T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10 000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.

Atypical language organization in temporal lobe epilepsy revealed by a passive semantic paradigm

Background Mesial temporal lobe epilepsy (MTLE) is the most common type of focal epilepsy in adults and can be successfully cured by surgery. One of the main complications of this surgery however is a decline in language abilities. The magnitude of this decline is related to the degree of language lateralization to the left hemisphere. Most fMRI paradigms used to determine language dominance in epileptic populations have used active language tasks. Sometimes, these paradigms are too complex and may result in patient underperformance. Only a few studies have used purely passive tasks, such as listening to standard speech. Methods In the present study we characterized language lateralization in patients with MTLE using a rapid and passive semantic language task. We used functional magnetic resonance imaging (fMRI) to study 23 patients [12 with Left (LMTLE), 11 with Right mesial temporal lobe epilepsy (RMTLE)] and 19 healthy right-handed controls using a 6 minute long semantic task in which subjects passively listened to groups of sentences (SEN) and pseudo sentences (PSEN). A lateralization index (LI) was computed using a priori regions of interest of the temporal lobe. Results The LI for the significant contrasts produced activations for all participants in both temporal lobes. 81.8% of RMTLE patients and 79% of healthy individuals had a bilateral language representation for this particular task. However, 50% of LMTLE patients presented an atypical right hemispheric dominance in the LI. More importantly, the degree of right lateralization in LMTLE patients was correlated with the age of epilepsy onset. Conclusions The simple, rapid, non-collaboration dependent, passive task described in this study, produces a robust activation in the temporal lobe in both patients and controls and is capable of illustrating a pattern of atypical language organization for LMTLE patients. Furthermore, we observed that the atypical right-lateralization patterns in LMTLE patients was associated to earlier age at epilepsy onset. These results are in line with the idea that early onset of epileptic activity is associated to larger neuroplastic changes.

From bird to sparrow: Learning-induced modulations in fine-grained semantic discrimination.

Recognition of environmental sounds is believed to proceed through discrimination steps from broad to more narrow categories. Very little is known about the neural processes that underlie fine-grained discrimination within narrow categories or about their plasticity in relation to newly acquired expertise. We investigated how the cortical representation of birdsongs is modulated by brief training to recognize individual species. During a 60-minute session, participants learned to recognize a set of birdsongs; they improved significantly their performance for trained (T) but not control species (C), which were counterbalanced across participants. Auditory evoked potentials (AEPs) were recorded during pre- and post-training sessions. Pre vs. post changes in AEPs were significantly different between T and C i) at 206-232ms post stimulus onset within a cluster on the anterior part of the left superior temporal gyrus; ii) at 246-291ms in the left middle frontal gyrus; and iii) 512-545ms in the left middle temporal gyrus as well as bilaterally in the cingulate cortex. All effects were driven by weaker activity for T than C species. Thus, expertise in discriminating T species modulated early stages of semantic processing, during and immediately after the time window that sustains the discrimination between human vs. animal vocalizations. Moreover, the training-induced plasticity is reflected by the sharpening of a left lateralized semantic network, including the anterior part of the temporal convexity and the frontal cortex. Training to identify birdsongs influenced, however, also the processing of C species, but at a much later stage. Correct discrimination of untrained sounds seems to require an additional step which results from lower-level features analysis such as apperception. We therefore suggest that the access to objects within an auditory semantic category is different and depends on subject's level of expertise. More specifically, correct intra-categorical auditory discrimination for untrained items follows the temporal hierarchy and transpires in a late stage of semantic processing. On the other hand, correct categorization of individually trained stimuli occurs earlier, during a period contemporaneous with human vs. animal vocalization discrimination, and involves a parallel semantic pathway requiring expertise.

Semantic domain and grammatical class effects in the picture-word interference paradigm

The role of grammatical class in lexical access and representation is still not well understood. Grammatical effects obtained in picture-word interference experiments have been argued to show the operation of grammatical constraints during lexicalization when syntactic integration is required by the task. Alternative views hold that the ostensibly grammatical effects actually derive from the coincidence of semantic and grammatical differences between lexical candidates. We present three picture-word interference experiments conducted in Spanish. In the first two, the semantic relatedness (related or unrelated) and the grammatical class (nouns or verbs) of the target and the distracter were manipulated in an infinitive form action naming task in order to disentangle their contributions to verb lexical access. In the third experiment, a possible confound between grammatical class and semantic domain (objects or actions) was eliminated by using action-nouns as distracters. A condition in which participants were asked to name the action pictures using an inflected form of the verb was also included to explore whether the need of syntactic integration modulated the appearance of grammatical effects. Whereas action-words (nouns or verbs), but not object-nouns, produced longer reaction times irrespective of their grammatical class in the infinitive condition, only verbs slowed latencies in the inflected form condition. Our results suggest that speech production relies on the exclusion of candidate responses that do not fulfil task-pertinent criteria like membership in the appropriate semantic domain or grammatical class. Taken together, these findings are explained by a response-exclusion account of speech output. This and alternative hypotheses are discussed.

