2015

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.

2014

MOUČEK, R., KOŠAŘ, V. Attention of Driver during Simulated Drive. In HEALTHINF 2014. Setúbal: SciTePress, 2014. p. 543-550. ISBN 978-989-758-010-9
Abstract: Attention of drivers is a key factor of road safety. Since inattentive drivers cause a considerable number of accidents, it is worth to examine the causes and course of driver's attention even in laboratory conditions during a simulated drive. This paper deals with the experiment in which the methods of electroencephalography and event related potentials are used under various conditions to investigate driver's attention. Eleven participants, university students, were stimulated with audio signals during monotonous drive in four experimental sessions. The hypothesis is that the peak latency of the P3 component increases in time as the driver is more tired from monotonous drive, daytime and sleep deprivation. The background of the used methods, experimental design, participants, data processing, results and final discussion are presented in this paper.

HOLEČKOVÁ, I., ČEPIČKA, L., MAUTNER, P., ŠTĚPÁNEK, D., MOUČEK, R. Auditory ERPs in children with developmental coordination disorder. Activitas Nervosa Superior, 2014, Volume 56, Issue 1-2, p. 37-44. ISSN: 1802-9698
Abstract: The study deals with investigation and comparison of the auditory attention performance of children with developmental coordination disorder (DCD) and normally developing children (NDC) using cognitive evoked potentials (ERPs) in passive conditions. ERPs data showed that children with DCD have less ability to detect small physical differences between acoustic stimuli (no MMN response in DCD children) and have a reduced attentional engagement and stimulus evaluation of salient stimuli (a reduction of P3 amplitude in DCD children). The results of our study suggest that children with DCD do not only suffer from a visuospatial attention deficit as previous studies reported but also have auditory attention deficit.

KOUTNÝ, T. Blood glucose level reconstruction as a function of transcapillary glocose transport. Computers in Biology and Medicine, 2014, Volume 53, Issue 1, p. 171-178. ISSN: 0010-4825
Abstract: A diabetic patient occasionally undergoes a detailed monitoring of their glucose levels. Over the course of a few days, a monitoring system provides a detailed track of their interstitial fluid glucose levels measured in their subcutaneous tissue. A discrepancy in the blood and interstitial fluid glucose levels is unimportant because the blood glucose levels are not measured continuously. Approximately five blood glucose level samples are taken per day, and the interstitial fluid glucose level is usually measured every 5 min. An increased frequency of blood glucose level sampling would cause discomfort for the patient; thus, there is a need for methods to estimate blood glucose levels from the glucose levels measured in subcutaneous tissue. The Steil-Rebrin model is widely used to describe the relationship between blood and interstitial fluid glucose dynamics. However, we measured glucose level patterns for which the Steil-Rebrin model does not hold. Therefore, we based our research on a different model that relates present blood and interstitial fluid glucose levels to future interstitial fluid glucose levels. Using this model, we derived an improved model for calculating blood glucose levels. In the experiments conducted, this model outperformed the Steil-Rebrin model while introducing no additional requirements for glucose sample collection. In subcutaneous tissue, 26.71% of the calculated blood glucose levels had absolute values of relative differences from smoothed measured blood glucose levels less than or equal to 5% using the Steil-Rebrin model. However, the same difference interval was encountered in 63.01% of the calculated blood glucose levels using the proposed model. In addition, 79.45% of the levels calculated with the Steil-Rebrin model compared with 95.21% of the levels calculated with the proposed model had 20% difference intervals.

JANÁK, T., KOHOUT, J. Deformable Muscle Models for Motion Simulation. In Proceedings of the 9th International Conference on Computer Graphics Theory and Applications. Setúbal: SciTePress, 2014. p. 301-311. ISBN 978-989-758-002-4
Abstract: This paper presents a methodology for interactive muscle simulation. The fibres of individual muscles are represented by particles connected by springs, thus creating a deformable model of the muscle. In order to be able to describe human musculoskeletal system, contact between pairs of muscles as well as muscles and bones must be accounted for. Therefore, collision detection and response mechanism which allows both types of contact (soft body vs. rigid body and soft vs. soft body) is presented. The solution is a part of a project dedicated to improvement of the effectiveness of osteoporosis prediction and treatment.

ŠTĚBETÁK, J., MOUČEK, R., KOREŇ, J. Desing of Full-text Search for Database and Linkedin Social Network in Electrophysiology. In Proceedings of the International Conference on Health Informatics. Setúbal: SciTePress, 2014. p. 238-243. ISBN 978-989-758-010-9
Abstract: EEG/ERP (electroencephalography, event-related potential) laboratories produce experimental data and metadata. Authors' research group has contributed to the building of a neuroinformatics infrastructure by developing and integrating data management and analytic tools for EEG/ERP research - the EEG/ERP Portal. With the development of the Portal and the increasing amount of data/metadata, a proper full text search mechanism for efficient information retrieval is necessary to improve the user experience. The presented solution combines search over data/metadata stored in an electrophysiological database and in the LinkedIn social network. Open source search engines, criteria, suitable engine selection, and index design are presented. Integration of the full-text solution to the EEG/ERP Portal is described.

VAŘEKA, L., BRŮHA, P., MOUČEK, R. Event-related potential datasets based on a three-stimulus paradigm. GigaScience, 2014, Volume 3, Issue 1, p. 1-5. ISSN: 2047-217X
Abstract: The event-related potentials technique is widely used in cognitive neuroscience research. The P300 waveform has been explored in many research articles because of its wide applications, such as lie detection or brain-computer interfaces (BCI). However, very few datasets are publicly available. Therefore, most researchers use only their private datasets for their analysis. This leads to minimally comparable results, particularly in brain-computer research interfaces. Here we present electroencephalography/event-related potentials (EEG/ERP) data. The data were obtained from 20 healthy subjects and was acquired using an odd-ball hardware stimulator. The visual stimulation was based on a three-stimulus paradigm and included target, non-target and distracter stimuli. The data and collected metadata are shared in the EEG/ERP Portal

KOUTNÝ, T. Experience with Lamport Clock Ordered Events with Intel Threading Building Blocks in a Glucose-Level Prediction Software. In IWBBIO 2014. Granada: Copicentro Granada S.L, 2014. p. 515-526. ISBN 978-84-15814-84-9
Abstract: Software tool was needed to verify a model predicting interstitial fluid glucose level, while conducting an experiment. With the tool, several tasks execute concurrently to effectively utilize available processors. Implementing the tool implied addressing such aspects of parallel computing which possibly have a broader impact. In this paper, I present an experience with implementing Lamport-clock ordered event scheme to control a parallel program employing a task-stealing scheduler, while eliminating the possibility of accidentally masking a synchronization error. For a program based on Intel Threading Building Blocks library, I devised a scheme to control task execution with events. These events are ordered using the concept of Lamport Clock. As the causal ordering of events is complete , program?s behavior can be reconstructed for additional debugging. In the implementation devised, recording theevents induces no additional synchronization operations that could accidentally mask a synchronization error. The work is presented in a context of glucose level prediction that originates from a glucose-transporter research.

VARNUŠKOVÁ, J., KOHOUT, J. Human Body Model Movement Support: Automatic Muscle Control Curves Computation. In Combinatorial Image Analysis. Heidelberg: Springer, 2014. p. 196-211. ISBN 978-3-319-07147-3 , ISSN: 0302-9743
Abstract: In this paper we present a novel approach of an automatic computation of muscle control curves. It is based on skeletonization of a triangular surface mesh representing the muscle. Automatically determined control curves are then connected to the skeleton of the human body model so as to govern the deformation of the muscle surface when the skeleton moves. The method, which was implemented in C++ using VTK framework, was integrated into the human body framework being developed at our institution and tested on the walking lower limbs. The results show that the control curves produced by the method have a positive effect on the deformation and, therefore, are preferred to manually defined lines of action that are used as control curves in the human body framework at present.

