Carro, Clara Garcia, additional, Carroll, Robert, additional, Carron, Pierre-Louis, additional, Carullo, Nazareno, additional, Cassia, Matthias, additional, Caster, Dawn, additional, Castillo, Belen Vizcaino, additional, Catucci, Davide, additional, Cavalli, Andrea, additional, Chakera, Aron, additional, Chan, Doris, additional, Chan, Gary Chi Wang, additional, Chan, Anthony Ting Pong, additional, Chan, Lai Wan, additional, Chang, Jae Hyun, additional, Chang, Ming-Shan, additional, Chapman, Fiona, additional, Charytan, Chaim, additional, Chaudhry, Asghar, additional, Cheetham, Melissa, additional, Chen, Cheng-Hsu, additional, Chen, Hsin-Yu, additional, Chen, Chien-Liang, additional, Chen, Hung-Yuan, additional, Chen, Hung-Chun, additional, Chenine, Leila, additional, Cheung, Siu Fai, additional, Cheung, Chee Kay, additional, Chiche-Jourde, Noemie, additional, Chiu, Hsien-Fu, additional, Chiu, Yen-Ling, additional, Chiu, Yi-Wen, additional, Chiu, Ian, additional, Choi, Hoon Young, additional, Chou, Kang-Ju, additional, Chowdhury, Paramit, additional, Chowdhury, Pradip, additional, Chrysochou, Constantina, additional, Chukwu, Chukwuma, additional, Chun, Ka Yeong, additional, Chung, Wookyung, additional, Cieniawski, Dominik, additional, Claisse, Guillaume, additional, Clayton, Philip, additional, Cleary, Catalina Martín, additional, Clement, Nisha, additional, Coates, Toby, additional, Cogno, Chiara, additional, Colla, Loredana, additional, Collins, Michael, additional, Colucci, Marco, additional, Combe, Christian, additional, Comi, Nicolino, additional, Comunale, Roderick, additional, Contreras, Gabriel, additional, Cooper, Bruce, additional, Coppock, Gaia, additional, Costa, Ana Cortesão, additional, Costanzi, Stefano, additional, Cozzolino, Mario, additional, Crail, Susan, additional, Cunha, Liliana, additional, Curry, Elizabeth, additional, Dai, Tiane, additional, Daina, Erica, additional, Daneshvari, Sam, additional, Dasgupta, Indranil, additional, DaSilva, Louise, additional, Davidson, Robert, additional, De Bhailis, Aine Maire, additional, de Précigout, Valérie, additional, Decupere, Marc, additional, Delmas, Yahsou, additional, Deodato, Francesca, additional, Dhaun, Neeraj, additional, Dhaygude, Ajay, additional, Dhelaria, Ranjit, additional, Di Maio, Federica, additional, Diezhandino, Maria Angeles Goicoechea, additional, Dika, Zivka, additional, Dinic, Miriana, additional, Dittmer, Ian, additional, Dobre, Mirela, additional, Doctor, Gabriel, additional, Donati, Gabriele, additional, Doubel, Peter, additional, Douthit, Nicole, additional, Draganova, Diliana, additional, Drexler, Yelena, additional, Drinkovic, Martin, additional, Drinovska, Klara, additional, Dudreuilh, Caroline, additional, Dumond, Clement, additional, Durlen, Ivan, additional, Dussol, Bertrand, additional, Encarnacion, Montserrat Diaz, additional, Endre, Zoltan, additional, Enrique, Jorge, additional, Eqbal, Yusuf, additional, Erlich, Jonathan, additional, Esposito, Vittoria, additional, Esposito, Ciro, additional, Fakih, Faisal, additional, Fang, Hua-Chang, additional, Farinha, Ana, additional, Fearday, Aaron, additional, Felgueiras, Joana de Sousa Soares, additional, Felicjanczuk, Elzbieta, additional, Fernandes, João Carlos, additional, Fernandes, Sara, additional, Fernandes, Adriana, additional, Fernandez, Jose Luño, additional, Fernandez, Victor, additional, Fernando, Mangalee, additional, Figueiredo, Ana Carolina, additional, Firre, Eric, additional, Flossmann, Oliver, additional, Floyd, Lauren, additional, Fonseca, Nuno, additional, Fonseca, Jose Nuno de Almeida Agapito, additional, Foote, Celine, additional, Forbes, Suzanne, additional, Forcen, Angel, additional, Fornoni, Alessia, additional, Fouassier, David, additional, Fraser, Ian, additional, Fung, Ka Shun