The usefulness of phonological information for the acquisition of grammatical structure in child language development

During the process of language development, one of the most important tasks that children must face is that of identifying the grammatical category to which words in their language belong. This is essential in order to be able to form grammatically correct utterances. How do children proceed in order to classify words in their language and assign them to their corresponding grammatical category? The present study investigates the usefulness of phonological information for the categorization of nouns in English, given the fact that it is phonology the first source of information that might be available to prelinguistic infants who lack access to semantic information or complex morphosyntactic information. We analyse four different corpora containing linguistic samples of English speaking mothers addressing their children in order to explore the reliability with which words are represented in mothers’ speech based on several phonological criteria. The results of the analysis confirm the prediction that most of the words to which English learning infants are exposed during the first two years of life can be accounted for in terms of their phonological resemblance

Cultural differences in web-based health information seeking of Finnish and Japanese students

Abstrakti

Of pearls and pigs : a conceptual-semantic Tiernet approach to formal representation of structure and variation of phraseological units

"Helmiä sioille", pärlor för svin, säger man på finska om någonting bra och fint som tas emot av en mottagare som inte vill eller har ingen förmåga att förstå, uppskatta eller utnyttja hela den potential som finns hos det mottagna föremålet, är ointresserad av den eller gillar den inte. För sådana relativt stabila flerordiga uttryck, som är lagrade i språkbrukarnas minnen och som demonstrerar olika slags oregelbundna drag i sin struktur använder man inom lingvistiken bl.a. termerna "idiom" eller "fraseologiska enheter". Som en oregelbundenhet kan man t.ex. beskriva det faktum att betydelsen hos uttrycket inte är densamma som man skulle komma till ifall man betraktade det som en vanlig regelbunden fras. En annan oregelbundenhet, som idiomforskare har observerat, ligger i den begränsade förmågan att varieras i form och betydelse, som många idiom har jämfört med regelbundna fraser. Därför talas det ofta om "grundform" och "grundbetydelse" hos idiom och variationen avses som avvikelse från dessa. Men när man tittar på ett stort antal förekomstexempel av idiom i språkbruk, märker man att många av dem tillåter variation, t.o.m. i sådan utsträckning att gränserna mellan en variant och en "grundform" suddas ut, och istället för ett idiom råkar vi plötsligt på en "familj" av flera besläktade uttryck. Allt detta väcker frågan om hur dessa uttryck egentligen ska vara representerade i språket. I avhandlingen utförs en kritisk granskning av olika tidigare tillvägagångssätt att beskriva fraseologiska enheter i syfte att klargöra vilka svårigheter deras struktur och variation erbjuder för den lingvistiska teorin. Samtidigt presenteras ett alternativt sätt att beskriva dessa uttryck. En systematisk och formell modell som utvecklas i denna avhandling integrerar en beskrivning av idiom på många olika språkliga nivåer och skildrar deras variation i form av ett nätverk och som ett resultat av samspel mellan idiomets struktur och kontexter där det förekommer, samt av interaktion med andra fasta uttryck. Modellen bygger på en fördjupande, språkbrukbaserad analys av det finska idiomet "X HEITTÄÄ HELMIÄ SIOILLE" (X kastar pärlor för svin).

Social tagging within task management

Social tagging evolved in response to a need to tag heterogeneous objects, the automated tagging of which is usually not feasible by current technological means. Social tagging can be used for more flexible competence management within organizations. The profiles of employees can be built in the form of groups of tags, as employees tag each other, based on their familiarity of each other’s expertise. This can serve as a replacement for the more traditional competence management approaches, which usually become outdated due to social and organizational hurdles, and obsolete data. These limitations can be overcome by people tagging, as the information revealed by such tags is usually based on most recent employee interaction and knowledge. Task management as part of personal information management aims at the support of users’ individual task handling. This can include collaborating with other individuals, sharing one’s knowledge, both functional and process-related, and distributing documents and web resources. In this context, Task patterns can be used as templates that collect information and experience around tasks associated to it during run time, facilitating agility. The effective collaboration among contributors necessitates the means to find the appropriate individuals to work with on the task, and this can be made possible by using social tagging to describe individual competencies. The goal of this study is to support finding and tagging people within task management, through the effective exploitation of the work/task context. This involves the utilization of knowledge of the workers’ expertise, nature of the task/task pattern and information available from the documents and web resources attached to the task. Vice versa, task management provides an excellent environment for social tagging due to the task context that already provides suitable tags. The study also aims at assisting users of the task management solution with the collaborative construction of light-weight ontology by inferring semantic relations between tags. The thesis project aims at an implementation of people finding & tagging within the java application for task management that consumes web services, which provide the required ontology for the organization.

