Multiple Mantel tests and isolation-by-distance, taking into account long-term historical divergence

Mantel tests of matrix correspondence have been widely used in population genetics to examine microevolutionary processes, such as isolation-by-distance (IBD). We used partial and multiple Mantel tests to simultaneously test long-term historical effects and current divergence and equilibrium processes, such as IBD. We used these procedures to calculate genetic divergence among Eugenia dysenterica (Myrtaceae) populations in Central Brazil. The Nei's genetic distances between pairs of local populations were strongly correlated with geographic distances, suggesting an IBD process, but field observations and the geographic distribution of the samples suggest that populations may have been subjected to more complex evolutionary processes of genetic divergence. Partial Mantel regression was used to partition the effects of geographic structure and long-term divergence associated with a possible historical barrier. The R(2) of the model with both effects was 73.3%, and after the partition 21.9% of the variation in the genetic distances could be attributed to long-term historical divergence alone, whereas only 1.5% of the variation in genetic distances could be attributed to IBD. As expected, there was a large overlap between these processes when explaining genetic divergence, so it was not possible to entirely partition divergence between historical and contemporary processes.     

An MLP training algorithm taking into account known errors on inputs and outputs

A training algorithm is introduced that takes into account a priori known errors on both inputs and outputs in an MLP network. The new cost function introduced for this case is based on a linear approximation of the network function over the input distribution for a given input pattern. Update formulas, in the form of the gradient of the new cost function, is given for a MLP network, together with expressions for the Hessian matrix. This is later used to calculate error bars in a Bayesian framework. The error bars thus derived are discussed in relation to the more commonly used width of the target posterior predictive distribution. It will also be shown that the taking into account of known input uncertainties in the way suggested in this article will have a strong regularizing effect on the solution.     

Predicting rules on organization of cis-regulatory elements, taking the order of elements into account

MOTIVATION: In eukaryotes, rules regarding organization of cis-regulatory elements are complex. They sometimes govern multiple kinds of elements and positional restrictions on elements. RESULTS: We propose a method for detecting rules, by which the order of elements is restricted. The order restriction is expressed as element patterns. We extract all the element patterns that occur in promoter regions of at least the specified number of genes. Then, we find significant patterns based on the expression similarity of genes with promoter regions containing each of the extracted patterns. When we applied our method to Saccharomyces cerevisiae, we detected significant patterns overlooked by previous methods, thus demonstrating the utility of our method for analyses of eukaryotic gene regulation. We also suggest that several types of element organization exist: (i) those in which only the order of elements is important, (ii) order and distance both are important and (iii) only the combination of elements is important. AVAILABILITY: The program for extracting element patterns is available upon request.     

Evaluation of musculotendinous stiffness in prepubertal children and adults, taking into account muscle activity.

Musculotendinous (MT) stiffness of the triceps surae (TS) muscle group was quantified in 28 prepubertal children (7-10 yr) by using quick-release movements at different levels of submaximal contractions. Surface electromyograms (EMG) of each part of the TS and of the tibialis anterior were also recorded. A stiffness index, defined as the slope of the angular stiffness-torque relationship (SIMT-Torque), was used to quantify changes in MT stiffness with age. Results showed a significant decrease in SIMT-Torque with age, ranging from 4.02 +/- 0.29 to 2.88 +/- 0.31 rad-1 for the youngest to the oldest children. Because an increase in stiffness with age was expected due to the maturation of elastic tissues, overactivation of the TS was suspected to contribute to the higher SIMT-Torque values found in the youngest children. TS EMG-torque analyses confirmed that neuromuscular efficiency was significantly lower for the 7- or 8-yr-old children compared with 10-yr-old children, notably due to a higher degree of tibialis anterior coactivation found in the youngest children. Thus the stiffness index originally defined as the slope of the angular stiffness-EMG relationship increased significantly with age toward adult values. The results underlined the necessity to take into account the capacities of muscle activation to quantify changes in elastic properties of muscles, when those capacities are suspected to be altered.     

An analysis of aortic pressure curves taking into account visco-elastic properties of the aorta and variations in peripheral resistance

The aortic pressure curve necessarily reveals the mechanical properties of the aorta and peripheral resistance as well as of the dynamics of blood flow. The present study uses a reasonable model of visco-elastic properties of the aorta, a reasonable form for variations in peripheral resistance and blood flow to predict an aortic pressure tracing. Numerical values of constants measured experimentally were available in the published literature. These were used in the nonlinear differential equations of motion of the system under analysis. The equations yielded to piece-wise solution, giving the aortic circumference and the aortic pressure as functions of time. The form of both curves resembles clinical tracings, but numerical values of circumference were higher and of pressure lower thanin vivo. The discrepancies between predicted and clinical curves may reveal certain inadequacies in published measurements on visco-elastic constants. These measurements have been made on longitudinal rather than circumferential strips often containing dead rather than living muscle. The discrepancies, therefore, indicate specific gaps in our knowledge of aortic behaviorin vitro. The suggested model of the system aided in the design of experiments which could supply data necessary to substantiate or to revise the model.     

Modeling calcium-45 metabolism in tissue, taking into account the structure and hemodynamics of the capillary system]

The accumulation of Ca-45 in the tissues and the degree of its desorption during the perfusion in the sufficiently extensive limits does not depend upon the rate of the perfused solution and is the function of the perfused solution volume. Taking into account strong dependence of the volume rate of filling the capillaries with the solution upon the capilliary radii (r-4) one may come to the conclusion that Ca-45 saturation of the paracapillary spaces in the wide capillaries occurs much sooner than in the narrow ones. As a result of developing these postulates, we have got the formulae which associates these two functions. It is shown that according to the theory the accumulation and desorption processes are interrelated and may be calculated.     

Investigations into the growth behaviour of a toluene-degrading Pseudomonas strain,taking the high vapour pressure of toluene into consideration

A toluene-degrading Pseudomonas species isolated from waste water was studied with regard to its growth behaviour. The dependence of the growth rate on the pH value, on the toluene concentration and on temperature, as well as the O₂ consumption of the isolate were determined. The fact that toluene is a highly volatile substrate, which is present both in the liquid and in the has phase of a reactor, was considered in the experiments. It is shown that the volatility of toluene has to be taken into consideration for an accurate determination of the toluene concentration in the medium.     

Lung cancer mortality in the European uranium miners cohorts analyzed with a biologically based model taking into account radon measurement error

The biologically based two-stage clonal expansion (TSCE) model is used to analyze lung cancer mortality of European miners from the Czech Republic, France, and Germany. All three cohorts indicate a highly significant action of exposure to radon and its progeny on promotion. The action on initiation is not significant in the French cohort. An action on transformation was tested but not found significant. In a pooled analysis, the results based on the French and German datasets do not differ significantly in any of the used parameters. For the Czech dataset, only lag time and two parameters that determine the clonal expansion without exposure and with low exposure rates (promotion) are consistent with the other studies. For low exposure rates, the resulting relative risks are quite similar. Exposure estimates for each calendar year are used. A model for random errors in each of these yearly exposures is presented. Depending on the used technique of exposure estimate, Berkson and classical errors are used. The consequences for the model parameters are calculated and found to be mostly of minor importance, except that the large difference in the exposure-induced initiation between the studies is decreased substantially.     

Electron and proton transport in chloroplasts taking into account lateral heterogeneity of thylakoids. Mathematical model]

A mathematical model of a chloroplast was constructed, which takes into account the inhomogeneous distribution of complexes of photosystems I and II between granal and intergranal thylakoids. The structural and functional complexes of photosystems I and II, which are localized in intergranal and granal thylakoids, respectively, and the b/f complex, which is uniformly distributed in thylakoid membranes, are assumed to be immobile. The interactions between spatially distant electron transport complexes are provided by plastoquinone and plastocyanine, which diffuse in the thylakoid membrane and intrathylakoid space, respectively. The main stages of proton transport associated with the functioning of photosystem II and oxidation-reduction transformations of plastoquinone are considered. The model takes into account the interactions of protons with membrane-bound buffer groups, the lateral diffusion of hydrogen ions in the intrathylakoid space and in the lumen between adjacent granal thylakoids, and the transmembrane proton transport associated with the function of ATP synthase and passive leakage of protons from thylakoids outside. The numerical integration of two systems of differential equations describing the behavior of some variables in two different regions: granal and intergranal thylakoids was performed. The model describes adequately the kinetics of processes being studied and predicts the occurrence of inhomogeneous lateral profiles of proton potentials and redox state of electron carriers. Modeling the electron and proton transport with allowance for the topological features of chloroplasts (lateral heterogeneity of thylakoids) is important for correct interpretation of "power-flux" interactions and the experimentally measured kinetic parameters averaged over the entire spatially inhomogeneous thylakoid system.     

