P2P and SOA architecture for digital libraries

In an information-driven society where the volume and value of produced and consumed data assumes a growing importance, the role of digital libraries gains particular importance. This work analyzes the limitations in current digital library management systems and the opportunities brought by recent distributed computing models. The result of this work is the implementation of the University of Aveiro integrated system for digital libraries and archives. It concludes by analyzing the system in production and proposing a new service oriented digital library architecture supported in a peer-to-peer infrastructure

Medical information extraction in European Portuguese

The electronic storage of medical patient data is becoming a daily experience in most of the practices and hospitals worldwide. However, much of the data available is in free-form text, a convenient way of expressing concepts and events, but especially challenging if one wants to perform automatic searches, summarization or statistical analysis. Information Extraction can relieve some of these problems by offering a semantically informed interpretation and abstraction of the texts. MedInX, the Medical Information eXtraction system presented in this document, is the first information extraction system developed to process textual clinical discharge records written in Portuguese. The main goal of the system is to improve access to the information locked up in unstructured text, and, consequently, the efficiency of the health care process, by allowing faster and reliable access to quality information on health, for both patient and health professionals. MedInX components are based on Natural Language Processing principles, and provide several mechanisms to read, process and utilize external resources, such as terminologies and ontologies, in the process of automatic mapping of free text reports onto a structured representation. However, the flexible and scalable architecture of the system, also allowed its application to the task of Named Entity Recognition on a shared evaluation contest focused on Portuguese general domain free-form texts. The evaluation of the system on a set of authentic hospital discharge letters indicates that the system performs with 95% F-measure, on the task of entity recognition, and 95% precision on the task of relation extraction. Example applications, demonstrating the use of MedInX capabilities in real applications in the hospital setting, are also presented in this document. These applications were designed to answer common clinical problems related with the automatic coding of diagnoses and other health-related conditions described in the documents, according to the international classification systems ICD-9-CM and ICF. The automatic review of the content and completeness of the documents is an example of another developed application, denominated MedInX Clinical Audit system.

Portuguese georesources suitability for medical hydrology applications

In Portugal, there is an old tradition in using clayey materials for therapeutic purposes. They are applied in pelotherapy, at several beaches of the Atlantic coast in the form of clay-sea water mixtures (peloids) to treat skin and rheumatic diseases. During many generations, peloids have been applied without scienti c studies that prove their therapeutic validity. In the last decade, the Portuguese scienti c community has become increasingly more interested in assessing the properties that make clayey materials suitable for therapeutic purposes. The abundance of clayey formations and the established practices of medical hydrology in our country turned this interest into a new perspective of application. The studied materials include di erent clays (in age and origin) mainly collected from well-known Mesozoic-Cenozoic formations, in some cases outcropping at beaches where empirical applications occur. This thesis focus in the study of silt-clay fraction (< 63 m).To determine their suitability for therapy, compositional, physicochemical, technological, thermal and rheological properties were assessed. Conventional techniques (XRD, XRF and Sedigraph) were used to assess compositional features of silt-clay fraction. Electron microscopy (SEM, VPSEM, HREM) was used to study the micromorphology and composition of clay fraction (< 2 m). Physicochemical properties (cation exchange and speci c surface) were assessed using the Ammonium Acetate and BET methods. Technological properties (plasticity and abrasivity indices) were assessed using the Atterberg limits and Einlehner abrasion tests. Thermal properties (speci c heat and cooling kinetics) were estimated by DSC analysis and cooling tests. Pharmacotechnical tests (compressibility index, sediment volume and Brook eld viscosity) were used to assess the powder owability as well as the physical stability and viscosity of clay-water dispersions. We selected as suitable Portuguese clays for health applications the samples A-Pe, A-Be2, A-Sd, J-Fr , M-To, C-Lu1, C-Lu2, Pl-Ba, M-Ga and J-Ab because they represent safe materials, with an adequate composition, good technological, physicochemical and thermal properties for application, also presenting an adequate rheology when dispersed in water. Their most relevant characteristics are the high clay minerals content, abundant smectite, illite and kaolinite, and safe hazardous concentrations. They also showed moderate capacity to exchange Ca 2+, high plasticity, low abrasivity, high speci c heat and slow cooling kinetics. They evidenced fair powder owability and good potential to formulate viscous dispersions when stabilized. Because the majority of the assessed characteristics are in accordance with those presented by clays applied in European spas for pelotherapy, we considered this group of clays also suitable for medical hydrology treatments in Portuguese spas.