Samuel, additional, Furlano, Monica, additional, Furtado, Teresa, additional, Gadh, Rajdeep, additional, Gaisset, Roxane, additional, Gallagher, Martin, additional, Gameiro, Joana, additional, Gangadharan, Muralikrishna, additional, Garcia, Fabiola Alonso, additional, Garcia, Olga Gracia, additional, Garg, Gunjan, additional, Garrouste, Cyril, additional, Gautam, Archana, additional, Geara, Abdallah, additional, Geddes, Colin, additional, Gellineo, Lana, additional, Germain, Michael, additional, Ghalli, Farid, additional, Giaroni, Francesco, additional, Giles, Harold, additional, Gillies, Alastair, additional, Gimeno, Ana Vilar, additional, Girardet, Annette, additional, Glaze, Jeffrey, additional, Goh, Tze, additional, Gois, Mario, additional, Goldsmith, Christopher, additional, Goma, Elena, additional, Gomes, Ana Marta, additional, Goncalves, Luis Pedro Falcao, additional, Goncalves, Sara, additional, Gontarek-Kacprzak, Julita, additional, Gonzalez, Carlos, additional, Gopu, Arun, additional, Gowda, Nayan, additional, Gray, Nicholas, additional, Greco, Barbara, additional, Green, Heather, additional, Greze, Clarisse, additional, Griffin, Sian, additional, Guldris, Secundino Cigarran, additional, Guzman, Ursula Verdalles, additional, Ha, Jeffrey Tsun Kit, additional, Hall, Amanda, additional, Hamilton, Patrick, additional, Han, Seung Hyeok, additional, Haws, Robert, additional, Hayat, Ashik, additional, Heath, Lauren, additional, Heinrichs, Sven, additional, Henderson, Andrew, additional, Henderson, Amy, additional, Hendren, Elizabeth, additional, Heng, Anne-Elisabeth, additional, Heres, Salia Virxinia Pol, additional, Herfurth, Johann Konstantin, additional, Herrero, Evangelina Merida, additional, Ho, Tzung-Yo, additional, Hogan, Jonathan, additional, Hohenstein, Bernd, additional, Hollett, Peter, additional, Horvatic, Ivica, additional, Hsu, Bang-Gee, additional, Hsu, Chia-Tien, additional, Hsu, Chih-Yang, additional, Hsu, Shih-Ping, additional, Huang, Chien-Wei, additional, Hudson, Amy, additional, Hung, Chi-Chih, additional, Hwang, Shang-Jyh, additional, Hwang, Daw-Yang, additional, Hyun, Young Youl, additional, Ilmoja, Madis, additional, Irish, Georgina, additional, Jacob, Radu, additional, Jahan, Sadia, additional, Jain, Arunima, additional, Jamar, Sofie, additional, Jander, Anna, additional, Jang, Hye Ryoun, additional, Janko, Catherine, additional, Jardine, Meg, additional, Jaskowski, Piotr, additional, Jeantet, Guillaume, additional, Jelakovic, Bojan, additional, Jeon, Junseok, additional, Jeong, Jong Cheol, additional, Jesudason, Shilpanjali, additional, Jittirat, Arksarapuk, additional, Jo, Sang-Kyung, additional, Jones, Rachel, additional, Joo, Narae, additional, Jorge, Sofia, additional, Julian, Bruce, additional, Jung, JiYong, additional, Jyothinagaram, Praveena, additional, Kadakia, Jigar, additional, Kamal, Fahameedah, additional, Kanigicherla, Durga, additional, Karanovic, Sandra, additional, Karras, Alexandre, additional, Kasimatis, Theodoros, additional, Kassem, Mohamad, additional, Kattamanchi, Siddhartha, additional, Keller, Christopher, additional, Kentric, Dubravka Trajbar, additional, Kettner, Christiane, additional, Khalil, Kassem, additional, Kim, Dana, additional, Kim, Se Joong, additional, Kim, Yeong Hoon, additional, Kim, Yunmi, additional, Kim, Hyung Wook, additional, Kim, Sunggyun, additional, Kim, Jwa-Kyung, additional, Kim, Aejin, additional, Kim, Myung-Gyu, additional, Kimber, Cassandra, additional, Klamm, Kathryn, additional, Koch, Annegret, additional, Koester, Eric, additional, Kolvald, Kulli, additional, Kon, Sui, additional, Kotwal, Sradha, additional, Krajewska, Magdalena, additional, Kratka, Karolina, additional, Krishnan, Anoushka, additional, Krishnasamy, Rathika, additional, Krueger, Thilo, additional, Kruljac, Ivan, additional, Kulka, Simone, additional, Kunzendorf, Ulrich, additional, Kuo, Mei-Chuan, additional, Kuo, Hung-Tien, additional, Kuo, Sheng, additional, Kwan, Lorraine