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.