Oxidative power and intracellular distribution of mitochondria control cell oxygen regime when arterial hypoxemia occurs

The regulatory impact of the mitochondria spatial distribution and enlargement in their oxidative power $q_{O_2 } $ on tissue oxygenation of skeletal muscle during hypoxia were studied. Investigations were performed by mathematical modeling of 3D O₂ diffusion-reaction in muscle fiber. The oxygen consumption rate $V_{O_2 } $ and tissue $p_{O_2 } $ were analyzed in response to a decrease in arterial blood oxygen concentration from 19.5 to 10 vol % at moderate load. Cells with evenly (case 1) and unevenly (case 2) distributed mitochondria were considered. According to calculations, owing to a rise in mitochondria oxidative power from 3.5 to 6.5 mL/min per 100 g of tissue it is possible to maintain muscle oxygen $V_{O_2 } $ at a constant level of 3.5 mL/min per 100 g despite a decrease in O₂ delivery. The minimum value of tissue $p_{O_2 } $ was about 0 and an area of hypoxia appeared inside the cell in case 1. Whereas hypoxia disappeared and minimum value of $p_{O_2 } $ increased from 0 to 4 mmHg if mitochondria were distributed unevenly (case 2). The possibilities of such regulation depended on the relationship “the degree of hypoxemia — the level of oxygen delivery.” It was assumed that an increase in mitochondrial enzyme activity and their migration to places of the greatest oxygen consumption rate can improve the oxygen regime in the cell as it adapts to hypoxia.     

Retention of Dissolved Inorganic Nitrogen by Foliage and Twigs of Four Temperate Tree Species

Nitrogen (N) retention by tree canopies is believed to be an important process for tree nutrient uptake, and its quantification is a key issue in determining the impact of atmospheric N deposition on forest ecosystems. Due to dry deposition and retention by other canopy elements, the actual uptake and assimilation by the tree canopy is often obscured in throughfall studies. In this study, ¹⁵N-labeled solutions ( $ ^{15} {\text{NH}}_{4}^{ + } $ and $ ^{15} {\text{NO}}_{3}^{ - } $ ) were used to assess dissolved inorganic N retention by leaves/needles and twigs of European beech, pedunculate oak, silver birch, and Scots pine saplings. The effects of N form, tree species, leaf phenology, and applied $ {\text{NO}}_{3}^{ - } $ to $ {\text{NH}}_{4}^{ + } $ ratio on the N retention were assessed. Retention patterns were mainly determined by foliar uptake, except for Scots pine. In twigs, a small but significant ¹⁵N enrichment was detected for $ {\text{NH}}_{4}^{ + } $ , which was found to be mainly due to physicochemical adsorption to the woody plant surface. The mean $ {{^{15} {\text{NH}}_{4}^{ + } } \mathord{\left/ {\vphantom {{^{15} {\text{NH}}_{4}^{ + } } {^{15} {\text{NO}}_{3}^{ - } }}} \right. \kern-0em} {^{15} {\text{NO}}_{3}^{ - } }} $ retention ratio varied considerably among species and phenological stadia, which indicates that the use of a fixed ratio in the canopy budget model could lead to an over- or underestimation of the total N retention. In addition, throughfall water under each branch was collected and analyzed for $ ^{15} {\text{NH}}_{4}^{ + } $ , $ ^{15} {\text{NO}}_{3}^{ - } $ , and all major ions. Net throughfall of $ ^{15} {\text{NH}}_{4}^{ + } $ was, on average, 20 times higher than the actual retention of $ ^{15} {\text{NH}}_{4}^{ + } $ by the plant material. This difference in $ ^{15} {\text{NH}}_{4}^{ + } $ retention could not be attributed to pools and fluxes measured in this study. The retention of $ ^{15} {\text{NH}}_{4}^{ + } $ was correlated with the net throughfall of K⁺, Mg²⁺, Ca²⁺, and weak acids during leaf development and the fully leafed period, while no significant relationships were found for $ ^{15} {\text{NO}}_{3}^{ - } $ retention. This suggests that the main driving factors for $ {\text{NH}}_{4}^{ + } $ retention might be ion exchange processes during the start and middle of the growing season and passive diffusion at leaf senescence. Actual assimilation or abiotic uptake of N through leaves and twigs was small in this study, for example, 1–5% of the applied dissolved ¹⁵N, indicating that the impact of canopy N retention from wet deposition on forest productivity and carbon sequestration is likely limited.     

