Járműdinamikai rendszerek integrált fuzzy-sztochasztikus modellezése és identifikációja = Integrated Modeling and Identification of Vehicle Dynamic Systems

A kutatómunka a lineáris és a nemlineáris járműdinamikai rendszerek a bizonytalansági tényezőket is figyelembe vevő új típusú modellezési eljárásainak és rendszeridentifikációs algoritmusainak kidolgozásával foglalkozik. A járműdinamikai modellezés metodológiai megközelítése a hagyományos statisztikai rendszeridentifikációs módszerek mellett alkalmazza a különböző lágy számítástudományi megközelítési módokat, így többek között felhasználja a fuzzy logika, fuzzy irányítástechnika algoritmusait, a neurális és fuzzy-neurális hálózatokat, továbbá a szinguláris értékdekompozíció (SVD) módszereit, kapcsolatot teremtve az LPV rendszereken értelmezett Takagi-Sugeno típusú fuzzy irányítási algoritmusok és a magasabb rendű szinguláris érték dekompozíció között. A nemlineáris járműdinamikai rendszerek komplex modellezésénél foglalkozunk a hatékony komplexitás csökkentő technikák kidolgozásával is, fuzzy interpolációs eljárások alkalmazásával, ahol a tömeges adatfeldolgozást multiprocesszoros számítások segítségével végezzük el. A lineáris járműdinamikai modellezés során összehasonlítjuk a szabályalapú fuzzy irányítástechnikai eljárásokkal kapott eredményeket a sztochasztikus identifikációs módszerek becslésével, a transzferfüggvények illetve a transzfermátrixok különböző típusú approximációja alapján. | This research project deals with the construction and development of new models of "uncertain principles" for the description of linear and nonlinear vehicle system dynamics using efficient new stochastic, fuzzy modelling approaches and identification algorythms. The methodological approach of the vehicle dynamics modelling is not only based on the traditional statistical system idetificaion methods, but on those soft computing approaches using among others fuzzy logic and fuzzy control algorythms, neural and fuzzy-neural networks, new singular value decomposition methods, establishing interconnection between Takagi-Sugeno type control models interpreted for LPV systems and higher order singular value decomposition (HOSVD). In the large-scale and complex modelling of the nonlinear vehicle system dynamics efficient complexity reduction techniques and fuzzy interpolative methods will be applied for the realization of the mass-data processing on the basis of multiprocessor computational intelligence. In the linear vehicle dynamic modelling a comparison will be examined between the rulebased fuzzy control approaches and modelling of the well-known modern stochastic identification methods on the basis of different transfer function and transfer matrix approximations

Transcriptionally active chromatin loops contain both ‘active’ and ‘inactive’ histone modifications that exhibit exclusivity at the level of nucleosome clusters

Chromatin state is thought to impart regulatory function to the underlying DNA sequence. This can be established through histone modifications and chromatin organisation, but exactly how these factors relate to one another to regulate gene expression is unclear. In this study, we have used super-resolution microscopy to image the Y loops of Drosophila melanogaster primary spermatocytes, which are enormous transcriptionally active chromatin fibres, each representing single transcription units that are individually resolvable in the nuclear interior. We previously found that the Y loops consist of regular clusters of nucleosomes, with an estimated median of 54 nucleosomes per cluster with wide variation. In this study, we report that the histone modifications H3K4me3, H3K27me3, and H3K36me3 are also clustered along the Y loops, with H3K4me3 more associated with diffuse chromatin compared to H3K27me3. These histone modifications form domains that can be stretches of Y loop chromatin micrometres long, or can be in short alternating domains. The different histone modifications are associated with different sizes of chromatin clusters and unique morphologies. Strikingly, a single chromatin cluster almost always only contains only one type of the histone modifications that were labelled, suggesting exclusivity, and therefore regulation at the level of individual chromatin clusters. The active mark H3K36me3 is more associated with actively elongating RNA polymerase II than H3K27me3, with polymerase often appearing on what are assumed to be looping regions on the periphery of chromatin clusters. These results provide a foundation for understanding the relationship between chromatin state, chromatin organisation, and transcription regulation – with potential implications for pause-release dynamics, splicing complex organisation and chromatin dynamics during polymerase progression along a gene

Fast imaging of live organisms with sculpted light sheets.

Light-sheet microscopy is an increasingly popular technique in the life sciences due to its fast 3D imaging capability of fluorescent samples with low photo toxicity compared to confocal methods. In this work we present a new, fast, flexible and simple to implement method to optimize the illumination light-sheet to the requirement at hand. A telescope composed of two electrically tuneable lenses enables us to define thickness and position of the light-sheet independently but accurately within milliseconds, and therefore optimize image quality of the features of interest interactively. We demonstrated the practical benefit of this technique by 1) assembling large field of views from tiled single exposure each with individually optimized illumination settings; 2) sculpting the light-sheet to trace complex sample shapes within single exposures. This technique proved compatible with confocal line scanning detection, further improving image contrast and resolution. Finally, we determined the effect of light-sheet optimization in the context of scattering tissue, devising procedures for balancing image quality, field of view and acquisition speed.This work was funded by grants from the Wellcome Trust, the Medical Research Council, the CamBridgeSense network, Carlsberg Foundation, the Alzheimer Research UK Trust and the Biotechnology and Biological Sciences Research Council and the Wolfson Foundation.This is the final version of the article. It first appeared at http://dx.doi.org/10.1038/srep09385

