Václav Bittner

OptOrch is a transparent and modular optimization toolkit for forest tree seed orchard (SO) deployment. It implements SO-specific optimal contribution models in AMPL (A Mathematical Programing Language), separating biological assumptions, input data, and numerical solvers. Unlike existing optimal-contribution or mate-allocation software, OptOrch exposes the objective function and constraints directly, allowing breeders to modify SO-specific requirements, including status-number thresholds, proportional contribution bounds, graft availability, pairwise coancestry restrictions, female and male gametic contributions, and external pollen flow. When the declared formulation is supported by the selected solver, solutions can be evaluated using solver-reported feasibility status, objective bounds, and optimality gaps. The algebraic framework also allows alternative formulations to be tested when biological constraints create mixed-integer, nonlinear, or nonconvex instances. We demonstrate OptOrch with simulation-based scenarios involving alternative status-number thresholds and pollen contamination. The framework quantifies gain–diversity trade-offs, evaluates external pollen effects, and compares feasible deployment strategies under realistic biological and operational constraints.

Maximizing genetic response to selection while constraining inbreeding is a central challenge in breeding and conservation. Classic optimal contribution selection methods address this by managing average population coancestry. However, this often results in complex, nonlinear optimization problems that cannot be guaranteed to reach a global optimum. Furthermore, many applications require a stricter pairwise constraint to avoid immediate inbreeding in offspring. Here, we present a binary integer linear programming formulation to select an optimal subset of individuals under a strict maximum tolerable pairwise genomic relationship threshold. We construct a binary matrix indicating whether each pair exceeds this threshold. This reformulation transforms the problem from a complex nonlinear program into a binary integer linear program. While this formulation remains NP-hard, the linearity allows modern solvers to efficiently navigate the solution space and, when convergence is achieved within the imposed runtime and tolerance settings, certify global optimality, a key advantage over heuristic approaches. We demonstrate the method using two distinct datasets: a large Norway spruce breeding population and a conservation population of German Black Pied cattle. We explore the trade-offs between the selection response, the relationship threshold, and the maximum number of individuals that can be selected under the threshold. Although large, dense problem instances remain computationally demanding, our results show that typical applications can often be solved to proven global optimality in seconds, whereas denser instances may terminate with a remaining optimality gap. This method is a practical solution for breeders and conservation geneticists to select optimal subsets under a strict relationship threshold, enabling applications from maximizing gain in breeding populations to establishing genetic reserves for endangered species.

Genomic relationship matrices computed from single nucleotide polymorphism (SNP) data are now widely used to estimate narrow-sense heritability (h2), yet the impact of genotyping error on these estimates is not well understood. We used stochastic simulation and supporting algebra to examine this impact and its interplay with marker density. Starting from a diploid founder population with 300 additive quantitative trait loci, we simulated SNP panels with densities ranging from 6.25 to 50 SNPs per cM and traits with true h2 of either 0.2 or 0.6. Genotypes were then altered at error rates ε=0−1 under three error kernels. For each of 100 simulation replicates, we calculated the genomic relationship matrix using VanRaden’s method and estimated h2 with restricted maximum likelihood (REML). In the absence of error, low-density marker panels underestimated h2. Sparse panels were also the most tolerant up to ε≈0.1 yet still underestimated h2. Conversely, the densest panel recovered the true h2 when ε=0, but even a small error ε>0.01 caused an upward bias. The analysis reveals that all distortions are attributable to: (i) a shift in the mean off-diagonal elements of the genomic relationship matrix with magnitude (1−ε)2 and (ii) a change in the ratio between the mean diagonal and mean off-diagonal elements of the genomic relationship matrix. When ε≳0.6, every kernel pushed h2 toward zero. Thus, even modest genotyping error can inflate or deflate additive genetic variance estimates. SNP panels therefore require rigorous laboratory quality control, error-aware imputation, and statistical models that account for genotype uncertainty when estimating h2.

“Muscle tone” is a clinically important and widely used term and palpation is a crucial skill for its diagnosis. However, the term is defined rather vaguely, and palpation is not measurable objectively. Therefore, several methods have been developed to measure muscle tone objectively, in terms of biomechanical properties of the muscle. This article aims to summarize these approaches. Through database searches, we identified those studies related to objective muscle tone measurement in vivo, in situ. Based on them, we described existing methods and devices and compared their reliability. Furthermore, we presented an extensive list of the use of these methods in different fields of research. Although it is believed by some authors that palpation cannot be replaced by a mechanical device, several methods have already proved their utility in muscle biomechanical property diagnosis. There appear to be two issues preventing wider usage of these objective methods in clinical practice. Firstly, a high variability of their reliability, and secondly, a lack of valid mathematical models that would provide the observed mechanical characteristics with a clear physical significance and allow the results to be compared with each other.

