LiDom builder: Automatising the construction of multilingual domain modules

136 p.

Structural relaxation and chain dynamics in polymer melts : a computational investigation on the role of the intramolecular barriers

149 p. : il. col.

A Computational Module Assembled from Different Protease Family Motifs Identifies PI PLC from Bacillus cereus as a Putative Prolyl Peptidase with a Serine Protease Scaffold

Proteolytic enzymes have evolved several mechanisms to cleave peptide bonds. These distinct types have been systematically categorized in the MEROPS database. While a BLAST search on these proteases identifies homologous proteins, sequence alignment methods often fail to identify relationships arising from convergent evolution, exon shuffling, and modular reuse of catalytic units. We have previously established a computational method to detect functions in proteins based on the spatial and electrostatic properties of the catalytic residues (CLASP). CLASP identified a promiscuous serine protease scaffold in alkaline phosphatases (AP) and a scaffold recognizing a beta-lactam (imipenem) in a cold-active Vibrio AP. Subsequently, we defined a methodology to quantify promiscuous activities in a wide range of proteins. Here, we assemble a module which encapsulates the multifarious motifs used by protease families listed in the MEROPS database. Since APs and proteases are an integral component of outer membrane vesicles (OMV), we sought to query other OMV proteins, like phospholipase C (PLC), using this search module. Our analysis indicated that phosphoinositide-specific PLC from Bacillus cereus is a serine protease. This was validated by protease assays, mass spectrometry and by inhibition of the native phospholipase activity of PI-PLC by the well-known serine protease inhibitor AEBSF (IC50 = 0.018 mM). Edman degradation analysis linked the specificity of the protease activity to a proline in the amino terminal, suggesting that the PI-PLC is a prolyl peptidase. Thus, we propose a computational method of extending protein families based on the spatial and electrostatic congruence of active site residues.

Bilingual Lexicography:Relevance of Corpora. The Example of German-Basque as Language Pair

Presentation for the 5th International Conference on Corpus Linguistics (CILC 2013), V Congreso Internacional de Lingüistica de Corpus.

THE AINU LANGUAGES: TRADITIONAL RECONSTRUCTION, EURASIAN AREAL LINGUISTICS, AND DIACHRONIC (HOLISTIC) TYPOLOGY

El objetivo principal de esta tesis doctoral es, en primer lugar, ofrecer una reconstrucción alternativa del protoainu para, en segundo lugar, aplicar conceptos de tipología diacrónicaholística con el fin de discernir algún patrón evolutivo que ayude a responder a la pregunta:¿por qué la lengua ainu es como es en su contexto geolingüístico (lengua AOV con prefijos),cuando en la región euroasiática lo normal es encontrar el perfil 'lengua AOV con sufijos'? En suma, se trata de explorar las posibilidades que ofrece la tipología diacrónica holística,combinada con métodos más tradicionales, en la investigación de las etapas prehistóricas delenguas aisladas, es decir, sin parientes conocidos, como el ainu, el vasco, el zuñi o elburushaski. Este trabajo se divide en tres grandes bloques con un total de ocho capítulos, unapéndice con las nuevas reconstrucciones protoainúes y la bibliografía.El primer bloque se abre con el capítulo 1, donde se hace una breve presentación delas lenguas ainus y su filología. El capítulo 2 está dedicado a la reconstrucción de la fonologíaprotoainu. La reconstrucción pionera pertenece a A. Vovin (1992), que de hecho sirve comobase sobre la que ampliar, corregir o modificar nuevos elementos. En el capítulo 3 se describela morfología histórica de las lenguas ainus. En el capítulo 4 se investiga esta opción dentrode un marco más amplio que tiene como objetivo analizar los patrones elementales deformación de palabras. El capítulo 5, con el que se inicia el segundo bloque, da cabida a lapresentación de una hipótesis tipológica diacrónica, a cargo de P. Donegan y D. Stampe, conla que especialistas en lenguas munda y mon-khmer han sido capaces de alcanzar unreconstrucción del protoaustroasiático según la cual el tipo aglutinante de las lenguas mundasería secundario, frente al original monosilábico de las lenguas mon-khmer. En el capítulo 6se retoma la perspectiva tradicional de la lingüística geográfica, pero no se olvidan algunas delas consideraciones tipológicas apuntadas en el capítulo anterior (el hecho de que la hipótesisde Donegan y Stampe no funcione con el ainu no significa que la tipología diacrónica nopueda ser todavía de utilidad). En el capítulo 7 se presentan algunas incongruencias queresultan tras combinar las supuestas evidencias arqueológicas con el escenario lingüísticodescrito en capítulos anteriores. Las conclusiones generales se presentan en el capítulo 8. Elapéndice es una tabla comparativa con las dos reconstrucciones disponibles a fecha de hoypara la lengua protoainu, es decir, las propuestas por A. Vovin en su estudio seminal de 1992y en el capítulo 3 de la presente tesis. Dicha tabla incluye 686 reconstrucciones (puedehacerse una sencilla referencia cruzada con Vovin, puesto que ambas están ordenadasalfabéticamente).