Dynamics of seasonal plant growth in halophytic meadows taking into account the temperature factor and soil salinity level

A mathematical model has been constructed to describe the growth dynamics of various plant communities of halophytic meadows depending on the temperature factor and degree of soil salinity. Field investigation of the yields of halophytic meadow plant communities were performed in the coastal area of Kurinka Lake in the Altaiskii district of the Republic of Khakasia in 2004 and 2006. The results of field investigations and model studies show that there is a correlation between plant growth and air temperature for plant communities growing on soils with the lowest and medium salinity levels. It was proven in model studies that for the plant communities that grow on highly saline (3.58%) soils, not only air temperature but also the salinity level of the soil should be taken into account.     

Diving behaviour, aquatic respiration and blood respiratory properties: a comparison of hatchling and juvenile Australian turtles

Australia has a number of bimodally respiring freshwater turtle species that use aquatic respiration to extend their aerobic dive limit. While species variations in reliance on aquatic respiration are reflected in the diving behaviour and ecology of adults, it is unknown whether these relationships also occur in hatchling and juvenile turtles. This study compared the diving behaviour, aquatic respiration and blood respiratory properties of hatchling and juveniles from five species of Australian freshwater turtles: Rheodytes leukops , Elusor macrurus , Elseya albagula , Elseya latisternum and Emydura signata . Both diving behaviour and physiology differed significantly between species as well as age classes. Dive duration in R. leukops was 17 times longer than the other species, with two hatchlings remaining submerged for the entire 72 h recording period. The long dive duration recorded for R. leukops was supported by a high reliance on aquatic respiration (63–73%) and high blood oxygen affinity ( P ₅₀=17.24 mmHg). A correlation between dive duration, aquatic respiration and blood respiratory properties was not observed in the remaining turtle species where, despite the longer dive duration of Els. albagula and Elu. macrurus compared with Em. signata and Els. latisternum , there was no difference observed in per cent aquatic respiration or blood oxygen affinity between these species. When compared with adult individuals (data from previous studies), dive duration was positively correlated with body size in Em. signata , Els. albagula and R. leukops , but a negative relationship occurred in Els. latisternum and Elu. macrurus .     

A mathematical model for sarcomere mechanics in cross-striated muscles taking into account the stretch and twist of actin filaments

A model of sarcomere mechanics, which takes into account the elongation of the actin and myosin filaments and twisting of the actin filaments during muscle contraction is suggested. The model accounts for the experimentally observed phenomena of the stretch and twist of actin filaments due to strong binding of myosin heads and pulling force. Some model parameters were estimated from published experimental data. The results of modelling suggest that the twist of actin filaments may play an essential role in mechanical responses of contracting muscle fibres to stepwise changes in their length.     

Use of the systems approach in modeling the growth dynamics of a microbial biomass taking into account the cell division process]

The possibility of using systemic approach in the construction of the mathematical model allowing for changes in the biomass and the number of cells is shown. Definite rules were followed in the process of construction, calculations were made with the use of a computer. The satisfactory coincidence of rated and experimental data was achieved (in this instance, E. coli M17 were used).     

Thermal biology,torpor and behaviour in sugar gliders: a laboratory-field comparison

Most studies on animal physiology and behaviour are conducted in captivity without verification that data are representative of free-ranging animals. We provide the first quantitative comparison of daily torpor, thermal biology and activity patterns, conducted on two groups of sugar gliders (Petaurus breviceps, Marsupialia) exposed to similar thermal conditions, one in captivity and the other in the field. Our study shows that activity in captive gliders in an outdoor aviary is restricted to the night and largely unaffected by weather, whereas free-ranging gliders omit foraging on cold/wet nights and may also forage in the afternoon. Torpor occurrence in gliders was significantly lower in captivity (8.4% after food deprivation; 1.1% for all observations) than in the field (25.9%), mean torpor bout duration was shorter in captivity (6.9 h) than in the field (13.1 h), and mean body temperatures during torpor were higher in captivity (25.3°C) than in the field (19.6°C). Moreover, normothermic body temperature as a function of air temperature differed between captive and free-ranging gliders, with a >3°C difference at low air temperatures. Our comparison shows that activity patterns, thermal physiology, use of torpor and patterns of torpor may differ substantially between the laboratory and field, and provides further evidence that functional and behavioural data on captive individuals may not necessarily be representative of those living in the wild.