Fine-Tuning Translation Kinetics Selection as the Driving Force of Codon Usage Bias in the Hepatitis A Virus Capsid

Hepatitis A virus (HAV), the prototype of genus Hepatovirus, has several unique biological characteristics that distinguish it from other members of the Picornaviridae family. Among these, the need for an intact eIF4G factor for the initiation of translation results in an inability to shut down host protein synthesis by a mechanism similar to that of other picornaviruses. Consequently, HAV must inefficiently compete for the cellular translational machinery and this may explain its poor growth in cell culture. In this context of virus/cell competition, HAV has strategically adopted a naturally highly deoptimized codon usage with respect to that of its cellular host. With the aim to optimize its codon usage the virus was adapted to propagate in cells with impaired protein synthesis, in order to make tRNA pools more available for the virus. A significant loss of fitness was the immediate response to the adaptation process that was, however, later on recovered and more associated to a re-deoptimization rather than to an optimization of the codon usage specifically in the capsid coding region. These results exclude translation selection and instead suggest fine-tuning translation kinetics selection as the underlying mechanism of the codon usage bias in this specific genome region. Additionally, the results provide clear evidence of the Red Queen dynamics of evolution since the virus has very much evolved to re-adapt its codon usage to the environmental cellular changing conditions in order to recover the original fitness.

Fine-Tuning Translation Kinetics Selection as the Driving Force of Codon Usage Bias in the Hepatitis A Virus Capsid

Hepatitis A virus (HAV), the prototype of genus Hepatovirus, has several unique biological characteristics that distinguish it from other members of the Picornaviridae family. Among these, the need for an intact eIF4G factor for the initiation of translation results in an inability to shut down host protein synthesis by a mechanism similar to that of other picornaviruses. Consequently, HAV must inefficiently compete for the cellular translational machinery and this may explain its poor growth in cell culture. In this context of virus/cell competition, HAV has strategically adopted a naturally highly deoptimized codon usage with respect to that of its cellular host. With the aim to optimize its codon usage the virus was adapted to propagate in cells with impaired protein synthesis, in order to make tRNA pools more available for the virus. A significant loss of fitness was the immediate response to the adaptation process that was, however, later on recovered and more associated to a re-deoptimization rather than to an optimization of the codon usage specifically in the capsid coding region. These results exclude translation selection and instead suggest fine-tuning translation kinetics selection as the underlying mechanism of the codon usage bias in this specific genome region. Additionally, the results provide clear evidence of the Red Queen dynamics of evolution since the virus has very much evolved to re-adapt its codon usage to the environmental cellular changing conditions in order to recover the original fitness.

Taking on new challenges in multi-word unit processing for Machine Translation

This paper discusses the qualitativecomparative evaluation performed on theresults of two machine translation systemswith different approaches to the processing ofmulti-word units. It proposes a solution forovercoming the difficulties multi-word unitspresent to machine translation by adopting amethodology that combines the lexicongrammar approach with OpenLogos ontologyand semantico-syntactic rules. The paper alsodiscusses the importance of a qualitativeevaluation metrics to correctly evaluate theperformance of machine translation engineswith regards to multi-word units.

Translation as a Process and Translation as a Product in Teaching Translation

L'ensenyament de la traducció s'ha utilitzat tradicionalment en algunes titulacions de filologia com a eina d'aprenentatge d'habilitats de la llengua. Aquesta circumstància, però, no ha d'estar renyida amb la producció d'una traducció acceptable. En aquest article es pretén analitzar si pot aconseguir-se aquest objectiu mitjançant la incorporació d'informació extratextual en l'enunciat de l'exercici de traducció. Els resultats obtinguts amb un grup d'estudiants de filologia mostren que en les seves decisions lingüístiques va tenir un pes important el tipus d'informació extratextual adjunta als textes originals anglesos. Si bé caldria fer un esforç investigador més sistemàtic per poder afirmar-ho categòricament, aquest estudi intenta esbossar la qüestió tan discutida de fins on l'aprenentatge d'una llengua s'ha de realitzar junt amb l'aprenentatge de la traducció. Aquest estudi, també, planteja la necessitat d'incorporar informació extratextual en l'aprenentatge de la traducció, independentment de la titulació que en aquests estudis s'insereixen.

