Search

Your search keyword '"Quer, Josep"' showing total 664 results
Start Over Author "Quer, Josep"
664 results on '"Quer, Josep"'

4. Chapter 5 Verb Agreement

Author

Quer, Josep

Subjects
Experimental, handbook, language, phonological, research, sign, theoretical, comprehension, conventions, interrogatives
Abstract

This chapter discusses the scholarship that takes this type of argument encoding as grammatical agreement, and presents the formal analyses proposed and the arguments made to defend its linguistic nature by opposition to a gestural one. It properties associated with it will be described and exemplified. Agreement auxiliaries feature in the first analyses of agreement because ASL have one, but research has shown that they are not rare across sign languages. Quite significantly, agreement auxiliaries co-occur with plain verbs, many of which have transfer or motion semantics. Engberg-Pedersen also questions that cases like are instances of agreement proper and proposes instead that they are examples of pragmatic agreement, whereby the relation between the predicate and its argument is specified and in particular it occurs when contrast is at play. The complexities that agreement by itself raises in both sign and spoken languages but help better understand its properties and the range of variation of its instantiations vis-+a-vis related phenomena.

Published
2021
Full Text
View/download PDF

5. Chapter 19 Quantification

Author

Kimmelman, Vadim and Quer, Josep

Subjects
Experimental, handbook, language, phonological, research, sign, theoretical, comprehension, conventions, interrogatives
Abstract

The study of quantificational expressions is one of the central domains in the field of natural language semantics. Probably every language has means of expressing quantification, but quantifiers in natural languages are straightforwardly parallel to logical quantifiers. Based on the previous research on quantification in sign languages, we further discuss the following issues: lexical quantifiers, quantificational morphology, and structural aspects of quantification. The idea behind A-quantification stems from the analysis of indefinites by Kamp and Heim, according to which indefinite expressions are non-quantificational, and they just introduce a variable with descriptive content that must be unselectively bound by a quantifier. In opposition to D-quantification, Bach et al. group other ways of encoding quantification under the label A-quantification, which includes adverbs, auxiliaries, affixes, and argument-structure adjusters. A large variety of verbal modifiers that express different types of distributive semantics has been found in RSL by Filimonova.

Published
2021
Full Text
View/download PDF

6. Molecular characterization and clinical impact of human bocavirus at a tertiary hospital in Barcelona (Catalonia, Spain) during the 2014–2017 seasons

Author

Piñana, Maria, Vila, Jorgina, Andrés, Cristina, Saura, Jordi, González-Sánchez, Alejandra, Creus-Costa, Anna, Saubi, Narcís, Esperalba, Juliana, Rando, Ariadna, Iglesias-Cabezas, Manuel Jesús, Quer, Josep, Soriano-Arandes, Antoni, Soler-Palacín, Pere, Pumarola, Tomàs, and Antón, Andrés

Published
2023
Full Text
View/download PDF

8. Genomic evolution of human respiratory syncytial virus during a decade (2013–2023): bridging the path to monoclonal antibody surveillance

Author

Piñana, Maria, González-Sánchez, Alejandra, Andrés, Cristina, Vila, Jorgina, Creus-Costa, Anna, Prats-Méndez, Ignasi, Arnedo-Muñoz, Maria, Saubi, Narcís, Esperalba, Juliana, Rando, Ariadna, Nadal-Baron, Patricia, Quer, Josep, González-López, Juan José, Soler-Palacín, Pere, Martínez-Urtaza, Jaime, Larrosa, Nieves, Pumarola, Tomàs, and Antón, Andrés

Published
2024
Full Text
View/download PDF

10. Emergence of Delta and Omicron variants carrying resistance-associated mutations in immunocompromised patients undergoing sotrovimab treatment with long-term viral excretion

Author

Andrés, Cristina, González-Sánchez, Alejandra, Jiménez, Moraima, Márquez-Algaba, Ester, Piñana, Maria, Fernández-Naval, Candela, Esperalba, Juliana, Saubi, Narcís, Quer, Josep, Rando-Segura, Ariadna, Miarons, Marta, Codina, Maria Gema, Ruiz-Camps, Isabel, Pumarola, Tomàs, Abrisqueta, Pau, and Antón, Andrés

