GALANT: a Cytoscape plugin for visualizing data as functional landscapes projected onto biological networks

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The briefing in paleodesign: selection and arrangement of data for the reconstruction of Paleovertebrates

Representing visually the external appearance of an extinct animal requires, for a reasonably reliable and expressive reconstitution, a good compilation and arrangement of the scientific conclusions on the fossil findings. It is proposed in this work an initial model of a briefing to be applied in a paleodesign process of a paleovertebrate. Briefing can be understood as a gathering of all necessary data to perform a project. We point out what must be known about the relevant structures in order to access all the data and the importance of such information. It is expected that the present briefing suggested might be faced with flexibility, serving as a facilitating interface of the relation between paleoartists and paleontologists.

Public Commons for Geospatial Data: A Conceptual Model

A wide variety of spatial data collection efforts are ongoing throughout local, state and federal agencies, private firms and non-profit organizations. Each effort is established for a different purpose but organizations and individuals often collect and maintain the same or similar information. The United States federal government has undertaken many initiatives such as the National Spatial Data Infrastructure, the National Map and Geospatial One-Stop to reduce duplicative spatial data collection and promote the coordinated use, sharing, and dissemination of spatial data nationwide. A key premise in most of these initiatives is that no national government will be able to gather and maintain more than a small percentage of the geographic data that users want and desire. Thus, national initiatives depend typically on the cooperation of those already gathering spatial data and those using GIs to meet specific needs to help construct and maintain these spatial data infrastructures and geo-libraries for their nations (Onsrud 2001). Some of the impediments to widespread spatial data sharing are well known from directly asking GIs data producers why they are not currently involved in creating datasets that are of common or compatible formats, documenting their datasets in a standardized metadata format or making their datasets more readily available to others through Data Clearinghouses or geo-libraries. The research described in this thesis addresses the impediments to wide-scale spatial data sharing faced by GIs data producers and explores a new conceptual data-sharing approach, the Public Commons for Geospatial Data, that supports user-friendly metadata creation, open access licenses, archival services and documentation of parent lineage of the contributors and value- adders of digital spatial data sets.

A Semantic Scraping Model for Web Resources - Applying Linked Data to Web Page Screen Scraping

In spite of the increasing presence of Semantic Web Facilities, only a limited amount of the available resources in the Internet provide a semantic access. Recent initiatives such as the emerging Linked Data Web are providing semantic access to available data by porting existing resources to the semantic web using different technologies, such as database-semantic mapping and scraping. Nevertheless, existing scraping solutions are based on ad-hoc solutions complemented with graphical interfaces for speeding up the scraper development. This article proposes a generic framework for web scraping based on semantic technologies. This framework is structured in three levels: scraping services, semantic scraping model and syntactic scraping. The first level provides an interface to generic applications or intelligent agents for gathering information from the web at a high level. The second level defines a semantic RDF model of the scraping process, in order to provide a declarative approach to the scraping task. Finally, the third level provides an implementation of the RDF scraping model for specific technologies. The work has been validated in a scenario that illustrates its application to mashup technologies

Mass Surveillance of Personal Data by EU Member States and its Compatibility with EU Law. CEPS Liberty and Security in Europe No. 61, 6 November 2013

In the wake of the disclosures surrounding PRISM and other US surveillance programmes, this paper assesses the large-scale surveillance practices by a selection of EU member states: the UK, Sweden, France, Germany and the Netherlands. Given the large-scale nature of these practices, which represent a reconfiguration of traditional intelligence gathering, the paper contends that an analysis of European surveillance programmes cannot be reduced to a question of the balance between data protection versus national security, but has to be framed in terms of collective freedoms and democracy. It finds that four of the five EU member states selected for in-depth examination are engaging in some form of large-scale interception and surveillance of communication data, and identifies parallels and discrepancies between these programmes and the NSA-run operations. The paper argues that these programmes do not stand outside the realm of EU intervention but can be analysed from an EU law perspective via i) an understanding of national security in a democratic rule of law framework where fundamental human rights and judicial oversight constitute key norms; ii) the risks posed to the internal security of the Union as a whole as well as the privacy of EU citizens as data owners and iii) the potential spillover into the activities and responsibilities of EU agencies. The paper then presents a set of policy recommendations to the European Parliament.

Access to Electronic Data by Third-Country Law Enforcement Authorities, Challenges to EU Rule of Law and Fundamental Rights. Center for European Policy Studies, 2015

This study examines the challenges posed to European law by third country access to data held by private companies for the purposes of law enforcement. It pays particular attention to the implications for rule of law and fundamental rights of foreign authorities’ direct access to electronic information falling outside pre-established channels of supranational cooperation. A special focus is given to EU-US relations and the practical issues emerging in transatlantic relations covering mutual legal assistance and evidence gathering for law enforcement purposes in criminal proceedings.