ŠTĚBETÁK, J., MOUČEK, R. Model of Syntactic Compatibility in Worksflows for Electrophysiology. In Proceedings of the International Conference on Health Informatics. Setúbal: SciTePress, 2014. p. 442-446. ISBN 978-989-758-010-9
Abstract: Large amounts of EEG/ERP (electroencephalography, event-related potential) data are produced by scientific laboratories. For complex analysis, data are processed by a set of methods sequentially or in parallel. These processes are known as workflows. However, various input/output formats of used methods involve difficulties while putting methods in a pipe. Simple syntactic rules comparing formats of input/output are already used by workflow engines. In electrophysiology, it is necessary to extend these rules due to variety of methods. Therefore, extension of syntactic rules between subsequent methods in a workflow is presented in this paper. The proposed solution allows creating more complex workflows in the domain of electrophysiology.

JEŽEK, P., MOUČEK, R., DANĚK, J. MongoDB for Electrophysiology Experiments. In Proceedings of the International Conference on Health Informatics. Setúbal: Scitepress, 2014. p. 422-427. ISBN 978-989-758-010-9
Abstract: Many efforts are devoted to provide a unified solution for maintaining data from electrophysiological experiments. Because large data collections of heterogeneous nature are obtained, neuroinformatics databases must be robust and flexible. Current database systems are of two types. The first one uses a fixed schema while the second one is schema free. This paper discusses usage of a NoSQL database, MongoDB, for electrophysiological experiments and investigates transformation of existing electroencephalography (EEG) and event-related potentials (ERP) database records in Oracle into MongoDB. Two perspectives, flexibility and performance are discussed. A final approach that profits from combination of both concepts, is also discussed.

VČELÁK, P., KRATOCHVÍL, M., KLEČKOVÁ, J. Ontology-driven Information System and Management of Heterogeneous Research Data. In The 2014 7th International Conference on BioMedical Engineering and Informatics. Piscataway: IEEE, 2014. p. 766-770. ISBN 978-1-4799-5837-5
Abstract: We adopt an ontology-driven information system design for research purposes. It is adaptable and extensible solution in the situation where the main features are the lack of a stable data model and changing and varying requests. We use ontology-driven design primarily as a collaboration tool for the research. Members directly collaborate and use this information system to ease them tasks with management of source/raw data, software applications and research results for its whole life-time. A different heterogeneous data kinds and a large volume data sets could be stored and shared together with its description meta data between research teams and its members in an uniform manner. It leads to an opportunity to process a stored data using proper methods and tools in a parallel and distributed computing environment. All achieved results are automatically stored and supplemented by an ontology-driven description meta data.

PROKOP, T., MOUČEK, R. P3 Component Detection Using HHT Improvement of EMD with Additional Stopping Criteria. In Brain Informatics and Health. Heidelberg: Springer, 2014. p. 100-110. ISBN 978-3-319-09890-6 , ISSN: 0302-9743
Abstract: This paper describes improvement of the Hilbert-Huang transform (HHT) for detection of ERP components in the EEG signal. Time-frequency domain methods, such as the wavelet transform or matching pursuit, are commonly for this task. We used a modified Hilbert-Huang transform that allows the processing of quasi-stationary signals such as EEG. The essential part of the HHT is an Empirical Mode Decomposition (EMD) that decomposes signal into intrinsic mode functions (IMFs). We designed additional stopping criteria for better selection of IMFs in the EMD. These IMFs positively affect later computed instantaneous attributes and increase classification success. We tested the influence of additional stopping criteria on classification reliability using the real EEG data acquired in our laboratory. Our results demonstrated that we were able to detect the P3 component by using the HHT with additional stopping criteria more successfully than by using the original implementation of modified HHT, continuous wavelet transform and matching pursuit.

KOHOUT, J., KUKAČKA, M. Real-time Modelling of Fibrous Muscle. Computer Graphics Forum, 2014, Volume 33, Issue 8, p. 1-15. ISSN: 0167-7055
Abstract: Relatively recently it has become apparent that providing human kind with a better healthcare requires personalised, predictive and integrative medicine, for which the building of Virtual Physiological Human (VPH) framework accessible via virtual patient avatar is necessary. Real-time modelling and visual exploration of such a complex avatar is a challenging task. In this paper, we propose a real-time method for automatic modelling of an arbitrarily large number of muscle fibres in the volume of a muscle represented by its surface mesh. The method is based on an iterative morphing of predefined fibres template into the muscle volume exploiting harmonic scalar field computed on the surface of muscle. Experiments with muscles of thighs and pelvis show that the method produces realistic shapes of fibres. Our sequential VTK-based C++ implementation is capable of producing 64 fine fibres within a muscle of 10K triangles in less than 170 ms on commodity hardware making the method suitable for VPH purposes as well as for interactive educational medical software.

VAŘEKA, L., MAUTNER, P. Self-organizing Maps for Event-Related Potential Data Analysis. In Healthinf 2014 - Proceedings of the international conference on health informatics. Setúbal: SciTePress, 2014. p. 387-392. ISBN 978-989-758-010-9
Abstract: Event-related potentials (ERPs) and especially the P300 component have been gaining attention in braincomputer interface design and neurobiological research. The detection of the P300 component in electroencephalographic signal is challenging since its signal-to-noise ratio is very low. Instead of using traditional supervised pattern recognition, this paper discusses using unsupervised neural networks for the P300 classification purposes. To validate the proposed approach, a method for the P300 detection based on matching pursuit and self-organizing maps is proposed and evaluated. The results may be applied to the design of brain-computer interfaces.

MOUČEK, R., JEŽEK, P., VAŘEKA, L., ŘONDÍK, T., BRŮHA, P., PAPEŽ, V., MAUTNER, P., NOVOTNÝ, J., PROKOP, T., ŠTĚBETÁK, J. Software and hardware infracstructure for research in electrophysiology. Frontiers in Neuroinformatics, 2014, Volume 8, Issue 20, p. 1-15. ISSN: 1662-5196
Abstract: As in other areas of experimental science, operation of electrophysiological laboratory, design and performance of electrophysiological experiments, collection, storage and sharing of experimental data and metadata, analysis and interpretation of these data, and publication of results are time consuming activities. If these activities are well organized and supported by a suitable infrastructure, work efficiency of researchers increases significantly. This article deals with the main concepts, design, and development of software and hardware infrastructure for research in electrophysiology. The described infrastructure has been primarily developed for the needs of neuroinformatics laboratory at the University of West Bohemia, the Czech Republic. However, from the beginning it has been also designed and developed to be open and applicable in laboratories that do similar research. After introducing the laboratory and the whole architectural concept the individual parts of the infrastructure are described. The central element of the software infrastructure is a web-based portal that enables community researchers to store, share, download and search data and metadata from electrophysiological experiments. The data model, domain ontology and usage of semantic web languages and technologies are described. Current data publication policy used in the portal is briefly introduced. The registration of the portal within Neuroscience Information Framework is described. Then the methods used for processing of electrophysiological signals are presented. The specific modifications of these methods introduced by laboratory researches are summarized; the methods are organized into a laboratory workflow. Other parts of the software infrastructure include mobile and offline solutions for data/metadata storing and a hardware stimulator communicating with an EEG amplifier and recording software.