Hole-type gaseous detectors for medical imaging and HEP experiments

This work presents the results on the development of a high pressure Xe gaseous detector envisaging medical imaging. The detector uses two VUV photosensors operating face-to-face, based on the CsI-MHSP with position discrimination capability. The known effect of the charge gain decrease with the gas pressure is compensated with a light gain using the electroluminescence process. Studies of signal amplitude, energy and position resolution are presented. On the second part, gaseous detectors based on THGEM where studied in order to fulfill the requirements of present and future high energy physics experiments. The work is focused on the application of THGEM in RICH detectors elements: a triple THGEM detector using CsI photocathodes in Ne mixtures was suggested. The ion backflow to the photocathode remains a concern and a limitation; to minimize it, the application of a new hole-structure, THCOBRA, was suggested. Preliminary results foresee good perspectives for the successful application of THCOBRA in ion back-flow suppression. This work contains several methods and measurements of the CsI photocathodes behaviour in radiation gaseous detectors. A long discussion on its issues and possible solutions are presented.

Diversifying medical imaging of breast lesions

Dissertação de mestrado, Engenharia Informática, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

Marketingstrategies for academic libraries

This assignment is about the development of a general strategic marketing plan for academic libraries in Germany and can be used as a guideline for libraries that want to develop concrete marketing strategies for several products and services. Two examples of marketing projects are at its end presented for linking theoretical approaches to practice. Finally the development of an own marketing strategy for “information literacy” builds the last part of the assignment.

Development of new approaches for the synthesis and decoding of one-bead one-compound cyclic peptide libraries

La plupart des processus cellulaires et biologiques reposent, à un certain niveau, sur des interactions protéine-protéine (IPP). Leur manipulation avec des composés chimiques démontre un grand potentiel pour la découverte de nouveaux médicaments. Malgré la demande toujours croissante en molécules capables d’interrompre sélectivement des IPP, le développement d’inhibiteurs d’IPP est fortement limité par la grande taille de la surface d’interaction. En considérant la nature de cette surface, la capacité à mimer des structures secondaires de protéines est très importante pour lier une protéine et inhiber une IPP. Avec leurs grandes capacités peptidomimétiques et leurs propriétés pharmacologiques intéressan-tes, les peptides cycliques sont des prototypes moléculaires de choix pour découvrir des ligands de protéines et développer de nouveaux inhibiteurs d’IPP. Afin d’exploiter pleinement la grande diversité accessible avec les peptides cycliques, l’approche combinatoire «one-bead-one-compound» (OBOC) est l’approche la plus accessible et puissante. Cependant, l’utilisation des peptides cycliques dans les chimiothèques OBOC est limitée par les difficultés à séquencer les composés actifs après le criblage. Sans amine libre en N-terminal, la dégradation d’Edman et la spectrométrie de masse en tandem (MS/MS) ne peuvent pas être utilisées. À cet égard, nous avons développé de nouvelles approches par ouverture de cycle pour préparer et décoder des chimiothèques OBOC de peptides cycliques. Notre stratégie était d’introduire un résidu sensible dans le macrocycle et comme ancrage pour permettre la linéarisation des peptides et leur largage des billes pour le séquençage par MS/MS. Tout d’abord, des résidus sensibles aux nucléophiles, aux ultraviolets ou au bromure de cyanogène ont été introduits dans un peptide cyclique et leurs rendements de clivage évalués. Ensuite, les résidus les plus prometteurs ont été utilisés dans la conception et le développement d’approches en tandem ouverture de cycle / clivage pour le décodage de chimiothèques OBOC de peptides cycliques. Dans la première approche, une méthionine a été introduite dans le macrocycle comme ancrage pour simultanément permettre l’ouverture du cycle et le clivage des billes par traitement au bromure de cyanogène. Dans la seconde approche, un résidu photosensible a été utilisé dans le macrocycle comme ancrage pour permettre l’ouverture du cycle et le clivage suite à une irradiation aux ultraviolets. Le peptide linéaire généré par ces approches peut alors être efficacement séquencé par MS/MS. Enfin, une chimiothèque OBOC a été préparée et criblée la protéine HIV-1 Nef pour identifier des ligands sélectifs. Le développement de ces méthodologies permttra l’utilisation de composés macrocycliques dans les chimiothèques OBOC et constitue une contribution importante en chimie médicinale pour la découverte de ligands de protéines et le développement d’inhibiteurs d’IPP.