A review of the information-gathering process for the provision of medicines for self-medication via community pharmacies in developing countries

Background: Currently, no review has been completed regarding the information-gathering process for the provision of medicines for self-medication in community pharmacies in developing countries. Objective: To review the rate of information gathering and the types of information gathered when patients present for self-medication requests. Methods: Six databases were searched for studies that described the rate of information gathering and/or the types of information gathered in the provision of medicines for self-medication in community pharmacies in developing countries. The types of information reported were classified as: signs and symptoms, patient identity, action taken, medications, medical history, and others. Results: Twenty-two studies met the inclusion criteria. Variations in the study populations, types of scenarios, research methods, and data reporting were observed. The reported rate of information gathering varied from 18% to 97%, depending on the research methods used. Information on signs and symptoms and patient identity was more frequently reported to be gathered compared with information on action taken, medications, and medical history. Conclusion: Evidence showed that the information-gathering process for the provision of medicines for self-medication via community pharmacies in developing countries is inconsistent. There is a need to determine the barriers to appropriate information-gathering practice as well as to develop strategies to implement effective information-gathering processes. It is also recommended that international and national pharmacy organizations, including pharmacy academics and pharmacy researchers, develop a consensus on the types of information that should be reported in the original studies. This will facilitate comparison across studies so that areas that need improvement can be identified. © 2013 Elsevier Inc.

Federated architecture for biomedical data integration

The last decades have been characterized by a continuous adoption of IT solutions in the healthcare sector, which resulted in the proliferation of tremendous amounts of data over heterogeneous systems. Distinct data types are currently generated, manipulated, and stored, in the several institutions where patients are treated. The data sharing and an integrated access to this information will allow extracting relevant knowledge that can lead to better diagnostics and treatments. This thesis proposes new integration models for gathering information and extracting knowledge from multiple and heterogeneous biomedical sources. The scenario complexity led us to split the integration problem according to the data type and to the usage specificity. The first contribution is a cloud-based architecture for exchanging medical imaging services. It offers a simplified registration mechanism for providers and services, promotes remote data access, and facilitates the integration of distributed data sources. Moreover, it is compliant with international standards, ensuring the platform interoperability with current medical imaging devices. The second proposal is a sensor-based architecture for integration of electronic health records. It follows a federated integration model and aims to provide a scalable solution to search and retrieve data from multiple information systems. The last contribution is an open architecture for gathering patient-level data from disperse and heterogeneous databases. All the proposed solutions were deployed and validated in real world use cases.

High body mass index is not a barrier to physical activity: Analysis of international rugby players' anthropometric data

Recent data indicate that levels of overweight and obesity are increasing at an alarming rate throughout the world. At a population level (and commonly to assess individual health risk), the prevalence of overweight and obesity is calculated using cut-offs of the Body Mass Index (BMI) derived from height and weight. Similarly, the BMI is also used to classify individuals and to provide a notional indication of potential health risk. It is likely that epidemiologic surveys that are reliant on BMI as a measure of adiposity will overestimate the number of individuals in the overweight (and slightly obese) categories. This tendency to misclassify individuals may be more pronounced in athletic populations or groups in which the proportion of more active individuals is higher. This differential is most pronounced in sports where it is advantageous to have a high BMI (but not necessarily high fatness). To illustrate this point we calculated the BMIs of international professional rugby players from the four teams involved in the semi-finals of the 2003 Rugby Union World Cup. According to the World Health Organisation (WHO) cut-offs for BMI, approximately 65% of the players were classified as overweight and approximately 25% as obese. These findings demonstrate that a high BMI is commonplace (and a potentially desirable attribute for sport performance) in professional rugby players. An unanswered question is what proportion of the wider population, classified as overweight (or obese) according to the BMI, is misclassified according to both fatness and health risk? It is evident that being overweight should not be an obstacle to a physically active lifestyle. Similarly, a reliance on BMI alone may misclassify a number of individuals who might otherwise have been automatically considered fat and/or unfit.

A Petrov-Galerkin method for a singularly perturbed ordinary differential equation with non-smooth data

In this paper, a singularly perturbed ordinary differential equation with non-smooth data is considered. The numerical method is generated by means of a Petrov-Galerkin finite element method with the piecewise-exponential test function and the piecewise-linear trial function. At the discontinuous point of the coefficient, a special technique is used. The method is shown to be first-order accurate and singular perturbation parameter uniform convergence. Finally, numerical results are presented, which are in agreement with theoretical results.