VAŘEKA, L., MAUTNER, P. Using the Windowed Means paradigm for Single Trial P300 Detection. In 2014 TSP. Brno: VUT Brno, 2014. p. 499-502. ISBN 978-80-214-4983-1 , ISSN: 1805-5435
Abstract: The Windowed means paradigm is a method for slow-changing cortical potentials feature extraction, most importantly in reaction to events. It has been successfully used for various brain-computer interfaces. The objective of this paper was to evaluate if this paradigm is also appropriate for P300 brain-computer interfaces. The modified method was tested on five healthy subjects. The optimal selection of parameters was discussed. The Windowed means paradigm was successful for the P300 detection on the testing data-set.

2013

MAHDIAN, N., DOSTÁLOVÁ, T., DANĚK, J., NEDOMA, J., KOHOUT, J., HUBÁČEK, M., HLIŇÁKOVÁ, P. 3D reconstruction of TMJ after resection of the cyst and the stress-strain analyses. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE, 2013, Volume 110, Issue 3, p. 279-289. ISSN: 0169-2607
Abstract: The aim of this article is 3D analysis of the temporomandibular joint patient, who underwent surgery, during which the right TMJ was resected along with the ramus of mandible and consequently the joint was reconstructed with subtotal replacement.

KOHOUT, J., CHIARINI, A., CLAPWORTHY, G. J., KLAJNŠEK, G. Aneurysm identification by analysis of the blood-vessel skeleton. Computer Methods and Programs in Biomedicine, 2013, Volume 109, Issue 1, p. 32-47. ISSN: 0169-2607
Abstract: At least 1% of the general population have an aneurysm (or possibly more) in their cerebral blood vessels. If an aneurysm ruptures, it kills the patient in up to 60% of cases. In order to choose the optimal treatment, clinicians have to monitor the development of the aneurysm in time. Nowadays, aneurysms are typically identified manually, which means that the monitoring is often imprecise since the identification is observer dependent. As a result, the number of misdiagnosed cases may be large. This paper proposes a fast semi-automatic method for the identification of aneurysms which is based on the analysis of the skeleton of blood vessels. Provided that the skeleton is accurate, the results achieved by our method have been deemed acceptable by expert clinicians.

MAULE, P., KLEČKOVÁ, J., ROHAN, V., TUPÝ, R. Automated infarction core delineation using cerebral and perfused blood volume maps. nternational Journal of Computer Assisted Radiology and Surgery, 2013, Volume 8, Issue 5, p. 787-797. ISSN: 1861-6410
Abstract: Detection of infarction core areas at patiens with ischemic stroke using computed tomography Cere-bral Blood Volume (CBV) or Perfused Blood Volume (PBV) maps. This article presents an automated method reaching better specificity allowing measuring of the infarction core volume which can serve as another criteria for physicians helping them with thrombolytical treatment indication decisions.

ŘONDÍK, T., MAUTNER, P. Cognitive Event-Related Potential Waveform Latency Determination. In BMEI 2013. Piscataway: IEEE, 2013. p. 209-214. ISBN 978-1-4799-2760-9
Abstract: According to the statistics of car accident causes [11] given by Police of the Czech Republic, about 17.5 % of all car accidents are caused by lack of dedication to driving, including microsleep. A lot of car factories develop systems for fatigue prediction and microsleep detection. These systems are usually based on eye movement tracking or steering wheel movement analysis. But both these methods detect consequences of fatigue. From road safety point of view, it would be useful to be able to detect fatigue itself before it affects dedication to driving. We know there could be a correlation between cognitive eventrelated potential (ERP) waveform latency and the rate of attention ? the longest the latency is, the more tired the measured subject is. This paper deals with determination of latency of a cognitive ERP waveform from outputs of two algorithms we use for its detection and which we have the best experience with.

VČELÁK, P., KRATOCHVÍL, M., KLEČKOVÁ, J. Collaboration and Research Information System Used for Sustainable Long-Term Research. In WCSE 2013. Los Alamitos: IEEE, 2013. p. 307-310. ISBN 978-1-4799-2883-5
Abstract: We have to deal with some crucial difficulties when more teams collaborate in a couple of research areas at the same time. These difficulties complicates our long-term medical research and its sustainability. Each researcher use quite different data, use different tools and develops its own advanced methods for data processing. Without a commonly accepted rules there were a lot of misunderstanding, data loss or even software methods loss. Research Information System is primarily used for members collaboration and managing source data, software and research results for its life-time.

PAPEŽ, V., MOUČEK, R. Data and Metadata Models in Electrophysiology Domain. In Proceedings 2013 IEEE International Conference on Bioinformatics and Biomedicine. Piscataway: IEEE, 2013. p. 539-543. ISBN 978-1-4799-1309-1
Abstract: Increasing requirements on data sharing in the domain of electrophysiology lead to proposing new terminologies and data models. A current trend is to describe data by ontologies and semantic web resources. However, classic technologies and models cannot be replaced in a short time. Due to this, dependencies between various data models should be explicitly described and properties, which the models have in common, should be unified. This work summarizes the current state in data modeling. It describes various ways to model and store data and transformation mechanisms between data models. It deals with well-known concepts (relational and object oriented model) as well as with emerging concepts (ontologies). Finally, the hierarchical metadata model consisting of levels with different expressive power is introduced.

KOHOUT, J., CLAPWORTHY, G.J., MARTELLI, S., VICECONTI, M. Fast Realistic Modelling of Muscle Fibres. In Computer Vision, Imaging and Computer Graphics, Theory and Application. Heidelberg: Springer, 2013. p. 33-47. ISBN 978-3-642-38240-6 , ISSN: 1865-0929
Abstract: This paper describes a method that represents a muscle by a realistic chaff of muscle fibres that are automatically generated in the volume defined by the surface mesh of the muscle which itself automatically wraps around bones as they move. Our C++ implementation can decompose the volume into muscle fibres, which is done by a slice-by-slice morphing of predefined fibres template into the muscle volume, and visualise the result in only about 1000 ms on commodity hardware. Hence, the method is fast enough to be suitable for interactive educational medical software. Although a biomechanical assessment has yet to be done, we believe that the method could be used also in clinical biomechanical applications to extract information on the current muscle lever arm and fibre path and, thanks to its rapid processing speed, it might be an attractive alternative to current methods.

KOUTNÝ, T. Glucose predictability, blood capillary permeability, and glucose utilization rate in subcutaneous, skeletal muscle, and visceral fat tissues. Computers in Biology and Medicine, 2013, Volume 48, Issue 11, p. 1680-1686. ISSN: 0010-4825
Abstract: This study suggests an approach for the comparison and evaluation of particular compartments with modest experimental setup costs. A glucose level prediction model was used to evaluate the compartment's glucose transport rate across the blood capillary membrane and the glucose utilization rate by the cells. The glucose levels of the blood, subcutaneous tissue, skeletal muscle tissue, and visceral fat were obtained in experiments conducted on hereditary hypertriglyceridemic rats. After the blood glucose level had undergone a rapid change, the experimenter attempted to reach a steady blood glucose level by manually correcting the glucose infusion rate and maintaining a constant insulin infusion rate. The interstitial fluid glucose levels of subcutaneous tissue, skeletal muscle tissue, and visceral fat were evaluated to determine the reaction delay compared with the change in the blood glucose level, the interstitial fluid glucose level predictability, the blood capillary permeability, the effect of the concentration gradient, and the glucose utilization rate. Based on these data, the glucose transport rate across the capillary membrane and the utilization rate in a particular tissue were determined. The rates obtained were successfully verified against positron emission tomography experiments. The subcutaneous tissue exhibits the lowest and the most predictable glucose utilization rate, whereas the skeletal muscle tissue has the greatest glucose utilization rate. In contrast, the visceral fat is the least predictable and has the shortest reaction delay compared with the change in the blood glucose level. The reaction delays obtained for the subcutaneous tissue and skeletal muscle tissue were found to be approximately equal using a metric based on the time required to reach half of the increase in the interstitial fluid glucose level.

