JANÁK, T., KOHOUT, J. An Efficient Mesh Deformation Method for Mass-Spring Muscle Models. In 15th IEEE International Conference on Bioinformatics and Bioengineering. Piscataway: IEEE Computer Society, 2015. p. 1-6. ISBN 978-1-4673-7983-0
Abstract: This paper will consider a framework for simulation of musculoskeletal system via mass-spring system as the target application. The framework uses a mass-spring systems to simulate the muscle fibres of each muscle and an additional triangle model to visually represent the surface of the muscles. This requires establishing some relationship between the two models so that when some nodes of the mass-spring model move, i.e. the object deforms, this deformation is correctly carried over to the visualization. Mean Value Coordinates are often used for this purpose. In this paper, we will present a simpler method that produces deformation that is visually similar to that by the Mean Value Coordinates while consuming less memory and time.

PAPEŽ, V., MOUČEK, R. Archetypes Development in Electrophysiology Domain - Electroencephalography as a Personal EHR System Module. In HEALTHINF 2015 ? 8th International Conference on Health Informatics. Setúbal: SciTePress, 2015. p. 611-616. ISBN 978-989-758-068-0
Abstract: The work presents the concept of a new personal electronic health record (EHR) system. The system is based on openEHR standards/framework. A fundamental part of openEHR is domain description by two layer modelling - reference data models and archetypes. Archetypes are building blocks of the EHR system, which provide structure and semantics for stored data. As common ontologies and terminologies, even archetypes are based on reusability. Although the public archetype repositories (clinical knowledge managers, CKM) contain hundreds of archetypes from various domains, the electrophysiology domain is not described yet. The work is focused on the development of the archetypes dealing with the electroencephalography domain.

HADERLEIN, T., SCHWEMMLE, C., DÖLLINGER, M., MATOUŠEK, V., PTOK, M., NÖTH, E. Automatic Evaluation of Voice Quality Using Text-Based Laryngograph Measurements and Prosodic Analysis. Computational and Mathematical Methods in Medicine, 2015, Volume neuveden, Issue 6, p. 1-11. ISSN: 1748-670X
Abstract: In this study, text-based, computer-aided prosodic analysis and measurements of connected speech were combined in order to model perceptual evaluation of the German Roughness-Breathiness-Hoarseness (RBH) scheme. 58 connected speech samples (43 women and 15 men; 48.7 ? 17.8 years) containing the German version of the text ?The North Wind and the Sun? were evaluated perceptually by 19 speech and voice therapy students according to the RBH scale. For the human-machine correlation, Support Vector Regression with measurements of the vocal fold cycle irregularities (CFx) and the closed phases of vocal fold vibration (CQx) of the Laryngograph and 33 features from a prosodic analysis module were used to model the listeners? ratings. The best human-machine results for roughness were obtained from a combination of six prosodic features and CFx (? = 0.71, ? = 0.57). These correlations were approximately the same as the interrater agreement among human raters (? = 0.65, ? = 0.61). CQx was one of the substantial features of the hoarseness model. For hoarseness and breathiness, the human-machine agreement was substantially lower. Nevertheless, the automatic analysismethod can serve as the basis for a meaningful objective support for perceptual analysis.

JEŽEK, P., MOUČEK, R., KRAUZ, J., HOŠEK, J., FRANC, Y.L., WACHTLER, T., GREWE, J. Framework for Collection of Electrophysiology Data. In Proceedings of the International Conference on Health Informatics. Setúbal: SciTePress, 2015. p. 558-565. ISBN 978-989-758-068-0
Abstract: Experiments in electrophysiology produce a lot of unstructured metadata collected in electrophysiology databases. The data are usually accessed through a web interface implemented on the top of data model respecting given data format. A lot of experiments are conducted outside the laboratory where access to these databases is not always available. The usage of mobile devices such as tablets or smart phones seems to be a practical solution, but users would welcome the same structured user interface such as they know from a common computer. When user interfaces of electrophysiology databases are tailored to a unique data struc- ture, they cannot be easily reused on a mobile device. As a solution, a mapping of a general data structure to a graphical template is proposed. This mapping is implemented in a framework that generates a template representing the database structure. The parsing process is driven by supplemented annotations added to the code. Next, an Android tool visualizing a graphical layout generated from the template is developed. A use case study is presented on a database of EEG/ERP experiments.

