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Search Results: 1 - 10 of 8075 matches for " Tomá? Ku?era "
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Koncept ekologickych fenomén v interpretaci st edoevropské vegetace Ecological phenomena concept: the interpretation of the Central-European vegetation
Tomá? Kuera
Malacologica Bohemoslovaca , 2005,
Abstract: A review of literature referring to floristic, vegetation and habitat diversity in Bohemian Massif has resulted to a revision and detailed classification of ecological phenomena. Each phenomenon represents an open nonhierarchical system of lithological, hydrological, topoclimatic and biotic aberrations, that differ from common features of surrounded “zonal“ environment. Two main groups of ecological phenomena have been distinguished: (i) large-scale ecological geo-phenomena originated by prominent lithological factors, and (ii) meso-scale ecological topo-phenomena produced by local action of hydrology, topoclimate, and air currents. With regard to the first group, the following geo-phenomena play a particular role in the Central European vegetation: (a) sandstone, (b) limestone and dolomite (karst phenomenon), (c) marl (flysch and loess), (d) neovolcanic, and (e) serpentinite phenomena. With regard to the latter group, the following meso-scale phenomena contribute to the diversity of habitats in landscape scenery: (f) river (or valley), (g) summit, (h) frost hollow, and (i) scree (and glacial cirque) phenomena. The “insular“ feature of the ecological phenomena in vegetation cover is expressed mainly by the occurrence of treeless ecosystems, such as swamps, bogs, marshes, steppes, rock faces and scree ecosystems, etc. Relatively higher species richness can indicate most of ecological phenomena (they should be detected by the distance from the regional species-area curve), and by the presence of rare plant species, especially by the relic and/or endemic species, which survive on extreme habitats due to the lower competition of prevailing dominant woody or graminoid species.
Tomá? Kuera
Obrana a Strategie , 2011,
Abstract: In July 2011 Germany abandoned conscription. This step is the most significant part of the ongoing reform of the German Armed Forces (Bundeswehr) and by no stretch also the greatest change in the entire history of the Bundeswehr. The current reform, however, is only the last one in the long line of attempts to adapt the Bundeswehr to post-Cold-War circumstances and missions. The German Armed Forces have been undergoing an almost uninterrupted process of transformation since the end of the Cold War. In the course of the last two decades the anticipated end-state of the reform has been changing accordingly with respect to the changing perception of strategic assumptions. The strategic reasoning behind the distinct reform attempts is to be analysed in this article.
Determinacy in Stochastic Games with Unbounded Payoff Functions
Tomá? Brázdil,Antonín Kuera,Petr Novotny
Computer Science , 2012,
Abstract: We consider infinite-state turn-based stochastic games of two players, Box and Diamond, who aim at maximizing and minimizing the expected total reward accumulated along a run, respectively. Since the total accumulated reward is unbounded, the determinacy of such games cannot be deduced directly from Martin's determinacy result for Blackwell games. Nevertheless, we show that these games are determined both for unrestricted (i.e., history-dependent and randomized) strategies and deterministic strategies, and the equilibrium value is the same. Further, we show that these games are generally not determined for memoryless strategies. Then, we consider a subclass of Diamond-finitely-branching games and show that they are determined for all of the considered strategy types, where the equilibrium value is always the same. We also examine the existence and type of (epsilon-)optimal strategies for both players.
Ancestral Vascular Lumen Formation via Basal Cell Surfaces
Tomá? Kuera, Boris Strili?, Kathrin Regener, Michael Schubert, Vincent Laudet, Eckhard Lammert
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0004132
Abstract: The cardiovascular system of bilaterians developed from a common ancestor. However, no endothelial cells exist in invertebrates demonstrating that primitive cardiovascular tubes do not require this vertebrate-specific cell type in order to form. This raises the question of how cardiovascular tubes form in invertebrates? Here we discovered that in the invertebrate cephalochordate amphioxus, the basement membranes of endoderm and mesoderm line the lumen of the major vessels, namely aorta and heart. During amphioxus development a laminin-containing extracellular matrix (ECM) was found to fill the space between the basal cell surfaces of endoderm and mesoderm along their anterior-posterior (A-P) axes. Blood cells appear in this ECM-filled tubular space, coincident with the development of a vascular lumen. To get insight into the underlying cellular mechanism, we induced vessels in vitro with a cell polarity similar to the vessels of amphioxus. We show that basal cell surfaces can form a vascular lumen filled with ECM, and that phagocytotic blood cells can clear this luminal ECM to generate a patent vascular lumen. Therefore, our experiments suggest a mechanism of blood vessel formation via basal cell surfaces in amphioxus and possibly in other invertebrates that do not have any endothelial cells. In addition, a comparison between amphioxus and mouse shows that endothelial cells physically separate the basement membranes from the vascular lumen, suggesting that endothelial cells create cardiovascular tubes with a cell polarity of epithelial tubes in vertebrates and mammals.