Pui Yuen, additional, Kwella, Norbert, additional, Kwella, Bogna, additional, Kyaw, Kay, additional, Labat, Aurore, additional, Lagatta, Mark, additional, Lam, Chi Kwan Darwin, additional, Lambie, Mark, additional, Lanaret, Camille, additional, Latif, Farah, additional, Laute, Margo, additional, Law, Wai Ping, additional, Lawman, Sarah, additional, Lazo, Mercedes Salgueira, additional, Lee, Hajeong, additional, Lee, Moon Hyoung, additional, Lee, Kyu-Beck, additional, Lee, Hyung-seok, additional, Lee, JungEun, additional, Lee, Hyun Hee, additional, Lee, Po-Tsang, additional, Leis, Liisi, additional, Lemahieu, Wim, additional, Leung, Janson, additional, Li, Yan, additional, Lie, Davina Ngoi Wah, additional, Lifland, Howard, additional, Lilienthal, Kadri, additional, Lim, Wai, additional, Limardo, Monica, additional, Livrozet, Marine, additional, Longhi, Selena, additional, Lopes, Daniela, additional, Lopes, Jose Antonio, additional, Lorde, Nathan, additional, Luxton, Grant, additional, Ma, Mingyao, additional, Madhrira, Machaiah, additional, Madonia, Phillip, additional, Mahadevan, Kumaradevan, additional, Mahdi, Amar, additional, Mahdi, Eamon, additional, Maillard, Nicolas, additional, Maixnerova, Dita, additional, Majstorovic Barac, Karolina, additional, Malecki, Robert, additional, Malfait, Thomas, additional, Malvica, Silvia, additional, Mandayam, Sreedhar, additional, Manley, Paul, additional, Mansfield, Nick, additional, Marcantoni, Carmelita, additional, Mariat, Christophe, additional, Marin, Tamara Malek, additional, Marin, Lida Maria Rodas, additional, Mark, Patrick, additional, Marques, Joana, additional, Martinez, Eduardo Gutierrez, additional, Martinez, Stacy, additional, Masset, Catherine, additional, Masson, Ingrid, additional, Mather, Amanda, additional, Maung Myint, Thida Maung, additional, Mayet, Valentin, additional, McCafferty, Kieran, additional, McCarthy, Ellen, additional, McDonald, Stephen, additional, McGreal, Kerri, additional, McMahon, Kellyn, additional, McNally, Andrew, additional, McQuarrie, Emily, additional, Medina, Allyson, additional, Meeus, Gert, additional, Mehta, Kshama, additional, Mendoza, Elder, additional, Menezes, Maria, additional, Meng, Jerry, additional, Messa, Piergiorgio, additional, Messias, Ana, additional, Miarka, Przemyslaw, additional, Miglinas, Marius, additional, Mikacic, Ivana, additional, Mikhail, Ashraf, additional, Milicevic, Martina, additional, Minasian, Raffi, additional, Moeller, Marcus, additional, Mohey, Hesham, additional, Mojarrab, Javad, additional, Mok, Maggie Ming Yee, additional, Moncasi, Eduardo Parra, additional, Moonen, Martial, additional, Morales, Wenceslao Adrian Aguilera, additional, Moreno, Eduardo Verde, additional, Moreno, Antolina, additional, Morris, Adam, additional, Moutzouris, Dimitrios, additional, Moya, Mercedes Gonzalez, additional, Mucha, Simon, additional, Musolino, Michela, additional, Napodano, Pietro, additional, Natario, Ana, additional, Negrea, Lavinia, additional, Nelson, Bradley, additional, Neuen, Brendon, additional, Newsome, Britt, additional, Ng, Kit Chung Jack, additional, Nguyen, Thu, additional, Nguyen, Viet, additional, Nicolo, Clementine, additional, Nitschke, Martin, additional, Noble, Euan, additional, Nolasco, Fernando, additional, O'Lone, Emma, additional, Ochoa, Adriana Sierra, additional, Oh, Kook-Hwan, additional, Oh, SeWon, additional, Okoh, Pedro, additional, Ombelet, Sara, additional, O'Shaughnessy, Michelle, additional, Ou, Shih-Hsiang, additional, Packham, David, additional, Padiyar, Aparna, additional, Pai, Mei-Fen, additional, Pamplona, Irene Agraz, additional, Pan, Szu-Yu, additional, Pandya, Bhavna, additional, Papadia, Federica, additional, Pardinhas, Clara, additional, Parikh, Nishita, additional, Parikh, Samir, additional, Park, Hyeong Cheon, additional, Park, Jung