Fluid–structure interaction analysis of the left coronary artery with variable angulation

The aim of this study is to elucidate the correlation between coronary artery branch angulation, local mechanical and haemodynamic forces at the vicinity of bifurcation. Using a coupled fluid–structure interaction (FSI) modelling approach, five idealized left coronary artery models with various angles ranging from 70° to 110° were developed to investigate the influence of branch angulations. In addition, one CT image-based model was reconstructed to further demonstrate the medical application potential of the proposed FSI coupling method. The results show that the angulation strongly alters its mechanical stress distribution, and the instantaneous wall shear stress distributions are substantially moderated by the arterial wall compliance. As high tensile stress is hypothesized to cause stenosis, the left circumflex side bifurcation shoulder is indicated to induce atherosclerotic changes with a high tendency for wide-angled models.     

Dynamics of the ‘echo’ effect in a phytoplankton system with nitrogen fixation

Consideration of nitrogen fixation adds a positive nonlinear feedback to plankton ecosystem models. We investigate the consequences of this feedback for secondary phytoplankton blooms and the response of phytoplankton dynamics to physical forcing. The dynamics of phytoplankton, Trichodesmium (the nitrogen fixer), and nutrients is modeled with a system of three differential equations. The model includes two types of nonlinear interactions: the competition of phytoplankton and Trichodesmium for light, and the positive feedback resulting from Trichodesmium recycling. A typical simulation of the model in time, with forcing by a varying mixed-layer depth, reveals a clear successional sequence including a secondary or ‘echo’ bloom of the phytoplankton. We explain this sequence of events through the stability analysis of three different steady states of the model. Our analysis shows the existence of a critical biological parameter, the ratio of normalized growth rates, determining the occurrence of ‘echo’ blooms and the specific sequence of events following a physical perturbation. The interplay of positive and negative feedbacks appears essential to the timing and the type of events following such a perturbation.     

The factor structure of the functional state of boys aged 13–14 years

We determined the independent factors that reflect the fundamental characteristics of the functional state (FS) in adolescents aged 13–14 years (n = 162): the sympathetic regulation and parasympathetic regulation of FS, physical working capability; the efficiency of cognitive performance; the hemodynamic basis of cognitive activity; nonspecific resistance to upper respiratory tract infections. Using the systematic approach, we investigated the physiological basis of these factors and determined the indices suitable for estimating the FS of adolescents at different stages of puberty. We observed progressive dynamics of FS parameters related to factors listed above in boys of the same chronological age at different puberty stages. Beginning from stage II to stage IV, we observed a heterochronic and nonlinear decrease in the tension of system of autonomic FS regulation, an increase in the efficiency of cognitive activity and its hemodynamic supply, as well as an improvement of anaerobic working capability.     

Modeling of the structure of protein–DNA complexes using the data from FRET and footprinting experiments

We discuss the question of constructing three-dimensional models of DNA in complex with proteins using computer modeling and indirect methods of studying the conformation of macromolecules. We consider the methods of interpreting the experimental data obtained by indirect methods of studying the three-dimensional structure of biomolecules. We discuss some aspects of integrating such data into the process of constructing the molecular models of DNA–protein complexes based on the geometric characteristics of DNA. We propose an algorithm for estimating conformations of such complexes based on the information about the local flexibility of DNA and on the experimental data obtained by Forster resonance energy transfer (FRET) and hydroxyl footprinting. Finally, we use this algorithm to predict the hypothetical configuration of DNA in a nucleosome bound with histone H1.     