A Computational Study of the Glycine-Rich Loop of Mitochondrial Processing Peptidase
Tomá? Kuera, Michal Otyepka, Anna Matu?ková, Abdul Samad, Eva Kutejová, Ji?í Janata
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0074518
Abstract: An all atomic, non-restrained molecular dynamics (MD) simulation in explicit water was used to study in detail the structural features of the highly conserved glycine-rich loop (GRL) of the α-subunit of the yeast mitochondrial processing peptidase (MPP) and its importance for the tertiary and quaternary conformation of MPP. Wild-type and GRL-deleted MPP structures were studied using non-restrained MD simulations, both in the presence and the absence of a substrate in the peptidase active site. Targeted MD simulations were employed to study the mechanism of substrate translocation from the GRL to the active site. We demonstrate that the natural conformational flexibility of the GRL is crucial for the substrate translocation process from outside the enzyme towards the MPP active site. We show that the α-helical conformation of the substrate is important not only during its initial interaction with MPP (i.e. substrate recognition), but also later, at least during the first third of the substrate translocation trajectory. Further, we show that the substrate remains in contact with the GRL during the whole first half of the translocation trajectory and that hydrophobic interactions play a major role. Finally, we conclude that the GRL acts as a precisely balanced structural element, holding the MPP subunits in a partially closed conformation regardless the presence or absence of a substrate in the active site.
The Structural and Functional Basis of Catalysis Mediated by NAD(P)H:acceptor Oxidoreductase (FerB) of Paracoccus denitrificans
Vojtěch Sedlá?ek, Tomá? Klumpler, Jaromír Marek, Igor Kuera
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0096262
Abstract: FerB from Paracoccus denitrificans is a soluble cytoplasmic flavoprotein that accepts redox equivalents from NADH or NADPH and transfers them to various acceptors such as quinones, ferric complexes and chromate. The crystal structure and small-angle X-ray scattering measurements in solution reported here reveal a head-to-tail dimer with two flavin mononucleotide groups bound at the opposite sides of the subunit interface. The dimers tend to self-associate to a tetrameric form at higher protein concentrations. Amino acid residues important for the binding of FMN and NADH and for the catalytic activity are identified and verified by site-directed mutagenesis. In particular, we show that Glu77 anchors a conserved water molecule in close proximity to the O2 of FMN, with the probable role of facilitating flavin reduction. Hydride transfer is shown to occur from the 4-pro-S position of NADH to the solvent-accessible si side of the flavin ring. When using deuterated NADH, this process exhibits a kinetic isotope effect of about 6 just as does the NADH-dependent quinone reductase activity of FerB; the first, reductive half-reaction of flavin cofactor is thus rate-limiting. Replacing the bulky Arg95 in the vicinity of the active site with alanine substantially enhances the activity towards external flavins that obeys the standard bi-bi ping-pong reaction mechanism. The new evidence for a cryptic flavin reductase activity of FerB justifies the previous inclusion of this enzyme in the protein family of NADPH-dependent FMN reductases.
Efficient Controller Synthesis for Consumption Games with Multiple Resource Types
Tomá? Brázdil,Krishnendu Chatterjee,Antonín Kuera,Petr Novotny
Mathematics , 2012,
Abstract: We introduce consumption games, a model for discrete interactive system with multiple resources that are consumed or reloaded independently. More precisely, a consumption game is a finite-state graph where each transition is labeled by a vector of resource updates, where every update is a non-positive number or omega. The omega updates model the reloading of a given resource. Each vertex belongs either to player \Box or player \Diamond, where the aim of player \Box is to play so that the resources are never exhausted. We consider several natural algorithmic problems about consumption games, and show that although these problems are computationally hard in general, they are solvable in polynomial time for every fixed number of resource types (i.e., the dimension of the update vectors).