KOUTNÝ, T. Glucose-Level Interpolation for Determining Glucose Distribution Delay. In MEDICON 2013. Heidelberg: Springer, 2013. p. 1229-1232. ISBN 978-3-319-00845-5 , ISSN: 1680-0737
Abstract: As a part of research on glucose transporters, I already proposed a hypothesis that the change of the blood glucose level includes information about the estimated rate with which the hypothalamus expects the blood glucose level to return to normal range, by means of regulatory mechanisms of glucose homeostasis. As the interstitial glucose level change reflects the blood glucose level change, I proposed a method to estimate the blood-to-interstitial glucose level delay prior formulating the hypothesis. For the estimation, measured glucose levels can be either approximated or interpolated. Each method has its pros and cons. However, the estimated delay converges into narrower bounds, as more glucose levels are measured, if the measured glucose levels are interpolated. In this paper, I present further details on the interpolation method which were not presented in previously published papers.

JEŽEK, P., MOUČEK, R. Mobile system for collecting EEG/ERP data and metadata. In MobileMed 2013. Praha: ČVUT Praha, 2013. p. 1-3.
Abstract: A lot of laboratories deal with management of experimental data. When experiments are conducted inside the laboratory, their results and their data/metadata are immediately stored using a common computer connected to the Internet. On the other hand, situations when the computer is not available, are frequent. It includes e. g. work outside the laboratory or discussions during scientific meetings. This work describes an android-based system developed to enable management of experiments outside the laboratory. Collected experiments are synchronized with a system intended for a long term storage and management of experimental data/metadata - the EEG/ERP Portal.

JEŽEK, P., ŠTĚBETÁK, J., BRŮHA, P., MOUČEK, R. Model of Software and Hardware Infrastructure for Electrophysiology. In 6th International Conference on Health Informatics. Setúbal: SciTePress, 2013. p. 352-356. ISBN 978-989-8565-37-2
Abstract: Large amounts of EEG/ERP (electroencephalography, event-related potential) data, various data formats and non-standardized domain description lead to incompatible results and interpretations of EEG/ ERP experimental data/metadata and to difficult communication between interested laboratories. Authors' research group has solved these problems and has contributed to the building of a neuroinformatics infrastructure by developing and integrating data management and analytic tools for EEG/ERP research. The model of the software and hardware infrastructure for electrophysiology, and the context and architecture of the developed EEG/ERP Portal, serving to manage, share and process EEG/ERP experiments, are presented. Other additional tools are briefly described.

HÁJKOVÁ, J., KOHOUT, J. Musculoskeletal System Modelling. In GRAPP 2013. Setúbal: SciTePress, 2013. p. 73-78. ISBN 978-989-8565-46-4
Abstract: In this paper we present an interpolation method that was derived from the muscle deformation algorithm computed on the gradient domain deformation technique. The method uses linear constraints to preserve the local shape of the muscle and the non-linear volume constraints to preserve the volume of the mesh. The Gauss-Newton method with Lagrange multipliers is used as the main computation algorithm and the interpolation approach serves especially to smooth up deformation steps. Thanks to the interpolation of main bones movement positions by several temporally interpositions, the large distances are optimized and the muscles of the musculoskeletal model are deformed in a more realistic way. The method was implemented in C++ language, using VTK framework and was integrated into the human body framework. Despite the fact that the current implementation is not optimised, all muscles tested were processed in a few minutes on commodity hardware, which is much faster in comparison with the traditional FEM approaches.

VAŘEKA, L., MAUTNER, P. Off-line Analysis of the P300 Event-Related Potential using Discrete Wavelet Transform. In TSP 2013. Piscataway: IEEE, 2013. p. 569-572. ISBN 978-1-4799-0404-4
Abstract: The P300 component is an event-related potential associated with the process of decision making. Its accurate detection in electroencephalographic signal is essential for P300-based brain-computer interfaces. This paper proposes a new method for the P300 detection based on discrete wavelet transform. Its benefits were tested with five healthy subjects using voting classification algorithm. The accuracy of 74.4% was achieved for single trials and over 90% accuracy for averaging.

KOHOUT, J., CLAPWORTHY, G. J., ZHAO, Y., TAO, Y., GONZALEZ-GARCIA, G., DONG, F., WEI, H., KOHOUTOVÁ, E. Patient-specific fibre-based models of muscle wrapping. Interface Focus, 2013, Volume 3, Issue 2, p. 1-8. ISSN: 2042-8898
Abstract: In many biomechanical problems, the availability of a suitable model for the wrapping of muscles when undergoing movement is essential for the estimation of forces produced on and by the body during motion. This is an important factor in the VPHOP project which is investigating the likelihood of fracture for osteoporotic patients undertaking a variety of movements. The weakening of their skeletons makes them particularly vulnerable to bone fracture caused by excessive loading being placed on the bones, even in simple everyday tasks. This paper provides an overview of a novel volumetric model that describes muscle wrapping around bones and other muscles during movement and which includes a consideration of how the orientations of the muscle fibres change during the motion. The method can calculate the form of wrapping of a muscle of medium size and visualize the outcome within tenths of seconds on commodity hardware, while conserving muscle volume. This makes the method suitable not only for educational biomedical software but also for clinical applications used to identify weak muscles that should be strengthened during rehabilitation or to identify bone stresses in order to estimate the risk of fractures.

VAŘEKA, L., BRŮHA, P., MOUČEK, R. Single Channel Eye-Blinking Artifacts Detections. In 2013 International Conference on Applied Electronics. Plzeň: ZČU v Plzni, 2013. p. 313-316. ISBN 978-80-261-0166-6 , ISSN: 1803-7232
Abstract: For neurophysiological data sharing, it is vital for researchers to validate their data from different perspectives. Detection of eye artifacts is especially important since the artifacts may distort the data to an unacceptable extent. Most methods for their correction either require EOG channels or they are very time consuming. This paper proposes a fast method that does not require EOG channels. It outperforms amplitudebased methods in accuracy and Independent Component Analysis in computational complexity.

2012

ŠTĚBETÁK, J., MOUČEK, R. Analytic Tools and Workflows for EEG/ERP Domain. In BMEI 2012. Los Alamitos: IEEE, 2012. p. 998-1000. ISBN 978-1-4673-1182-3
Abstract: EEG/ERP (electroencephalography, event related potential) laboratories produce experimental data and metadata. Large amounts of data and various data formats lead to incompatible results and difficult communication among laboratories. Authors' research group has contributed to the building of a neuroinformatics infrastructure by developing and integrating data management and analytic tools for EEG/ERP research. In addition, a module integrated within the EEG/ERP Portal allowing to process experimental data using analytic tools is developed. An integration of the EEG/ERP Portal with other systems is ensured using web services.

MAULE, P., KLEČKOVÁ, J., ROHAN, V., TUPÝ, R. Automated Infarction Core Delineation. In ICCGI 2012. Wilmington: IARIA, 2012. p. 127-130. ISBN 978-1-61208-202-8
Abstract: This article is focused on development of a tool supporting physicians with an appropriate treatment decisions at patients with acute ischemic stroke. The automated tools for infarction core area delineation could provide important information about the volume of the infarction core. This article describes such automated method results used on both cerebral and perfusion blood volume computed tomography maps compared with manual infarction core delineations made by two physicians.

POLÍVKA, J., KRATOCHVÍL, P., ROHAN, V., POLÍVKA, J., KLEČKOVÁ, J. Design of the artificial neural network model for the prediction of outcome after stroke. In HEALTHINF 2012. Setúbal: SciTePress, 2012. p. 467-470. ISBN 978-989-8425-88-1
Abstract: In our contemporary research we are trying to develop the artificial neural network (ANN) model for the prediction of outcome after the occurrence of stroke. This paper mentions some important facts about stroke as well as the urgent need for Computer Assisted Decision Support (CAMS) systems in the relation to clinical practice. The short review of related studies of ANN in medicine is included. The model input and output parameters were selected and are also described. The basic ANN design for the predictive model is mentioned together with the future directions of our research.