Teaching foreign languages through translation: considering multiple intelligences

Aquest treball de recerca tracta de la relació existent entre pedagogia, traducció, llengües estrangeres i intel•ligències múltiples. El debat sobre si la traducció és una eina útil a la classe de llengües estrangeres és un tema actual sobre el qual molts investigadors encara indaguen. Estudis recents, però, han demostrat que qualsevol tasca de traducció -en la qual s’hi poden incloure treballs amb les diferents habilitats- és profitosa si la considerem un mitjà, no una finalitat en ella mateixa. Evidentment, l’ús de la traducció dins l’aula és avantatjosa, però també hem de tenir presents certs desavantatges d’aquesta aplicació. Un possible desavantatge podria ser la creença que, al principi, molta gent té referent a l’equivalència, paraula per paraula, d’una llengua vers una altra. Però després de presentar vàries tasques de traducció als estudiants, aquests poden arribar a controlar, fins i tot, les traduccions inconscients i poden assolir un cert nivell de precisió i flexibilitat que val la pena mencionar. Però l’avantatge principal és que s’enfronten a una activitat molt estesa dins la societat actual que combina dues llengües, la llengua materna i la llengua objecte d’estudi, per exemple. De tot això en podem deduir que utilitzar la llengua materna a la classe no s’ha de considerar un crim, com fins ara, sinó una virtut, evidentment si és emprada correctament. En aquest treball de recerca s’hi pot trobar una síntesi tant de les principals teories d’adquisició i aprenentatge de llengües com de les teories de traducció. A la pregunta de si les teories, tant de traducció com de llengües estrangeres, s’haurien d’ensenyar implícita o explícitament, es pot inferir que segons el nivell d’estudis on estiguin els aprenents els convindrà aprendre les teories explícitament o les aprendran, de totes maneres, implícitament. Com que qualsevol grup d’estudiants és heterogeni -és a dir que cada individu té un ritme i un nivell d’aprenentatge concret i sobretot cadascú té diferents estils de percepció (visual, auditiu, gustatiu, olfactiu, de moviment) i per tant diferents intel•ligències-, els professors ho han de tenir en compte a l’hora de planificar qualsevol programa d’actuació vers els alumnes. Per tant, podem concloure que les tasques o projectes de traducció poden ajudar als alumnes a aprendre millor, més eficaçment i a aconseguir un aprenentatge més significatiu.

Catalonia’s participation in calls of the EU 7th Framework Programme for RTD. Period 2007-2009

English translation of the Executive summary of the report “Catalonia’s participation in calls of the EU 7th Framework Programme for RTD. Period 2007-2009” drawn up by researchers of the AQR Research Group – Research Institute of Applied Economics (IREA) of the University of Barcelona. It aims to find out the reality of the Catalonia’s participation in the EU 7th Framework Programme, the main European financial instrument for research during the period 2007-2009.

Multilingualism in the EU: a Necessary Evil?

Aquest treball té com a objectiu analitzar el multilingüisme a la Unió europea des d’una perspectiva interdisciplinària entre traducció i dret de la Unió europea. Aquest article estudia la Unió com a un sistema multilingüe, amb especial èmfasi en les raons jurídiques i polítiques darrera l’actual règim lingüístic. També s’intentarà examinar els efectes que la diversitat lingüística té en la interpretació de la legislació europea. Hi han vint i tres llengües oficials i els textos publicats en les diferents llengües son igualment autèntics (Article 55 TFUE). Però les regles poden tenir la mateixa implicació jurídica en mes d’una llengua?

