Indexing strategies for rapid searches of short words in genome sequences.

Searching for matches between large collections of short (14-30 nucleotides) words and sequence databases comprising full genomes or transcriptomes is a common task in biological sequence analysis. We investigated the performance of simple indexing strategies for handling such tasks and developed two programs, fetchGWI and tagger, that index either the database or the query set. Either strategy outperforms megablast for searches with more than 10,000 probes. FetchGWI is shown to be a versatile tool for rapidly searching multiple genomes, whose performance is limited in most cases by the speed of access to the filesystem. We have made publicly available a Web interface for searching the human, mouse, and several other genomes and transcriptomes with oligonucleotide queries.

More than Words? An Analysis on the Language and Structure of General Election Manifestos of the British Labour Party 1983-2005

The topic of this study is the language of the educational policies of the British Labour party in the General Election manifestos between the years 1983-2005. The twenty-year period studied has been a period of significant changes in world politics, and in British politics, especially for the Labour party. The emergence educational policy as a vote-winner of the manifestos of the nineties has been noteworthy. The aim of the thesis is two-fold: to look at the structure of the political manifesto as an example of genre writing and to analyze the content utilizing the approach of critical discourse analysis. Furthermore, the aim of this study is not to pinpoint policy positions but to look at what is the image that the Labour Party creates of itself through these manifestos. The analysis of the content is done by a method of close-reading. Based on the findings, the methodology for the analysis of the content was created. This study utilized methodological triangulation which means that the material is analyzed from several methodological aspects. The aspects used in this study are ones of lexical features (collocation, coordination, euphemisms, metaphors and naming), grammatical features (thematic roles, tense, aspect, voice and modal auxiliaries) and rhetoric (Burke, Toulmin and Perelman). From the analysis of the content a generic description is built. By looking at the lexical, grammatical and rhetorical features a clear change in language of the Labour Party can be detected. This change is foreshadowed already in the 1992 manifesto but culminates in the 1997 manifesto which would lead Labour to a landslide victory in the General Election. During this twenty-year period Labour has moved away from the old commitments and into the new sphere of “something for everybody”. The pervasiveness of promotional language and market inspired vocabulary into the sphere of manifesto writing is clear. The use of the metaphors seemed to be the tool for the creation of the image of the party represented through the manifestos. A limited generic description can be constructed from the findings based on the content and structure of the manifestos: especially more generic findings such as the use of the exclusive we, the lack of certain anatomical parts of argument structure, the use of the future tense and the present progressive aspect can shed light to the description of the genre of manifesto writing. While this study is only the beginning, it proves that the combination of looking at the lexical, grammatical and rhetorical features in the study of manifestos is a promising one.

Electrostimulation mapping of comprehension of auditory and visual words.

In order to spare functional areas during the removal of brain tumours, electrical stimulation mapping was used in 90 patients (77 in the left hemisphere and 13 in the right; 2754 cortical sites tested). Language functions were studied with a special focus on comprehension of auditory and visual words and the semantic system. In addition to naming, patients were asked to perform pointing tasks from auditory and visual stimuli (using sets of 4 different images controlled for familiarity), and also auditory object (sound recognition) and Token test tasks. Ninety-two auditory comprehension interference sites were observed. We found that the process of auditory comprehension involved a few, fine-grained, sub-centimetre cortical territories. Early stages of speech comprehension seem to relate to two posterior regions in the left superior temporal gyrus. Downstream lexical-semantic speech processing and sound analysis involved 2 pathways, along the anterior part of the left superior temporal gyrus, and posteriorly around the supramarginal and middle temporal gyri. Electrostimulation experimentally dissociated perceptual consciousness attached to speech comprehension. The initial word discrimination process can be considered as an "automatic" stage, the attention feedback not being impaired by stimulation as would be the case at the lexical-semantic stage. Multimodal organization of the superior temporal gyrus was also detected since some neurones could be involved in comprehension of visual material and naming. These findings demonstrate a fine graded, sub-centimetre, cortical representation of speech comprehension processing mainly in the left superior temporal gyrus and are in line with those described in dual stream models of language comprehension processing.

Functional neuroanatomy of contextual acquisition of concrete and abstract words

The meaning of a novel word can be acquired by extracting it from linguistic context. Here we simulated word learning of new words associated to concrete and abstract concepts in a variant of the human simulation paradigm that provided linguistic context information in order to characterize the brain systems involved. Native speakers of Spanish read pairs of sentences in order to derive the meaning of a new word that appeared in the terminal position of the sentences. fMRI revealed that learning the meaning associated to concrete and abstract new words was qualitatively different and recruited similar brain regions as the processing of real concrete and abstract words. In particular, learning of new concrete words selectively boosted the activation of the ventral anterior fusiform gyrus, a region driven by imageability, which has previously been implicated in the processing of concrete words.

One, two, or many mechanisms? The brain's processing of complex words

The heated debate over whether there is only a single mechanism or two mechanisms for morphology has diverted valuable research energy away from the more critical questions about the neural computations involved in the comprehension and production of morphologically complex forms. Cognitive neuroscience data implicate many brain areas. All extant models, whether they rely on a connectionist network or espouse two mechanisms, are too underspecified to explain why more than a few brain areas differ in their activity during the processing of regular and irregular forms. No one doubts that the brain treats regular and irregular words differently, but brain data indicate that a simplistic account will not do. It is time for us to search for the critical factors free from theoretical blinders.