Környezeti folyamatok modellezése "Soft Computing" módszerekkel = Modeling of environmental processes by soft computing methods

A környezeti folyamatok összetettsége, és nemlineáris volta miatt tanulmányozásukhoz adekvát modellek szükségesek. Az ún. soft computing módszerek (rács alapú celluláris neurális hálózatok, sejtautomaták és fuzzy szabályok) a környezeti folyamatok modellezésének ígéretes eszközei [8, 19]. Létrehoztunk egy általános celluláris neuronhálózat (CNN) modellt szennyeződések terjedésének vizsgálatára [1, 5, 10, 20], amely alapját képezheti egy hatékony döntéstámogató rendszer létrehozásának. A rendszer finomítása érdekében a környezeti rendszer egyes komponenseiben zajló folyamatokat is megvizsgáltuk, hangsúlyt fektetve a folyadék és gázáramlás áramlás modelljeire [6, 7, 23]. Vizsgálatukhoz közelítő numerikus módszereket fejlesztetünk [5, 16, 17, 25] Megvizsgáltuk a zavarás (élőhely vesztés és invázív fajok) hatását a populáció szintű folyamatokra sejtautomata modellek és szimulációk segítségével. Kimutattuk, hogy az élőhelyek számának csökkenésével az invázív (gyom jellegű) fajok előnyösebb helyzetbe kerülnek [4]. Kiderült, hogy az invázív fajok visszaszorításának sikeressége a kolonizációs képességük visszaszorításán múlik és függ a térbeli aggregációtól [2, 3, 14, 18, 21, 24]. Alkalmazásként sor került egy fejlett numerikus szimulációs technológiákra épülő informatikai rendszer prototípusának megalkotására, amely tetszőleges úthálózatok gépjárműforgalmának, és a társult környezeti terhelés eloszlásának számítógépes modellezésére használható. | Studying environmental processes requires adequate models, because of their high level of complexity and nonlinearity. Soft computing methods (such as cellular neural networks, cellular automata and fuzzy rules) provide reliable tools of modeling environmental systems [8, 19]. We have created a general model of cellular neural network (CNN) in order to investigate the propagation of pollutions [1, 5, 10, 20]. Effective decision support systems can be constructed on the base of this model. Processes in the particular components of the environmental system were also studied, in particular models of liquid and gas flow [6, 7, 23]. New numerical methods have been developed for their investigation [5, 16, 17, 25]. The effect of disturbance (such as habitat destruction and invasive species) on population level processes has been investigated with the help of cellular automaton models and simulations. We have demonstrated that decreasing number of habitats promotes invasive (weed) species [4]. As it turned out, the success of eradication of invasive species depends mainly on depression of colonization ability and also depends on spatial aggregation of species [2, 3, 14, 18, 21, 24]. As a particular application, a prototype of an advanced simulation technology-based IT system has been created. It is reliable to model the distribution of environmental pollution over an arbitrary road-system with traffic

From Single-Molecule Interactions to Population-Level Dynamics: Understanding the Complex Organization of RNA Pol II in the Nucleus of Living Cells

Transcription involves a complex exchange within a reservoir of proteins in the nucleoplasm, and the specific recruitment of individual proteins at specific gene loci. However, understanding the spatial distribution of individual proteins and the temporal behavior in the nucleus of living cells remains challenging. Using 3D super-resolution fluorescence microscopy and cluster analysis, we observe that the distribution of RNA Polymerase II (Pol II) cluster sizes, measured as the number of polymerases per cluster, follows a −3/2 power law. Radial dependent analysis of the spatial distribution of Pol II also shows scale-invariance, consistent with a so-called self-organized criticality in a fractal geometry of dimension ∼2.7. These results suggest a diffusion-based mechanism whereby, via transient interactions, massive recruitment and dismissal of pol II molecules can occur at specific loci in the nucleoplasm. Kinetic measurements using single-molecule detection in live cells reveal Pol II binding dynamics within minutes. Serum-induced transcription increased Pol II binding kinetics in live cells by an order of magnitude. Together, these results provide a comprehensive view of the spatio-temporal organization of Pol II in the nucleus: from the global population distribution, to single molecule recruitment at specific loci in live cells. This comprehensive single-cell approach can be adopted for other proteins beside RNA Pol II, for real-time quantification of protein organization in vivo, with single-molecule sensitivity

The ciliary marginal zone of the zebrafish retina: clonal and time-lapse analysis of a continuously growing tissue.

