A Dependency Parsing Approach to Biomedical Text Mining

Biomedical research is currently facing a new type of challenge: an excess of information, both in terms of raw data from experiments and in the number of scientific publications describing their results. Mirroring the focus on data mining techniques to address the issues of structured data, there has recently been great interest in the development and application of text mining techniques to make more effective use of the knowledge contained in biomedical scientific publications, accessible only in the form of natural human language. This thesis describes research done in the broader scope of projects aiming to develop methods, tools and techniques for text mining tasks in general and for the biomedical domain in particular. The work described here involves more specifically the goal of extracting information from statements concerning relations of biomedical entities, such as protein-protein interactions. The approach taken is one using full parsing—syntactic analysis of the entire structure of sentences—and machine learning, aiming to develop reliable methods that can further be generalized to apply also to other domains. The five papers at the core of this thesis describe research on a number of distinct but related topics in text mining. In the first of these studies, we assessed the applicability of two popular general English parsers to biomedical text mining and, finding their performance limited, identified several specific challenges to accurate parsing of domain text. In a follow-up study focusing on parsing issues related to specialized domain terminology, we evaluated three lexical adaptation methods. We found that the accurate resolution of unknown words can considerably improve parsing performance and introduced a domain-adapted parser that reduced the error rate of theoriginal by 10% while also roughly halving parsing time. To establish the relative merits of parsers that differ in the applied formalisms and the representation given to their syntactic analyses, we have also developed evaluation methodology, considering different approaches to establishing comparable dependency-based evaluation results. We introduced a methodology for creating highly accurate conversions between different parse representations, demonstrating the feasibility of unification of idiverse syntactic schemes under a shared, application-oriented representation. In addition to allowing formalism-neutral evaluation, we argue that such unification can also increase the value of parsers for domain text mining. As a further step in this direction, we analysed the characteristics of publicly available biomedical corpora annotated for protein-protein interactions and created tools for converting them into a shared form, thus contributing also to the unification of text mining resources. The introduced unified corpora allowed us to perform a task-oriented comparative evaluation of biomedical text mining corpora. This evaluation established clear limits on the comparability of results for text mining methods evaluated on different resources, prompting further efforts toward standardization. To support this and other research, we have also designed and annotated BioInfer, the first domain corpus of its size combining annotation of syntax and biomedical entities with a detailed annotation of their relationships. The corpus represents a major design and development effort of the research group, with manual annotation that identifies over 6000 entities, 2500 relationships and 28,000 syntactic dependencies in 1100 sentences. In addition to combining these key annotations for a single set of sentences, BioInfer was also the first domain resource to introduce a representation of entity relations that is supported by ontologies and able to capture complex, structured relationships. Part I of this thesis presents a summary of this research in the broader context of a text mining system, and Part II contains reprints of the five included publications.

Mediating the Immediate – Endogenous meanings and simulated narratives in ludic spaces

The thesis discusses games and the gaming experience. It is divided into two main sections; the first examines games in general, while the second concentrates exclusively on electronic games. The text approaches games from two distinct directions by looking at both their spatiality and their narrativity at the same time. These two points of view are combined right from the beginning of the text as they are used in conceptualising the nature of the gaming experience. The purpose of the thesis is to investigate two closely related issues concerning both the field of game studies and the nature of games. In regard to studying games, the focus is placed on the juxtaposition of ludology and narratology, which acts as a framework for looking at gaming. In addition to aiming to find out whether or not it is possible to undermine the said state of affairs through the spatiality of games, the text looks at the interrelationships of games and their spaces as well as the role of narratives in those spaces. The thesis is characterised by discussing alternative points of view and its hypothetical nature. During the text, it becomes apparent that the relationship between games and narratives is strongly twofold: on one hand, the player continuously narrativizes the states the game is in while playing, while the narratives residing within the game space form their own partially separate narrative spaces, on the other. These spaces affect the conception the player has of the game states and the events taking place in the game space itself.

Déclaration et traitement des événements indésirables en médecine interne [Incident-reporting electronic-based system in internal medicine].

How to recognize, announce and analyze incidents in internal medicine units is a daily challenge that is taught to all hospital staff. It allows suggesting useful improvements for patients, as well as for the medical department and the institution. Here is presented the assessment made in the CHUV internal medicine department one year after the beginning of the institutional procedure which promotes an open process regarding communication and risk management. The department of internal medicine underlines the importance of feedback to the reporters, ensures the staff of regular follow-up concerning the measures being taken and offers to external reporters such as general practioners the possibility of using this reporting system too.