Modeling and dynamic assessment of urban economy–resource–environment system with a coupled system dynamics – geographic information system model

At present, environmental issues associated with rapid economic development are becoming critical concerns that arouse government's and people's particular attention. A large amount of influencing factors and especially their complicated interactions have always thrown confused insights into assessing the dynamic evolvement and sustainable development of urban economy–resource–environment (ERE) system and programming the developing strategies. A combination of system dynamics (SD) and geographic information system (GIS) is expected to explicitly understand the synergic interaction and feedback among a variety of influencing factors in time and space, since SD model can extend the spatial analysis functions of GIS to realize both dynamic simulation and trend prediction of an ERE system development. According to connotation and framework of sustainable development, this study proposes a dynamic combination method of SD–GIS to model and evaluate the urban development in Chongqing city of China suffering from depletion of resource and degradation of environment. To compare different policy inclinations with regard to potential ERE effects, typical scenarios (current, resource, technology and environment scenarios) are designed by adjusting the parameters in the model and changing the specification of some variables. Integrated assessment results indicate that the current ERE system of Chongqing is not sustainable; environment scenario is more effective to sustainable development of urban ERE system in a long run. Under the considerations of development features and regional differences, as well as regular discipline on urbanization, a coordinated combination of environmental, resource and technology scenarios is anticipated to realize sustainable development of urban ERE system.     

Modeling the dynamics of woody plant–herbivore interactions with age-dependent toxicity

In this paper we study the effects that woody plant chemical defenses may have on interactions between boreal hares that in winter feed almost entirely on twigs. We focus particularly on the fact that toxin concentration often varies with the age of twig segments. The model incorporates the fact that the woody internodes of the youngest segments of the twigs of the deciduous angiosperm species that these hares prefer to eat are more defended by toxins than the woody internodes of the older segments that subtend and support the younger segments. Thus, the per capita daily intake of the biomass of the older segments of twigs by hares is much higher than their intake of the biomass of the younger segments of twigs. This age-dependent toxicity of twig segments is modeled using age-structured model equations which are reduced to a system of delay differential equations involving multiple delays in the woody plant-hare dynamics. A novel aspect of the modeling was that it had to account for mortality of non-consumed younger twig segment biomass when older twig biomass was bitten off and consumed. Basic mathematical properties of the model are established together with upper and lower bounds on the solutions. Necessary and sufficient conditions are found for the linear stability of the equilibrium in which the hare is extinct, and sufficient conditions are found for the global stability of this equilibrium. Numerical simulations confirmed the analytical results and demonstrated the existence of limit cycles over ranges of parameters reasonable for hares browsing on woody vegetation in boreal ecosystems. This showed that age dependence in plant chemical defenses has the capacity to cause hare-plant population cycles, a new result.     

Functional structure of the intermediate and ventral hippocampo–prefrontal pathway in the prefrontal convergent system

The hippocampo–prefrontal pathway is a unique projection that connects distant ends of the cerebral cortex. The direct hippocampo–prefrontal projection arises from the ventral to intermediate third of the hippocampus, but not from the dorsal third. It forms a funnel-shaped structure that collects information from the large hippocampal area and projects it to the prefrontal cortex. The anatomical regional differentiation of the projection has not been described. The hippocampal region is differentiated into structural and behavioural roles. For example, it has been shown that the ventral, but not the dorsal, hippocampus reciprocally connects with the amygdala and influences emotional behaviours. These data imply that hippocampal variation along the dorso–ventral axis is contained within the hippocampo–prefrontal pathway. Here, we present electrophysiological studies that demonstrate regional differences in short- but not long-term plasticity in the intermediate/posterior-dorsal and ventral routes of the hippocampo–prefrontal pathway. Furthermore, behavioural studies revealed that each route appears to play a different role in working memory. These results suggest that hippocampal regional information is processed through different routes, with the integration of individual regulatory functions in the prefrontal convergent system.     

Modeling the Fear Effect in Predator–Prey Interactions with Adaptive Avoidance of Predators

Recent field experiments on vertebrates showed that the mere presence of a predator would cause a dramatic change of prey demography. Fear of predators increases the survival probability of prey, but leads to a cost of prey reproduction. Based on the experimental findings, we propose a predator–prey model with the cost of fear and adaptive avoidance of predators. Mathematical analyses show that the fear effect can interplay with maturation delay between juvenile prey and adult prey in determining the long-term population dynamics. A positive equilibrium may lose stability with an intermediate value of delay and regain stability if the delay is large. Numerical simulations show that both strong adaptation of adult prey and the large cost of fear have destabilizing effect while large population of predators has a stabilizing effect on the predator–prey interactions. Numerical simulations also imply that adult prey demonstrates stronger anti-predator behaviors if the population of predators is larger and shows weaker anti-predator behaviors if the cost of fear is larger.     

