Effect of Intracluster Correlation on the R-Square Statistic

R²-statistic is a popular and very widely used statistic in regression analysis to estimate the square multiple correlation (SMC), ρ², between a response variable Y and p predictor variables, _X1, …, _Xp. Numerous articles are available in the statistical literature on the properties of R² as an estimator of ρ² when the observations are uncorrelated. However, relatively little is known about the behavior of R² when the available observations are correlated such as the data that result from complex sampling schemes. In this paper, we study the behavior R² in the presence of two-stage sampling data. An approximate expressions for the variance and the bias of R² in the presence of two-stage cluster sampling data with positive intracluster correlation (ρ*) are obtained. It is evident from these formulas and from a simulation study that R² is a poor estimator of ρ² except when ρ* is small. As such, we consider several alternative estimators of ρ² and evaluate their theoretical properties and finite sample performance using a simulation study.     

Electrocatalysis with a Glucose-Oxidase-immobilized Graphite Electrode

Glucose oxidase was immobilized on the surface of a graphite electrode by irreversible adsorption. An electrocatalytic steady-state current for the oxidation of D-glucose was observed using this electrode in the presence of p-benzoquinone as an electron transfer mediator. The electrocatalytic current at 0.5 V vs. SCE was analyzed as a function of the concentrations of D-glucose and p-benzoquinone, and the maximum current, I_s^max, and the Michaelis constants (K₁ and K₂ for D-glucose and p-benzoquinone, respectively) of the electrocatalysis were determined. The dependence of the current on the electrode potential, pH, and temperature was also investigated. The results indicate that the kinetics of the immobilized enzyme are essentially the same as those of the enzyme in the solubilized state. The effect of various electron transfer mediators on the electrocatalytic current was also examined and evaluated in terms of I_s^max, K₁, and K₂ values.     

Li+ counterion self-diffusion in ordered DNA

The anisotropic self-diffusion coefficient of ⁷Li⁺ (I = 3/2) counterions has been studied in hydrated, macroscopically oriented Li-(B)DNA fibers at relatively high water contents, corresponding to approximate DNA-DNA helix axis distances of 22–35 Å, using the pulsed field gradient hmr spin-echo method. Self-diffusion coefficients parallel (D_∥) and perpendicular (D_?) to the DNA helix axis increase with increasing salt content and with increasing DNA-DNA helix axis distance. The observed anisotropy D_∥/D_? decreases from 1.6 to 1.2 with the DNA-DNA separation increasing from 22 to 35 Å in the salt-free sample. This result can be understood by the obstruction effect caused by the DNA molecules themselves. The values of the Li⁺ self-diffusion coefficients in the most water-rich system with no added salt (corresponding to an approximate distance of 35 Å between the DNA helix axes) were D_∥ ～ 1.15 × 10^?10 m² s^?1 and D_? ～ 0.98 × 10^?10 m² s^?1, compared to 9.14 × 10^?10 m² s^?1 for the diffusion of Li⁺ in an aqueous solution of LiCl (～ 2.1M). The possible occurrence of restriction effects in the DNA fibers have also been studied by determining the self-diffusion coefficient at different effective diffusion times. The self-diffusion coefficient of Li⁺ in the sample with the largest DNA-DNA helix axis distance seems to be independent of the effective diffusion time, which indicates that the lithium ions are not trapped within impermeable barriers. The possibility of diffusion through permeable barriers has also been investigated, and is discussed. © 1994 John Wiley & Sons, Inc.     

Rare earth element uptake by the marine diatom

Abstract

Rare earth distribution coefficients, DT = (moles cm^-3, cells)/(moles cm^-3, solution), obtained using seawater (S = 36.4, t = 25°C, pH ～ 8.2, pCO₂ ～ 345 μatm) and the marine diatom, Skeletonema costatum, exhibited a strong tendency toward the order Ce > Gd > Yb. Observations of rapid initial uptake, with subsequent gradual uptake over time, are suggestive of initial adsorption onto cell surfaces followed by slow transport to interior cell sites. The average volume concentration factors (DT) obtained in our study are: DTCe = (3.33 ± 0.9) × 10⁵; DTGd = (2.41 ± 0.7) × 10⁵; DTYb = (1.64 ± 0.3) × 10⁵. Distribution coefficient results, expressed as a competition between solution and solid-state complexation terms, indicate that rare earth element complexation, both in solution and on surfaces, strongly increases with atomic number. Relatively small differences in rare earth element distribution coefficients (DT) with atomic number are the result of small differences between large solution and solid-state complexation terms.     

