Functional diversity (FD) has the potential to address many ecological questions, from impacts of global change on biodiversity to ecological restoration. There are several methods estimating the different components of FD. However, most of these methods can only be computed at limited spatial scales and cannot account for intraspecific trait variability (ITV), despite its significant contribution to FD. Trait probability density (TPD) functions (which explicitly account for ITV) reflect the probabilistic nature of niches. By doing so, the TPD approach reconciles existing methods for estimating FD within a unifying framework, allowing FD to be partitioned seamlessly across multiple scales (from individuals to species, and from local to global scales), and accounting for ITV. We present methods to estimate TPD functions at different spatial scales and probabilistic implementations of several FD concepts, including the primary components of FD (functional richness, evenness, and divergence), functional redundancy, functional rarity, and solutions to decompose beta FD into nested and unique components. The TPD framework has the potential to unify and expand analyses of functional ecology across scales, capturing the probabilistic and multidimensional nature of FD. The R package TPD (https://CRAN.R-project.org/package=TPD) will allow users to achieve more comparative results across regions and case studies.

• Klíčová slova
• functional diversity, functional trait, niche, probability density function, redundancy, uniqueness,
• MeSH
• biodiverzita * MeSH
• ekologie * MeSH
• fenotyp MeSH
• pravděpodobnostní funkce MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

In this study, we consider a method for investigating the stochastic response of a nonlinear dynamical system affected by a random seismic process. We present the solution of the probability density of a single/multiple-degree of freedom (SDOF/MDOF) system with several statically stable equilibrium states and with possible jumps of the snap-through type. The system is a Hamiltonian system with weak damping excited by a system of non-stationary Gaussian white noise. The solution based on the Gibbs principle of the maximum entropy of probability could potentially be implemented in various branches of engineering. The search for the extreme of the Gibbs entropy functional is formulated as a constrained optimization problem. The secondary constraints follow from the Fokker-Planck equation (FPE) for the system considered or from the system of ordinary differential equations for the stochastic moments of the response derived from the relevant FPE. In terms of the application type, this strategy is most suitable for SDOF/MDOF systems containing polynomial type nonlinearities. Thus, the solution links up with the customary formulation of the finite elements discretization for strongly nonlinear continuous systems.

• Klíčová slova
• Boltzmann solution, Fokker–Planck equation, Gibbs entropy functional, maximum entropy probability density principle, random earthquake process, stochastically proportional system,
• Publikační typ
• časopisecké články MeSH

Interpretation of XANES spectra suffers from a poor intuitive understanding of the relation between spectral features and structural elements of a material. An attempt to alleviate this shortcoming is made by exploring a spatial distribution of probability density of wave functions of photoelectrons excited during the photoabsorption process. One has to add incoherently squares of wave functions which describe participating photoelectron diffraction (PED) processes, weighted by normalized PED cross sections. As an example, we investigate probability density of wave functions relevant to Ag L1 and L3 XANES of Ag2O.

• Publikační typ
• časopisecké články MeSH

A successful kidney transplantation (Tx) offers good quality of life for children suffering from chronic renal failure. However, some metabolic abnormalities may not be corrected and may persist after Tx despite good graft function. Post-Tx bone disease seems to be a universal finding in adult Tx recipients, and is most probably related to steroids. Reports on bone mineral density (BMD) in children after renal Tx are not uniform. Recent studies suggest that BMD is normal when corrected for height. However, longitudinal studies show a transient decrease in BMD in the early post-Tx period. These controversial results raise the issue of the correct interpretation of dual-energy X-ray absorptiometry in children with stunted growth. Etiopathogenetic factors of the decreased BMD, preventive and therapeutic measures are discussed. In conclusion, the results of dual energy X-ray absorptiometry should be interpreted with caution, especially in children with disturbed growth.