Mining and exploiting domain-specific corpora in the PANACEA platform

The objective of the PANACEA ICT-2007.2.2 EU project is to build a platform that automates the stages involved in the acquisition,production, updating and maintenance of the large language resources required by, among others, MT systems. The development of a Corpus Acquisition Component (CAC) for extracting monolingual and bilingual data from the web is one of the most innovative building blocks of PANACEA. The CAC, which is the first stage in the PANACEA pipeline for building Language Resources, adopts an efficient and distributed methodology to crawl for web documents with rich textual content in specific languages and predefined domains. The CAC includes modules that can acquire parallel data from sites with in-domain content available in more than one language. In order to extrinsically evaluate the CAC methodology, we have conducted several experiments that used crawled parallel corpora for the identification and extraction of parallel sentences using sentence alignment. The corpora were then successfully used for domain adaptation of Machine Translation Systems.

Spotting Translationese in two Corpora of Original and Translated Catalan Texts: an Empirical Approach

This research investigates the phenomenon of translationese in two monolingual comparable corpora of original and translated Catalan texts. Translationese has been defined as the dialect, sub-language or code of translated language. This study aims at giving empirical evidence of translation universals regardless the source language.Traditionally, research conducted on translation strategies has been mainly intuition-based. Computational Linguistics and Natural Language Processing techniques provide reliable information of lexical frequencies, morphological and syntactical distribution in corpora. Therefore, they have been applied to observe which translation strategies occur in these corpora.Results seem to prove the simplification, interference and explicitation hypotheses, whereas no sign of normalization has been detected with the methodology used.The data collected and the resources created for identifying lexical, morphological and syntactic patterns of translations can be useful for Translation Studies teachers, scholars and students: teachers will have more tools to help students avoid the reproduction of translationese patterns. Resources developed will help in detecting non-genuine or inadequate structures in the target language. This fact may imply an improvement in stylistic quality in translations. Translation professionals can also take advantage of these resources to improve their translation quality.

The impact of Economics on health policy and management in Spain

BackgroundDespite the intrinsic value of scientific disciplines, such as Economics, it is appropriate to gauge the impact of its applications on social welfare, or at least Health Economics (HE) case- its influence on health policy and management.MethodsThe three relevant features of knowledge (production, diffusion and application) are analyzed, more from an emic perspective the one used in Anthropology relying on the experience of the members of a culture- than from an etic approach seated on material descriptions and dubious statistics.ResultsThe soundness of the principles and results of HE depends on its disciplinary foundations,whereas its relevance than does not imply translation into practice- is more linked with the problems studied. Important contributions from Economics to the health sphere are recorded.HE in Spain ranks seventh in the world despite the relatively minor HE contents of its clinical and health services research journals.HE has in Spain more presence than influence, having failed to impregnate sufficiently thedaily events.ConclusionsHE knowledge required by a politician, a health manager or a clinician is rather limited; the main impact of HE could be to develop their intuition and awareness.

Identification by Real-time PCR of 13 mature microRNAs differentially expressed in colorectal cancer and non-tumoral tissues

MicroRNAs (miRNAs) are short non-coding RNA molecules playing regulatory roles by repressing translation or cleaving RNA transcripts. Although the number of verified human miRNA is still expanding, only few have been functionally described. However, emerging evidences suggest the potential involvement of altered regulation of miRNA in pathogenesis of cancers and these genes are thought to function as both tumours suppressor and oncogenes. In our study, we examined by Real-Time PCR the expression of 156 mature miRNA in colorectal cancer. The analysis by several bioinformatics algorithms of colorectal tumours and adjacent non-neoplastic tissues from patients and colorectal cancer cell lines allowed identifying a group of 13 miRNA whose expression is significantly altered in this tumor. The most significantly deregulated miRNA being miR-31, miR-96, miR-133b, miR-135b, miR-145, and miR-183. In addition, the expression level of miR-31 was correlated with the stage of CRC tumor. Our results suggest that miRNA expression profile could have relevance to the biological and clinical behavior of colorectal neoplasia.

Tagging reveals limited exchange of immature loggerhead sea turtles (Caretta caretta) between regions in the western Mediterranean.