Tak, additional, Parreira, Lucia, additional, Passerini, Patrizia, additional, Patak, Ramachandra, additional, Patecki, Margret, additional, Patel, Rajan, additional, Patel, Jusmin, additional, Patel Suthar, Meera, additional, Patella, Gemma, additional, Patrikyan, Artashes, additional, Pavlovic, Drasko, additional, Paxton, William, additional, Peh, Chen, additional, Peleg, Yonatan, additional, Pelicano, Josep Miquel Blasco, additional, Peng, Yu-Sen, additional, Pereira de Vicente, Manuel, additional, Perez, Jonay Pantoja, additional, Perez, Erika, additional, Perez de Jose, Ana, additional, Pérez Gómez, María Vanessa, additional, Perez Lluna, Leticia, additional, Peri, Usha, additional, Perico, Norberto, additional, Philipponnet, Carole, additional, Phua, Elaine, additional, Piel, Julia, additional, Pillai, Unnikrishnan, additional, Pilmore, Helen, additional, Plavljanic, Djuro, additional, Plaza, Mercedes Velo, additional, Pollock, Carol, additional, Ponnusamy, Arvind, additional, Ponti, Serena, additional, Powell, Thomas, additional, Pradhan, Nishigandha, additional, Prado, Raul Fernandez, additional, Prkacin, Ingrid, additional, Pruthi, Rishi, additional, Pugh, Dan, additional, Quinn, Sarah, additional, Quintana, Luis F, additional, Raakesh, Lathika, additional, Rabindranath, Kannaiyan, additional, Radermacher, Luc, additional, Ragy, Omar Sherin Ibrahim, additional, Raichoudhury, Ritesh, additional, Raimundo, Mario, additional, Randone, Paolo, additional, Razavian, Mona, additional, Reichel, Helmut, additional, Reis, Marina, additional, Remuzzi, Giuseppe, additional, Reynolds, Annie, additional, Ricchiuto, Anna, additional, Rico, Ivon Maritza Bobadilla, additional, Rigothier, Claire, additional, Ritchie, Angus, additional, Rivero, Maria Antonieta Azancot, additional, Rizk, Dana, additional, Ro, Han, additional, Rodriguez, Alfred, additional, Rodriguez Garcia, Eva, additional, Roger, Simon, additional, Rony, Mohammad, additional, Rosenberg, Mai, additional, Roueff, Stephane, additional, Rovin, Brad, additional, Roxburgh, Sarah, additional, Ruiz, Mario, additional, Rusinol, Helena Marco, additional, Rychlik, Ivan, additional, Sá, Helena, additional, Salehi, Tania, additional, Sánchez de la Nieta, Maria Dolores, additional, Sanden, Silja, additional, Santockiene, Lina, additional, Santos, Patricia Valerio, additional, Santos, Iara Da Silva, additional, Sargsyan, Mari, additional, Sarnow, Franziska, additional, Sat, Sebahat, additional, Satora, Ewa, additional, Savuk, Ana, additional, Sayer, Matthew, additional, Schlieper, Georg, additional, Schlosser, Mandy, additional, Schmidt-Guertler, Hans, additional, Schockaert, Olivier, additional, Schulte, Kevin, additional, Schulz, Lisa, additional, Selvaskandan, Haresh, additional, Semple, David, additional, Sen, Shaundeep, additional, Seppet, Elviira, additional, Serrano, Antonio Galan, additional, Serre, Jean-Emmanuel, additional, Sevillano, Angel, additional, Shah, Sapna, additional, Shen, Yvonne, additional, Sheridan, Brittany, additional, Shu, Kai-Hsiang, additional, Sightler, Ford, additional, Silva, Sónia, additional, Silva, Arnold, additional, Sinha, Smeeta, additional, Siriwardana, Amanda, additional, Sitas, Zvonimir, additional, Sivo, Carmen, additional, Sizeland, Peter, additional, Sly, Cathylee, additional, Smith, Priscilla, additional, Snow, Brian, additional, Soares, Elsa Sofia Quadrado, additional, Solazzo, Andrea, additional, Solis, Elena Gutierrez, additional, Solomon, Laurence, additional, Song, Young Rim, additional, Sousa, Helena, additional, Spinowitz, Bruce, additional, Stallworthy, Elizabeth, additional, Stamellou, Eleni, additional, Stanczyk, Malgorzata, additional, Stangenberg, Stefanie, additional, Stankovic, Marija, additional, Stankuviene, Asta, additional, Stea, Emma