• MeSH
• dítě MeSH
• dospělí MeSH
• imunosupresiva škodlivé účinky   MeSH
• kostní denzita * MeSH
• lidé MeSH
• metabolické nemoci kostí chemicky indukované   prevence a kontrola   MeSH
• pooperační období MeSH
• transplantace ledvin * MeSH
• Check Tag
• dítě MeSH
• dospělí MeSH
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• imunosupresiva MeSH

The distribution of time that people spend in physical activity of various intensities has important health implications. Physical activity (commonly categorised by the intensity into light, moderate and vigorous physical activity), sedentary behaviour and sleep, should not be analysed separately, because they are parts of a time-use composition with a natural constraint of 24 h/day. To find out how are relative reallocations of time between physical activity of various intensities associated with health, herewith we describe compositional scalar-on-function regression and a newly developed compositional functional isotemporal substitution analysis. Physical activity intensity data can be considered as probability density functions, which better reflects the continuous character of their measurement using accelerometers. These probability density functions are characterised by specific properties, such as scale invariance and relative scale, and they are geometrically represented using Bayes spaces with the Hilbert space structure. This makes possible to process them using standard methods of functional data analysis in the L2 space, via centred logratio (clr) transformation. The scalar-on-function regression with clr transformation of the explanatory probability density functions and compositional functional isotemporal substitution analysis were applied to a dataset from a cross-sectional study on adiposity conducted among school-aged children in the Czech Republic. Theoretical reallocations of time to physical activity of higher intensities were found to be associated with larger and more progressive expected decreases in adiposity. We obtained a detailed insight into the dose-response relationship between physical activity intensity and adiposity, which was enabled by using the compositional functional approach.

• Klíčová slova
• Compositional scalar-on-function regression, isotemporal substitution, physical activity, probability density functions, sedentary behaviour, sleep,
• MeSH
• adipozita * MeSH
• Bayesova věta MeSH
• časové faktory MeSH
• cvičení * fyziologie   MeSH
• dítě MeSH
• lidé MeSH
• obezita * MeSH
• průřezové studie MeSH
• Check Tag
• dítě MeSH
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

In this study, we investigated the potential of long-range fluorine-carbon J-coupling for determining the structures of deoxyfluorinated disaccharides. Three disaccharides, previously synthesized as potential galectin inhibitors, exhibited through-space fluorine-carbon J-couplings. In our independent conformational analysis of these disaccharide derivatives, we employed a combination of density functional theory (DFT) calculations and nuclear magnetic resonance (NMR) experiments. By comparing the calculated nuclear shieldings with the experimental carbon chemical shifts, we were able to identify the most probable conformers for each compound. A model comprising fluoromethane and methane molecules was used to study the relationship between molecular arrangements and intermolecular through-space J-coupling. Our study demonstrates the important effect of internuclear distance and molecular orientation on the magnitude of fluorine-carbon coupling. The experimental values for the fluorine-carbon through-space couplings (TSCs) of the disaccharides corresponded with values calculated for the most probable conformers identified by the conformational analysis. These results unlock the broader application of fluorine-carbon TSCs as powerful tools for conformational analysis of flexible molecules, offering valuable insights for future structural investigations.

• Klíčová slova
• Conformation, DFT calculations, Fluorine, NMR spectroscopy, Saccharides,
• MeSH
• disacharidy * chemie   MeSH
• fluor * chemie   MeSH
• konformace sacharidů MeSH
• magnetická rezonanční spektroskopie * MeSH
• molekulární konformace MeSH
• teorie funkcionálu hustoty * MeSH
• uhlík chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

A method for averaging of NMR parameters by molecular dynamics (MD) has been derived from the method of statistical averaging in MD snapshots, benchmarked and applied to structurally dynamic interpretation of the 31 P NMR shift (δ31P ) in DNA phosphates. The method employs adiabatic dependence of an NMR parameter on selected geometric parameter(s) that is weighted by MD-calculated probability distribution(s) for the geometric parameter(s) (Ad-MD method). The usage of Ad-MD for polymers is computationally convenient when one pre-calculated structural dependence of an NMR parameter is employed for all chemically equivalent units differing only in dynamic behavior. The Ad-MD method is benchmarked against the statistical averaging method for δ31P in the model phosphates featuring distinctively different structures and dynamic behavior. The applicability of Ad-MD is illustrated by calculating 31 P NMR spectra in the Dickerson-Drew DNA dodecamer. δ31P was calculated with the B3LYP/IGLO-III/PCM(water) and the probability distributions for the torsion angles adjacent to the phosphorus atoms in the DNA phosphates were calculated using the OL15 force field.