Published
2023
Full Text
View/download PDF

11. Part-of-Speech Tagging on an Endangered Language: a Parallel Griko-Italian Resource

Author

Anastasopoulos, Antonis, Lekakou, Marika, Quer, Josep, Zimianiti, Eleni, DeBenedetto, Justin, and Chiang, David

Subjects
Computer Science - Computation and Language
Abstract

Most work on part-of-speech (POS) tagging is focused on high resource languages, or examines low-resource and active learning settings through simulated studies. We evaluate POS tagging techniques on an actual endangered language, Griko. We present a resource that contains 114 narratives in Griko, along with sentence-level translations in Italian, and provides gold annotations for the test set. Based on a previously collected small corpus, we investigate several traditional methods, as well as methods that take advantage of monolingual data or project cross-lingual POS tags. We show that the combination of a semi-supervised method with cross-lingual transfer is more appropriate for this extremely challenging setting, with the best tagger achieving an accuracy of 72.9%. With an applied active learning scheme, which we use to collect sentence-level annotations over the test set, we achieve improvements of more than 21 percentage points., Comment: to be presented at COLING 2018

Published
2018

12. Effect of Hepatitis E Virus RNA Universal Blood Donor Screening, Catalonia, Spain, 2017-2020

Author

Bes, Marta, Costafreda, Maria I., Riveiro-Barciela, Mar, Piron, Maria, Rico, Angie, Quer, Josep, Puig, Lluis, and Sauleda, Silvia

Subjects
Catalonia, Spain -- Health aspects, Hepatitis E -- Statistics -- Risk factors -- Diagnosis, Blood transfusion -- Statistics -- Complications and side effects, Blood donors -- Statistics, Medical screening -- Statistics, Health
Abstract

Hepatitis E virus (HEV; family Hepeviridae, genus Orthohepevirus) (1) is an RNA virus that causes acute viral hepatitis in humans. Five HEV genotypes are known to infect humans. Genotypes 1 [...]

Published
2022
Full Text
View/download PDF

13. Characteristics of hepatitis C virus resistance in an international cohort after a decade of direct-acting antivirals