A method for assessing the fit of a constitutive material model to experimental stress–strain data

Higher-order polynomial functions can be used as a constitutive model to represent the mechanical behaviour of biological materials. The goal of this study was to present a method for assessing the fit of a given constitutive three-dimensional material model. Goodness of fit was assessed using multiple parameters including the root mean square error and Hotelling's T ²-test. Specifically, a polynomial model was used to characterise the stress–strain data, varying the number of model terms used (45 combinations of between 3 and 11 terms) and the manner of optimisation used to establish model coefficients (i.e. determining coefficients either by parameterisation of all data simultaneously or averaging coefficients obtained by parameterising individual data trials). This framework for model fitting helps to ensure that a given constitutive formulation provides the best characterisation of biological material mechanics.     

The effect of body temperature on the dynamic respiratory system compliance–breathing frequency relationship in the rat

The mechanical inhomogeneity of the respiratory system is frequently investigated by measuring the frequency dependence of dynamic compliance, but no data are currently available describing the effects of body temperature variations. The aim of the present report was to study those effects in vivo. Peak airway pressure was measured during positive pressure ventilation in eight anesthetized rats while breathing frequency (but not tidal volume) was altered. Dynamic compliance was calculated as the tidal volume/peak airway pressure, and measurements were taken in basal conditions (mean rectal temperature 37.3 °C) as well as after total body warming (mean rectal temperature 39.7 °C). Due to parenchymal mechanical inhomogeneity and stress relaxation-linked effects, the normal rat respiratory system exhibited frequency dependence of dynamic lung compliance. Even moderate body temperature increments significantly reduced the decrements in dynamic compliance linked to breathing rate increments. The results were analyzed using Student’s and Wilcoxon’s tests, which yielded the same results (p < 0.05). Body temperature variations are known to influence respiratory mechanics. The frequency dependence of dynamic compliance was found, in the experiments described, to be temperature-dependent as temperature variations affected parenchymal mechanical inhomogeneity and stress relaxation. These results suggest that body temperature variations should be taken into consideration when the dynamic compliance–breathing frequency relationship is being examined during clinical assessment of inhomogeneity of lung parenchyma in patients.     

Rhizobial strain involvement in symbiosis efficiency of chickpea–rhizobia under drought stress: plant growth,nitrogen fixation and antioxidant enzyme activities

Chickpea plants were inoculated with two strains of Mesorhizobium ciceri: local strain (C-15) and non-local strain (CP-36) in order to evaluate plant growth parameters, activities of nitrogenase and antioxidant enzymes under drought stress as well as control condition within 15 days of imposition of drought stress. Biomass production, nodulation, nitrogen fixation and antioxidant enzyme activities under drought condition were compared. Under control condition, symbiotic efficiency in symbiosis formed by C-15 was higher than that in symbiosis derived by CP-36. Although drought stress decreased shoot dry weight, root dry weight, nodule dry weight and nitrogen fixation in both symbioses, the rate of decline in plants inoculated with CP-36 was higher than that in symbiosis chickpea with C-15. Therefore, symbioses showed different tolerance level under drought condition which was essentially correlated with symbiotic performance at non-stressful conditions. Under drought stress, nodular peroxidase (POX) activity increased in both symbioses but was higher in nodules produced by C-15. Ascorbate peroxidase (APX) increased significantly in nodules of symbiosis of chickpea with C-15. Catalase (CAT) and glutation reductase (GR) declined in both symbioses which decline extent in symbiosis with C-15 was lower than that in the nodules of CP-36. These results suggested contribution of rhizobial partner in enhancing the tolerance of symbioses to drought stress, which was related with the increase of antioxidant enzyme activities (APX and POX) under drought conditions.     