OBJECTIVES: The main aim of this study was to analyse selected biomechanical aspects of the asymmetrical loading of the human postural system when riding the C1 speed canoe and their influence on the development of muscular imbalances. METHODS: 3D kinematic analysis of a simulated forward stroke of the canoeist in a pool with a counter-current (N = 9) and analysis of MRI data with selected individuals (N = 5), videoanalysis of actual paddling top athletes (N = 12), the kinesiological analysis of movement. RESULTS: Can be stated that when riding a C1 speed canoe the postural system is exposed to two types of asymmetric loading. In the first place, there is lateral asymmetry, which stems from the very nature of the one-sided paddling on this type of vessel. The canoeist has to compensate for the consequent instability by shifting the body's centre of gravity higher above the kneeling lower limb. This effect is achieved by the so-called pelvic lateralisation from the paddling side and by this side's skewing to the kneeling lower limb. Another asymmetry is connected to the forward-backward body movement and its time-dependent deviation from the neutral posture. A significant disproportion between generally fixation movements of the lower part of the body and phasic movements of the upper part of the body has been confirmed. These asymmetrical positions result in a significant unilateral overloading of the quadratus lumborum on the side of the supporting lower limb (side without the paddle), as well as an overloading of the spine straighteners in the lumbar area, in particular on the part of a supporting lower limb, and bilateral yet asymmetric overloading of m. iliopsoas, which in addition takes place in different isometrics. The analysis of MRI data indicates that, during longitudinal training, lateral disproportion in the volume and intensity of postural system loading is the cause of different cross sections of the iliopsoas muscle and quadratus lumborum muscle on the side of the kneeling and supporting lower limbs. With both muscles, larger cross sections with a statistical significance level a = 0.05 and thus also strength on the side of the supporting lower limb can be expected. CONCLUSION: When canoeing on the C1, a significant unilateral overloading occurs with m. quadratus lumborum on the part of the supporting lower limb (side without paddle). Furthermore, spine straighteners in the lumbar area are overloaded, in particular in the part of the supporting lower limb. Last but not least however, the bilateral asymmetric overloading of m. iliopsoas occurs.

The effect of short-term nutrient deprivation was studied in five populations of the mite Tyrophagus putrescentiae with different microbiomes. The fresh weight, nutrient status, respiration, and population growth of the mites were observed for the five mite population-scale samples. The starvation caused the larvae and nymphs to be eliminated, resulting in a significant increase in the fresh weight of starved adult specimens. Three populations were negatively influenced by starvation, and the starved specimens were characterized by a decrease in nutrient status, respiration, and population growth. One population was not influenced or was slightly influenced by starvation, which had no effect on population growth or nutrient contents but caused a significant decrease in respiration. One population was positively influenced by starvation; the population growth increased in starved specimens, and starvation had no effect on respiration. Although starvation altered the bacterial profiles of the microbiomes, these differences were much smaller than those between the populations. The bacterial profiles of Staphylococcus, Bacillus, Kocuria, Brevibacterium, and unidentified Micrococcaceae and Enterobacteriaceae increased in starved specimens, whereas those of Bartonella and Solitalea-like genera were reduced in the starved mite populations. The profiles of the intracellular symbiont Cardinium decreased in the starved specimens, and the Wolbachia profile changes were dependent on the mite population. In mite populations, when the symbionts were rare, their profiles varied stochastically. Correlations between changes in the profiles of the bacterial taxa and mite fitness parameters, including nutrient status (lipids, proteins, saccharides, and glycogen contents), mite population growth, and respiration, were observed. Although the microbiomes were resistant to the perturbations caused by nutrition deficiency, the responses of the mites differed in terms of their population growth, respiration, and nutrient status.

Narrow sense heritability (h²) is a key concept in quantitative genetics, as it expresses the proportion of the observed phenotypic variation that is transmissible from parents to offspring. h² determines the resemblance among relatives and the rate of response to artificial and natural selection. Classical methods for estimating h² use random samples of individuals with known relatedness, as well as response to artificial selection, when it is called realized heritability. Here, we present a method for estimating realized h² based on a simple assessment of a random-mating population with no artificial manipulation of the population structure, and derive standard errors of the estimates. This method can be applied to arbitrary phenotypic segments of the population (for example, the top ranking p parents and offspring), rather than random samples. It can thus be applied to non-pedigreed random mating populations, where relatedness is determined from molecular markers in the p selected parents and offspring, thus substantially saving on genotyping costs. Further, we assessed the method by stochastic simulations and as expected from the mathematical derivation, it provides unbiased estimates of h². We compared our approach to the regression and maximum-likelihood approaches utilizing Galton9s dataset on human heights and all three methods provided identical results.

The aim of this study was to find possibilities of using the Fourier transform in the analysis of vibration load tests of heterogeneous mechanical systems, especially those of a biological nature. The study applied the idea that the dispersion...

The aim of the study was to identify the meniscoids of the cervical spine using in-vivo MRI imaging and to determine their potential role in the development of functional joint blocks of the axial system (AS). Another objective was to find out how the articular blocks affect the rheological properties of the spine by the Transfer Vibration through the Spine (TVS) method. In this study were used methods TVS and MRI. The study was conducted on a research file of 12 subjects and was conceived as a pilot one. It has been shown that the MRI method, in appropriate circumstances, enables the detection of changes in the size and shape of meniscoids in-vivo. On the basis of the investigations carried out, it can be assumed that several mechanisms are involved in the formation of functional joint blocks, and are not primarily caused by the incarceration of meniscoidal tissue. Using the TVS method, it has also been found that a functional articular blockade affects the rheological properties of the axial system, specifically reducing the damping capabilities of the particular spine segment. In the follow-up studies, it will be necessary to verify the theoretical interpretations on a larger statistical set.