Bone refilling in cortical basic multicellular units: insights into tetracycline double labelling from a computational model

Bone remodelling is carried out by ‘bone multicellular units’ ( $\text{ BMU }$ s) in which active osteoclasts and active osteoblasts are spatially and temporally coupled. The refilling of new bone by osteoblasts towards the back of the $\text{ BMU }$ occurs at a rate that depends both on the number of osteoblasts and on their secretory activity. In cortical bone, a linear phenomenological relationship between matrix apposition rate and $\text{ BMU }$ cavity radius is found experimentally. How this relationship emerges from the combination of complex, nonlinear regulations of osteoblast number and secretory activity is unknown. Here, we extend our previous mathematical model of cell development within a single cortical $\text{ BMU }$ to investigate how osteoblast number and osteoblast secretory activity vary along the $\text{ BMU }$ ’s closing cone. The mathematical model is based on biochemical coupling between osteoclasts and osteoblasts of various maturity and includes the differentiation of osteoblasts into osteocytes and bone lining cells, as well as the influence of $\text{ BMU }$ cavity shrinkage on osteoblast development and activity. Matrix apposition rates predicted by the model are compared with data from tetracycline double labelling experiments. We find that the linear phenomenological relationship observed in these experiments between matrix apposition rate and $\text{ BMU }$ cavity radius holds for most of the refilling phase simulated by our model, but not near the start and end of refilling. This suggests that at a particular bone site undergoing remodelling, bone formation starts and ends rapidly, supporting the hypothesis that osteoblasts behave synchronously. Our model also suggests that part of the observed cross-sectional variability in tetracycline data may be due to different bone sites being refilled by $\text{ BMU }$ s at different stages of their lifetime. The different stages of a $\text{ BMU }$ ’s lifetime (such as initiation stage, progression stage, and termination stage) depend on whether the cell populations within the $\text{ BMU }$ are still developing or have reached a quasi-steady state whilst travelling through bone. We find that due to their longer lifespan, active osteoblasts reach a quasi-steady distribution more slowly than active osteoclasts. We suggest that this fact may locally enlarge the Haversian canal diameter (due to a local lack of osteoblasts compared to osteoclasts) near the $\text{ BMU }$ ’s point of origin.     

Towards a conceptualization of ETL and physical storage of semantic data warehouses as a service

The data warehouse technology has become the incontestable tool for businesses and organizations to make strategic decisions to ensure their competitively. The construction of a data warehouse ( $\mathcal{D}\mathcal{W}$ ) passes by selecting relevant information sources, extracting relevant data and loading them into the $\mathcal{D}\mathcal{W}$ . These processes require a precise expertise from designers related to logical and physical implementations of information sources, which is not usually an easy task. The diversity and heterogeneity of information sources makes the construction process of the $\mathcal{D}\mathcal{W}$ complex and time consuming. Domain ontologies have been proposed to reduce heterogeneity between sources, platforms, services, etc. They resolve syntax and semantic conflicts. The phenomenon of adopting domain ontologies by organizations creates a new type of databases, called semantic databases ( $\mathcal{S}\mathcal{D}\mathcal{B}$ ). As a consequence, they become a candidate for building the semantic $\mathcal{D}\mathcal{W}$ ( $\mathcal{S}\mathcal{D}\mathcal{W}$ ). To handle the diversity of information sources and hide the implementations aspects of sources, proposing a generic framework for constructing $\mathcal{D}\mathcal{W}$ becomes a necessity. In this paper, we first proposed an ontology-based approach for designing $\mathcal{S}\mathcal {D}\mathcal{B}$ . Secondly, ETL phases are defined at ontological level to hide the implementation details. Thirdly, a storage service for ontologies and its associated data is given. Finally, our proposal is validated through a case study and a tool.     

Long-term analysis of Hubbard Brook stable oxygen isotope ratios of streamwater and precipitation sulfate

In response to decreasing atmospheric emissions of sulfur (S) since the 1970s there has been a concomitant decrease in S deposition to watersheds in the Northeastern U.S. Previous study at the Hubbard Brook Experimental Forest, NH (USA) using chemical and isotopic analyzes ( $ \delta^{34} {\text{S}}_{{{\text{SO}}_{4} }} $ ) combined with modeling has suggested that there is an internal source of S within these watersheds that results in a net loss of S via sulfate in drainage waters. The current study expands these previous investigations by the utilization of δ¹⁸O analyzes of precipitation sulfate and streamwater sulfate. Archived stream and bulk precipitation samples at the Hubbard Brook Experimental Forest from 1968–2004 were analyzed for stable oxygen isotope ratios of sulfate ( $ \delta^{18} {\text{O}}_{{{\text{SO}}_{4} }} $ ). Overall decreasing temporal trends and seasonally low winter values of $ \delta^{18} {\text{O}}_{{{\text{SO}}_{4} }} $ in bulk precipitation are most likely attributed to similar trends in precipitation $ \delta^{18} {\text{O}}_{{{\text{H}}_{2} {\text{O}}}} $ values. Regional climate trends and changes in temperature control precipitation $ \delta^{18} {\text{O}}_{{{\text{H}}_{2} {\text{O}}}} $ values that are reflected in the $ \delta^{18} {\text{O}}_{{{\text{SO}}_{4} }} $ values of precipitation. The significant relationship between ambient temperature and the $ \delta^{18} {\text{O}}_{{{\text{H}}_{2} {\text{O}}}} $ values of precipitation is shown from a nearby site in Ottawa, Ontario (Canada). Although streamwater $ \delta^{18} {\text{O}}_{{{\text{SO}}_{4} }} $ values did not reveal temporal trends, a large difference between precipitation and streamwater $ \delta^{18} {\text{O}}_{{{\text{SO}}_{4} }} $ values suggest the importance of internal cycling of S especially through the large organic S pool and the concomitant effect on the $ \delta^{18} {\text{O}}_{{{\text{SO}}_{4} }} $ values in drainage waters.     

Studies on mass attenuation coefficient, effective atomic number and electron density of some vitamins

Mass attenuation coefficient, $ \mu_{m} $ , atomic cross-section, $ \sigma_{i} $ , electronic cross-section, $ \sigma_{e} $ , effective atomic number, $ Z_{\text{eff}} $ and effective electron density, $ N_{\text{el}} $ , were determined experimentally and theoretically for some vitamins (retinol, beta-carotene, thiamine, riboflavin, niacinamide, pantothenic acid, pyridoxine, biotin, folic acid, cyanocobalamin, ascorbic acid, cholecalciferol, alpha-tocopherol, ketamine, hesperidin) at 30.82, 59.54, 80.99, 356.61, 661.66 and 1,408.01?keV photon energies using a NaI(Tl) scintillation detector. The theoretical mass attenuation coefficients were estimated using mixture rules. The calculated values were compared with the experimental values for all vitamins.     

Edge removal in random contact networks and the basic reproduction number

Understanding the effect of edge removal on the basic reproduction number ${\mathcal{R}_0}$ for disease spread on contact networks is important for disease management. The formula for the basic reproduction number ${\mathcal{R}_0}$ in random network SIR models of configuration type suggests that for degree distributions with large variance, a reduction of the average degree may actually increase ${\mathcal{R}_0}$ . To understand this phenomenon, we develop a dynamical model for the evolution of the degree distribution under random edge removal, and show that truly random removal always reduces ${\mathcal{R}_0}$ . The discrepancy implies that any increase in ${\mathcal{R}_0}$ must result from edge removal changing the network type, invalidating the use of the basic reproduction number formula for a random contact network. We further develop an epidemic model incorporating a contact network consisting of two groups of nodes with random intra- and inter-group connections, and derive its basic reproduction number. We then prove that random edge removal within either group, and between groups, always decreases the appropriately defined ${\mathcal{R}_0}$ . Our models also allow an estimation of the number of edges that need to be removed in order to curtail an epidemic.     

Analytic Calculation of Finite-Population Reproductive Numbers for Direct- and Vector-Transmitted Diseases with Homogeneous Mixing

The basic reproductive number, $\mathcal {R}_{0}$ , provides a foundation for evaluating how various factors affect the incidence of infectious diseases. Recently, it has been suggested that, particularly for vector-transmitted diseases, $\mathcal {R}_{0}$ should be modified to account for the effects of finite host population within a single disease transmission generation. Here, we use a transmission factor approach to calculate such “finite-population reproductive numbers,” under the assumption of homogeneous mixing, for both vector-borne and directly transmitted diseases. In the case of vector-borne diseases, we estimate finitepopulation reproductive numbers for both host-to-host and vector-to-vector generations, assuming that the vector population is effectively infinite. We find simple, interpretable formulas for all three of these quantities. In the direct case, we find that finite-population reproductive numbers diverge from $\mathcal {R}_{0}$ before $\mathcal {R}_{0}$ reaches half of the population size. In the vector-transmitted case, we find that the host-to-host number diverges at even lower values of $\mathcal {R}_{0}$ , while the vector-to-vector number diverges very little over realistic parameter ranges.     

Provenance variation and genetic parameters of Eucalyptus viminalis in Argentina

Genetic parameters for growth, stem straightness, pilodyn penetration, relative bark thickness and survival were estimated in a base-population of five open-pollinated provenance/progeny trials of Eucalyptus viminalis. The trials, located in northern, central and southern Buenos Aires Province, Argentina, comprised 148 open-pollinated families from 13 Australian native provenances and eight local Argentinean seedlots. The Australian native provenances come from a limited range of the natural distribution. Overall survival, based on the latest assessment of each trial, was 62.4%. Single-site analyses showed that statistically significant provenances differences (p?<?0.05) for at least one of the studied traits in three out of the five trials analyzed. The local land race performed inconsistently in this study. The average narrow-sense individual-tree heritability estimate $ \left( {{{\hat{h}}^2}} \right) $ was 0.27 for diameter and 0.17 for total height. Values of $ {\hat{h}^2} $ also increased with age. Pilodyn penetration, assessed at only one site, was more heritable $ \left( {{{\hat{h}}^2} = 0.32} \right) $ than the average of growth traits. Estimated individual-tree heritabilities were moderate to low for stem straightness (average of 0.20) and relative bark thickness (0.16). The estimated additive genetic correlations $ \left( {{{{r}}_{{A}}}} \right) $ between diameter and height were consistently high and positive ( $ {{r}_{^A}} $ average of 0.90). High additive genetic correlations were observed between growth variables and pilodyn penetration ( $ {{r}_{^A}} $ average of 0.58). Relative bark thickness showed a negative correlation with diameter $ \left( {{{{r}}_{^A}} = - 0.39} \right) $ and height $ \left( {{{{r}}_{^A}} = - 0.51} \right) $ . The average estimated additive genetic correlation between sites was high for diameter (0.67). The implications of all these parameter estimates for genetic improvement of E. viminalis in Argentina are discussed.     

Topological classification and enumeration of RNA structures by genus

To an RNA pseudoknot structure is naturally associated a topological surface, which has its associated genus, and structures can thus be classified by the genus. Based on earlier work of Harer–Zagier, we compute the generating function $\mathbf{D}_{g,\sigma }(z)=\sum _{n}\mathbf{d}_{g,\sigma }(n)z^n$ for the number $\mathbf{d}_{g,\sigma }(n)$ of those structures of fixed genus $g$ and minimum stack size $\sigma $ with $n$ nucleotides so that no two consecutive nucleotides are basepaired and show that $\mathbf{D}_{g,\sigma }(z)$ is algebraic. In particular, we prove that $\mathbf{d}_{g,2}(n)\sim k_g\,n^{3(g-\frac{1}{2})} \gamma _2^n$ , where $\gamma _2\approx 1.9685$ . Thus, for stack size at least two, the genus only enters through the sub-exponential factor, and the slow growth rate compared to the number of RNA molecules implies the existence of neutral networks of distinct molecules with the same structure of any genus. Certain RNA structures called shapes are shown to be in natural one-to-one correspondence with the cells in the Penner–Strebel decomposition of Riemann’s moduli space of a surface of genus $g$ with one boundary component, thus providing a link between RNA enumerative problems and the geometry of Riemann’s moduli space.     