Calcium and 1,25-dihydroxyvitamin D3 regulation of adipokine expression

Objective: Obesity is associated with elevated oxidative stress and low‐grade systemic inflammation. We have demonstrated recently that 1α,25‐(OH)₂‐D₃ promotes reactive oxygen species production in cultured adipocytes, whereas suppression of 1α,25‐(OH)₂‐D₃ by increasing dietary calcium down‐regulates diet‐induced oxidative stress in aP2‐agouti transgenic mice. However, whether the anti‐obesity effect of dietary calcium plays a role in regulation of obesity‐associated inflammation is not clear. Research Methods and Procedures: We investigated the role of dietary calcium in the regulation of inflammatory cytokine production in aP2‐agouti transgenic mice fed low‐ and high‐calcium obesigenic diets and in the modulation of cytokine production by 1α,25‐(OH)₂‐D₃ in cultured murine and human adipocytes. Results: The high‐calcium diet inhibited the expression of pro‐inflammatory factors tumor necrosis factor α and interleukin (IL)‐6 by 64% and 51%, respectively (p < 0.001), in visceral fat, stimulated the expression of the anti‐inflammatory factors IL‐15 and adiponectin by 52% (p = 0.001) and 54% (p = 0.025), respectively, in visceral fat, and induced a 2‐fold increase in IL‐15 expression in soleus muscle (p = 0.01) compared with litter mate controls on a low‐calcium diet. 1α,25‐(OH)₂‐D₃ also markedly stimulated the expression of tumor necrosis factor α (p < 0.001) and IL‐6 (p = 0.016) in differentiated 3T3‐L1 adipocytes and increased IL‐6 (p = 0.004) and IL‐8 (p < 0.001) production in differentiated human adipocytes. These effects were blocked by calcium channel antagonism with nifedipine. Discussion: These data demonstrate that 1α,25‐(OH)₂‐D₃ favors inflammatory cytokine expression and inhibits anti‐inflammatory cytokine expression; accordingly, suppression of 1α,25‐(OH)₂‐D₃ by dietary calcium inhibits adipocyte‐derived inflammation associated with obesity.     

A critical appraisal of a combined stomatal-photosynthesis model for C3 plants

Gas-exchange measurements on Eucalyptus grandis leaves and data extracted from the literature were used to test a semi-empirical model of stomatal conductance for CO₂ g_Sc=g_o+a₁A/(c_s-I) (1+D_s/D_o)] where A is the assimilation rate; D_s and c_s are the humidity deficit and the CO₂ concentration at the leaf surface, respectively; g₀ is the conductance as A → 0 when leaf irradiance → 0; and D₀ and a₁ are empirical coefficients. This model is a modified version of g_sc=a₁A h_s/c_s first proposed by Ball, Woodrow & Berry (1987, in Progress in Photosynthesis Research, Martinus Mijhoff, Publ., pp. 221–224), in which h_s is relative humidity. Inclusion of the CO₂ compensation point, τ, improved the behaviour of the model at low values of c_s, while a hyperbolic function of D_s for humidity response correctly accounted for the observed hyperbolic and linear variation of g_sc and c_i/c_s as a function of D_s, where C_i is the intercellular CO₂ concentration. In contrast, use of relative humidity as the humidity variable led to predictions of a linear decrease in g_sc and a hyperbolic variation in c_i/c_s as a function of D_s, contrary to data from E. grandis leaves. The revised model also successfully described the response of stomata to variations in A, D_s and c_s for published responses of the leaves of several other species. Coupling of the revised stomatal model with a biochemical model for photosynthesis of C₃ plants synthesizes many of the observed responses of leaves to light, humidity deficit, leaf temperature and CO₂ concentration. Best results are obtained for well-watered plants.     

