Studies of conformation and configuration using crystallographic methods

This Thesis demonstrates the use of the Cambridge Crystallographic Database for structure correlation studies in two very different fields. The first part of the Thesis (Chapters 2 and 3) is concerned with the systematic conformational analysis of medium-sized rings and satisfies the objectives of the study by: (i) applying novel classification techniques to the conformational descriptions of both the seven- and eight-membered rings, (ii) interpreting the results in terms of the relevant conformational hypersurface by locating the highly populated regions of that hypersurface and mapping the interconversion pathways, (iii) studying, modifying and improving the available methodologies for data analysis, and (iv) relating the conformational minima found using these methods to both the chemical environments of the fragments under investigation, and to energetic features of the hypersurface obtained by computational methods. The second major structure correlation experiment involves the analysis and description of 3-coordinated transition metal complexes using both simple geometrical models and group-theoretically based symmetry deformation coordinates. Non-bonded interactions will be seen to play a significant part in the geometry of the 3-coordinated fragment, and extrapolation of these results leads to the rationalisation of an addition/elimination scheme linking 4- and 2-coordinated fragments through the intermediate 3-coordinated species. Chapter 5 describes the crystallographic structure determinations of eight novel compounds: 3,5-cycloheptadienyl-3,5 dinitrobenzoate [C(_14)H(_12)O(_6)N(_2)]; a 34-membered diolide [C(_32)H(_60)O(_4)]; l-iodo-3-tosyloxy-propan-2-ane [C(_10)H(_11)O(_4)IS)]; 1β, 9 β -diacetyl- 7α-chloro-cis-hydrindane [C(_13)H(_19)O(_2)CI]; (R,R)-l,4-bis (2'-chloro-1 '-hydoxyethyl) benzene [C(_10)H(_12)O(_2)CI(_2)]; a fused penta-cyclic ring compound [C(_17)H(_14)]; 1,4 dibenzyl- 1,2,4,5-tetraazacyclohexane [C(_16) H(_20) N(_4)]; 1,5-di (2'-chloroacetoxy)-3,3-dimethyl-2,4- diphenyl-3-silapentane [C(_22)H(_26)O(_4) CI(_2) Si]

Foreword

The aim of this Workshop is to focus on building and evaluating resources used to facilitate biomedical text mining, including their design, update, delivery, quality assessment, evaluation and dissemination. Key resources of interest are lexical and knowledge repositories (controlled vocabularies, terminologies, thesauri, ontologies) and annotated corpora, including both task-specific resources and repositories reengineered from biomedical or general language resources. Of particular interest is the process of building annotated resources, including designing guidelines and annotation schemas (aiming at both syntactic and semantic interoperability) and relying on language engineering standards. Challenging aspects are updates and evolution management of resources, as well as their documentation, dissemination and evaluation

PowerAqua: Open Question Answering on the Semantic Web

With the rapid growth of semantic information in the Web, the processes of searching and querying these very large amounts of heterogeneous content have become increasingly challenging. This research tackles the problem of supporting users in querying and exploring information across multiple and heterogeneous Semantic Web (SW) sources. A review of literature on ontology-based Question Answering reveals the limitations of existing technology. Our approach is based on providing a natural language Question Answering interface for the SW, PowerAqua. The realization of PowerAqua represents a considerable advance with respect to other systems, which restrict their scope to an ontology-specific or homogeneous fraction of the publicly available SW content. To our knowledge, PowerAqua is the only system that is able to take advantage of the semantic data available on the Web to interpret and answer user queries posed in natural language. In particular, PowerAqua is uniquely able to answer queries by combining and aggregating information, which can be distributed across heterogeneous semantic resources. Here, we provide a complete overview of our work on PowerAqua, including: the research challenges it addresses; its architecture; the techniques we have realised to map queries to semantic data, to integrate partial answers drawn from different semantic resources and to rank alternative answers; and the evaluation studies we have performed, to assess the performance of PowerAqua. We believe our experiences can be extrapolated to a variety of end-user applications that wish to open up to large scale and heterogeneous structured datasets, to be able to exploit effectively what possibly is the greatest wealth of data in the history of Artificial Intelligence

Důležitá slova. Podklady ke kolokačnímu švédsko-českému slovníku základních sloves