Deriving fluorometer-specific values of relative PSI fluorescence intensity from quenching of F 0 fluorescence in leaves of Arabidopsis thaliana and Zea mays

The effect of stepwise increments of red light intensities on pulse-amplitude modulated (PAM) chlorophyll (Chl) fluorescence from leaves of A. thaliana and Z. mays was investigated. Minimum and maximum fluorescence were measured before illumination (F ₀ and F _M, respectively) and at the end of each light step ( $ F^{\prime}_{0} $ and $ F^{\prime}_{\text{M}} $ , respectively). Calculated $ F^{\prime}_{0} $ values derived from F ₀, F _M and $ F^{\prime}_{\text{M}} $ fluorescence according to Oxborough and Baker (1997) were lower than the corresponding measured $ F^{\prime}_{0} $ values. Based on the concept that calculated $ F^{\prime}_{0} $ values are under-estimated because the underlying theory ignores PSI fluorescence, a method was devised to gain relative PSI fluorescence intensities from differences between calculated and measured $ F^{\prime}_{0} $ . This method yields fluorometer-specific PSI data as its input data (F ₀, F _M, $ F^{\prime}_{0} $ and $ F^{\prime}_{\text{M}} $ ) depend solely on the spectral properties of the fluorometer used. Under the present conditions, the PSI contribution to F ₀ fluorescence was 0.24 in A. thaliana and it was independent on the light acclimation status; the corresponding value was 0.50 in Z. mays. Correction for PSI fluorescence affected Z. mays most: the linear relationship between PSI and PSII photochemical yields was clearly shifted toward the one-to-one proportionality line and maximum electron transport was increased by 50 %. Further, correction for PSI fluorescence increased the PSII reaction center-specific parameter, 1/F ₀ ? 1/F _M, up to 50 % in A. thaliana and up to 400 % in Z. mays.     

Longitudinal distribution of nitrate δ15N and δ18O in two contrasting tropical rivers: implications for instream nitrogen cycling

The longitudinal variations in the nitrogen (δ¹⁵N) and oxygen (δ¹⁸O) isotopic compositions of nitrate (NO₃ ^?), the carbon isotopic composition (δ¹³C) of dissolved inorganic carbon (DIC) and the δ¹³C and δ¹⁵N of particulate organic matter were determined in two Southeast Asian rivers contrasting in the watershed geology and land use to understand internal nitrogen cycling processes. The $ \delta^{15} {\text{N}}_{{{\text{NO}}_{3} }} $ became higher longitudinally in the freshwater reach of both rivers. The $ \delta^{18} {\text{O}}_{{{\text{NO}}_{3} }} $ also increased longitudinally in the river with a relatively steeper longitudinal gradient and a less cultivated watershed, while the $ \delta^{18} {\text{O}}_{{{\text{NO}}_{3} }} $ gradually decreased in the other river. A simple model for the $ \delta^{15} {\text{N}}_{{{\text{NO}}_{3} }} $ and the $ \delta^{18} {\text{O}}_{{{\text{NO}}_{3} }} $ that accounts for simultaneous input and removal of NO₃ ^? suggested that the dynamics of NO₃ ^? in the former river were controlled by the internal production by nitrification and the removal by denitrification, whereas that in the latter river was significantly affected by the anthropogenic NO₃ ^? loading in addition to the denitrification and/or assimilation. In the freshwater-brackish transition zone, heterotrophic activities in the river water were apparently elevated as indicated by minimal dissolved oxygen, minimal δ¹³C_DIC and maximal pCO₂. The δ¹⁵N of suspended particulate nitrogen (PN) varied in parallel to the $ \delta^{15} {\text{N}}_{{{\text{NO}}_{3} }} $ there, suggesting that the biochemical recycling processes (remineralization of PN coupled to nitrification, and assimilation of NO₃ ^?-N back to PN) played dominant roles in the instream nitrogen transformation. In the brackish zone of both rivers, the $ \delta^{15} {\text{N}}_{{{\text{NO}}_{3} }} $ displayed a declining trend while the $ \delta^{18} {\text{O}}_{{{\text{NO}}_{3} }} $ increased sharply. The redox cycling of NO₃ ^?/NO₂ ^? and/or deposition of atmospheric nitrogen oxides may have been the major controlling factor for the estuarine $ \delta^{15} {\text{N}}_{{{\text{NO}}_{3} }} $ and $ \delta^{18} {\text{O}}_{{{\text{NO}}_{3} }} $ , however, the exact mechanism behind the observed trends is currently unresolved.     