Metabolic responses of the body to breathing with hypoxic argon–oxygen and nitrogen–oxygen mixtures

We have studied metabolic responses of six male volunteers who were exposed to hypoxic nitrogen–oxygen and argon–oxygen respiratory mixtures under hermetic chamber conditions for a long time. We measured the values of 44 biochemical parameters of venous blood, which reflected the state of different parts of metabolism, as well as the state of organs and tissues. Under the conditions of argon–oxygen respiratory mixture with the level of oxygen of 12.8% within the first five days and 12.0% from six to ten days of the experiment, the activation of processes of anaerobic glycolysis and lipolysis with the development of metabolic acidosis was observed. Against this background, biochemical signs of unfavorable changes in the myocardium were recorded. When we used the nitrogen–oxygen respiratory mixture with the level of oxygen of 13.0% during the first five days of the experiment and 12.1% from the sixth to the tenth day, these changes were expressed much more significantly: the activation of lipolysis and a decrease in the level of serum iron were observed and the signs of damage of mitochondria, depression of the kidney function, and development of hypodynamia were recorded. Complete stabilization of metabolic processes was reached only after seven to eight days of the recovery period for both mixtures. These findings lead to the conclusion that it is physiologically more preferable to use oxygen–argon respiratory mixtures at small immersion depths.     

Modeling the Effect of Prey Refuge on a Ratio-Dependent Predator–Prey System with the Allee Effect

The extinction of species is a major threat to the biodiversity. The species exhibiting a strong Allee effect are vulnerable to extinction due to predation. The refuge used by species having a strong Allee effect may affect their predation and hence extinction risk. A mathematical study of such behavioral phenomenon may aid in management of many endangered species. However, a little attention has been paid in this direction. In this paper, we have studied the impact of a constant prey refuge on the dynamics of a ratio-dependent predator–prey system with strong Allee effect in prey growth. The stability analysis of the model has been carried out, and a comprehensive bifurcation analysis is presented. It is found that if prey refuge is less than the Allee threshold, the incorporation of prey refuge increases the threshold values of the predation rate and conversion efficiency at which unconditional extinction occurs. Moreover, if the prey refuge is greater than the Allee threshold, situation of unconditional extinction may not occur. It is found that at a critical value of prey refuge, which is greater than the Allee threshold but less than the carrying capacity of prey population, system undergoes cusp bifurcation and the rich spectrum of dynamics exhibited by the system disappears if the prey refuge is increased further.     

A comparison of the peri-implant bone stress generated by the preload with screw tightening between ‘bonded’ and ‘contact’ model

A number of finite element analyses (FEAs) for the dental implant were performed without regard for preload and with all interfaces ‘fixed-bonded’. The purpose of this study was comparing the stress distributions between the conventional FEA model with all contacting interfaces ‘fixed-bonded’ (bonded model) and the model with the interfaces of the components in ‘contact’ with friction simulated as a preloaded implant (contact model). We further verified the accuracy of the result of the FEA using model experiment. In the contact model, the stress was more widely distributed than in the bonded model. From the model study, the preload induced by screw tightening generated strain at the peri-implant bone, even before the application of external force. As a result, the bonded model could not reproduce the mechanical phenomena, whereas the contact model is considered to be appropriate for analysing mechanical problems.     