Computational study of the vortex path variation with the VG height

An extensive range of conventional, vane-type, passive vortex generators (VGs) are in use for successful applications of flow separation control. In most cases, the VG height is designed with the same thickness as the local boundary layer at the VG position. However, in some applications, these conventional VGs may produce excess residual drag. The so-called low-profile VGs can reduce the parasitic drag associated to this kind of passive control devices. As suggested by many authors, low-profile VGs can provide enough momentum transfer over a region several times their own height for effective flow-separation control with much lower drag. The main objective of this work is to study the variation of the path and the development of the primary vortex generated by a rectangular VG mounted on a flat plate with five different device heights h = delta, h(1) = 0.8 delta, h(2) = 0.6 delta, h(3) = 0.4 delta and h(4) = 0.2 delta, where delta is the local boundary layer thickness. For this purpose, computational simulations have been carried out at Reynolds number Re = 1350 based on the height of the conventional VG h = 0.25m with the angle of attack of the vane to the oncoming flow beta = 18.5 degrees. The results show that the VG scaling significantly affects the vortex trajectory and the peak vorticity generated by the primary vortex.

Etymological notes on Aleut (III). With methodological notes on (Eskimo-Aleut) historical linguistics

[EN] The goal of this contribution is twofold: on the one hand, to review two relatively recent contributions in the field of Eskimo-Aleut historical linguistics in which it is proposed that Eskimo-Aleut languages are related genealogically to Wakashan (Holst 2004) and?/or Nostratic (Krougly-Enke 2008). These contributions can be characterized by saying that their authors have taken little care to be diligent and responsible in the application of the comparative method, and that their familiarity with the languages involved is insufficient. Eskimo-Aleut languages belong to a very exclusive group of language families that have been (and still are) used, sometimes compulsively, in the business of so-called “long-range comparisons”. Those carrying out such studies are very often unaware of the most basic facts regarding the philological and linguistic traditions of those languages, as a result of what mountains of very low quality works with almost no-relevancy for the specialist grow every year to the desperation of the scientific community, whose attitude toward them ranges from the most profound indifference to the toughest (and most explicit) critical tone. Since Basque also belongs to this group of “compare-with-everything-you-come- across” languages, it is my intention to provide the Basque readership with a sort of “pedagogical case” to show that little known languages, far from underrepresented in the field, already have a very long tradition in historical and comparative linguistics, i.e. nobody can approach them without previous acquaintance with the materials. Studies dealing with the methodological inappropriateness of the Moscow School’s Nostratic hypothesis or the incorrectness of many of the proposed new taxonomic Amerindian subfamilies (several of them involving the aforementioned Wakashan languages), that is to say, the frameworks on which Krougly-Enke and Holst work, respectively, are plenty (i.a. Campbell 1997: 260-329, Campbell & Poser 2008: 234-96), therefore there is no reason to insist once more on the very same point. This is the reason why I will not discuss per se Eskimo-Aleut–Wakashan or Eskimo-Aleut–Nostratic. On the contrary, I will focus attention upon very concrete aspects of Krougly-Enke and Holst´s proposals, i.e. when they work on “less ambitious” problems, for example, dealing with the minutiae of internal facts or analyzing certain words from the sole perspective of Eskimo-Aleut materials (in other words, those cases in which even they do not invoke the ad hoc help of Nostratic stuff). I will try to explain why some of their proposals are wrong, demonstrate where the problem lies, and fix it if possible. In doing so, I will propose new etymologies in an attempt at showing how we may proceed. The main difference between this and handbook examples lies in the reality of what we are doing: this is a pure etymological exercise from beginning to end. I will try to throw a bit of light on a couple of problematic questions regarding Aleut historical phonology, demonstrating how much work should be done at the lowest level of the Eskimo-Aleut pyramid; it is technically impossible to reach the peak of the pyramid without having completed the base. As far as Aleut is regarded, I will mainly profit not only from the use of the traditional philological analysis of Aleut (and, eventually, of Eskimo) materials, but also of diachronic typology, bringing into discussion what in my opinion seems useful, and in some cases I think decisive, parallels. It is worth noting that this paper makes up yet another part of a series of exploratory works dealing with etymological aspects of the reconstruction of Proto-Eskimo-Aleut, with special emphasis on Aleut (vid. i.a. Alonso de la Fuente 2006/2007, 2008a, 2008b, 2010a), whose main goal is to become the solid basis for an etymological dictionary of the Aleut language, currently in progress.