Author

Martinello, Marianne, Matthews, Gail, Fernando, Fay Fabián, Esteban, Juan I., Müllhaupt, Beat, Wiesch, Julian Schulze zur, Buggisch, Peter, Neumann-Haefelin, Christoph, Berg, Thomas, Berg, Christoph P., Schattenberg, Jörn M., Moreno, Christophe, Stauber, Rudolf, Lloyd, Andrew, Dore, Gregory, Applegate, Tanya, Ignacio, Juan, Garcia-Cehic, Damir, Gregori, Josep, Rodriguez-Frias, Francisco, Rando, Ariadna, Gozlan, Yael, Angelico, Mario, Andreoni, Massimo, Babudieri, Sergio, Bertoli, Ada, Cento, Valeria, Coppola, Nicola, Craxì, Antonio, Paolucci, Stefania, Parruti, Giustino, Pasquazzi, Caterina, Perno, Carlo Federico, Teti, Elisabetta, Vironet, C., Lannergård, Anders, Duberg, Ann-Sofi, Aleman, Soo, Gutteberg, Tore, Soulier, Alexandre, Gourgeon, Aurélie, Chevaliez, Stephane, Pol, Stanislas, Carrat, Fabrice, Salmon, Dominique, Kaiser, Rolf, Knopes, Elena, Gomes, Perpetua, de Kneght, Rob, Rijnders, Bart, Poljak, Mario, Lunar, Maja, Usubillaga, Rafael, Seguin_Devaux, Carole, Tay, Enoch, Wilson, Caroline, Wang, Dao Sen, George, Jacob, Kok, Jen, Pérez, Ana Belén, Chueca, Natalia, García-Deltoro, Miguel, Martínez-Sapiña, Ana María, Lara-Pérez, María Magdalena, García-Bujalance, Silvia, Aldámiz-Echevarría, Teresa, Vera-Méndez, Francisco Jesús, Pineda, Juan Antonio, Casado, Marta, Pascasio, Juan Manuel, Salmerón, Javier, Alados-Arboledas, Juan Carlos, Poyato, Antonio, Téllez, Francisco, Rivero-Juárez, Antonio, Merino, Dolores, Vivancos-Gallego, María Jesús, Rosales-Zábal, José Miguel, Ocete, María Dolores, Simón, Miguel Ángel, Rincón, Pilar, Reus, Sergi, De la Iglesia, Alberto, García-Arata, Isabel, Jiménez, Miguel, Jiménez, Fernando, Hernández-Quero, José, Galera, Carlos, Balghata, Mohamed Omar, Primo, Joaquín, Masiá, Mar, Espinosa, Nuria, Delgado, Marcial, von-Wichmann, Miguel Ángel, Collado, Antonio, Santos, Jesús, Mínguez, Carlos, Díaz-Flores, Felícitas, Fernández, Elisa, Bernal, Enrique, De Juan, José, Antón, José Joaquín, Vélez, Mónica, Aguilera, Antonio, Navarro, Daniel, Arenas, Juan Ignacio, Fernández, Clotilde, Espinosa, María Dolores, Ríos, María José, Alonso, Roberto, Hidalgo, Carmen, Hernández, Rosario, Téllez, María Jesús, Rodríguez, Francisco Javier, Antequera, Pedro, Delgado, Cristina, Martín, Patricia, Crespo, Javier, Becerril, Berta, Pérez, Oscar, García-Herola, Antonio, Montero, José, Freyre, Carolina, Grau, Concepción, Cabezas, Joaquin, Jimenez, Miguel, Rodriguez, Manuel Alberto Macias, Quilez, Cristina, Pardo, Maria Rodriguez, Muñoz-Medina, Leopoldo, Figueruela, Blanca, Howe, Anita Y.M., Rodrigo, Chaturaka, Cunningham, Evan B., Douglas, Mark W., Dietz, Julia, Grebely, Jason, Popping, Stephanie, Sfalcin, Javier Alejandro, Parczewski, Milosz, Sarrazin, Christoph, de Salazar, Adolfo, Fuentes, Ana, Sayan, Murat, Quer, Josep, Kjellin, Midori, Kileng, Hege, Mor, Orna, Lennerstrand, Johan, Fourati, Slim, Di Maio, Velia Chiara, Chulanov, Vladimir, Pawlotsky, Jean-Michel, Harrigan, P. Richard, Ceccherini-Silberstein, Francesca, and Garcia, Federico

Published
2022
Full Text
View/download PDF

14. The frequency of defective genomes in Omicron differs from that of the Alpha, Beta and Delta variants

Author

Campos, Carolina, Colomer-Castell, Sergi, Garcia-Cehic, Damir, Gregori, Josep, Andrés, Cristina, Piñana, Maria, González-Sánchez, Alejandra, Borràs, Blanca, Parés-Badell, Oleguer, Adombi, Caroline Melanie, Ibañez-Lligoña, Marta, Esperalba, Juliana, Codina, Maria Gema, Rando-Segura, Ariadna, Saubí, Narcis, Esteban, Juan Ignacio, Rodriguez-Frías, Francisco, Pumarola, Tomàs, Antón, Andrés, and Quer, Josep

Published
2022
Full Text
View/download PDF

19. Genotyping Hepatitis B virus by Next-Generation Sequencing: Detection of Mixed Infections and Analysis of Sequence Conservation.

Author

Dopico, Eva, Vila, Marta, Tabernero, David, Gregori, Josep, Rando-Segura, Ariadna, Pacín-Ruíz, Beatriz, Guerrero, Laura, Ubillos, Itziar, Martínez, Miguel J., Costa, Josep, Quer, Josep, Pérez-Garreta, Javier, González-Sánchez, Alejandra, Antón, Andrés, Pumarola, Tomás, Riveiro-Barciela, Mar, Ferrer-Costa, Roser, Buti, Maria, Rodríguez-Frías, Francisco, and Cortese, Maria Francesca

Subjects
HEPATITIS B virus, MIXED infections, NUCLEOTIDE sequencing, SEQUENCE analysis, RNA interference
Abstract