Libraries and Canon-Formation: the Case of English in the Collections of the Library of the Faculty of Humanities, Lisbon University

Abstract: The project for researching the role played by libraries in canon-formation (namely through their policies regarding the creation, organization, preservation, and utilization of the collections) will be presented and discussed. We selected the Library of the Faculty of Humanities, Lisbon University, a modern academic library, created in 1859, by royal decree of D. Pedro V, following his canonical choice. Actually, the two contemporary rulers of new Britannia— Prince Albert, his cousin, and Queen Victoria—held this king in high consideration for his outstanding contribution to Portuguese modernisation. Representing various fields of study, the collections were decisive to canon-formation in the Faculty of Humanities. Thus, we have been trying to answer the following questions: who has been creating, organizing, preserving, and utilizing the collections, from the mid-nineteenth century onwards? When, where and how? Presently, we are studying the collections in English, namely the works belonging or referring to the long nineteenth century. Richard Garnett’s “The International Library of Famous Literature” (London, 1899) is our first case-study. The anthology determined the Western literary, cultural and visual canon at the turning of the century, as evidenced by comparing it to the Portuguese and Spanish editions, published at the beginning of the twentieth century.

Visual Literacy Standards in Higher Education: New Opportunities for Libraries and Student Learning

Visual literacy is essential for 21st century learners. Across the higher education curriculum, students are being asked to use and produce images and visual media in their academic work, and they must be prepared to do so. The Association of College and Research Libraries has published the Visual Literacy Competency Standards for Higher Education, which for the first time, outline specific visual literacy learning outcomes. These Standards present new opportunities for libraries to expand their role in student learning through standards-based teaching and assessment, and to contribute to campus-wide collaborative efforts to develop students’ skills and critical thinking with regard to visual materials.

An algebra and conceptual model for semantic tagging of collaborative digital libraries

Cost-effective semantic description and annotation of shared knowledge resources has always been of great importance for digital libraries and large scale information systems in general. With the emergence of the Social Web and Web 2.0 technologies, a more effective semantic description and annotation, e.g., folksonomies, of digital library contents is envisioned to take place in collaborative and personalised environments. However, there is a lack of foundation and mathematical rigour for coping with contextualised management and retrieval of semantic annotations throughout their evolution as well as diversity in users and user communities. In this paper, we propose an ontological foundation for semantic annotations of digital libraries in terms of flexonomies. The proposed theoretical model relies on a high dimensional space with algebraic operators for contextualised access of semantic tags and annotations. The set of the proposed algebraic operators, however, is an adaptation of the set theoretic operators selection, projection, difference, intersection, union in database theory. To this extent, the proposed model is meant to lay the ontological foundation for a Digital Library 2.0 project in terms of geometric spaces rather than logic (description) based formalisms as a more efficient and scalable solution to the semantic annotation problem in large scale.

3D Reconstruction of Medical Images from Slices Automatically Landmarked with Growing Neural Models

In this study, we utilise a novel approach to segment out the ventricular system in a series of high resolution T1-weighted MR images. We present a brain ventricles fast reconstruction method. The method is based on the processing of brain sections and establishing a fixed number of landmarks onto those sections to reconstruct the ventricles 3D surface. Automated landmark extraction is accomplished through the use of the self-organising network, the growing neural gas (GNG), which is able to topographically map the low dimensionality of the network to the high dimensionality of the contour manifold without requiring a priori knowledge of the input space structure. Moreover, our GNG landmark method is tolerant to noise and eliminates outliers. Our method accelerates the classical surface reconstruction and filtering processes. The proposed method offers higher accuracy compared to methods with similar efficiency as Voxel Grid.

Analyzing and Modeling Medical Data on Distributed Computing Infrastructures

Researchers want to analyse Health Care data which may requires large pools of compute and data resources. To have them they need access to Distributed Computing Infrastructures (DCI). To use them it requires expertise which researchers may not have. Workflows can hide infrastructures. There are many workflow systems but they are not interoperable. To learn a workflow system and create workflows in a workflow system may require significant effort. Considering these efforts it is not reasonable to expect that researchers will learn new workflow systems if they want to run workflows of other workflow systems. As a result, the lack of interoperability prevents workflow sharing and a vast amount of research efforts is wasted. The FP7 Sharing Interoperable Workflow for Large-Scale Scientific Simulation on Available DCIs (SHIWA) project developed the Coarse-Grained Interoperability (CGI) to enable workflow sharing. The project created the SHIWA Simulation Platform (SSP) to support CGI as a production-level service. The paper describes how the CGI approach can be used for analysis and simulation in Health Care.