• Klíčová slova
• 31P NMR shift, DNA phosphate, MD averaging,
• MeSH
• DNA chemie   MeSH
• fosfor MeSH
• konformace nukleové kyseliny MeSH
• nukleární magnetická rezonance biomolekulární * MeSH
• simulace molekulární dynamiky * MeSH
• teorie funkcionálu hustoty MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA MeSH
• fosfor MeSH

We present an exact calculation of the probability density for the work done by an external agent on a two-level system. Due to the external drive, both the transition rates between the two states and their energies depend on time. Within this setting we calculate the probability of every possible sample path of the system evolution and also the work done along any such path. The general procedure yields an evolution equation for the characteristic function of the work. Assuming that the energies change with constant rates, the properties of the work distribution are controlled by a single parameter representing the ratio of the time scales of the driving protocol, and of the internal dynamics, respectively. We calculate the mean work and characterize those sample paths which are not in agreement with the second law. In the slow driving limit, the probability density for the work collapses to a delta function localized at the reversible work. In the strongly nonequilibrium regime, the most probable work is smaller and the mean work is bigger than the reversible work.

• Publikační typ
• časopisecké články MeSH

Capillary affinity electrophoresis (CAE) and quantum mechanical density functional theory (DFT) have been applied to the investigation of interactions of valinomycin (Val), a macrocyclic dodecadepsipeptide antibiotic ionophore, with lithium cation Li(+). Firstly, from the dependence of effective electrophoretic mobility of Val on the Li(+) ion concentration in the background electrolyte (BGE) (methanolic solution of 50mM chloroacetic acid, 25 mM Tris, pH(MeOH) 7.8, 0-40 mM LiCl), the apparent binding (stability) constant (K(b)) of Val-Li(+) complex in methanol was evaluated as logK(b)=1.50+/-0.24. The employed CAE method include correction of the effective mobilities measured at ambient temperature, at different input power (Joule heating) and at variable ionic strength of the BGEs to the mobilities related to the reference temperature 25 degrees C and to the constant ionic strength 25 mM. Secondly, using DFT calculations, the most probable structures of the non-hydrated Val-Li(+) and hydrated Val-Li(+) x 3H(2)O complex species were predicted.

• MeSH
• elektroforéza kapilární * MeSH
• kationty jednomocné chemie   MeSH
• kvantová teorie * MeSH
• lithium chemie   MeSH
• molekulární modely MeSH
• molekulární struktura MeSH
• osmolární koncentrace MeSH
• počítačová simulace MeSH
• teplota MeSH
• valinomycin chemie   MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• kationty jednomocné MeSH
• lithium MeSH
• valinomycin MeSH

The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Firstly, to properly simulate photo-induced reactions the potential energy surfaces corresponding to excited states must be appropriately accessed; secondly, understanding the mechanisms of these processes requires the exploration of complex configurational spaces and the localization of conical intersections; finally, photo-induced reactions are probability events, that require the simulation of hundreds of trajectories to obtain the statistical information for the analysis of the reaction profiles. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code FIREBALL, suitable for the computational study of these problems. As an example of the application of this approach, we also report results on the [2 + 2] cycloaddition of ethylene with maleic anhydride and on the [2 + 2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition.

• MeSH
• algoritmy MeSH
• elektronika * MeSH
• elektrony MeSH
• ethyleny chemie   MeSH
• fullereny chemie   MeSH
• kvantová teorie * MeSH
• maleinanhydridy chemie   MeSH
• molekulární modely MeSH
• počítačová simulace MeSH
• simulace molekulární dynamiky * MeSH
• světlo * MeSH
• termodynamika MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• ethylene MeSH Prohlížeč
• ethyleny MeSH
• fullerene C60 MeSH Prohlížeč
• fullereny MeSH
• maleinanhydridy MeSH