Richard Hůlek

Interactive algorithms for teaching and learning acute medicine in the network of medical faculties MEFANET

Background Medical Faculties Network (MEFANET) has established itself as the authority for setting standards for medical educators in the Czech Republic and Slovakia, 2 independent countries with similar languages that once comprised a federation and that still retain the same curricular structure for medical education. One of the basic goals of the network is to advance medical teaching and learning with the use of modern information and communication technologies. Objective We present the education portal AKUTNE.CZ as an important part of the MEFANET’s content. Our focus is primarily on simulation-based tools for teaching and learning acute medicine issues. Methods Three fundamental elements of the MEFANET e-publishing system are described: (1) medical disciplines linker, (2) authentication/authorization framework, and (3) multidimensional quality assessment. A new set of tools for technology-enhanced learning have been introduced recently: Sandbox (works in progress), WikiLectures (collaborative content authoring), Moodle-MEFANET (central learning management system), and Serious Games (virtual casuistics and interactive algorithms). The latest development in MEFANET is designed for indexing metadata about simulation-based learning objects, also known as electronic virtual patients or virtual clinical cases. The simulations assume the form of interactive algorithms for teaching and learning acute medicine. An anonymous questionnaire of 10 items was used to explore students’ attitudes and interests in using the interactive algorithms as part of their medical or health care studies. Data collection was conducted over 10 days in February 2013. Results In total, 25 interactive algorithms in the Czech and English languages have been developed and published on the AKUTNE.CZ education portal to allow the users to test and improve their knowledge and skills in the field of acute medicine. In the feedback survey, 62 participants completed the online questionnaire (13.5%) from the total 460 addressed. Positive attitudes toward the interactive algorithms outnumbered negative trends. Conclusions The peer-reviewed algorithms were used for conducting problem-based learning sessions in general medicine (first aid, anesthesiology and pain management, emergency medicine) and in nursing (emergency medicine for midwives, obstetric analgesia, and anesthesia for midwifes). The feedback from the survey suggests that the students found the interactive algorithms as effective learning tools, facilitating enhanced knowledge in the field of acute medicine. The interactive algorithms, as a software platform, are open to academic use worldwide. The existing algorithms, in the form of simulation-based learning objects, can be incorporated into any educational website (subject to the approval of the authors).

GENASIS Information System: A Global Environmental Assessment of Persistent Organic Pollutants

Global ENvironmental ASsessment and Information System (GENASIS) is a tool developed by expert teams of the Research Centre for Toxic Compounds in the Environment (RECETOX) and the Institute for Biostatistics and Analyses (IBA) of the Masaryk University in Brno. The aim of GENASIS is to compile validated data on persistent organic pollutants, including their properties, sources, long-term levels, life times, transport mechanisms, effects and risks, scattered throughout various institutions and ministries, and to provide tools for their visualization, analyses, interpretation, assessment of environmental and human risks or modelling of fate. Such a tool should significantly enhance comprehensive understanding of the fate of POPs in the environment, their impacts on ecosystem and the human population.

Integration of R Statistical Environment into ICT Infrastructure of GMP and GENASIS

The Global Monitoring Plan (GMP) was established as a tool for providing a worldwide overview of Stockholm Convention (SC) compliance by monitoring and evaluation of SC 22 persistent organic pollutants (POPs) concentration levels and their trends. In order to evaluate a dataset on POPs concentrations from the initial GMP campaign, it was essential to use advanced statistical methods which are not incorporated in commonly used database languages. Instead of a complete realization of these methods in the main programming language, in which the application is developed, this language was used only as an interface to the server version of the powerful statistical software R. The involvement of the R language into the environmental pollution data assessment infrastructure of the Global Environmental Assessment Information System (GENASIS) adopted for the GMP data makes easier to avoid disambiguities in data analysis and brings a powerful tool for advanced statistical analysis and visualization of GMP and GENASIS data.

Three Levels of R Language Involvement in Global Monitoring Plan Warehouse Architecture

Three different options for involving R statistical software in the infrastructure of the data warehouse and visualization tool of the Global Monitoring Plan for persistent organic pollutants are presented, all differing in their demands with respect to data transfer rates, numbers of concurrently connected users, total amounts of data transferred, and the possibilities of repeating statistical calculations within a short period. After the development stage, two of these options were used at different levels of the system, demonstrating the specificity of their use and enabling the deployment of the powerful features of R statistical software by a system created using conventional programming languages.