MOUČEK, R., ŘEŘICHA, J. Driver´s Attention during Monotonous Driving. In BMEI 2012. Los Alamitos: IEEE, 2012. p. 343-347. ISBN 978-1-4673-1182-3
Abstract: Attention of drivers is a key factor of road safety. Inattentive drivers are dangerous to their surroundings and cause a considerable number of accidents. However, decline of attention, especially during long rides, is natural and it is worth to know if it can be investigated from electric activity of the brain. Since there is an evidence of relationship between attention and P3 component which is widely used in design and analysis of experiments by the method of event related potentials (ERPs), the ERP experiment based on auditory stimulation was designed and performed on tested subjects, which drove a car simulator on a monotonous track. The background of the used method, experimental design, data processing, and results of the performed experiments are described in this paper.

KOHOUT, J., KELLNHOFER, P., MARTELLI, S. Fast Deformation for Modelling of Musculoskeletal System. In GRAPP 2012: Proceedings of International Conference on Computer Graphics Theory and Applications. Setúbal: SciTePress, 2012. p. 16-25. ISBN 978-989-8565-02-0
Abstract: This paper proposes a gradient domain deformation for wrapping surface models of muscles around bones as they move during a simulation of physiological activities. Each muscle is associated with one or more poly-lines that represent the muscle skeleton to which the surface model of the muscle is bound so that transformation of the skeleton (caused by the movement of bones) produces transformation of the vertices of the mesh subject to Laplacian linear constraints to preserve the local shape of the mesh and non-linear volume constraints to preserve the volume of the mesh. All these constraints form a system of equations that is solved using the iterative Gauss-Newton method with Lagrange multipliers. Our C++ implementation can wrap a muscle of medium size in about a couple of ms up to 400 ms on commodity hardware depending on the type of parallelization, whilst it can keep the change in volume below 0.04%. A preliminary biomechanical assessment of the proposed technique suggests that it can produce realistic results and thanks to its rapid processing speed, it might be an attractive alternative to the methods that are used in clinical practise at present.

MOUČEK, R., ŘONDÍK, T. Influence of Mental Load on Driver's Attention. Transaction on Transport Sciences, 2012, Volume 5, Issue 1, p. 21-26. ISSN: 1802-971X
Abstract: This paper deals with influence of mental load on drivers? attention. EEG (electroencephalography) and ERP (event related potentials) techniques are used for investigation of the level of drivers? attention. A short overview of experiments dealing with drivers? attention is given and the ERP technique and the P3 component are described. General assumptions related to P3 amplitude and P3 latency are introduced. Then experimental design and the course of the experiment are described. The resulting EEG/ERP data are analyzed and their interpretation is provided.

VAŘEKA, L. Matching Pursuit for P300-based Brain-Computer Interfaces. In TSP 2012. neuveden: IEEE, 2012. p. 513-516. ISBN 978-1-4673-1118-2
Abstract: "Since the evoked responses obtained by stimulation are much weaker than the continuous electroencephalographic signal, the correct signal analysis enhances stimulation-driven signal components. The paper proposes methods for event-related potential processing for brain-computer interfaces based on matching pursuit. The suggested method is compared with another simple method which is frequently used for feature extraction. A multi-layer perceptron was used for classification. The results can be used to improve the feature extraction for BCI systems."

KRATOCHVÍL, M., VČELÁK, P., KLEČKOVÁ, J., ROHAN, V. MedIDEA - Medical Image Data Extgraction and Analysis. In BMEI 2012. Los Alamitos: IEEE, 2012. p. 225-229. ISBN 978-1-4673-1182-3
Abstract: The most indicated imaging technique before operations is computed tomography. Preoperative deliberation requires not only its own evaluation of pathological findings, but also the overall anatomy, perfusion and volume of various anatomical parts, which must be accurately identified. There is a wide range for computer-assisted diagnosis, which should reduce and refine the assessment carried out by man and help better decide on the appropriate therapeutic procedure (resection, multiphase power, chemotherapy, ablation methods), and, among other things, reduce the number of unnecessary surgical procedures while on the other hand enabling the implementation of extensive resection. We aims to create a comprehensive system for computed imaging, which would allow the detection and analysis of focal lesions, determination of their segmental localisation, assessment of perfusion conditions and performance of a virtual resection including the establishment of volume resected and organ remaining. Such a system is not yet commercially available.

VČELÁK, P., KRATOCHVÍL, M., KLEČKOVÁ, J., ROHAN, V. MetaMed - Medical Meta Data Extraction and Manipulation Tool Used in the Semantically Interoperable Research Information System. In BMEI 2012. Los Alamitos: IEEE, 2012. p. 1281-1285. ISBN 978-1-4673-1182-3
Abstract: The MetaMed is a tool for data and meta data extraction primarily from a heterogeneous medical data. It is a non-interactive command line open source application for processing a large amount of data. An extracted meta data is stored in the Resource Description Framework and is structured by OWL ontologies. It enables a semantic interoperability. Meta data as an index data prevents us to solve different file format and version of raw files again and again for a following research. It enables a better performance. Indexed data can be directly used in a user interface and querying for an appropriate raw data can be done. The MetaMed and the research information system is confirmed with research primarily focused on a cerebrovascular diseases.

KOHOUT, J., CLAPWORTHY, G.J., MARTELLI, S., VICECONTI, M. Muscle Fibres Modelling. In GRAPP 2012 Proceedings of the International Conference on Computer Graphics Theory and Applications. Setúbal: SciTePress, 2012. p. 58-66. ISBN 978-989-8565-02-0
Abstract: This paper describes a method that represents a muscle by a realistic chaff of muscle fibres that are automatically generated in the volume defined by the surface mesh of the muscle which itself automatically wraps around bones as they move. Our C++ implementation can decompose the volume into muscle fibres, which is done by a slice-by-slice morphing of predefined fibres template into the muscle volume, and visualise the result in only about 1000 ms on commodity hardware. Hence, the method is fast enough to be suitable for interactive educational medical software. Although a biomechanical assessment has yet to be done, we believe that the method could be used also in clinical biomechanical applications to extract information on the current muscle lever arm and fibre path and, thanks to its rapid processing speed, it might be an attractive alternative to current methods.

JEŽEK, P., MOUČEK, R. Ontology Development in EEG/ERP Portal. In BMEI 2012. Los Alamitos: IEEE, 2012. p. 1291-1295. ISBN 978-1-4673-1182-3
Abstract: The EEG/ERP (Electroencephalography/Even- Related Potentials) Portal serves for storage and management of ERP experiments. The protocols describing these experiments are designed and implemented using various software applications and/or hardware devices. Some protocols are kept in XML files and stored in the EEG/ERP portal database as LOB (Large Object) data types. Since it is important for researchers to directly find details about design of the ERP protocols in the related XML files and it is also hard to use LOB data for generating the semantic web output, storage types provided by the Oracle 11g database system were investigated and compared. Therefore a new model of storage of ERP protocols is introduced. This model is finally simplified after analysis of results of performance tests.