Experts' consensus on use of electronic cigarettes : a Delphi survey from Switzerland

Objectifs: Dans certains pays, les cigarettes électroniques contenant de la nicotine (e-cigarettes) sont considérées comme des produits de consommation courante, sans régulation spécifique. Dans d'autres (comme en Suisse), la vente d'e-cigarettes contenant de la nicotine est interdite, malgré l'importante demande de nombreux fumeurs de pouvoir les obtenir. Au vu du manque de données scientifiques sur l'efficacité et la sécurité à long-terme de ces produits, les spécialistes de la lutte contre le tabagisme se trouvent divisés sur la question de leur régulation. Afin d'obtenir un consensus parmi ces experts que nous puissions transmettre aux autorités sanitaires, nous avons réalisé une étude d'avis d'experts sur le plan national. Méthode : Nous avons utilisé une méthodologie Delphi, à l'aide de questionnaires électroniques, afin de synthétiser l'opinion d'experts suisses sur la question de la cigarette électronique. Participants : 40 experts suisses représentant l'ensemble de la Suisse. Mesures : Nous avons mesuré le degré de consensus entre les experts au sujet de recommandations touchant à la régulation, la vente et l'utilisation de l'e-cigarette contenant de la nicotine, ainsi que leur opinion générale sur le produit. De nouvelles recommandations et déclarations ont été formulées en tenant compte des réponses et des commentaires des participants. Résultats : Un consensus entre les experts a établi que l'e-cigarette contenant de la nicotine devrait être accessible en Suisse, mais seulement dans des conditions spécifiques. La vente devrait être réservée aux adultes, en utilisant des standards de qualité, une limite de concentration maximale de nicotine, et être accompagnée d'une liste d'ingrédients autorisés. La publicité devrait être restreinte et l'utilisation de l'e- cigarette devrait être interdite dans les lieux publics. Conclusions : Ces recommandations permettent de regrouper trois principes : 1) le principe de réalité, étant donné que le produit est déjà disponible sur le marché ; 2) le principe de prévention, puisque l'e- cigarette procure une alternative au tabac pour les fumeurs actuels, et 3) le principe de précaution, afin de protéger les mineurs et les non-fumeurs, étant donné que les effets à long-terme ne sont pas encore connus. Les autorités suisses devraient mettre en place une législation spécifique afin d'autoriser l'e- cigarette contenant de la nicotine.

Delivery of antigen to nasal-associated lymphoid tissue microfold cells through secretory IgA targeting local dendritic cells confers protective immunity.

BACKGROUND: Transmission of mucosal pathogens relies on their ability to bind to the surfaces of epithelial cells, to cross this thin barrier, and to gain access to target cells and tissues, leading to systemic infection. This implies that pathogen-specific immunity at mucosal sites is critical for the control of infectious agents using these routes to enter the body. Although mucosal delivery would ensure the best onset of protective immunity, most of the candidate vaccines are administered through the parenteral route. OBJECTIVE: The present study evaluates the feasibility of delivering the chemically bound p24gag (referred to as p24 in the text) HIV antigen through secretory IgA (SIgA) in nasal mucosae in mice. RESULTS: We show that SIgA interacts specifically with mucosal microfold cells present in the nasal-associated lymphoid tissue. p24-SIgA complexes are quickly taken up in the nasal cavity and selectively engulfed by mucosal dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin-positive dendritic cells. Nasal immunization with p24-SIgA elicits both a strong humoral and cellular immune response against p24 at the systemic and mucosal levels. This ensures effective protection against intranasal challenge with recombinant vaccinia virus encoding p24. CONCLUSION: This study represents the first example that underscores the remarkable potential of SIgA to serve as a carrier for a protein antigen in a mucosal vaccine approach targeting the nasal environment.

New technologies and nursing: use and perception of primary healthcare nurses about electronic health record in Catalonia, Spain

This study was aimed to analyze and assess the use and perception of electronic health records (EHRs) by nurses. The study sample included 113 nurses from different shifts of primary health facilities in Catalonia, Spain, devoted to adult as well as pediatric outpatients using EHRs throughout the year 2010. A majority of the sample (87.5%) were women and 12.5% were men. The average age was 44.27 years and the average time working in primary healthcare was 47.15 months. A majority (80.4%) received specific training on the use of the EHR and 19.6% did not. The use of the application required side technical support (mean: 3.42) and it is considered necessary to learn more about the performance of the application (mean: 3.50). The relationship between the average ratings that nurses have about the EHR and age shows that there is no statistically significant linear relationship (r = - 0.002, p-value = 0.984). As to how long they have used the EHRs, there are significant differences (r= -0.304, p-value = 0.00), so the more time the nurse takes using the EHR, the greater degree of satisfaction is shown. In addition, there are significant differences between nurses" perceptions regarding the EHR and gender (t = - 0.421, p-value = 0.675). Nurses assessed as positive the contribution of the EHRs in their nursing care day work (average score: 2.55/5). Considering that the usability of the EHR device is assessed as satisfactory, the results of the perception of nurses show that we must also take into account the training and emphasize the need for a side technical support in the implementation process of the EHR. Doing so, the positive perception that nurses have in regard to information and communication technology in general and with respect to the EHR in particular may be increased.