Enhanced accuracy of kinetic information from CT-CPMG experiments by transverse rotating-frame spectroscopy

Micro-to-millisecond motions of proteins transmit pivotal signals for protein function. A powerful technique for the measurement of these motions is nuclear magnetic resonance spectroscopy. One of the most widely used methodologies for this purpose is the constant-time Carr–Purcell–Meiboom–Gill (CT-CPMG) relaxation dispersion experiment where kinetic and structural information can be obtained at atomic resolution. Extraction of accurate kinetics determined from CT-CPMG data requires refocusing frequencies that are much larger than the nuclei’s exchange rate between states. We investigated the effect when fast processes are probed by CT-CPMG experiments via simulation and show that if the intrinsic relaxation rate $ \left( {R_{2,0}^{CT - CPMG} } \right) $ ( R 2 , 0 CT ? CPMG ) is not known a priori the extraction of accurate kinetics is hindered. Errors on the order of 50 % in the exchange rate are attained when processes become fast, but are minimized to 5 % with a priori $ R_{2,0}^{CT - CPMG} $ R 2 , 0 CT ? CPMG information. To alleviate this shortcoming, we developed an experimental scheme probing $ R_{2,0}^{CT - CPMG} $ R 2 , 0 CT ? CPMG with large amplitude spin-lock fields, which specifically contains the intrinsic proton longitudinal Eigenrelaxation rate. Our approach was validated with ubiquitin and the Oscillatoria agardhii agglutinin (OAA). For OAA, an underestimation of 66 % in the kinetic rates was observed if $ R_{2,0}^{CT - CPMG}\, $ R 2 , 0 CT ? CPMG is not included during the analysis of CT-CPMG data and result in incorrect kinetics and imprecise amplitude information. This was overcome by combining CT-CPMG with $ R_{2,0}^{CT - CPMG} $ R 2 , 0 CT ? CPMG measured with a high power R_1ρ experiment. In addition, the measurement of $ R_{2,0}^{CT - CPMG} $ R 2 , 0 CT ? CPMG removes the ambiguities in choosing between different models that describe CT-CPMG data.     

Integrating qPLM and biomechanical test data with an anisotropic fiber distribution model and predictions of TGF-\upbeta 1 and IGF-1 regulation of articular cartilage fiber modulus

A continuum mixture model with distinct collagen (COL) and glycosaminoglycan elastic constituents was developed for the solid matrix of immature bovine articular cartilage. A continuous COL fiber volume fraction distribution function and a true COL fiber elastic modulus ( $E^\mathrm{f})$ were used. Quantitative polarized light microscopy (qPLM) methods were developed to account for the relatively high cell density of immature articular cartilage and used with a novel algorithm that constructs a 3D distribution function from 2D qPLM data. For specimens untreated and cultured in vitro, most model parameters were specified from qPLM analysis and biochemical assay results; consequently, $E^\mathrm{f}$ was predicted using an optimization to measured mechanical properties in uniaxial tension and unconfined compression. Analysis of qPLM data revealed a highly anisotropic fiber distribution, with principal fiber orientation parallel to the surface layer. For untreated samples, predicted $E^\mathrm{f}$ values were 175 and 422 MPa for superficial (S) and middle (M) zone layers, respectively. TGF- $\upbeta $ 1 treatment was predicted to increase and decrease $E^\mathrm{f}$ values for the S and M layers to 281 and 309 MPa, respectively. IGF-1 treatment was predicted to decrease $E^\mathrm{f}$ values for the S and M layers to 22 and 26 MPa, respectively. A novel finding was that distinct native depth-dependent fiber modulus properties were modulated to nearly homogeneous values by TGF- $\upbeta $ 1 and IGF-1 treatments, with modulated values strongly dependent on treatment.     