Brownian Dynamics Simulations of Colloidal Liquids: Hydrodynamics and Stress Relaxation

Abstract

We describe the statistical mechanics background and additional algorithmic features of a recently proposed simple mean-field Brownian Dynamics algorithm formulated to include many-body hydrodynamics, using a local density approximation for the friction coefficient. We show that the equations of motion satisfy the incompressibility of phase space. We make further developments to the model, computing the hydrodynamic effects on the shear stress relaxation function. We show that stress relaxation takes place over two well-defined regimes, in both cases with and without mean field hydrodynamics, MFH. At short times ta ²/D ₀ < 10^?3, where a is the radius of the colloidal particle and D ₀ is the self-diffusion coefficient at infinite dilution, decay of the stress autocorrelation function, C_s(t) is essentially independent of volume fraction and does not fit to a simple analytic form. At longer times than ta ²/D ₀ < 10^?2 the decay has the fractional exponential form ～exp(-t ^β) with β ? 1. The transition between these two regimes coincides with a rapid fall in the time-dependent diffusion coefficient from the so-called short-time to long-time values. We do not find any evidence for power law decay in the C_s(t) as predicted by recent mode-coupling based analytical expansions.     

Transient state analysis of biochemical reactor using coimmobilized system

The transient state analysis of the consecutive sequence of reactions S P ₁ P ₂ taking place inside a porous spherical coimmobilized biocatalyst is discussed for the case in which each step follows Michaelis Menten type kinetics. The theoretical analysis includes intraparticle diffusional limitations. The model equations are solved by the explicit finite difference method. The effect of various parameters of importance on the batch reactor performance is discussed. Comparison of the model with experimental results has been shown.List of Symbols c _p Dimensionless substrate concentration inside the particle, (s _p/ss _o) - c _{pi, j} Dimensionless substrate concentration inside the particle at i, j - c _s Dimensionless substrate concentration at the surface of the particle, (s _s/s ₀) - d _p cm particle diameter - D _s, D _p cm²/s Diffusion coefficient of the substrate S and intermediate P ₁ inside the particle respectively - h Space step size inside the particle - i Grid point inside the particle - j Grid point along the time coordinate - k Time step size - K _m1, K _m2 g/l Michaelis constants for the first and second reaction respectively - K _I1,K _I2 g/l Substrate inhibition parameters for first and second reaction respectively - P _m g/l Product inhibition parameter for the second reaction - P _1p , P _1s g/l Concentration of the intermediate inside the particle and at the surface of the particle respectively - P _2p , P _2s g/l Concentration of the product P ₂ inside the particle and at the surface of the particle respectively - p _1p Dimensionless intermediate concentration inside the particle, (p _1p/s₀) - p _1s Dimensionless intermediate concentration at the surface of the particle, (p _1s /S ₀) - P _2p Dimensionless product concentration inside the particle, (p _2p /S₀) - p _2s Dimensionless product concentration at the surface of the particle, (p _2s/S₀) - p _{1pi, j} Dimensionless intermediate concentration inside the particle at i, j - P _{2pi, j} Dimensionless product concentration inside the particle at i, j - q Ratio of diffusion coefficients, D _p/D _s - r cm Radial position inside the particle - R cm Radius of the pellet - S ₀ g/l Initial substrate concentration in the bulk liquid - S _p g/l Substrate concentration inside the particle - S _s g/l Substrate concentration at the surface of the particle - t s Time, - V _max1 g/(ls) Maximum reaction velocity for the first reaction - V _max2 g/(ls) Maximum reaction velocity for the second reaction - y Dimensionless radial distance, (r/R) - y _{1, j} Dimensionless radial distance at i, j Greek Letters ₁ Parameter, S ₀/K _m1 - ₂ Parameter, S ₀/K _m2 - _I1 Parameter, S ₀/K _I1 - _I2 Parameter, S ₀/K _I2 - _I3 Parameter, S ₀/P _m - Dimensionless time defined as (D _s t/R ²) - ₁ ² V _max1R ²/K_m1D_s - ₂ ² V _max2R ²/K_m2D_s     

