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Modeling of Binaural Hearing.
Tóth, Peter ; Maršálek, Petr (advisor) ; Košťál, Lubomír (referee) ; Hromádka, Tomáš (referee)
The central theme of this thesis is a description of information processing in the sound localization circuit of the auditory pathway. The focus is on principal neurons of the medial superior olive (MSO), the first major convergence point for binaural information. Selected properties and relations of MSO neurons are derived and expressed through models. In the thesis we present three modeling studies. The first one clarifies a relation- ship between biophysical parameters of the MSO neuron and its ability to detect coincidental spikes from the left and the right ear. The second study describes the statistical behavior of spike trains on the input and output of the MSO neuron. In the third work, we studied how interaural coherence could guide localization of sound sources in complex listening situations with multiple sound sources in reverberant environments. The main results are analytical and numerical models describing the aforemen- tioned relations and behaviors. Secondary results include that inhibitory input to the MSO neuron narrows and shifts the time range of coincidence detection, that ergodic assumption from statistical physics and circular statistics are beneficial in the description of spike trains in the auditory pathway, and that interaural level difference of parts of the signal with...
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Modelica in physiological modelling. Models with spatially distributed parameters, Authorin educational simulators.
Šilar, Jan ; Kofránek, Jiří (advisor) ; Maršálek, Petr (referee) ; Roubík, Karel (referee)
Mathematical models in physiology are useful to formulate and verify hypotheses, to make predictions, to estimate hidden parameters and in education. This thesis deals with modelling in physiology using the Modelica language. New methods for model implementation and simulator production were developed. Modelica is an open standard equation-based object-oriented language for modelling complex systems. It is highly convenient in physiology modelling due to its ability to describe extensive models in a lucid hierarchical way. The models are described by algebraic, ordinary differential and discrete equations. Partial differential equations are not supported by the Modelica standard yet. The thesis focuses on two main topics: 1) modelling of systems described by partial differential equations in Modelica 2) production of web-based e-learning simulators driven by models implemented in Modelica. A Modelica language extension called PDEModelica1 for 1-dimensional partial differential equations was designed (based on a previous extension). The OpenModelica modelling tool was extended to support PDEModelica1 using the method of lines. A model of countercurrent heat exchange between the artery and vein in a leg of a bird standing in water was implemented using PDEModelica1 to prove its usability. The...
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Activity and Memory in Biologically Motivated Neural Network.
Štroffek, Július ; Maršálek, Petr (advisor) ; Zápotocký, Martin (referee) ; Hozman, Jiří (referee)
This work presents biologically motivated neural network model which works as an auto-associative memory. Architecture of the presented model is similar to the architecture of the Hopfield network which might be similar to some parts of the hippocampal network area CA3 (Cornu Amonis). Patterns learned and retrieved are not static but they are periodically repeating sequences of sparse synchronous activities. Patterns were stored to the network using the modified Hebb rule adjusted to store cyclic sequences. Capacity of the model is analyzed together with the numerical simulations. The model is further extended with short term potentiation (STP), which is forming the essential part of the successful pattern recall process. The memory capacity of the extended version of the model is highly increased. The joint version of the model combining both approaches is discussed. The model might be able to retrieve the pattern in short time interval without STP (fast patterns) or in a longer time period utilizing STP (slow patterns). We know from our everyday life that some patterns could be recalled promptly and some may need much longer time to reveal. Keywords auto-associative neural network, Hebbian learning, neural coding, memory, pattern recognition, short-term potentiation 1
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Functional properties and plasticity of the rat auditory cortex
Pysanenko, Kateryna ; Tureček, Rostislav (advisor) ; Maršálek, Petr (referee) ; Chvátal, Alexandr (referee)
Auditory cortex (AC) is the ultimate target of afferent auditory pathways and plays a crucial role in the perception and localization of complex sounds. In the thesis were investigated and discussed three aspects of the AC function: i) diversity of the intrinsic passive and active electrical properties of core and belt AC neurons, ii) the modulatory function of the descending connections from the auditory cortex to the inferior colluculus and iii) the effect of a complex acoustical environment applied during the critical period on the responsiveness of auditory cortex neurons in rats. Within the AC can be distinguished two fundamental areas: centrally located core area and peripheral belt area. Recordings of sound-evoked AC activity revealed striking differences between response patterns of neurons from the core and belt areas. Most of core neurons displayed short latency, phasic responses, unlike the prevalence oflonger latency tonic responses in the belt area. It has been hypothesized that incoming signals could be processed differently by neurons in these areas. In thethesis we have investigated the intrinsic electrical properties of layer V pyramidal neurons by patch-clamp recording in acute rat AC slices. Results showed that the pyramidal neurons from the core AC are more excitable at rest...