Our aim was to develop an accurate, highly sensitive method for HBV genotype determination and detection of genotype mixtures. We examined the preS and 5′ end of the HBV X gene (5X) regions of the HBV genome using next-generation sequencing (NGS). The 1852 haplotypes obtained were subjected to genotyping via the Distance-Based discrimination method (DB Rule) using two sets of 95 reference sequences of genotypes A–H. In clinical samples from 125 patients, the main genotypes were A, D, F and H in Caucasian, B and C in Asian and A and E in Sub-Saharan patients. Genotype mixtures were identified in 28 (22.40%) cases, and potential intergenotypic recombination was observed in 29 (23.20%) cases. Furthermore, we evaluated sequence conservation among haplotypes classified into genotypes A, C, D, and E by computing the information content. The preS haplotypes exhibited limited shared conserved regions, whereas the 5X haplotypes revealed two groups of conserved regions across the genotypes assessed. In conclusion, we developed an NGS-based HBV genotyping method utilizing the DB Rule for genotype classification. We identified two regions conserved across different genotypes at 5X, offering promising targets for RNA interference-based antiviral therapies. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

20. Virus Quasispecies Rarefaction: Subsampling with or without Replacement?

Author

Gregori, Josep, Ibañez-Lligoña, Marta, Colomer-Castell, Sergi, Campos, Carolina, and Quer, Josep

Subjects
HAPLOTYPES, NUCLEOTIDE sequencing, SAMPLE size (Statistics)
Abstract

In quasispecies diversity studies, the comparison of two samples of varying sizes is a common necessity. However, the sensitivity of certain diversity indices to sample size variations poses a challenge. To address this issue, rarefaction emerges as a crucial tool, serving to normalize and create fairly comparable samples. This study emphasizes the imperative nature of sample size normalization in quasispecies diversity studies using next-generation sequencing (NGS) data. We present a thorough examination of resampling schemes using various simple hypothetical cases of quasispecies showing different quasispecies structures in the sense of haplotype genomic composition, offering a comprehensive understanding of their implications in general cases. Despite the big numbers implied in this sort of study, often involving coverages exceeding 100,000 reads per sample and amplicon, the rarefaction process for normalization should be performed with repeated resampling without replacement, especially when rare haplotypes constitute a significant fraction of interest. However, it is noteworthy that different diversity indices exhibit distinct sensitivities to sample size. Consequently, some diversity indicators may be compared directly without normalization, or instead may be resampled safely with replacement. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

21. In-Host Flat-like Quasispecies: Characterization Methods and Clinical Implications.

Author

Gregori, Josep, Colomer-Castell, Sergi, Ibañez-Lligoña, Marta, Garcia-Cehic, Damir, Campos, Carolina, Buti, Maria, Riveiro-Barciela, Mar, Andrés, Cristina, Piñana, Maria, González-Sánchez, Alejandra, Rodriguez-Frias, Francisco, Cortese, Maria Francesca, Tabernero, David, Rando-Segura, Ariadna, Pumarola, Tomás, Esteban, Juan Ignacio, Antón, Andrés, and Quer, Josep

Subjects
MUTAGENS, HEPATITIS E, NUCLEOTIDE sequencing, ENTEROVIRUSES, RESPIRATORY syncytial virus, PHENOTYPES, HAPLOTYPES
Abstract

The repeated failure to treat patients chronically infected with hepatitis E (HEV) and C (HCV) viruses, despite the absence of resistance-associated substitutions (RAS), particularly in response to prolonged treatments with the mutagenic agents of HEV, suggests that quasispecies structure may play a crucial role beyond single point mutations. Quasispecies structured in a flat-like manner (referred to as flat-like) are considered to possess high average fitness, occupy a significant fraction of the functional genetic space of the virus, and exhibit a high capacity to evade specific or mutagenic treatments. In this paper, we studied HEV and HCV samples using high-depth next-generation sequencing (NGS), with indices scoring the different properties describing flat-like quasispecies. The significance of these indices was demonstrated by comparing the values obtained from these samples with those from acute infections caused by respiratory viruses (betacoronaviruses, enterovirus, respiratory syncytial viruses, and metapneumovirus). Our results revealed that flat-like quasispecies in HEV and HCV chronic infections without RAS are characterized by numerous low-frequency haplotypes with no dominant one. Surprisingly, these low-frequency haplotypes (at the nucleotide level) exhibited a high level of synonymity, resulting in much lower diversity at the phenotypic level. Currently, clinical approaches for managing flat-like quasispecies are lacking. Here, we propose methods to identifying flat-like quasispecies, which represents an essential initial step towards exploring alternative treatment protocols for viruses resistant to conventional therapies. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