BRŮHA, P., MOUČEK, R. Portal for Research in Electrophysiology - Data Integration with Neuroscience Information Framework. In BMEI 2012. Los Alamitos: IEEE, 2012. p. 1025-1028. ISBN 978-1-4673-1182-3
Abstract: There is a problem with global search and data sharing. Our research group developed the EEG/ERP (electroencephalography, event-related potentials) portal; a system for storage and management of EEG/ERP resources - data, metadata, tools and materials related to EEG/ERP experiments. The EEG/ERP portal and existing solutions of data integration are presented. Authors registered the EEG/ERP portal as a source of neuroscience data and metadata within the world known project - Neuroscience Information Framework (NIF). Developed web services for harvesting EEG/ERP scenarios and experiments within NIF are presented.

KOUTNÝ, T. Prediction of Interstitial Glucose Level. IEEE Transactions on Information Technology in Biomedicine, 2012, Volume 16, Issue 1, p. 136-142. ISSN: 1089-7771
Abstract: Glucose is an important source of energy for cells. In clinical practice, we measure glucose level in blood and interstitial fluid. Each method has its pros and cons, and both levels correlate with each other. As the body tries to maintain the glucose level within a particular range to avoid adverse effects, it is desirable to predict future glucose levels in order to aid provided health care. We can see this desire in research, e.g. research on glukose transporters of cells. As yet another example, we can see it with diabetic patients, patients in a metabolic intensive care unit, particularly. In this paper, a glucose level prediction method is proposed.

MAUTNER, P., MOUČEK, R. Processing and Categorization of Czech Written Documents Using Neural Networks. Neural Network World, 2012, Volume 22, Issue 1, p. 53-66. ISSN: 1210-0552
Abstract: The Kohonen Self-organizing Feature Map (SOM) has been developed for clustering input vectors and for projection of continuous high-dimensional signal to discrete low-dimensional space. The application area, where the map can be also used, is the processing of text documents. Within the project WEBSOM, some methods based on SOM have been developed. These methods are suitable either for text documents information retrieval or for organization of large document collections. All methods have been tested on collections of English and Finnish written documents. This article deals with the application of WEBSOM methods to Czech written documents collections. The basic principles of WEBSOM methods, transformation of text information into the real components feature vector and results of documents classification are described. The Carpenter-Grossberg ART-2 neural network, usually used for adaptive vector clustering, was also tested as a document categorization tool. The results achieved by using this network are also presented.

ČEPIČKA, L., HOLEČKOVÁ, I., MAUTNER, P., MOUČEK, R. Projevy poruchy pozornosti v závislosti na stupni pohybového vývoje u dětí předškolního věku. Česká kinantropologie, 2012, Volume 16, Issue 2, p. 119-125. ISSN: 1211-9261
Abstract: Study deals with attention deficit and hyperactivity disorder with connection to coordination disorder. Aim of study is to assess differences in attention according to motor development in preschool children. Sixteen children with mean age of 5,87 (SD ? 0,55) participated in study. To assess a motor development TGMD - 2 was used. The attention was measured through the electric activity of brain and analysis of evoked potentials. The results confirm assumption that children with coordination disorder to suffer from disorder in visuospatial attention and also attention deficit to acoustic stimuli. Together with worse processing and information storage it can cause of coordination disorder and problems in motor learning as well.

JEŽEK, P., MOUČEK, R. Semantic Web in EEG/ERP Portal, Extending of Data Layer using Java Annotations. In BIOSTEC 2012, HEALTHINF 2012. Setúbal: SciTePress, 2012. p. 350-353. ISBN 978-989-8425-88-1
Abstract: Because the Semantic Web uses its technologies for presenting data/metadata on the web and common systems are based on object-oriented languages a need for suitable mapping is emerging. This paper describes the difficulties during transformation of data layer represented by object-oriented code into the semantic web structures (OWL, RDF). Since there is difference between semantic expressivity of these data representations it is necessary to fill this semantic gap. Authors investigate these differences in semantics and provide a preliminary idea to add missing semantics into the Java code using Java annotations. These annotations are consequently processed by the proposed framework. The transformation is demonstrated within the EEG/ERP Portal.

JEŽEK, P., MOUČEK, R. System for EEG/ERP Data and Metadata Storage and Management. Neural Network World, 2012, Volume 22, Issue 3, p. 277-290. ISSN: 1210-0552
Abstract: The paper introduces a system for EEG/ERP (electroencephalography, event-related potentials) data and metadata storage and processing. Since researchers have difficulties with a suitable long-term storage and management of electrophysiology data the presented system helps them to increase both efficiency and effectiveness of their work by providing the means for the storage, management, search and sharing of EEG/ERP data. The requirements specification including the system context, system requirements, project scope, basic features, system users, and data formats and metadata structures is presented. The database structure is proposed; upload, download and interchange of EEG/ERP data and metadata using the web interface are described. The system architecture, used technologies and final realization are described. Data and metadata search and user accounts including system security management are presented. Additional tools and structures as converters of data formats and semantic web ontology are mentioned.

VAŘEKA, L., MAUTNER, P. The Event-Related Potential Data Processing Using ART 2 Network. In BMEI 2012. Los Alamitos: IEEE, 2012. p. 467-471. ISBN 978-1-4673-1182-3
Abstract: The event-related potentials (ERPs) obtained by stimulation are much weaker than the continuous electroencephalographic(EEG) signal. Therefore, the correct signal analysis is vital to detect the stimulation-driven signal components. This paper proposes the combination of matching pursuit for feature extraction and ART 2 neural network for clustering. Then, clusters are filtered and interpreted according to their statistical properties as ERP components or noise. The suggested method can be used to filter the EEG/ERP signal. Furthermore, its results lead to a method that improves averaging when compared to traditional approaches.

KELLNHOFER, P., KOHOUT, J. Time-convenient deformation of musculoskeletal system. In Algoritmy 2012, 19th Conference on Scientific Computing. Bratislava: STU Bratislava, 2012. p. 239-249. ISBN 978-80-227-3742-5
Abstract: The musculoskeletal modelling and simulation is an essential step in the process of looking for an optimal strategy to provide patients su?ering from various musculoskeletal disorders, such as osteoporosis, with better health care. In our previous work, we proposed a deformation method suitable for clinical practise that deforms each muscle represented by a surface mesh according to assigned skeleton action lines and preserves its inner volume at the same time. It is built on combination of linear constraints for surface description together with relation of surface to control skeleton and non-linear constraint of volume preservation. It uses Gauss-Newton based iterative solver to ?nd energy minimum ful?lling these conditions. It gains extra performance from exploiting the coarse outer hull for potentially slow and numerically unstable calculations. It achieves excellent ratios of volume preservation and maintains reasonable times in hundreds of milliseconds for our typical meshes, but since each mesh is deformed independently to others, it is unable to provide deformation of multiple interacting meshes without danger of their mutual intersections. This is why a new modi?cation of the method is introduced in this paper that alters both constraint formulation and the iterative solver algorithm to ?x and prevent major intersections between mesh surfaces. It detects and prevents initial intersection in the starting pose of meshes and then prevents new intersections during the solution by constraining the modi?cation step of meshes. It however still considers importance of volume preservation and tries to minimise e?ect of changes on its maintenance. The method was implemented using C++ language and VTK framework and integrated to our human body framework. The results of application to medical data we use show that despite a few open issues, the proposed technique has its merit.

KRATOCHVÍL, M., VČELÁK, P., KLEČKOVÁ, J. Unified parallel Experiment Interface for Medical Research System. In Proceeding of the International Conference on Health Informatics. Setúbal: SciTePress, 2012. p. 449-452. ISBN 978-989-8425-88-1
Abstract: When we are processing large quantity of a data, and/or we are computing complex tasks, computational performance of one computer is not enough. Solution is parallel processing. However proper approach to parallel programming doesn't need to well-known to medical experts or computational tool doesn't have native support for parallel programming. Our goal is to design unified interface, which allows parallel approach to our medical researchers. It must provide support for existing medical experiments and it must provide full interoperability.

