stochastic complexity
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We explored the transition of 13 X-linked markers across two separate portions of the house mouse hybrid zone, asking whether such a comparison can distinguish the effects of selection from random factors. A heuristic search in the likelihood landscape revealed more complex likelihood profiles for data sampled in two-dimensional (2D) space relative to data sampled along a linear transect. Randomized resampling of localities analyzed for individual loci showed that deletion of sites away from the zone center can decrease cline width estimates whereas deletion of sites close to the center can significantly increase the width estimates. Deleting localities for all loci resulted in wider clines if the number of samples from the center was limited. The results suggest that, given the great variation in width estimates resulting from inclusion/exclusion of sampling sites, the geographic sampling design is important in hybrid zone studies and that our inferences should take into account measures of uncertainty such as support intervals. The comparison of the two transects indicates cline widths are narrower for loci in the central part of the X chromosome, suggesting selection is stronger in this region and genetic incompatibilities may have at least partly common architecture in the house mouse hybrid zone.
- MeSH
- druhová specificita MeSH
- genetické markery genetika MeSH
- genotyp MeSH
- hybridizace genetická MeSH
- myši genetika MeSH
- pravděpodobnostní funkce MeSH
- rozmnožování genetika MeSH
- selekce (genetika) MeSH
- stochastické procesy MeSH
- vznik druhů (genetika) MeSH
- zeměpis MeSH
- zvířata MeSH
- Check Tag
- myši genetika MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- Geografické názvy
- Česká republika MeSH
- Německo MeSH
Fractals are models of natural processes with many applications in medicine. The recent studies in medicine show that fractals can be applied for cancer detection and the description of pathological architecture of tumors. This fact is not surprising, as due to the irregular structure, cancerous cells can be interpreted as fractals. Inspired by Sierpinski carpet, we introduce a flexible parametric model of random carpets. Randomization is introduced by usage of binomial random variables. We provide an algorithm for estimation of parameters of the model and illustrate theoretical and practical issues in generation of Sierpinski gaskets and Hausdorff measure calculations. Stochastic geometry models can also serve as models for binary cancer images. Recently, a Boolean model was applied on the 200 images of mammary cancer tissue and 200 images of mastopathic tissue. Here, we describe the Quermass-interaction process, which can handle much more variations in the cancer data, and we apply it to the images. It was found out that mastopathic tissue deviates significantly stronger from Quermass-interaction process, which describes interactions among particles, than mammary cancer tissue does. The Quermass-interaction process serves as a model describing the tissue, which structure is broken to a certain level. However, random fractal model fits well for mastopathic tissue. We provide a novel discrimination method between mastopathic and mammary cancer tissue on the basis of complex wavelet-based self-similarity measure with classification rates more than 80%. Such similarity measure relates to Hurst exponent and fractional Brownian motions. The R package FractalParameterEstimation is developed and introduced in the paper.
- MeSH
- algoritmy MeSH
- diagnóza počítačová metody MeSH
- duktální karcinom prsu MeSH
- fraktály MeSH
- hodnocení rizik metody MeSH
- lidé MeSH
- nádory prsu diagnóza patologie MeSH
- patologie metody MeSH
- počítačová simulace MeSH
- stochastické procesy MeSH
- Check Tag
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
... The Canonical Distribution and Stochastic Differential Equations -- 7. ... ... Numerical Methods for Stochastic Molecular Dynamics -- 8. ...
Interdisciplinary Applied Mathematics, ISSN 0939-6047 39
1st edition XXII, 443 stran : ilustrace ; 24 cm
- MeSH
- matematika MeSH
- simulace molekulární dynamiky MeSH
- Publikační typ
- monografie MeSH
- Konspekt
- Matematika
- NLK Obory
- přírodní vědy
This article presents a stochastic model of binaural hearing in the medial superior olive (MSO) circuit. This model is a variant of the slope encoding models. First, a general framework is developed describing the elementary neural operations realized on spike trains in individual parts of the circuit and how the neurons converging onto the MSO are connected. Random delay, coincidence detection of spikes, divergence and convergence of spike trains are operations implemented by the following modules: spike generator, jitter generator, and coincidence detector. Subsequent processing of spike trains computes the sound azimuth in the circuit. The circuit parameters that influence efficiency of slope encoding are studied. In order to measure the overall circuit performance the concept of an ideal observer is used instead of a detailed model of higher relays in the auditory pathway. This makes it possible to bridge the gap between psychophysical observations in humans and recordings taken of small rodents. Most of the results are obtained through numerical simulations of the model.
- MeSH
- akční potenciály fyziologie MeSH
- akustická stimulace metody MeSH
- lidé MeSH
- modely neurologické * MeSH
- nervová síť * fyziologie MeSH
- nucleus olivaris caudalis * fyziologie MeSH
- sluchová dráha * fyziologie MeSH
- stochastické procesy MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Cryo Electron Tomography (cryoET) plays an essential role in Structural Biology, as it is the only technique that allows to study the structure of large macromolecular complexes in their close to native environment in situ. The reconstruction methods currently in use, such as Weighted Back Projection (WBP) or Simultaneous Iterative Reconstruction Technique (SIRT), deliver noisy and low-contrast reconstructions, which complicates the application of high-resolution protocols, such as Subtomogram Averaging (SA). We propose a Progressive Stochastic Reconstruction Technique (PSRT) - a novel iterative approach to tomographic reconstruction in cryoET based on Monte Carlo random walks guided by Metropolis-Hastings sampling strategy. We design a progressive reconstruction scheme to suit the conditions present in cryoET and apply it successfully to reconstructions of macromolecular complexes from both synthetic and experimental datasets. We show how to integrate PSRT into SA, where it provides an elegant solution to the region-of-interest problem and delivers high-contrast reconstructions that significantly improve template-based localization without any loss of high-resolution structural information. Furthermore, the locality of SA is exploited to design an importance sampling scheme which significantly speeds up the otherwise slow Monte Carlo approach. Finally, we design a new memory efficient solution for the specimen-level interior problem of cryoET, removing all associated artifacts.
- MeSH
- algoritmy MeSH
- elektronová kryomikroskopie metody MeSH
- makromolekulární látky chemie MeSH
- metoda Monte Carlo MeSH
- počítačové zpracování obrazu metody MeSH
- reprodukovatelnost výsledků MeSH
- ribozomy chemie MeSH
- stochastické procesy * MeSH
- tomografie elektronová metody MeSH
- zobrazování trojrozměrné metody MeSH
- Publikační typ
- časopisecké články MeSH
Cell cycle is controlled by the activity of protein family of cyclins and cyclin-dependent kinases that are periodically expressed during cell cycle and that are conserved among different species. Genome-wide location analysis found that cyclins are controlled by a small number of transcription factors that form closed network of genes controlling each other. To investigate gene expression dynamics of this network, we developed a general procedure for stochastic simulation of gene expression process. Using the binding data, we simulated gene expression of all genes of the network for all possible combinations of regulatory interactions and by statistical comparison with experimentally measured time series excluded those interactions that formed gene expression temporal profiles significantly different from the measured ones. These experiments led to a new definition of the cyclins regulatory network coherent with the binding experiments which are kinetically plausible. Level of influence of individual regulators in control of the regulated genes is defined. Simulation results indicate particular mechanism of regulatory activity of protein complexes involved in the control of cyclins.
Cíl: Analýza DNA je dnes širokou verejností prijímána jako zcela standardní a bezchybná metoda, ale za nekterých okolností muže její spolehlivost výrazne klesat. Tento príspevek se zabývá procesem identifikace a stanovením váhy evidence proti podezrelému a uvedeme v nem hlavní stochastické prístupy k identifikaci osob. Metody: Z Bayesovy vety jsme odvodili vzorec pro stanovení váhy evidence a ukázali jeho použití v modelu ostrovního problému. K výpoctum složitejších situací jsme použili z Dirichletova rozdelení odvozenou beta-binomickou formuli. Výsledky: Z mnoha ruzných komplikací v modelu ostrovního problému jsme ukázali, jak se vyporádat s nejistotou ve velikosti populace. Beta-binomickou formuli jsme využili k zahrnutí subpopulacní struktury a v problematice DNA smesí. Závery: Zejména vliv populacní struktury je dnes nedostatecne prozkoumán. S využitím výsledku H. Kubátové jsme v této oblasti odvodili nové vzorce.
Objectives: The DNA analysis is now accepted by the broad public as a completely standard and faultless procedure but in some circumstances its reliability can decrease substantially. This paper deals with the process of identifying and determining the weight of evidence against the suspect. Main stochastic approaches to identification are shown. Methods: The weight-of-evidence formula was derived from Bayes theorem and its application in the model of the island problem was demonstrated. The beta-binomial formula derived from Dirichlet distribution was used for calculation of more complex situations. Results: From many various complications in the model of the island problem there was shown how to work with uncertainty in a population size. The beta-binomial formula was used to include a subpopulation structure and in issues of DNA mixtures. Conclusions: In particular, the influence of a population structure is now explored insufficiently. Using the results of H. Kubátová in this area, a new formula was derived.
- Klíčová slova
- vzorec pro stanovení váhy evidence, coancestry koeficient, beta-binomická výběrová formule, DNA směsi,
- MeSH
- DNA fingerprinting metody trendy využití MeSH
- financování organizované MeSH
- lidé MeSH
- statistika jako téma MeSH
- zločin statistika a číselné údaje MeSH
- zločinci statistika a číselné údaje MeSH
- Check Tag
- lidé MeSH
Multitemplate polymerase chain reaction (PCR) is used for preparative and analytical applications in diagnostics and research. Classical PCR and qPCR are two basic setups with many possible experimental modifications. Classical PCR is a method of choice to obtain enough material for subsequent sophisticated applications such as construction of libraries for next-generation sequencing or high-throughput screening. Sequencing and Single Nucleotide Primer Extension (SNuPE) employ one-strand synthesis and represent a distinct variant of analytical DNA synthesis. In all these applications, maintaining the initial ratio of templates and avoiding underestimation of minority templates is desired. Here, we demonstrate that different templates can amplify independently at low template concentrations (typical in qPCR setups, in which the polymerase concentration is usually several orders of magnitude higher than the template concentration). However, rare templates can be diluted in an effort to keep DNA amplification in the exponential phase, or template concentration can be biased by differences in amplification efficiency. Moreover, amplification of templates present in low concentrations is more vulnerable to stochastic events that lead to proportional changes in the product ratio, as well as by incomplete amplification leading to chimera formation. These undesired effects can be compensated for by using highly processive polymerases with high and equal affinity to different primer-template complexes. Novel enhanced polymerases are desired. With increasing concentration of a primer-template of interest, the system becomes more deterministic. Nevertheless, marked deviation from independent exponential amplification occurs when the total template concentration starts to approach the polymerase concentration. The primer-template complexes compete for enzyme molecules, and the amount of products grows arithmetically-the system starts to obey Michaelis-Menten kinetics. Synthesis of rare products in a multitemplate mixture can run more easily under the detection limit in such conditions, although it would be unequivocally detectable in a single template assay. When fishing out rare template variants, the best processive polymerases should be used to decrease both amplification and detection limits. The possibility of stochastic events, should be taken into account to correctly interpret the obtained data.