The case of web based information environment in web based weight management services

Abstrakti

Integrating open articles with open data in the life sciences with Europe PubMed Central.

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Integration of JINR Information Resources

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Translating with the Web. Professional translators' information-seeking behaviour in translation with online resources

Tämän tutkielman aiheena on ammattikääntäjien tiedonhaku, kun käytettävissä on ainoastaan verkkolähteitä. Tutkimuksessa on tarkasteltu, mistä ja miten ammattikääntäjät etsivät tietoa internetistä kääntäessään lähtötekstiä englannista suomeen. Lisäksi tutkimuksen tarkoituksena on osoittaa, että tiedonhakutaidot ja lähdekriittisyys ovat käännöskompetensseja, joita tulisi sekä ylläpitää että opettaa osana kääntäjäkoulutusta. Tutkimuksen aineisto kerättiin empiirisesti käyttämällä kolmea metodia. Käännösprosessi ja sen aikana tapahtunut tiedonhaku tallennettiin käyttäen Camtasia-näyttövideointiohjelmaa ja Translog-II -näppäilyntallennusohjelmaa. Lisäksi tutkimukseen osallistuneet kääntäjät täyttivät kaksi kyselyä, joista ensimmäinen sisälsi taustatietokysymyksiä ja toinen itse prosessiin liittyviä retrospektiivisiä kysymyksiä. Kyselyt toteutettiin Webropol-kyselytyökalulla. Aineistoa kerättiin yhteensä viidestä koetilanteesta. Tutkimuksessa tarkasteltiin lähemmin kolmen ammattikääntäjän tiedon-hakutoimintoja erottelemalla käännösprosesseista ne tauot, joiden aikana kääntäjät etsivät tietoa internetistä. Käytettyjen verkkolähteiden osalta tutkimuksessa saatiin vastaavia tuloksia kuin aiemmissakin tutkimuksissa: eniten käytettyjä olivat Google, Wikipedia sekä erilaiset verkkosanakirjat. Tässä tutkimuksessa kuitenkin paljastui, että ammattikääntäjien tiedonhaun toimintamallit vaihtelevat riippuen niin kääntäjän erikoisalasta kuin hänen tiedonhakutaitojensa tasosta. Joutuessaan työskentelemään tutun työympäristönsä ja oman erikoisalansa ulkopuolella turvautuu myös osa ammattikääntäjistä alkeellisimpiin tiedonhakutekniikoihin, joita käännöstieteen opiskelijoiden on havaittu yleisesti käyttävän. Tulokset paljastivat myös, että tiedonhaku voi viedä jopa 70 prosenttia koko käännösprosessiin kuluvasta ajasta riippuen kääntäjän aiemmasta lähtötekstin aihepiiriin liittyvästä tietopohjasta ja tiedonhaun tehokkuudesta. Tutkimuksessa saatujen tulosten pohjalta voidaan sanoa, että myös ammattikääntäjien tulisi kehittää tiedonhakutaitojaan pitääkseen käännösprosessinsa tehokkaana. Lisäksi kääntäjien pitäisi muistaa arvioida kriittisesti käyttämiään tietolähteitä: lähdekritiikki on tarpeen erityisesti verkkolähteitä käytettäessä. Tästä syystä tiedonhakutaitoja ja lähdekriittisyyttä tulisikin opettaa ja harjoitella jo osana kääntäjäkoulutusta. Kääntäjien ei myöskään pidä jättää tiedonhakua pelkkien verkkolähteiden varaan, vaan jatkossakin käyttää hyväkseen niin painettuja tietolähteitä kuin myös henkilölähteitä.

Recherche efficace d'information sur le Web

Il s'agit d'un atelier donné dans le cadre des semaines de formation continue aux diététistes par le Département de nutrition de l'Université de Montréal en 2002. Après une brève introduction à Internet, on présente les caractéristiques spécifiques aux répertoires versus celles des moteurs de recherche, puis les principaux sites et moteurs de recherche utiles dans le domaine de la nutrition. La deuxième partie de l'atelier consiste à montrer comment utiliser la banque de données PubMed avec des exemples en nutrition.