Clonal analysis is helping us understand the dynamics of cell replacement in homeostatic adult tissues (Simons and Clevers, 2011). Such an analysis, however, has not yet been achieved for continuously growing adult tissues, but is essential if we wish to understand the architecture of adult organs. The retinas of lower vertebrates grow throughout life from retinal stem cells (RSCs) and retinal progenitor cells (RPCs) at the rim of the retina, called the ciliary marginal zone (CMZ). Here, we show that RSCs reside in a niche at the extreme periphery of the CMZ and divide asymmetrically along a radial (peripheral to central) axis, leaving one daughter in the peripheral RSC niche and the other more central where it becomes an RPC. We also show that RPCs of the CMZ have clonal sizes and compositions that are statistically similar to progenitor cells of the embryonic retina and fit the same stochastic model of proliferation. These results link embryonic and postembryonic cell behaviour, and help to explain the constancy of tissue architecture that has been generated over a lifetime.This work was supported by a Wellcome Trust Senior Investigator Awards [100329/Z/12/Z to W.A.H.] and [098357/Z/12/Z to B.D.S].This is the final version of the article. It first appeared from The Company of Biologists via https://doi.org/10.1242/dev.13331

Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells

Transcription is reported to be spatially compartmentalized in nuclear transcription factories with clusters of RNA polymerase II (Pol II). However, little is known about when these foci assemble or their relative stability. We developed a quantitative single-cell approach to characterize protein spatiotemporal organization, with single-molecule sensitivity in live eukaryotic cells. We observed that Pol II clusters form transiently, with an average lifetime of 5.1 (± 0.4) seconds, which refutes the notion that they are statically assembled substructures. Stimuli affecting transcription yielded orders-of-magnitude changes in the dynamics of Pol II clusters, which implies that clustering is regulated and plays a role in the cell’s ability to effect rapid response to external signals. Our results suggest that transient crowding of enzymes may aid in rate-limiting steps of gene regulation

Soft computing számítógépes realizálása numerikus algoritmusokkal = Soft computing implementation by numerical algorithms

A Soft computing számítógépes realizálása számítógépes algoritmusokkal c. projektben elért eredmények a következők: 1. Kidolgozásra került a többdimenziós fuzzy kalkulusban is alkalmazható rácsmentes interpolációs technika. 2. Az evolúciós feladatok megoldására minőségi tulajdonságokat (monotonitás, energia megmaradás) is megőrző sokprocesszoros környezetben is hatékonyan alkalmazható numerikus algoritmusok kerültek kifejlesztésre. 3. A parciális differenciálegyenletek számítógépes megoldásához kifejlesztésre került egy ciklikus mátrix prekondicionert alkalmazó tartomány dekompozíciós párhuzamos algoritmus. 4. A nagyméretű lineáris egyenletrendszerek és nemlineáris minimalizálási feladatok megoldásához egy reziduum négyzet minimalizáláson alapuló új genetikai jellegű jól skálázható párhuzamos algoritmus került kifejlesztésre. | The main results of the project: Computer realization of soft computing by numerical algorithm: 1. Development of a meshless interpolation technique applicable for multidimensional fuzzy calculus. 2. Working out some parallel numerical algorithms preserving quality properties of the solution (monotonicity, conservative of energy) for evolution problems. 3. Development of a domain decomposition parallel algorithm for numerical solution of partial differential equations based on cyclic preconditioner matrices. 4. For large linear system of equation and for nonlinear minimizing problems development of a parallel scalable genetic algorithm based on residual minimization

Invaginating endoderm pulls on the extending ectoderm

How genetic programs generate cell-intrinsic forces to shape embryos is actively studied, but less so how tissue-scale physical forces impact morphogenesis. Here we address the role of the latter during axis extension, using Drosophila germband extension (GBE) as a model. We found previously that cells elongate in the anteroposterior (AP) axis in the extending germband, suggesting that an extrinsic tensile force contributed to body axis extension. Here we further characterized the AP cell elongation patterns during GBE, by tracking cells and quantifying their apical cell deformation over time. AP cell elongation forms a gradient culminating at the posterior of the embryo, consistent with an AP-oriented tensile force propagating from there. To identify the morphogenetic movements that could be the source of this extrinsic force, we mapped gastrulation movements temporally using light sheet microscopy to image whole Drosophila embryos. We found that both mesoderm and endoderm invaginations are synchronous with the onset of GBE. The AP cell elongation gradient remains when mesoderm invagination is blocked but is abolished in the absence of endoderm invagination. This suggested that endoderm invagination is the source of the tensile force. We next looked for evidence of this force in a simplified system without polarized cell intercalation, in acellular embryos. Using Particle Image Velocimetry, we identify posteriorwards Myosin II flows towards the presumptive posterior endoderm, which still undergoes apical constriction in acellular embryos as in wildtype. We probed this posterior region using laser ablation and showed that tension is increased in the AP orientation, compared to dorsoventral orientation or to either orientations more anteriorly in the embryo. We propose that apical constriction leading to endoderm invagination is the source of the extrinsic force contributing to germband extension. This highlights the importance of physical interactions between tissues during morphogenesis.This work was funded by a Biotechnology and Biological Sciences Research Council grant BB/ J010278/1 to GBB, RJA and BS, a Wellcome Trust Investigator Award 099234/Z/12/Z to BS and a Herchel Smith Postdoctoral Fellowship from the University of Cambridge to C