22. Comparison of Nanopore and Synthesis-Based Next-Generation Sequencing Platforms for SARS-CoV-2 Variant Monitoring in Wastewater

Author

Garcia-Pedemonte, David, primary, Carcereny, Albert, additional, Gregori, Josep, additional, Quer, Josep, additional, Garcia-Cehic, Damir, additional, Guerrero, Laura, additional, Ceretó-Massagué, Adrià, additional, Abid, Islem, additional, Bosch, Albert, additional, Costafreda, Maria Isabel, additional, Pintó, Rosa M., additional, and Guix, Susana, additional

Published
2023
Full Text
View/download PDF

23. In-Host HEV Quasispecies Evolution Shows the Limits of Mutagenic Antiviral Treatments

Author

Colomer-Castell, Sergi, primary, Gregori, Josep, additional, Garcia-Cehic, Damir, additional, Riveiro-Barciela, Mar, additional, Buti, Maria, additional, Rando-Segura, Ariadna, additional, Vico-Romero, Judit, additional, Campos, Carolina, additional, Ibañez-Lligoña, Marta, additional, Adombi, Caroline Melanie, additional, Cortese, Maria Francesca, additional, Tabernero, David, additional, Esteban, Juan Ignacio, additional, Rodriguez-Frias, Francisco, additional, and Quer, Josep, additional

Published
2023
Full Text
View/download PDF

25. Sophisticated viral quasispecies with a genotype-related pattern of mutations in the hepatitis B X gene of HBeAg-ve chronically infected patients

Author

Cortese, Maria Francesca, González, Carolina, Gregori, Josep, Casillas, Rosario, Carioti, Luca, Guerrero-Murillo, Mercedes, Riveiro-Barciela, Mar, Godoy, Cristina, Sopena, Sara, Yll, Marçal, Quer, Josep, Rando, Ariadna, Lopez-Martinez, Rosa, Pacín Ruiz, Beatriz, García-García, Selene, Esteban-Mur, Rafael, Tabernero, David, Buti, Maria, and Rodríguez-Frías, Francisco

Published
2021
Full Text
View/download PDF

28. The Francoist dictatorship through the Deaf lens

Author

Sánchez-Amat, Jordina, primary, Busto, Raquel Veiga, additional, Álvarez, Xavi, additional, Santiago, Frigola, additional, Aliaga, Delfina, additional, Sampedro, Miguel Ángel, additional, Barberà, Gemma, additional, and Quer, Josep, additional

Published
2021
Full Text
View/download PDF

29. Complete Genome Sequences of Four Mycobacteriophages Involved in Directed Evolution against Undisputed Mycobacterium abscessus Clinical Strains.

Author

Cao Yao, Juan Carlos, Garcia Cehic, Damir, Quer, Josep, Méndez, Jesús Navas, Gorrín, Alexis Dorta, Hevia, Lorena García, and Fernández, María Teresa Tórtola

Subjects
WHOLE genome sequencing, BACTERIOPHAGES, MYCOBACTERIUM, GENOMES, DRUG resistance in bacteria
Abstract

Phage therapy is still in its infancy, but it is increasingly promising as a future alternative for treating antibiotic-resistant bacteria. To investigate the effect of phages on Mycobacterium abscessus complex (MABC), we isolated 113 environmental phages, grown them to high titres, and assayed them on MABC clinical strains through the spot test. Of all the phages, only 16 showed killing activity. Their activity was so temperate to MABC that they could not generate any plaque-forming units (PFUs). The Appelmans method of directed evolution was carried out to evolve these 16 phages into more lytic ones. After only 11 of 30 rounds of evolution, every single clinical strain in our collection, including those that were unsusceptible up to this point, could be lysed by at least one phage. The evolved phages were able to form PFUs on the clinical strains tested. Still, they are temperate at best and require further training. The genomes of one random parental phage and three random evolved phages from Round 13 were sequenced, revealing a diversity of clusters and genes of a variety of evolutionary origins, mostly of unknown function. These complete annotated genomes will be key for future molecular characterisations. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