Basic verbs, i.e. very common verbs that typically denote physical movements, locations, states or actions, undergo various semantic shifts and acquire different secondary uses. In extreme cases, the distribution of secondary uses grows so general that they are regarded as auxiliary verbs (go and to be going to), phase verbs (turn, grow), etc. ese uses are usually well-documented by grammars and language textbooks, and so are idiomatic expressions (phraseologisms) in dictionaries. ere is, however, a grey area in between, which is extremely difficult to learn for non-native speakers. is consists of secondary uses with limited collocability, in particular light verb constructions, and secondary meanings that only get activated under particular morphosyntactic conditions. e basic-verb secondary uses and constructions are usually semantically transparent, such that they do not pose understanding problems, but they are generally unpredictable and language-specific, such that they easily become an issue in non-native text production. In this thesis, Swedish basic verbs are approached from the contrastive point of view of an advanced Czech learner of Swedish. A selection of Swedish constructions with basic verbs is explored. e observations result in a proposal for the structure of a machine-readable Swedish-Czech...Základní slovesa (basic verbs), tj. frekventovaná významová slovesa, jež zpravidla popisují fyzický pohyb, umístění, stav, nebo děj, procházejí řadou sémantických posunů, díky kterým se používají k vyjádření druhotných, přenesených významů. V krajních případech se dané sloveso stává pomocným, způsobovým, nebo fázovým slovesem a přestávají pro ně platit kolokační omezení, jež se vztahují na sloveso užité v jeho primárním (tj. doslovném) významu. Tato užití sloves bývají většinou dobře dokumentována v gramatikách i učebnicích, stejně jako kvalitní slovníky podávají podrobnou informaci o užití těchto sloves v ustálených frazeologických spojeních. Mezi plně gramatikalizovaným užitím na jedné straně a idiomatickým, frazeologickým užitím na druhé straně však existuje celá škála užití základních sloves v přenesených významech, jejíž zvládnutí je pro nerodilého mluvčího značně obtížné: užití v přeneseném významu, jež mají omezenou kolokabilitu. To jsou především verbonominální konstrukce někdy nazývané analytické predikáty (light verb constructions), ale také užití, která za určitých omezených morfosyntaktických podmínek (např. pouze v negaci) aktivují abstraktní sémantické rysy u jiných predikátů, např. zesilují význam, nebo implikují, že daný děj již trvá dlouho, a podobně. Tato druhotná užití významových sloves...Institute of Germanic StudiesÚstav germánských studiíFilozofická fakultaFaculty of Art

Natural Language Processing Resources for Finnish. Corpus Development in the General and Clinical Domains

Siirretty Doriast

The very model of a modern linguist — in honor of Helge Dyvik

publishedVersio

High-Performance Modelling and Simulation for Big Data Applications

This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications

Event extraction from biomedical texts using trimmed dependency graphs

This thesis explores the automatic extraction of information from biomedical publications. Such techniques are urgently needed because the biosciences are publishing continually increasing numbers of texts. The focus of this work is on events. Information about events is currently manually curated from the literature by biocurators. Biocuration, however, is time-consuming and costly so automatic methods are needed for information extraction from the literature. This thesis is dedicated to modeling, implementing and evaluating an advanced event extraction approach based on the analysis of syntactic dependency graphs. This work presents the event extraction approach proposed and its implementation, the JReX (Jena Relation eXtraction) system. This system was used by the University of Jena (JULIE Lab) team in the "BioNLP 2009 Shared Task on Event Extraction" competition and was ranked second among 24 competing teams. Thereafter JReX was the highest scorer on the worldwide shared U-Compare event extraction server, outperforming the competing systems from the challenge. This success was made possible, among other things, by extensive research on event extraction solutions carried out during this thesis, e.g., exploring the effects of syntactic and semantic processing procedures on solving the event extraction task. The evaluations executed on standard and community-wide accepted competition data were complemented by real-life evaluation of large-scale biomedical database reconstruction. This work showed that considerable parts of manually curated databases can be automatically re-created with the help of the event extraction approach developed. Successful re-creation was possible for parts of RegulonDB, the world's largest database for E. coli. In summary, the event extraction approach justified, developed and implemented in this thesis meets the needs of a large community of human curators and thus helps in the acquisition of new knowledge in the biosciences

High-Performance Modelling and Simulation for Big Data Applications

This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications