Computation analysis
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OBJECTIVE: This paper aims to improve the shortcomings of the extant methodologies for realistic Laplacian (RL) computation, and correct the erroneous claims published in the past. METHODS: We implemented several variants of RL computation methods, using various potential approximation techniques and different regularization approaches. The individual variants of the RL computation were tested using simulations based on a realistic head model computed with the boundary element method (BEM). The results which disagreed with previously published works were further analyzed, and the reasons for the disagreement were identified. RESULTS: We identified the best regularization techniques for the surface potential approximation, and we showed that once these techniques are used there is often little difference between various potential approximations, which is in contrast with previous claims that promoted the radial basis function (RBF) approximation. Further, our analysis shows that the RBF approximation suffers from Runge phenomenon, which cannot be mitigated simultaneously for both deep and shallow sources; therefore, its good performance is guarantied only if a priori knowledge about the source depth is available. CONCLUSIONS: The previously published methodology for RL computation was not optimal. Improvements are possible if the newly suggested approach is used. SIGNIFICANCE: The methodology presented in our paper allows more efficient utilization of the RL, providing a useful tool for processing of high density EEG recordings. Presented techniques allow to achieve high EEG spatial resolution, and avoid unnecessary spatial blurring caused by the problems in the previously published RL methodology.
Compromised detection of short DNA fragments can result in underestimation of radiation-induced clustered DNA damage. The fragments can be detected with atomic force microscopy (AFM), followed by image analysis to compute the length of plasmid molecules. Plasmid molecules imaged with AFM are represented by open or closed curves, possibly with crossings. For the analysis of such objects, a dedicated algorithm was developed, and its usability was demonstrated on the AFM images of plasmid pBR322 irradiated with 60Co gamma rays. The analysis of the set of the acquired AFM images revealed the presence of DNA fragments with lengths shorter than 300 base pairs that would have been neglected by a conventional detection method.
- MeSH
- chemické jevy MeSH
- DNA bakterií chemie účinky záření MeSH
- mikroskopie atomárních sil metody MeSH
- molekulová hmotnost MeSH
- plazmidy chemie účinky záření MeSH
- počítačové zpracování obrazu metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- DNA bakterií MeSH
The system was designed to allow simultaneous monitoring of eight bioelectrical signals together with the necessary event markers. The data inputs are pulse code modulated, recorded on magnetic tape, and then read into a minicomputer. The computer permits the determination of parameters for the following signals: electrocardiogram (ECG), respiration (RESP), skin conductance changes (SCC), electromyogram (EMG), plethysmogram (PLET), pulse transmission time (PTT), and electroencephalogram (EEG). These parameters are determined for time blocks of selectable duration and read into a mainframe computer for further statistical analysis.
Soliton dynamics and nonlinear phenomena in quantum deformation has been investigated through conformal time differential generalized form of q deformed Sinh-Gordon equation. The underlying equation has recently undergone substantial amount of research. In Phase 1, we employed modified auxiliary and new direct extended algebraic methods. Trigonometric, hyperbolic, exponential and rational solutions are successfully extracted using these techniques, coupled with the best possible constraint requirements implemented on parameters to ensure the existence of solutions. The findings, then, are represented by 2D, 3D and contour plots to highlight the various solitons' propagation patterns such as kink-bright, bright, dark, bright-dark, kink, and kink-peakon solitons and solitary wave solutions. It is worth emphasizing that kink dark, dark peakon, dark and dark bright solitons have not been found earlier in literature. In phase 2, the underlying model is examined under various chaos detecting tools for example lyapunov exponents, multistability and time series analysis and bifurcation diagram. Chaotic behavior is investigated using various initial condition and novel results are obtained.
For further understanding of neural coding, stochastic variability of interspike intervals has been investigated by both experimental and theoretical neuroscientists. In stochastic neuronal models, the interspike interval corresponds to the time period during which the process imitating the membrane potential reaches a threshold for the first time from a reset depolarization. For neurons belonging to complex networks in the brain, stochastic diffusion processes are often used to approximate the time course of the membrane potential. The interspike interval is then viewed as the first passage time for the employed diffusion process. Due to a lack of analytical solution for the related first passage time problem for most diffusion neuronal models, a numerical integration method, which serves to compute first passage time moments on the basis of the Siegert recursive formula, is presented in this paper. For their neurobiological plausibility, the method here is associated with diffusion processes whose state spaces are restricted to finite intervals, but it can also be applied to other diffusion processes and in other (non-neuronal) contexts. The capability of the method is demonstrated in numerical examples and the relation between the integration step, accuracy of calculation and amount of computing time required is discussed.
- MeSH
- akční potenciály MeSH
- časové faktory MeSH
- modely neurologické * MeSH
- neurony fyziologie MeSH
- numerická analýza pomocí počítače * MeSH
- počítačová simulace * MeSH
- reprodukovatelnost výsledků MeSH
- software MeSH
- stochastické procesy * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The lack of exact definition of the concept of biological age (BA) is a typical feature of works concerning BA. That is why comparison of results of various published methods makes little sense and eventual proof of their optimality is impossible. Based on natural and simple presumptions, an attempt to express mathematically the supposed relation between chronological age (CA) and BA has proven to be unexpectedly fruitful. In the present paper, an optimum method of estimation of BA, which is easily applicable even in nonlinear cases, is derived. Moreover, the method allows evaluating the precision of the estimates and also offers tools for validation of presumptions of the method. A special feature of the method is that CA should be used as a standard biomarker, leading to essential improving the precision of BA-estimate and illuminating relativity of the known "paradox of biomarkers". All theoretical results of the method were fully approved by means of a special simulation program. Further, the theory and the results of the simulation have proven that many published results of BA-estimates using multiple linear regression (MLR) are very probably disserviceable because CA is typically more precise estimate of BA than estimates computed by MLR. This unpleasant conclusion also concerns methods, which use MLR as the final step after transformation of the battery of biomarkers by factor analysis or by principal component analysis.
- MeSH
- biologické modely * MeSH
- lidé MeSH
- stárnutí fyziologie MeSH
- výpočetní biologie metody MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The purpose of the present study was to describe the structural density and geometry of the bone, as well as its sensitivity to the resolution of finite element discretisation. The study introduces a novel way to validate biomechanical model of the bone by experimental modal analysis. The structural density and geometry of the model was obtained from a composite bone. A detailed investigation of the weight dependence of the bone on the mesh resolution was performed to obtain the best match with the real weight of the tested bone. The computational model was compared with the experimental results obtained from the modal analysis. The overall changes of the modal properties and bone weight in the model caused by different mesh resolutions and order of approximation were below 10%, despite the bone was modelled with simple isotropic material properties. The experimental modal analysis shows a great potential to be a robust verification tool of computational biomechanical models because it provides boundary conditions-free results. The sensitivity analysis revealed that the linear approximation of the density field is not suitable for the modelling of the modal response of composite bone.
- Klíčová slova
- Modal analysis, bone weight, finite element, pelvic bone, sensitivity, structural density,
- MeSH
- analýza metodou konečných prvků MeSH
- biomechanika MeSH
- lidé MeSH
- lineární modely MeSH
- mechanický stres MeSH
- pánevní kosti anatomie a histologie diagnostické zobrazování MeSH
- počítačová rentgenová tomografie MeSH
- počítačová simulace * MeSH
- reprodukovatelnost výsledků MeSH
- velikost orgánu MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- validační studie MeSH
Stochastic modelling of gene regulatory networks provides an indispensable tool for understanding how random events at the molecular level influence cellular functions. A common challenge of stochastic models is to calibrate a large number of model parameters against the experimental data. Another difficulty is to study how the behaviour of a stochastic model depends on its parameters, i.e. whether a change in model parameters can lead to a significant qualitative change in model behaviour (bifurcation). In this paper, tensor-structured parametric analysis (TPA) is developed to address these computational challenges. It is based on recently proposed low-parametric tensor-structured representations of classical matrices and vectors. This approach enables simultaneous computation of the model properties for all parameter values within a parameter space. The TPA is illustrated by studying the parameter estimation, robustness, sensitivity and bifurcation structure in stochastic models of biochemical networks. A Matlab implementation of the TPA is available at http://www.stobifan.org.
- Klíčová slova
- gene regulatory networks, high-dimensional computation, parametric analysis, stochastic modelling,
- MeSH
- stochastické procesy MeSH
- teoretické modely * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
In this study, we examined different computer-assisted sperm analysis (CASA) systems (CRISMAS, Hobson Sperm Tracker, and Image J CASA) on the exact same video recordings to evaluate the differences in sperm motility parameters related to the specific CASA used. To cover a wide range of sperm motility parameters, we chose 12-second video recordings at 25 and 50 Hz frame rates after sperm motility activation using three taxonomically distinct fish species (sterlet: Acipenser ruthenus L.; common carp: Cyprinus carpio L.; and rainbow trout: Oncorhynchus mykiss Walbaum) that are characterized by essential differences in sperm behavior during motility. Systematically higher values of velocity and beat cross frequency (BCF) were observed in video recordings obtained at 50 Hz frame frequency compared with 25 Hz for all three systems. Motility parameters were affected by the CASA and species used for analyses. Image J and CRISMAS calculated higher curvilinear velocity (VCL) values for rainbow trout and common carp at 25 Hz frequency compared with the Hobson Sperm Tracker, whereas at 50 Hz, a significant difference was observed only for rainbow trout sperm recordings. No significant difference was observed between the CASA systems for sterlet sperm motility at 25 and 50 Hz. Additional analysis of 1-second segments taken at three time points (1, 6, and 12 seconds of the recording) revealed a dramatic decrease in common carp and rainbow trout sperm speed. The motility parameters of sterlet spermatozoa did not change significantly during the 12-second motility period and should be considered as a suitable model for longer motility analyses. Our results indicated that the CASA used can affect motility results even when the same motility recordings are used. These results could be critically altered by the recording quality, time of analysis, and frame rate of camera, and could result in erroneous conclusions.
- Klíčová slova
- CRISMAS, Fish spermatozoa, Hobson Sperm Tracker, Image J, Sperm velocity,
- MeSH
- analýza spermatu metody veterinární MeSH
- motilita spermií * MeSH
- počítačové zpracování obrazu přístrojové vybavení MeSH
- ryby * MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- hodnotící studie MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- MeSH
- metody MeSH
- počítače * MeSH
- radionuklidy MeSH
- spektrální analýza * MeSH
- záření * MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- radionuklidy MeSH