ŘONDÍK, T., MAUTNER, P. Using ART2 for Clustering of Gabor Atoms Describing ERP P3 Waveforms. In BMEI 2012. Los Alamitos: IEEE, 2012. p. 477-481. ISBN 978-1-4673-1182-3
Abstract: This paper deals with a suitable method for decomposition of EEG/ERP signal to waveforms which are grouped is such way that one or few groups contain ERP P3 waveforms. At the beginning, the EEG/ERP domain is briefly introduced and essential information about EEG and ERP signals is given. Then, the method for waveforms grouping based on matching pursuit algorithm with Gabor dictionary as a preprocessing method for feature extraction for ART2 neural network is explained in detail. Emphasis is placed on selection of suitable feature extraction method. Comparison of tested feature extraction methods and summarization is given at the end.

POLÍVKA, J., POLÍVKA, J., PETERKA, J., ROHAN, V., ŠEVČÍK, P., TOPOLČAN, O. Vitamin D a neurologická onemocnění. Vnitřní lékařství, 2012, Volume 58, Issue 5, p. 393-395. ISSN: 0042-773X
Abstract: We provide an overview of the association between vitamin D and some neurological diseases where the correlation has repeatedly been described. The majority of literature refers to cerebrovascular diseases, followed by multiple sclerosis and cognitive disorders. Vitamin D hypovitaminosis might be associated with the diseases directly or it might contribute to the disease risk factors (typically in cerebrovascular events). Vitamin D hypovitaminosis may also play a role in patients with residual functional involvement due to a neurological disorder (movement disorders, lack of self-sufficiency) and worsen functional status owing to muscle weakness, instability and falls.

JEŽEK, P., MOUČEK, R., MIKO, P., MARKVART, F., KOREŇ, J., KOLENA, J. EEG Data Processor - Framework for Running Signal Processing Methods. 2012.
Abstract: This software solves difficulties related to running of signal processing methods. Although several systems that implement signal processing methods exist, their sharing and remote calling is not satisfactorily solved. This software is a custom server-side approach that provides a powerful plug-in engine for integration of signal processing methods. The plug-in engine ensures high modularity and flexibility of the system. Since the implemented methods are accessible via the SOAP Web Service, integration with another system is available. There is also possible to use the system locally via a web browser. The set of basic methods is already implemented.

PAPEŽ, V., MOUČEK, R. Model of Storage of ERP Protocols in EEG/ERP Portal. In BMEI 2012. Los Alamitos: IEEE, 2012. p. 1286-1290. ISBN 978-1-4673-1182-3
Abstract: The EEG/ERP (Electroencephalography/Even- Related Potentials) Portal serves for storage and management of ERP experiments. The protocols describing these experiments are designed and implemented using various software applications and/or hardware devices. Some protocols are kept in XML files and stored in the EEG/ERP portal database as LOB (Large Object) data types. Since it is important for researchers to directly find details about design of the ERP protocols in the related XML files and it is also hard to use LOB data for generating the semantic web output, storage types provided by the Oracle 11g database system were investigated and compared. Therefore a new model of storage of ERP protocols is introduced. This model is finally simplified after analysis of results of performance tests.

2011

HOŠNA, M. Adaptation method for brain computer interface system. 1. vyd. Plzeň : 2011, 94 s.
Abstract: The dissertation focuses on the matters of interface between the human brain and computer (Brain Computer interface) that enables direct communication of a human being with a computer, at this time only in direction from the human towards the computer. The theoretical part of the dissertation covers current matters of direct communication between the human and the computer through the electroencephalography (EEG), processing methods of evoked potentials and possibilities of adaptation and their respective usage in the field of BCI systems. The second part of the work encompasses the proposal and verification of the original adaptation method for the BCI system. To reach this aim a system concept was proposed which was further replenished by various aspects improving its features and results. The author proved in his work that the adaptation represents a way to the creation of the BCI system capable of good understanding of a random subject, who begins to operate the developed system.

MATOUŠEK, V., MOUČEK, R., MAUTNER, P. Analysis of visual field and reaction time in correlation with the vigilance decreasing. In Reliability of driver car interaction. Praha : UI AVČR, ČVUT Praha, 2011, p. 110-153. ISBN 978-80-87136-12-6
Abstract: The book describes many aspects of the reliability of interactions among drivers and their vehicles; this reliability attracts the interest of researchers in many countries for a long time. The field of driver-car interaction reliability involves extremly wide spectrum of aspects concerning many areas of science and technology. Therefore a well cooperated group of specialists of 11 Czech universities, research institutes and industrial companies was estabilished with the aim to solve the main problems of the interaction reliability between road vehicle and its driver. The knowledge reached in this area are presented in this book and it will be very useful for all people who will continue in this research.

MAULE, P., KLEČKOVÁ, J., ROHAN, V. Automated approach for whole brain infarction core delineation. In Proceedings of the International Conference on Knowledge Discovery and Information Retrieval. Setúbal: SciTePress, 2011. p. 433-437. ISBN 978-989-8425-79-9
Abstract: This article proposes automated approach for whole brain infarction core delineation while using only non-contrast computed tomography and computed tomography angiography. The main aim is to provide additional information measuring infarction core volume while exceeding certain level is contraindication of early recanalization. Process of generation of Perfusion Blood Volume maps is described first followed by description of process of infarction core delineation. Verification of correctness is based on comparison against follow-up examinations. Discussion and future works summarizes weaknesses of the method and steps for improvement.

VČELÁK, P., KLEČKOVÁ, J. Automatic Real-Patient Medical Data De-Identification for Reserarch Purposes. World Academy of Science, Engineering and Technology, An International Journal of Science, Engineering and Technology, 2011, Volume Neuveden, Issue 58, p. 506-510. ISSN: 2010-376X
Abstract: Our Medicine-oriented research is based on a medical data set of real patients. It is a security problem to share patient private data with peoples other than clinician or hospital staff. We have to remove person identification information from medical data. The medical data without private data are available after a de-identification process for any research purposes. In this paper, we introduce an universal automatic rule-based de-identification application to do all this stuff on an heterogeneous medical data. A patient private identification is replaced by an unique identification number, even in burned-in annotation in pixel data. The identical identification is used for all patient medical data, so it keeps relationships in a data. Hospital can take an advantage of a research feedback based on results.

ŘONDÍK, T., CINIBURK, J. Comparison of Various Approaches for P3 Component Detection using Basic Methods for Signal Processing. In 2011 th International Conference on Biomedical Engineering and Informatics. New York: IEEE, 2011. p. 700-704. ISBN 978-1-4244-9350-0
Abstract: The paper deals with ERP (Event related potentials) components detection using wavelet transform (both continuous and discrete form), matching pursuit algorithm and Hilbert-Huang transform. The EEG/ERP domain is shortly introduced and essential information about EEG and ERP signals is given. The wavelet transform, matching pursuit algorithm, and Hilbert-Huang transform are introduced and their suitability for ERP components detection is described. Experimental results obtained by using these algorithms for P3 component detection are summarized.

ŘONDÍK, T., CINIBURK, J., MOUČEK, R., MAUTNER, P. ERP components detection using wavelet transform and matching pursuit algorithm. In Applied Electronics 2011. Plzeň: ZČU v Plzni, 2011. p. 333-336. ISBN 978-80-7043-987-6 , ISSN: 1803-7232
Abstract: The paper deals with ERP (Event related potentials) components detection using wavelet transform and matching pursuit algorithm. The EEG/ERP domain is shortly introduced and essential information about EEG and ERP signals is given. The wavelet transform, matching pursuit algorithms and its modification are introduced and their suitability for ERP components detection is described. Experimental results obtained by using these algorithms for P3 component detection are summarized.