Diletta, additional, Stompor, Tomasz, additional, Storrar, Joshua, additional, Sullivan, James, additional, Sulowicz, Wladyslaw, additional, Suyumova, Irina, additional, Szeto, Cheuk Chun, additional, Tamarit, Esther, additional, Tan, Eddie, additional, Tan, May, additional, Tang, Sydney Chi Wai, additional, Tang, Hon, additional, Teixeira, Catarina, additional, Telling, Kadri, additional, Terrades, Natalia Ramos, additional, Tez, Didem, additional, Thervet, Eric, additional, Thibaudin, Damien, additional, Thomas, Mark, additional, Thyagarajan, Nikhil, additional, Tkaczyk, Marcin, additional, Torreggiani, Massimo, additional, Trillini, Matias, additional, Tsai, Shang-Feng, additional, Tsai, Wan-Chuan, additional, Tsai, Jer-Chia, additional, Tseng, Po-Yu, additional, Tumlin, James, additional, Tung, Kuei-Ting, additional, Turnbull, Angus, additional, Udani, Suneel, additional, Uhlinova, Jana, additional, Unt, Kristin, additional, Urciuolo, Federica, additional, Vanacker, An, additional, Vandewiele, Bert, additional, Vaz, Alvaro, additional, Veermae, Kristi, additional, Viaene, Liesbeth, additional, Vickiene, Alvita, additional, Vigano, Sara, additional, Vila, Maria Antonia Munar, additional, Vilayur, Eswari, additional, Villanueva, Caridad Martinez, additional, Villarroya, Cristina Medrano, additional, Villen, Alejandro Soria, additional, Viramontes, Veronica, additional, Vita, Caterina, additional, Vujcic, Dunja, additional, Wahba, Mona, additional, Wan, Susan, additional, Wang, Chih-Hsien, additional, Warling, Xavier, additional, Waters, Gerald, additional, Waugh, Jane, additional, Weiland, Lea, additional, Weiner, Stefan, additional, Weinreich, Thomas, additional, Werth, Stephan Christian, additional, Wickens, Olivia, additional, Wijeratne, Vidu, additional, Wilder, Karen, additional, Willcocks, Lisa, additional, Williams, Allister, additional, Winiarska, Agata, additional, Wirtz, Nikolaus, additional, Wolf, Lothar, additional, Wolf, Gunter, additional, Wong, Yick Hei, additional, Wong, Sze Ho Sunny, additional, Workeneh, Biruh, additional, Wu, Ming-Ju, additional, Wu, Hon-Yen, additional, Wyndham, Roger, additional, Yang, Jihyun, additional, Yang, Ju-Yeh, additional, Yeap, Chii, additional, Yim, Ka Fai, additional, Yong, Kenneth, additional, Yoo, Tae-Hyun, additional, Yoon, Songuk, additional, Yu, Tung-Min, additional, Yue, Tak Tai Andrew, additional, Zakari, Michel, additional, Zakauskiene, Urte, additional, Zaoui, Philippe, additional, Zbrzezniak, Justyna, additional, Zielinska, Dorota, additional, and Zizzi, Carlotta Federica, additional

Published
2023
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48. Development of a Hybrid Application for Psychotic Disorders Self-Management

Author

de Almeida, Raquel Simões, Martins, Constantino, Marques, António, Benevides, Daniel, Costa, Alexandre, Queirós, Cristina, Sousa, Tiago, Almeida, Ana, Fonseca, Nuno, Faria, Luíz, 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, De Paz, Juan F., editor, Julián, Vicente, editor, Villarrubia, Gabriel, editor, Marreiros, Goreti, editor, and Novais, Paulo, editor

Published
2017
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49. QmihR: Pipeline for Quantification of Microbiome in Human RNA-seq

Author

Cavadas, Bruno, Ferreira, Joana, Camacho, Rui, Fonseca, Nuno A., Pereira, Luisa, 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 Pinto, Tiago, editor

Published
2017
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50. Monitoring the Progress of Programming Students Supported by a Digital Teaching Assistant

Author

Fonseca, Nuno Gil, Macedo, Luís, Mendes, António José, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Weikum, Gerhard, Series Editor, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Oliveira, Eugénio, editor, Gama, João, editor, Vale, Zita, editor, and Lopes Cardoso, Henrique, editor

Published
2017
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