31. Comparison of Extracellular Vesicle Isolation Methods for miRNA Sequencing

Author

Llorens-Revull, Meritxell, primary, Martínez-González, Brenda, additional, Quer, Josep, additional, Esteban, Juan Ignacio, additional, Núñez-Moreno, Gonzalo, additional, Mínguez, Pablo, additional, Burgui, Idoia, additional, Ramos-Ruíz, Ricardo, additional, Soria, María Eugenia, additional, Rico, Angie, additional, Riveiro-Barciela, Mar, additional, Sauleda, Silvia, additional, Piron, María, additional, Corrales, Irene, additional, Borràs, Francesc E., additional, Rodríguez-Frías, Francisco, additional, Rando, Ariadna, additional, Ramírez-Serra, Clara, additional, Camós, Silvia, additional, Domingo, Esteban, additional, Bes, Marta, additional, Perales, Celia, additional, and Costafreda, Maria Isabel, additional

Published
2023
Full Text
View/download PDF

32. Fitness-Dependent, Mild Mutagenic Activity of Sofosbuvir for Hepatitis C Virus

Author

Martínez-González, Brenda, primary, Gallego, Isabel, additional, Gregori, Josep, additional, Soria, María Eugenia, additional, Somovilla, Pilar, additional, de Ávila, Ana Isabel, additional, García-Crespo, Carlos, additional, Durán-Pastor, Antoni, additional, Briones, Carlos, additional, Gómez, Jordi, additional, Quer, Josep, additional, Domingo, Esteban, additional, and Perales, Celia, additional

Published
2023
Full Text
View/download PDF

35. HBV and HDV interaction and variability in a superinfection mouse model: role of type I interferon

Author

Ruiz, Beatriz Pacín, primary, Ramón, Gracián Camps, additional, Cortese, Maria Francesca, additional, Gregori, Josep, additional, Garcia-Garcia, Selene, additional, Tabernero, David, additional, Aranguren, África Vales, additional, Najarro, Adrian, additional, Micheltorena, Cristina Olague, additional, Rando-Segura, Ariadna, additional, Quer, Josep, additional, Esteban, Rafael, additional, Barciela, Mar Riveiro, additional, Buti, Maria, additional, González-Aseguinolaza, Gloria, additional, and Rodríguez-Frías, Francisco, additional

Published
2023
Full Text
View/download PDF

38. Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses

Author

Ibañez-Lligoña, Marta, primary, Colomer-Castell, Sergi, additional, González-Sánchez, Alejandra, additional, Gregori, Josep, additional, Campos, Carolina, additional, Garcia-Cehic, Damir, additional, Andrés, Cristina, additional, Piñana, Maria, additional, Pumarola, Tomàs, additional, Rodríguez-Frias, Francisco, additional, Antón, Andrés, additional, and Quer, Josep, additional

Published
2023
Full Text
View/download PDF

43. Quasispecies Fitness Partition to Characterize the Molecular Status of a Viral Population. Negative Effect of Early Ribavirin Discontinuation in a Chronically Infected HEV Patient

Author

Gregori, Josep, primary, Colomer-Castell, Sergi, additional, Campos, Carolina, additional, Ibañez-Lligoña, Marta, additional, Garcia-Cehic, Damir, additional, Rando-Segura, Ariadna, additional, Adombie, Caroline Melanie, additional, Pintó, Rosa, additional, Guix, Susanna, additional, Bosch, Albert, additional, Domingo, Esteban, additional, Gallego, Isabel, additional, Perales, Celia, additional, Cortese, Maria Francesca, additional, Tabernero, David, additional, Buti, Maria, additional, Riveiro-Barciela, Mar, additional, Esteban, Juan Ignacio, additional, Rodriguez-Frias, Francisco, additional, and Quer, Josep, additional