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The influence of stochastic behaviour of ion channels on the signal and information transfer at excitable neuronal membranes
Šejnová, Gabriela ; Kuriščák, Eduard (advisor) ; Maršálek, Petr (referee)
The stochastic behavior of voltage-gated ion channels causes fluctuations of conductances and voltages across neuronal membranes, contributing to the neuronal noise which is ubiquitous in the nervous system. While this phenomenon can be observed also on other parts of the neuron, here we concentrated on the axon and the way the channel noise influences axonal input-output characteristics. This was analysed by working with our newly created computational compartmental model, programmed in Matlab environment, built up using the Hodgkin-Huxley mathematical formalism and channel noise implemented via extended Markov Chain Monte Carlo method. The model was thoroughly verified to simulate plausibly a mammalian axon of CA3 neuron. Based on our simulations, we confirmed quantitatively the findings that the channel noise is the most prominent on membranes with smaller number of Na+ and K+ channels and that it majorly increases the variability of travel times of action potentials (APs) along axons, decreasing thereby the temporal precision of APs. The simulations analysing the effect of axonal demyelination and axonal diameter correlated well with other finding referred in Literature. We further focused on spike pattern and how is its propagation influenced by inter-spike intervals (ISI). We found, that APs fired...
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Analysis of dynamical interactions of axon shafts and their biopysical modelling.
Šmít, Daniel ; Zápotocký, Martin (advisor) ; Reingruber, Jūrgen (referee) ; Maršálek, Petr (referee)
in English While axon fasciculation plays a key role in the development of neural networks, very lit- tle is known about its dynamics and the underlying biophysical mechanisms. In a model system composed of neurons grown ex vivo from explants of embryonic mouse olfactory epithelia, we observed that axons dynamically interact with each other through their shafts, leading to zippering and unzippering behaviour that regulates their fasciculation. Taking advantage of this new preparation suitable for studying such interactions, we carried out a detailed biophysical analysis of zippering, occurring either spontaneously or induced by micromanipulations and pharmacological treatments. We show that zippering arises from the competition of axon-axon adhesion and me- chanical tension in the axons. This is upheld on quantitative level by conforming change of network global structure in response to various pharmacological treatments, without active involvement of growth cones. The calibrated manipulations of interacting shafts provide qualitative support for the hypothesis, and also allow us to quantify the mechan- ical tension of axons in our system. Furthermore, we introduce a biophysical model of the zippering dynamics, which efficiently serves the purpose of estimating the magnitude of remaining involved...
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Kinematic analysis of rhythmic motion: the cases of human hand tremor and fly wingbeat.
Chakraborty, Soma ; Zápotocký, Martin (advisor) ; Maršálek, Petr (referee) ; Jech, Robert (referee)
Rhythmic motions, regular or irregular, are an integral part of motor behavior both in health and in disease. Better understanding of its neural control mechanisms helps in developing methods for controlling the progression of diseases manifesting as rhythmic motions. I studied two specific aspects of rhythmic motions: bilateral coordination of hand tremors in human subjects and modular control of locomotion in invertebrates. Many types of tremors, including the physiological tremor (PT) and the essential tremor (ET) occur in limbs on both the sides of the body, with similar fundamental frequency of the oscillation. This raises the possibility that the contralateral tremors may have a common source or are otherwise coupled. However, while significant contralateral interaction is seen in these two types of tremors, only limited evidence of bilateral coherence has been shown in the previous literature. Therefore, in my study I explored the existence of a weak coupling between the left and right oscillators the may lead to intermittent bilateral coherence. I measured triaxial acceleration of the two hands and systematically assessed their bilateral coherence, using both stationary and non-stationary (wavelet-based) analyses methods. Measuring all three axes allowed examination of a more complete set...