GENASIS System Architecture

GENASIS (Global ENvironmental ASsessment and Information System) is the web environmental information system which is an environmental data repository that provides comprehensive information on chemical contamination of the environment by Persistent Organic Pollutants (POPs). GENASIS combines data from long-term environmental monitoring programmes operated by RECETOX with validated data from partner institutions, and provides data archives, data management services and analytical processing of data. In the past few years the GENASIS system has undergone rapid development and grew up from the data repository into a scientific data infrastructure.

GMP Data Warehouse – a Supporting Tool of Effectiveness Evaluation of the Stockholm Convention on Persistent Organic Pollutants

The Stockholm Convention on Persistent Organic Pollutants is multilateral environmental agreement focused on selected persistent organic pollutants (POPs) for which the contracting Parties must adopt measures to eliminate or reduce their production and use or minimise the unintentional releases. One of the tools for the effectiveness evaluation of the Stockholm Convention is Global Monitoring Plan for Persistent Organic Pollutants (GMP) – a project that aims to collect global data on POPs concentrations in selected environmental matrices. This paper introduces an information system GMP Data Warehouse, which was developed in order to provide user-friendly tools for the collection, storage, analyses and visualisation of data from international POPs monitoring activities.

Estimating Impacts of Environmental Interventions in Monitoring Programs Requires Conceptual Data Models and Robust Statistical Processing

This paper discusses main problems associated with evaluation of performance and impact of long-term environmental programs. Lack of data standards, incompleteness of archived datasets and insufficient statistical power were identified as main limits in functionality of monitoring networks. To avoid these failures, environmental programs should be designed with inception to incorporate data management as their integral part. Especially in global programs, local and regional data managers should invest significant proportion of their effort to handle documentation in terms of standardized coding, data formats, metadata coding and consistency of records over time. Up-to-date trends in building knowledge-based infrastructures are illustrated using example of monitoring of atmospheric pollution by persistent organic pollutants (POPs). Conceptual model usable to facilitate the integration and analysis of data on POPs concentrations is introduced with its multilayer hierarchy of entities (POPs as nomenclature classes, couples “observation – measurement” as content classes). Robust set of statistical methods for processing of time series of concentration data is discussed from the viewpoint of practical implementation within running monitoring programs. It consists of the following components: baseline pollution estimates, uncertainty analyses, spatial extrapolations, effect size estimates, time trend identification and quantification. Development of tools supporting standardized environmental data management is rapidly expanding field of science which results in the following challenges for applied informatics and statistics: log-term sustainability of information systems, data-related metadata coding and archiving, tools for automated integration and reporting of data.

GENASIS: On-Line Data Browser for Environmental Monitoring and Associated Information Systems

The current environmental research is producing large quantities of data on all environmental matrices and number of chemical and biological endpoints. However, there is a paradox in this situation that we suffer from lack of representative data, since their production has not been accordingly supported by development of systems that make them accessible for analysis. The introduced GENASIS data browser aims in its current version on the problem of persistent organic pollutants and the analysis, visualization and interpretation of data from their monitoring networks. The development of the GENASIS involves problems of the so called information pyramid: monitoring (obtaining environmental data), data validation (including uncertainty quantification), data analysis, and methods of aggregation of data from different sources, model generalization and interpretation of results, and their presentation. Within the frame of the GENASIS data browser, we introduce a user-friendly system for the visualization and analysis of contamination of all environmental compartments by persistent organic pollutants and evaluation of actual POPs contamination, its long-term trends and seasonal fluctuations. Project outcomes are useful as information source both for lay public and experts, as well as for the process of the Stockholm Convention implementation.

Tools for Collection, Analysis and Visualization of Data from the Stockholm Convention Global Monitoring Plan on Persistent Organic Pollutants

The Global Monitoring Plan for persistent organic pollutants is an important component of the effectiveness evaluation of the Stockholm Convention and its main objective is assessment of long-term changes in POPs concentrations in core matrices – ambient air and human tissues (milk, blood). This paper summarizes results of activities of the Research Centre for Toxic Compounds in the Environment and the Institute of Biostatistics and Analyses, Masaryk University, Czech Republic, which have been performed on the basis of the mandate given by Global Coordination Group for GMP and Secretariat of the Stockholm Convention: content analysis of the GMP monitoring reports published in 2009, on-line visualization tool for browsing and analyzing collected data from the monitoring reports, and proposal of a design of future data collection campaigns.