Assessing the structure–activity relationships of fluorotelomer unsaturated acids and aldehydes with glutathione

Fluorotelomer alcohols (FTOHs) have been shown to degrade via abiotic and biotic mechanisms to perfluorocarboxylates (PFCAs) which are environmentally persistent and bioaccumulate in humans and wildlife depending on their chain length. Fluorotelomer unsaturated aldehydes (FTUALs) and acids (FTUCAs) are intermediate metabolites that form from the degradation of FTOHs. Their potential for toxicity is not yet defined and may be more significant compared to PFCAs. Past studies have shown that these intermediates form adducts with glutathione (GSH). The purpose of this study was to further assess the reactivity of these intermediate compounds. In vitro experiments were carried out in an aqueous buffer system (pH 7.4) where FTUCAs and FTUALs of varying chain lengths were reacted with GSH. To quantify the reactivity of FTUCAs and FTUALs, unreacted free GSH was derivatized with 5,5′-dithiobis(2-nitrobenzoic acid), its absorbance measured at 412 nm, and the percentage of unconjugated free GSH evaluated over time. EC₅₀ values were obtained for the reactions of GSH with acrolein and methyl methacrylate to assess the accuracy of the method, as well as for acrylic acid, FTUCAs, and FTUALs. The results of this study indicated that α,β-unsaturated aldehydes are comparatively the most reactive and reaction with GSH may be influenced by the length of the fluorinated tail. This is the first study to examine the relationship of FTUCAs and FTUALs with biological nucleophiles by quantifying their intrinsic reactivity.     

Mathematical Modeling of the Dynamics of Plant Mineral Nutrition in the Fertilizer–Soil–Plant System

A numerical simulation of the spatial–temporal dynamics of a multi-parameter system has been developed. The components of this system are plant biomass, the mobile and stationary forms of mineral nutrition elements, rhizosphere microorganisms, and environmental parameters (temperature, humidity, and acidity). Parametric identification and verification of the adequacy of the model were carried out based on the experimental data on the growth of Krasnoufimskaya-100 spring wheat on peat lowland soil. The results are represented by temporal distributions of biomass from agricultural crops and the findings on the contents of the main nutrition elements within the plant (nitrogen, phosphorus, and potassium). An agronomic assessment and interpretation of the results are given.

     

Interactive influence of biotic and abiotic cues on the plasticity of preferred body temperatures in a predator–prey system

The ability to modify phenotypes in response to heterogeneity of the thermal environment represents an important component of an ectotherm's non-genetic adaptive capacity. Despite considerable attention being dedicated to the study of thermally-induced developmental plasticity, whether or not interspecific interactions shape the plastic response in both a predator and its prey remains unknown. We tested several predictions about the joint influence of predator/prey scents and thermal conditions on the plasticity of preferred body temperatures (T (p)) in both actors of this interaction, using a dragonfly nymphs-newt larvae system. Dragonfly nymphs (Aeshna cyanea) and newt eggs (Ichthyosaura alpestris) were subjected to fluctuating cold and warm thermal regimes (7-12 and 12-22°C, respectively) and the presence/absence of a predator or prey chemical cues. Preferred body temperatures were measured in an aquatic thermal gradient (5-33°C) over a 24-h period. Newt T (p) increased with developmental temperature irrespective of the presence/absence of predator cues. In dragonflies, thermal reaction norms for T (p) were affected by the interaction between temperature and prey cues. Specifically, the presence of newt scents in cold regime lowered dragonfly T (p). We concluded that predator-prey interactions influenced thermally-induced plasticity of T (p) but not in a reciprocal fashion. The occurrence of frequency-dependent thermal plasticity may have broad implications for predator-prey population dynamics, the evolution of thermal biology traits, and the consequences of sustaining climate change within ecological communities.     

Time to the MRCA of a sample in a Wright–Fisher model with variable population size

Determining the expected distribution of the time to the most recent common ancestor of a sample of individuals may deliver important information about the genetic markers and evolution of the population. In this paper, we introduce a new recursive algorithm to calculate the distribution of the time to the most recent common ancestor of the sample from a population evolved by any conditional multinomial sampling model. The most important advantage of our method is that it can be applied to a sample of any size drawn from a population regardless of its size growth pattern. We also present a very efficient method to implement and store the genealogy tree of the population evolved by the Galton–Watson process. In the final section we present results applied to a simulated population with a single bottleneck event and to real populations of known size histories.