New technologies and nursing: use and perception of primary healthcare nurses about electronic health record in Catalonia, Spain

This study was aimed to analyze and assess the use and perception of electronic health records (EHRs) by nurses. The study sample included 113 nurses from different shifts of primary health facilities in Catalonia, Spain, devoted to adult as well as pediatric outpatients using EHRs throughout the year 2010. A majority of the sample (87.5%) were women and 12.5% were men. The average age was 44.27 years and the average time working in primary healthcare was 47.15 months. A majority (80.4%) received specific training on the use of the EHR and 19.6% did not. The use of the application required side technical support (mean: 3.42) and it is considered necessary to learn more about the performance of the application (mean: 3.50). The relationship between the average ratings that nurses have about the EHR and age shows that there is no statistically significant linear relationship (r = - 0.002, p-value = 0.984). As to how long they have used the EHRs, there are significant differences (r= -0.304, p-value = 0.00), so the more time the nurse takes using the EHR, the greater degree of satisfaction is shown. In addition, there are significant differences between nurses" perceptions regarding the EHR and gender (t = - 0.421, p-value = 0.675). Nurses assessed as positive the contribution of the EHRs in their nursing care day work (average score: 2.55/5). Considering that the usability of the EHR device is assessed as satisfactory, the results of the perception of nurses show that we must also take into account the training and emphasize the need for a side technical support in the implementation process of the EHR. Doing so, the positive perception that nurses have in regard to information and communication technology in general and with respect to the EHR in particular may be increased.

Construction of an index of information from clinical practice in Radiology and Imaging Diagnosis based on text mining and thesaurus

Objective To construct a Portuguese language index of information on the practice of diagnostic radiology in order to improve the standardization of the medical language and terminology. Materials and Methods A total of 61,461 definitive reports were collected from the database of the Radiology Information System at Hospital das Clínicas – Faculdade de Medicina de Ribeirão Preto (RIS/HCFMRP) as follows: 30,000 chest x-ray reports; 27,000 mammography reports; and 4,461 thyroid ultrasonography reports. The text mining technique was applied for the selection of terms, and the ANSI/NISO Z39.19-2005 standard was utilized to construct the index based on a thesaurus structure. The system was created in *html. Results The text mining resulted in a set of 358,236 (n = 100%) words. Out of this total, 76,347 (n = 21%) terms were selected to form the index. Such terms refer to anatomical pathology description, imaging techniques, equipment, type of study and some other composite terms. The index system was developed with 78,538 *html web pages. Conclusion The utilization of text mining on a radiological reports database has allowed the construction of a lexical system in Portuguese language consistent with the clinical practice in Radiology.

Text i context. El concurs de cinema amateur «JULIUS» (1987-1996)

El «Julius» és un concurs de cinema amateur que fonamenta la seva singularitat en el fet de partir d’un text literari prefixat del qual els participants han de fer una adaptació audiovisual. En aquest article s’estudia la primera època del concurs: el seu origen, les diverses edicions en què es dugué a terme, les incidències que s’hi produïren..., i el context social i cultural que va contribuir a fer-ne un concurs amb unes característiques úniques que es concretaren en l’anomenat «esperit Julius», sorneguer, llibertari i surrealista.

Jane Eyre: del text a la pantalla : Un estudi comparatiu entre l'obra de Charlotte Brontë i l'adaptació cinematogràfica de Cary Fukunaga

Treball de fi de màster que estudia comparativament les relacions entre la novel·la "Jane Eyre" de Charlotte Brontë i l'adaptació cinematogràfica de la mateixa realitzada pel director Cary Fukunaga.

Adaptações em forno de microondas doméstico para utilização em laboratório

Domestic microwave oven was modified for laboratory applications. Electronic system was made for controlling magnetron irradiation time. Exhaustion and air circulation systems were installed to clean the internal oven atmosphere during operation. The cavity walls were coated with aluminized thermal paint to avoid chemical corrosion. These modifications allowed the usage of the oven for drying and processes using reflux.