Exchange of immature loggerhead sea turtles (Caretta caretta) between the northern and southern regions of the western Mediterranean was investigated using data obtained from several Spanish tagging programmes. Tagged turtles ranged in straight carapace length from 23.0 to 74.0 cm. Thirty-six turtles were recaptured after an average interval of 390.5±462.6 days (SD). As the mean dispersal distance (MDD) of a turtle population that spreads over the western Mediterranean would stabilize after 117 days (CI 95%: 98 to 149), two analyses were conducted that included data from turtles recaptured after 98 and 149 days respectively. In both analyses, turtles were recaptured more often than expected in the same region where they had been tagged. No difference was found in either of the two regions between the average distance between the capture and recapture locations and the expected MDD if the turtles were to remain in the region where they were first captured. Turtles recaptured after 15 and 25 days respectively were excluded from the analysis to ensure data independence. The overall evidence indicates that immature turtles exhibit strong site fidelity to certain areas and that there is a strong barrier to dispersal between the northern and southern parts of the western Mediterranean. Therefore, loggerhead turtles in the western Mediterranean should be split into at least two management units.

Language Resources Factory: case study on the acquisition of Translation Memories

This paper demonstrates a novel distributed architecture to facilitate the acquisition of Language Resources. We build a factory that automates the stages involved in the acquisition, production, updating and maintenance of these resources. The factory is designed as a platform where functionalities are deployed as web services, which can be combined in complex acquisition chains using workflows. We show a case study, which acquires a Translation Memory for a given pair of languages and a domain using web services for crawling, sentence alignment and conversion to TMX.

Traducción comentada de Guidelines Governing the Adoption of Children, 2011 in India

En este trabajo se analiza la variación discursiva y los diferentes criterios de estilo entre textos jurídicos normativos en inglés y español; se establecen fenómenos lingüísticos propios del discurso jurídico que generan problemas de traducción; y se comparan algunas diferencias entre sistemas jurídicos y políticos para analizar su repercusión en la traducción.

An efficient algorithm to perform multiple testing in epistasis screening

Background: Research in epistasis or gene-gene interaction detection for human complex traits has grown over the last few years. It has been marked by promising methodological developments, improved translation efforts of statistical epistasis to biological epistasis and attempts to integrate different omics information sources into the epistasis screening to enhance power. The quest for gene-gene interactions poses severe multiple-testing problems. In this context, the maxT algorithm is one technique to control the false-positive rate. However, the memory needed by this algorithm rises linearly with the amount of hypothesis tests. Gene-gene interaction studies will require a memory proportional to the squared number of SNPs. A genome-wide epistasis search would therefore require terabytes of memory. Hence, cache problems are likely to occur, increasing the computation time. In this work we present a new version of maxT, requiring an amount of memory independent from the number of genetic effects to be investigated. This algorithm was implemented in C++ in our epistasis screening software MBMDR-3.0.3. We evaluate the new implementation in terms of memory efficiency and speed using simulated data. The software is illustrated on real-life data for Crohn’s disease. Results: In the case of a binary (affected/unaffected) trait, the parallel workflow of MBMDR-3.0.3 analyzes all gene-gene interactions with a dataset of 100,000 SNPs typed on 1000 individuals within 4 days and 9 hours, using 999 permutations of the trait to assess statistical significance, on a cluster composed of 10 blades, containing each four Quad-Core AMD Opteron(tm) Processor 2352 2.1 GHz. In the case of a continuous trait, a similar run takes 9 days. Our program found 14 SNP-SNP interactions with a multiple-testing corrected p-value of less than 0.05 on real-life Crohn’s disease (CD) data. Conclusions: Our software is the first implementation of the MB-MDR methodology able to solve large-scale SNP-SNP interactions problems within a few days, without using much memory, while adequately controlling the type I error rates. A new implementation to reach genome-wide epistasis screening is under construction. In the context of Crohn’s disease, MBMDR-3.0.3 could identify epistasis involving regions that are well known in the field and could be explained from a biological point of view. This demonstrates the power of our software to find relevant phenotype-genotype higher-order associations.