A Bovine Babesiosis Model with Dispersion

Bovine Babesiosis (BB) is a tick borne parasitic disease with worldwide over 1.3 billion bovines at potential risk of being infected. The disease, also called tick fever, causes significant mortality from infection by the protozoa upon exposure to infected ticks. An important factor in the spread of the disease is the dispersion or migration of cattle as well as ticks. In this paper, we study the effect of this factor. We introduce a number, $\mathcal{P}$ , a “proliferation index,” which plays the same role as the basic reproduction number $\mathcal{R}_{0}$ with respect to the stability/instability of the disease-free equilibrium, and observe that $\mathcal{P}$ decreases as the dispersion coefficients increase. We prove, mathematically, that if $\mathcal{P}>1$ then the tick fever will remain endemic. We also consider the case where the birth rate of ticks undergoes seasonal oscillations. Based on data from Colombia, South Africa, and Brazil, we use the model to determine the effectiveness of several intervention schemes to control the progression of BB.     

Proton cycles through membranes in bacteria: Relationship between proton passive and active fluxes and their dependence on some external physico-chemical factors under fermentation

This paper represents H⁺ circles through the bacterial membranes, their peculiarities and relationship with ATP synthesis or hydrolysis, utilization or accumulation of energy are considered. Data on passive and active proton (H⁺) fluxes through the bacterial membranes are analyzed and their relationship with membrane H⁺ conductance $\left( {G_m^{H^ + } } \right)$ and permeability for H⁺ $\left( {P_{H^ + } } \right)$ is discussed. Methods for determination of bacterial membrane $G_m^{H^ + }$ are presented and some difficulties in obtaining and interpreting data are pointed out. Different ways and mechanisms of passive and active H⁺ fluxes, including a role of membrane lipids in H⁺ transfer, importance of phase transitions in lipid bilayers, operation of protonophores as well as H⁺ translocation via the F₀ factor of the F₀F₁-ATPase, are discussed. Dependence of $G_m^{H^ + }$ for Escherichia coli, Enterococcus hirae, Streptococcus lactis and other bacteria on some external physico-chemical growth factors, particularly, on pH and oxidation reduction potential as well as influence of osmotic stress on $G_m^{H^ + }$ and H⁺ active fluxes through the bacterial membrane under fermentation have been shown. The relationship between $G_m^{H^ + }$ , $P_{H^ + }$ and active H⁺ fluxes through a membrane is proposed, possible mechanisms of relationship between their alterations depending on pH and oxidation reduction potential are discussed. The results are important for understanding the structural and functional properties of bacterial membranes determining H⁺ cycles operation and mechanisms of H⁺ fluxes essential in adaptation of bacteria to altered environment conditions.     

Estimation of viscosity from passage time of liquids flowing through a microchannel array

Recently, a microchannel flow analyzer (MC-FAN) has been used to study the flow properties of blood. However, the correlation between blood passage time measured by use of the MC-FAN and hemorheology has not been clarified. In this study, a simple model is proposed for estimation of liquid viscosity from the passage time t _p of liquids. The t _p data for physiological saline were well represented by the model. According to the model, the viscosity of Newtonian fluids was estimated reasonably well from the t _p data. For blood samples, although the viscosity $ \eta_{\text{mc}} $ estimated from t _p was shown to be smaller than the viscosity $ \eta_{{450{\text{s}}^{ - 1} }} $ measured by use of a rotatory viscometer at a shear rate of 450 s^?1, $ \eta_{\text{mc}} $ was correlated with $ \eta_{{450{\text{s}}^{ - 1} }} $ . An empirical equation for estimation of $ \eta_{{450{\text{s}}^{ - 1} }} $ from $ \eta_{\text{mc}} $ of blood samples is proposed.     

Do calcium buffers always slow down the propagation of calcium waves?