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Role of Islet1, BDNF and nanoparticles in development, function and regeneration of the auditory system
Chumak, Tetyana ; Syka, Josef (advisor) ; Druga, Rastislav (referee) ; Maršálek, Petr (referee)
Detailed knowledge of the role that particular genes and factors play during the development and in the normal function of the auditory system is necessary to develop successful regenerative inner ear therapies. Islet1 transcription factor and brain derived neurothrophic factor (BDNF) have great potential to play a role in regenerative inner ear therapy as both have been shown to be sufficient for self-repair regeneration in cochlea in animal studies. In this study we looked at the roles these two factors play in the development and function of the auditory system. In the transgenic mice used in the study, overexpression of Isl1 affected cell specification during embryonic development, leading to enlargement of the cochleovestibular ganglion and accelerated nerve fiber extension and branching in mutant embryos. The hearing of young transgenic mice was not affected. However, it started to decline in 1-month-old animals. This early onset of age-related hearing loss was found to be a consequence of the neurodegeneration of the olivocochlear system caused by Pax2-driven Isl1 misexpression in the hindbrain. Our data provide the first evidence that the alternation of the olivocochlear system efferent system accelerates the age-related functional decline of hearing without the loss of OHCs. The functional role of...
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Software tool for modelling coding and processing of information in auditory cortex of mice
Popelová, Markéta ; Brom, Cyril (advisor) ; Maršálek, Petr (referee)
Autor Markéta Popelová Název práce Software tool for modelling coding and processing of information in auditory cortex of mice Abstrakt Porozumění zpracovávání a kódování informací ve sluchové k·ře (AC) je stále ne- dostatečné. Z několika r·zných d·vod· by bylo užitečné mít výpočetní model AC, například z d·vodu vysvětlení, či ujasnění procesu kódování informací v AC. Prv- ním cílem této práce bylo vytvořit softwarový nástroj (simulátor SUSNOMAC), zaměřený na modelování AC. Druhým cílem bylo navrhnout výpočetní model AC s následujícími vlastnostmi: Izhikevich·v model neuronu, dlouhodobá plasticita ve formě Spike-timing-dependent plasticity (STDP), šestivrstvá architektura, pa- rametrizované typy neuron·, hustota neuron· a pravděpodobnost vzniku synapsí. Navržený model byl testován v desítkách experiment·, s r·znými sadami para- metr· a v r·zných velikostech (až 100 000 neuron· s takřka 21 milióny synapsí). Experimenty byly analyzovány a jejich výsledky srovnány s pozorováním skutečné AC. V práci popisujeme a analyzujeme několik zajímavých pozorování o aktivitě modelované sítě a vzniku tonotopického uspořádání AC. 1
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Affecting the function of the central part of the auditory system of the adult rat by a brief noise exposure during development
Bartošová, Jolana ; Popelář, Jiří (advisor) ; Vyklický, Ladislav (referee) ; Maršálek, Petr (referee)
ln my the:!i" I aimed to dwal:teriu t.hc dumges in neuronil mvi'Y in tbe tenUlll nucleus of !hl' inferior coIlleulus (CIC) in ..:Iult fllI who ..ffertd fium a lack ohuditory stimulatiOll dl.lling their postnatal dcvdopment ""'..... by the Illmponry i~ase of auditory bearing thresholds after bOef noise e:o:poawe Oll postnItaJ day 14 (broad-bllrKl noise, US dB SPL., 11 min). AI the age of 3-6 IJlOI\tbs, lhe rtSpon5eII ofindividual neurons in tbc CIC 10 :taJnd wtre rcoordod in tb_ animall .nd eompared witb thoseoh~a\l;hcd eontrols. We foood lhal tbe neuronal response tbresholds were sinůlll" in tbe exposed and eontrol animals. However, tbe responJe propenies of high-frequtnCy neuronJ in the exposed rau had characteristic.s typical of the immature auditory system, Le. significantly widtr excitatory response II"talI (which indicatel impairod frcquoncy selectivity), a loogcr fil"Jl-spikc latcfJ(:y, a u.rrower dynamie range, lower maximum rcspon.<;c magniludes, a SUleper ,Iope nf tbc rare-inlensily flmClionllnd a lignifiClnLly lo"",r percelllage of monotonie neuron!. On the basis of thelle !inding" we investignled wllelher the reponed alterallon! nf neuronal relponlivenesl are llso Rccompanied by abnonnal behavioral responses 10 toUnd. The resoll howed a reduced strengtl1 nf the acousbc litanie reflex...
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