JEŽEK, P., MOUČEK, R. Semantic framework for mapping object-oriented model to semantic web languages. Frontiers in Neuroinformatics, 2015, Volume 9, Issue 3, p. 1-15. ISSN: 1662-5196
Abstract: The article deals with and discusses two main approaches in building semantic structures for electrophysiological metadata. It is the use of conventional data structures, repositories, and programming languages on one hand and the use of formal representations of ontologies, known from knowledge representation, such as description logics or semantic web languages on the other hand. Although knowledge engineering offers languages supporting richer semantic means of expression and technological advanced approaches, conventional data structures and repositories are still popular among developers, administrators and users because of their simplicity, overall intelligibility, and lower demands on technical equipment. The choice of conventional data resources and repositories, however, raises the question of how and where to add semantics that cannot be naturally expressed using them. As one of the possible solutions, this semantics can be added into the structures of the programming language that accesses and processes the underlying data. To support this idea we introduced a software prototype that enables its users to add semantically richer expressions into a Java object-oriented code. This approach does not burden users with additional demands on programming environment since reflective Java annotations were used as an entry for these expressions. Moreover, additional semantics need not to be written by the programmer directly to the code, but it can be collected from non-programmers using a graphic user interface. The mapping that allows the transformation of the semantically enriched Java code into the Semantic Web language OWL was proposed and implemented in a library named the Semantic Framework. This approach was validated by the integration of the Semantic Framework in the EEG/ERP Portal and by the subsequent registration of the EEG/ERP Portal in the Neuroscience Information Framework.

SVOBODOVÁ, M., JIŘÍK, M., VČELÁK, P., LUKEŠ, V., RYBA, T., HOŠEK, P., BAJCUROVÁ, K., LUDVÍK, J., MIRKA, H., TONAR, Z., TŘEŠKA, V., LIŠKA, V. Software LISA ? virtuální resekce jater pro urychlení a usnadnění předoperačního plánování. Rozhledy v chirurgii, 2015, Volume 94, Issue 11, p. 485-490. ISSN: 0035-9351
Abstract: The intent of this paper is a summary of implemented and planned the necessary steps leading to the development of software LISA (Liver Surgery Analyser). Clinically tested software offering in the preoperative phase, radiologists and surgeons called virtual liver resection to facilitate decisions on the type and design of the possible curative treatment.

MAUTNER, P., MOUČEK, R., NOVOTNÝ, J., DUDÁČEK, K. Stimulátor pro neuroinformatické a reaktometrické experimenty. Praha, 2015.
Abstract: Stimulation device for neuroinformatic and reactometric experiments is developed as an external hardware device providing a visual stimulation, acoustic stimulation or combination of these. The aim of this stimulation is to evoke the corresponding brain response (visual, acoustic evoked or event related potentials). Stimulator is also able to process the response from measuring subjects and evaluate the reaction time. Simultaneously with the stimuli presentation the device also generates the synchronization pulses for external EEG or other measuring devices. These pulses are important for processing and analysis of evoked potentials. Stimulation device can be used in all experiments relating to reactometry, measuring evoked response in electrophysiology, neuroinformatics or brain-computer interface systems.

MOUČEK, R., SMITKA, S., JEŽEK, P. Tool Facilitating Construction of Ontologies on the KIM Platform. In HealthINF 2015 ? Proceedings of the International Conference on Health Informatics. Setúbal: SciTePress, 2015. p. 659-665. ISBN 978-989-758-068-0
Abstract: During research based on experimental work vast amounts of data and associated metadata are usually produced. This is also the case of experimental work using the techniques of electroencephalography and event related potentials. The collected data and associated metadata have to be stored, analyzed, and eventually shared among research groups. Besides storing data and metadata from experiments, it is often beneficial to collect additional information from other sources related to the kind of experiment performed. These information sources are mostly scientific and technical publications, manuals describing the used infrastructure, and topical discussions appearing on the web. This article deals with selection and use of a semantic repository for such information sources. Development of a simple prototype ontology is shortly presented and a tool that facilitates construction of ontologies on the KIM platform is described. Sets of test documents are used to verify the functionality of the tool.