Calcium buffers are large proteins that act as binding sites for free cytosolic calcium. Since a large fraction of cytosolic calcium is bound to calcium buffers, calcium waves are widely observed under the condition that free cytosolic calcium is heavily buffered. In addition, all physiological buffered excitable systems contain multiple buffers with different affinities. It is thus important to understand the properties of waves in excitable systems with the inclusion of buffers. There is an ongoing controversy about whether or not the addition of calcium buffers into the system always slows down the propagation of calcium waves. To solve this controversy, we incorporate the buffering effect into the generic excitable system, the FitzHugh–Nagumo model, to get the buffered FitzHugh–Nagumo model, and then to study the effect of the added buffer with large diffusivity on traveling waves of such a model in one spatial dimension. We can find a critical dissociation constant ( $K=K(a)$ ) characterized by system excitability parameter $a$ such that calcium buffers can be classified into two types: weak buffers ( $K\in (K(a),\infty )$ ) and strong buffers ( $K\in (0,K(a))$ ). We analytically show that the addition of weak buffers or strong buffers but with its total concentration $b_0^1$ below some critical total concentration $b_{0,c}^1$ into the system can generate a traveling wave of the resulting system which propagates faster than that of the origin system, provided that the diffusivity $D_1$ of the added buffers is sufficiently large. Further, the magnitude of the wave speed of traveling waves of the resulting system is proportional to $\sqrt{D_1}$ as $D_1\rightarrow \infty $ . In contrast, the addition of strong buffers with the total concentration $b_0^1>b_{0,c}^1$ into the system may not be able to support the formation of a biologically acceptable wave provided that the diffusivity $D_1$ of the added buffers is sufficiently large.     

Release of non-exchangeable {}^{{{\text{15}}}}{\text{NH}}^{{\text{ + }}}_{{\text{4}}} from subgrade, decomposed granite substrates and uptake by non-mycorrhizal and mycorrhizal California native annual grass, Vulpia microstachys

Release rates of recently fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ from non-exchangeable interlayer sites in 2:1 silicate minerals were determined for decomposed granite (DG) saprolites from three locations in California, USA. Recently-fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release from the DG substrate was quantified by extracting diffused $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ with H-resin, as well as a native, annual grass Vulpia microstachys. The $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release data varied with via the method of extraction, which included H-resin pre-treatments (Na⁺ or H⁺) and V. microstachys uptake (mycorrhizal inoculated or uninoculated). After 6 weeks (1008 h), more $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ was recovered from fixed interlayer positions by the H-resins as compared to uptake by V. microstachys. The H⁺ treated H-resins recovered more released $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ (≈94 mg ${\text{NH}}^{{\text{ + }}}_{{\text{4}}} - {\text{N}}\;{\text{kg}}^{1} $ or (12%) of total fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ ) in two of the three DG samples as compared to the Na⁺ treated resins, (which recovered ≈70–78 mg ${\text{NH}}^{{\text{ + }}}_{{\text{4}}} - {\text{N}}\;{\text{kg}}^{{{\text{ - 1}}}} $ (or 9–10%) of the total fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ ). The V. microstachys assimilated 8–9% of the total fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ with mycorrhizal inoculum as compared to only 2% without a mycorrhizal inoculum, over the same time period. The fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release kinetics from the H-resin experiments were most accurately described by first order and power function models, and can be characterized as biphasic using a heterogeneous diffusion model. Uptake of both the ¹⁵N and ambient, unlabelled N from the soils was closely related to plant biomass. There was no significant difference in percent of N per unit of biomass between the control and mycorrhizal treatments. The findings presented here indicate that observed, long-term $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release rates from DG in studies utilizing resins, may overestimate the levels of fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ made available to plants and microorganisms. Additionally, the study suggested that mycorrhizae facilitate the acquisition and plant uptake of fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ , resulting in markedly increased plant biomass production.     

On the page number of RNA secondary structures with pseudoknots

Let ${\mathcal {S}}$ denote the set of (possibly noncanonical) base pairs {i, j} of an RNA tertiary structure; i.e. ${\{i, j\} \in \mathcal {S}}$ if there is a hydrogen bond between the ith and jth nucleotide. The page number of ${\mathcal {S}}$ , denoted ${\pi(\mathcal {S})}$ , is the minimum number k such that ${\mathcal {S}}$ can be decomposed into a disjoint union of k secondary structures. Here, we show that computing the page number is NP-complete; we describe an exact computation of page number, using constraint programming, and determine the page number of a collection of RNA tertiary structures, for which the topological genus is known. We describe an approximation algorithm from which it follows that ${\omega(\mathcal {S}) \leq \pi(\mathcal {S}) \leq \omega(\mathcal {S}) \cdot \log n}$ , where the clique number of ${\mathcal {S}, \omega(\mathcal {S})}$ , denotes the maximum number of base pairs that pairwise cross each other.