Qualitative Reachability in Stochastic BPA Games
Tomá? Brázdil,Václav Bro?ek,Antonín Kuera,Jan Obdr?álek
Computer Science , 2010, DOI: 10.1016/j.ic.2011.02.002
Abstract: We consider a class of infinite-state stochastic games generated by stateless pushdown automata (or, equivalently, 1-exit recursive state machines), where the winning objective is specified by a regular set of target configurations and a qualitative probability constraint `>0' or `=1'. The goal of one player is to maximize the probability of reaching the target set so that the constraint is satisfied, while the other player aims at the opposite. We show that the winner in such games can be determined in PTIME for the `>0' constraint, and both in NP and coNP for the `=1' constraint. Further, we prove that the winning regions for both players are regular, and we design algorithms which compute the associated finite-state automata. Finally, we show that winning strategies can be synthesized effectively.
Approximating the Termination Value of One-Counter MDPs and Stochastic Games
Tomá? Brázdil,Václav Bro?ek,Kousha Etessami,Antonín Kuera
Computer Science , 2011,
Abstract: One-counter MDPs (OC-MDPs) and one-counter simple stochastic games (OC-SSGs) are 1-player, and 2-player turn-based zero-sum, stochastic games played on the transition graph of classic one-counter automata (equivalently, pushdown automata with a 1-letter stack alphabet). A key objective for the analysis and verification of these games is the termination objective, where the players aim to maximize (minimize, respectively) the probability of hitting counter value 0, starting at a given control state and given counter value. Recently, we studied qualitative decision problems ("is the optimal termination value = 1?") for OC-MDPs (and OC-SSGs) and showed them to be decidable in P-time (in NP and coNP, respectively). However, quantitative decision and approximation problems ("is the optimal termination value ? p", or "approximate the termination value within epsilon") are far more challenging. This is so in part because optimal strategies may not exist, and because even when they do exist they can have a highly non-trivial structure. It thus remained open even whether any of these quantitative termination problems are computable. In this paper we show that all quantitative approximation problems for the termination value for OC-MDPs and OC-SSGs are computable. Specifically, given a OC-SSG, and given epsilon > 0, we can compute a value v that approximates the value of the OC-SSG termination game within additive error epsilon, and furthermore we can compute epsilon-optimal strategies for both players in the game. A key ingredient in our proofs is a subtle martingale, derived from solving certain LPs that we can associate with a maximizing OC-MDP. An application of Azuma's inequality on these martingales yields a computable bound for the "wealth" at which a "rich person's strategy" becomes epsilon-optimal for OC-MDPs.
Markov Decision Processes with Multiple Long-run Average Objectives
Tomá? Brázdil,Václav Bro?ek,Krishnendu Chatterjee,Vojtěch Forejt,Antonín Kuera
Computer Science , 2011, DOI: 10.2168/LMCS-10(1:13)2014
Abstract: We study Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) functions. We consider two different objectives, namely, expectation and satisfaction objectives. Given an MDP with k limit-average functions, in the expectation objective the goal is to maximize the expected limit-average value, and in the satisfaction objective the goal is to maximize the probability of runs such that the limit-average value stays above a given vector. We show that under the expectation objective, in contrast to the case of one limit-average function, both randomization and memory are necessary for strategies even for epsilon-approximation, and that finite-memory randomized strategies are sufficient for achieving Pareto optimal values. Under the satisfaction objective, in contrast to the case of one limit-average function, infinite memory is necessary for strategies achieving a specific value (i.e. randomized finite-memory strategies are not sufficient), whereas memoryless randomized strategies are sufficient for epsilon-approximation, for all epsilon>0. We further prove that the decision problems for both expectation and satisfaction objectives can be solved in polynomial time and the trade-off curve (Pareto curve) can be epsilon-approximated in time polynomial in the size of the MDP and 1/epsilon, and exponential in the number of limit-average functions, for all epsilon>0. Our analysis also reveals flaws in previous work for MDPs with multiple mean-payoff functions under the expectation objective, corrects the flaws, and allows us to obtain improved results.
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