Published
2022
Full Text
View/download PDF

44. Molecular characterization and clinical impact of human bocavirus at a tertiary hospital in Barcelona (Catalonia, Spain) during the 2014–2017 seasons

Author

Piñana, Maria, primary, Vila, Jorgina, additional, Andrés, Cristina, additional, Saura, Jordi, additional, González-Sánchez, Alejandra, additional, Creus-Costa, Anna, additional, Saubi, Narcís, additional, Esperalba, Juliana, additional, Rando, Ariadna, additional, Iglesias-Cabezas, Manuel Jesús, additional, Quer, Josep, additional, Soriano-Arandes, Antoni, additional, Soler-Palacín, Pere, additional, Pumarola, Tomàs, additional, and Antón, Andrés, additional

Published
2022
Full Text
View/download PDF

45. Quantificational Strategies across Language Modalities

Author

Quer, Josep, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Aloni, Maria, editor, Kimmelman, Vadim, editor, Roelofsen, Floris, editor, Sassoon, Galit W., editor, Schulz, Katrin, editor, and Westera, Matthijs, editor

Published
2012
Full Text
View/download PDF

46. Amino acid substitutions associated with treatment failure of hepatitis C virus infection

Author

Soria, María Eugenia, García-Crespo, Carlos, Martínez-González, Brenda, Vázquez-Sirvent, Lucía, Lobo-Vega, Rebeca, Ávila, Ana Isabel de, Gallego, Isabel, Chen, Qian, García-Cehic, Damir, Llorens-Revull, Meritxell, Briones, Carlos, Gómez, Jordi, Ferrer-Orta, Cristina, Verdaguer, Núria, Gregori, Josep, Rodríguez-Frías, Francisco, Buti, María, Esteban, Juan Ignacio, Domingo, Esteban, Quer, Josep, Perales, Celia, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Comunidad de Madrid, Instituto de Salud Carlos III, Fundación Ramón Areces, Banco Santander, Global Virus Network, Centro para el Desarrollo Tecnológico Industrial (España), and Ministerio de Ciencia, Innovación y Universidades (España)

Abstract

Trabajo presentado en el XVI Congreso Nacional de Virología, celebrado en Málaga (España) del 06 al 09 de septiembre de 2022., Despite the high sustained virological response rates achieved with current directly-acting antiviral agents (DAAs) against hepatitis C virus (HCV), around 2% to 5% of patients do not achieve such a response. Identification of amino acid substitutions associated with treatment failure requires analytical designs, such as subtype-specific ultra-deep sequencing (UDS) methods for HCV characterization and patient management. By deep sequencing analysis of 220 subtyped HCV samples from infected patients who failed therapy, collected from 39 Spanish hospitals, we determined amino acid sequences of the DAA-target proteins NS3, NS5A and NS5B, by UDS of HCV patient samples, in search of resistanceassociated substitutions (RAS). Using this procedure, we have identified six highly represented amino acid substitutions (HRSs) in NS5A and NS5B of HCV, which are not bona fide RAS. They were present frequently in basal and post-treatment virus of patients who failed therapy to different DAA-based therapies. Contrary to several RAS, HRSs belong to the acceptable subset of substitutions according to the PAM250 replacement matrix. Coherently, their mutant frequency, measured by the number of deep sequencing reads within the HCV quasispecies that encode the relevant substitutions, ranged between 90% and 100% in most cases. Also, they have limited predicted disruptive effects on the threedimensional structures of the proteins harboring them. The information on HRSs that will be gathered during sequencing should be relevant not only to help predict treatment outcomes and disease progression but also to further understand HCV population dynamics, which appears much more complex than thought prior to the introduction of deep sequencing., The work at CBMSO was supported by grants SAF2014-52400-R from MINECO, SAF2017-87846-R and BFU2017-91384-EXP MICIU, PI18/00210 from ISCIII, S2013/ABI-2906 (PLATESA) and S2018/BAA-4370 (PLATESA2) from Comunidad de Madrid/FEDER. C.P. is supported by the Miguel Servet program of the ISCIII (CP14/00121 and CPII19/00001), cofinanced by the European Regional Development Fund (ERDF). CIBERehd is funded by ISCIII. Institutional grants from the Fundación Ramón Areces and Banco Santander to the CBMSO are also acknowledged. The team at CBMSO belongs to the Global Virus Network (GVN). The work in Barcelona was supported by ISCIII, cofinanced by ERDF grant number PI19/00301 and by the Centro para el Desarrollo Tecnológico Industrial (CDTI) from the MICIU, grant number IDI20151125. Work at CAB was supported by MINECO grant BIO2016-79618R and PID2019-104903RB-I00 (funded by the EU under the FEDER program) and by the Spanish State research agency (AEI) through project number MDM-2017-0737 Unidad de Excelencia “María de Maeztu”-Centro de Astrobiología (CSIC-INTA). Work at IBMB was supported by MICIN grant BIO2017-83906-P (funded by the EU under the FEDER program). C.G.-C. is supported by predoctoral contract PRE2018-083422 from MICIU. B.M.-G. is supported by predoctoral contract PFIS FI19/00119 from Instituto de Salud Carlos III (Ministerio de Sanidad y Consumo), cofinanced by Fondo Social Europeo (FSE).