KOUTNÝ, T. Estimating reaction delay for glucose level prediction. MEDICAL HYPOTHESES, 2011, Volume 77, Issue 6, p. 1034-1037. ISSN: 0306-9877
Abstract: The pancreas, liver and hypothalamus have a regulatory function in the glucose homeostasis. As the blood glucose level changes, these compartments react and the level changes again. Subsequently, the interstitial glucose level changes with some delay. I propose a hypothesis that the change of the blood glucose level includes information about the estimated rate with which the hypothalamus expects the blood glucose level to return to normal range by means of regulatory mechanisms. Also, I propose a method to estimate the blood-to-interstitial glucose level delay. With this delay, it was possible to relate the present blood glucose level and future interstitial glucose level with such coefficients, which do not seem to change over the time of the experiment to a significant extent. Perhaps, it is a parameterization of the regulatory processes, which could be possibly encoded within hypothalamus set-points.

CINIBURK, J. Hilbert-Huang Transform for ERP detection. 1. vyd. Plzeň : 2011, 105 s.
Abstract: Several modifications of the Hilbert-Huang transform are presented in this paper. Modifications were designed to restrain the over/undershoot effect oc- curring when envelopes are being calculated. My modifications contribute to better estimation of additional extrema and improve the results acquired from processing the EEG signal (even when it is contamined with artifacts). They make the empirical mode decomposition faster and the decomposed IMFs cor- responds more with the original EEG signal.

MOUČEK, R., ŘONDÍK, T. Influence of mental load on driver´s attention. In Electromobility Congress proceedings. Praha: CTU Praha, FTS, 2011. p. 1-3. ISBN 978-80-01-04818-4
Abstract: This preliminary paper deals with influence of mental load on driver?s attention. EEG (electroencephalography) and ERP (Event related potentials) techniques are used for investigation of the level of driver?s attention. A short overview of experiments dealing with drivers? attention is given and the ERP technique and the P3 component are described. General assumptions related to P3 amplitude and P3 latency are introduced. Then experimental design is described. At present the resulting EEG/ERP data are analyzed and their interpretation will be provided during congress presentation and in the final version of the paper.

JEŽEK, P., MOUČEK, R. Integration of signal processing methods into EEG/ERP system. In BIOSTEC 2011. Setúbal: SciTePress, 2011. p. 563-566. ISBN 978-989-8425-34-8
Abstract: This paper deals with the processing of signals from EEG/ERP experiments. Selected methods for EEG/ERP signal processing are shortly presented. Since these methods are usually implemented for various platforms and within various tools, a new designed and developed software system, which allows users running them uniformly, is presented. The methods are added and processed as plug-ins. It ensures a high modularity and flexibility of the system. The main system components (JERPA, JUIGLE) are introduced and shortly described.

ŠTĚBETÁK, J., BRŮHA, P., MOUČEK, R. Neuroinformatics - Data management and analytic tools for EEG/ERP research. In Beyond AI: Interdisciplinary Aspects of Artifical Intelligence. Plzeň: ZČU, NTC, 2011. p. 91-95. ISBN neuveden
Abstract: Brain research is currently a rapidly growing scientific field. Large amounts of data, various data formats and non-standardized domain descriptions lead to incompatible results and interpretations of neuroscientific data and to difficult communication between laboratories and scientific teams. Neuroinformatics, a newly established scientific field, provides integration across all levels and scales of neuroscience. Our research group has contributed to the building of a neuroinformatics infrastructure by developing and integrating data management and analytic tools for EEG/ERP (electroencephalography, event-related potential) research.

VČELÁK, P., KLEČKOVÁ, J., ROHAN, V. Privacy and Security Issues in Cerebrovascular Diseases Data Research. International Journal for Information Security Research, 2011, Volume 1, Issue 1, p. 27-34. ISSN: 2042-4639
Abstract: The cerebrovascular diseases research are based on real patient's data received from a collaborating centre. The goal of research is to take advantage of heterogeneous medical data relationships. Medical data relationships leads to get more data mining facilities in studying of dependencies and crucial values of parameters in a huge volume of real imaging examinations with clinical and therapeutic data. There are lot of difficulties and security issues when providing research on medical data. All real patient's identifiers must be removed for privacy reasons. A research team does not necessity know the patient identity information. We keep limited characteristics only and can be accessible to patient's medical doctors. These characteristics are useful to provide us analysis and statistics results. The aggregated results are publicly available.

MOUČEK, R., JEŽEK, P., PAPEŽ, V. Semantic web technologies in EEG/ERP domain. In BIOSTEC 2011. Setúbal: SciTePress, 2011. p. 618-621. ISBN 978-989-8425-34-8
Abstract: The paper shortly describes EEG/ERP domain and the system for storage and management of data and metadata from EEG/ERP experiments. The system has been developed using common technologies and data structures (object oriented code, relational database). A registration of the system as a recognized data source requires representation of its data and metadata by semantic web resources. A short overview of differences between common data structures and semantic web representations is given and possible approaches to automated transformation of data and metadata from common data structures are mentioned. The existing semantic web frameworks and tools, widely tested for our purposes, are listed. Finally, the integration of selected tools and the software solution for automated transformation from the relational database to a semantic web representation is described.

VČELÁK, P., KLEČKOVÁ, J. Semantically interoperable research medical data and meta data extraction strategy. In BMEI 2011. Piscataway: IEEE, 2011. p. 1950-1954. ISBN 978-1-4577-1447-4
Abstract: Generally, the interoperability is the key feature to any widely used application or an information system. A system build on the basis of semantic data interpretation can also lead to an easy extensible and adaptable system, in the future. Otherwise, you have to deal with a lack of agreed terminologies or codes between standards e.g. DASTA vs. HL7, different coding structures and even variety of file formats or inconsistent database table schema. The most of these difficulties can be solved by the semantically interoperable system. We present our implementation strategy and meta data extraction methods for a research information system with an heterogeneous medical data. The medical data can have different origin, type, file format and even its version. We discuss the research information system that we primarily use for cerebrovascular brain diseases research.

MOUČEK, R., JAROŠ, P., JEŽEK, P., PAPEŽ, V. Software infrastructure for EEG/ERP research. In Proceedings of the International Conference on knowledge Enginering and Ontology Development 2011. Setúbal: SciTePress, 2011. p. 478-481. ISBN 978-989-8425-80-5
Abstract: This paper deals with the software infrastructure for EEG/ERP (electroencephalography, event related potentials) research. The requirements for building this infrastructure have arisen from laboratory needs, unavailability of appropriate software tools and incompatibility of previously used commercial solutions. The standardization of EEG/ERP data formats and construction of complex and publicly open software infrastructure is also supported by International Neuroinformatics Coordinating Facility (INCF) since these efforts can significantly accelerate brain research. The presented software infrastructure includes the web based EEG/ERP portal as the central data storage for data/metadata obtained in EEG/ERP experiments and JERPA software as the desktop software tool for computationally demanding operations. Supporting libraries (e.g. library of signal processing methods), developed and integrated to EEG/ERP portal and/or JERPA software, are briefly described.

JEŽEK, P., MOUČEK, R. Transformation of object-oriented code into semantic web using Java annotations. In ICEIS 2011. Lisabon: SciTePress, 2011. p. 1-4. ISBN 978-989-8425-53-9
Abstract: This paper deals with difficulties occurring during transformation of schema and data from an object-oriented code to a semantic web representation (RDF, OWL). The authors describe differences in semantic expressivity between the object-oriented approach and the semantic web approach and look for the ways to fill this semantic gap. Then some existing approaches with their difficulties are introduced and a preliminary idea using Java annotations is proposed. Java annotations add missing semantic information into Java code, which is consequently processed by the proposed framework and serialized into output semantic web structure (OWL).