Published
2022

47. Ultra Deep Sequencing of Circulating Cell-Free DNA as a Potential Tool for Hepatocellular Carcinoma Management

Author

Higuera, Mónica, primary, Vargas-Accarino, Elena, additional, Torrens, María, additional, Gregori, Josep, additional, Salcedo, María Teresa, additional, Martínez-Campreciós, Joan, additional, Torres, Gloria, additional, Bermúdez-Ramos, María, additional, Bilbao, Itxarone, additional, Guerrero-Murillo, Mercedes, additional, Serres-Créixams, Xavier, additional, Merino, Xavier, additional, Rodríguez-Frías, Francisco, additional, Quer, Josep, additional, and Mínguez, Beatriz, additional

Published
2022
Full Text
View/download PDF

48. The frequency of defective genomes in Omicron differs from that of the Alpha, Beta and Delta variants

Author

Campos, Carolina, primary, Colomer-Castell, Sergi, additional, Garcia-Cehic, Damir, additional, Gregori, Josep, additional, Andrés, Cristina, additional, Piñana, Maria, additional, González-Sánchez, Alejandra, additional, Borràs, Blanca, additional, Parés-Badell, Oleguer, additional, Adombi, Caroline Melanie, additional, Ibañez, Marta, additional, Esperalba, Juliana, additional, Codina, Maria Gema, additional, Rando, Ariadna, additional, Saubí, Narcis, additional, Esteban, Juan Ignacio, additional, Rodriguez-Frías, Francisco, additional, Pumarola, Tomàs, additional, Antón, Andrés, additional, and Quer, Josep, additional

Published
2022
Full Text
View/download PDF

49. Prevalence of Hepatitis C Virus Infection, Genotypes and Subtypes in Migrants from Pakistan in Barcelona, Spain

Author

Dopico, Eva, primary, Rodriguez-Frias, Francisco, additional, Ubillos, Itziar, additional, Rando-Segura, Ariadna, additional, Garcia-Cehic, Damir, additional, Gregori, Josep, additional, Rando-Matos, Yolanda, additional, Solsona, Luis, additional, Niubó, Jordi, additional, Esteban, Juan Ignacio, additional, Costa, Josep, additional, Martínez, Miguel J, additional, and Quer, Josep, additional

Published
2022
Full Text
View/download PDF

50. HDV-mediated inhibition of HBV in superinfection mouse model: the role of type I Interferon

Author

Ruiz, Beatriz Pacín, primary, Camps, Gracián, additional, Cortese, Maria Francesca, additional, Gregori, Josep, additional, Tabernero, David, additional, Garcia-Garcia, Selene, additional, Aranguren, África Vales, additional, Micheltorena, Cristina Olague, additional, Rando-Segura, Ariadna, additional, Quer, Josep, additional, Esteban, Rafael, additional, Barciela, Mar Riveiro, additional, Buti, Maria, additional, González-Aseguinolaza, Gloria, additional, and Rodríguez-Frías, Francisco, additional

Published
2022
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results