Design and synthesis of tetraol derivatives of 1,12-dicarba-closo-dodecaborane as non-secosteroidal vitamin D analogs

Vitamin D receptor (VDR), a nuclear receptor for 1α,25-dihydroxyvitamin D₃ (1α,25(OH)₂D₃, 1), is a promising target for multiple clinical applications. We recently developed non-secosteroidal VDR ligands based on a carbon-containing boron cluster, 1,12-dicarba-closo-dodecaborane (p-carborane), and examined the binding of one of them to VDR by means of crystallographic analysis. Here, we utilized that X-ray structure to design novel p-carborane-based tetraol-type vitamin D analogs, and we examined the biological activities of the synthesized compounds. Structure–activity relationship study revealed that introduction of an ω-hydroxyalkoxy functionality enhanced the biological activity, and the configuration of the substituent significantly influenced the potency. Among the synthesized compounds, 4-hydroxybutoxy derivative 9a exhibited the most potent activity, which was equal to that of the secosteroidal vitamin D analog, 19-nor-1α,25-dihydroxyvitamin D₃ (2).     

A Simple Construction Procedure for Eesolvable Incomplete Block Designs for any Number of Treatments

A simple, straightforward procedure, which requires no special tables or generators, is presented for constructing resolvable incomplete block designs for v=pk, v=p²k, …, treatments, for k≥p, in incomplete blocks of size k. Also, it is shown, how to obtain incomplete block designs for any v in blocks of size k and k+1. The procedure allows construction of balanced incomplete block designs for p = k a prime number. For p = n not a prime number, incomplete block designs can be obtained by the procedure, but are not balanced. However, for p_s being the smallest prime factor of n, p_s + 1 for v = n², p_s²+ p_s + 1 for v = n³, …, arrangements can be obtained for which the occurrence of any treatment pair in the blocks is either zero or one. This is called a zero-one concurrence design. Procedures are described for obtaining additional zero-one concurrence arrangements. It is shown that the efficiency of these designs is maximum. Both intra-block and inter-block analyses are described.     

Inducibility of Rat Liver Drug-Metabolizing Enzymes as an Index of Food-Screeing for Safety Assessment

D-Lactate dehydrogenase (D-LDH) from Pediococcus pentosaceus ATCC 25745 was found to produce D-3-phenyllactic acid from phenylpyruvate. The optimum pH and temperature for enzyme activity were pH 5.5 and 45 °C. The Michaelis-Menten constant (K _m), turnover number (k _cat), and catalytic efficiency (k _cat?K _m) values for the substrate phenylpyruvate were estimated to be 1.73 mmol/L, 173 s^?1, and 100 (mmol/L)^?1 s^?1 respectively.     

Characterization of photosynthesis of Populus euphratica grown in the arid region

Net photosynthetic rate (P _N), stomatal conductance (g _s), intercellular CO₂ concentration (C _i), transpiration rate (E), water use efficiency (WUE), and stomatal limitation (L_s) of Populus euphratica grown at different groundwater depths in the arid region were measured. g _s of the trees with groundwater depth at 4.74 m (D₄) and 5.82 m (D₅) were lower and a little higher than that at 3.82 m (D₃), respectively. Compared with C _i and L_s of the D₃ trees, C _i decreased and L_s increased at 4.74 m, however, Ci increased and L_s decreased at D₅. Hence photosynthetic reduction of P. euphratica was attributed to either stomatal closure or non-stomatal factors depending on the groundwater depths in the plant locations. P _N of the D₃ trees was significantly higher than those at D₄ or D₅. The trees of D₄ and D₅ did not show a significant difference in their P _N, indicating that there are mechanisms of P. euphratica tolerance to mild and moderate drought stress.     

Coupling of D1 and D5 dopamine receptors to multiple G proteins

Dopamine receptors are a subclass of the super family of G protein-coupled receptors, that transduce their effects by coupling to specific G proteins. Within the dopamine receptor family, the adenylyl cyclase stimulatory receptors include the D₁ and D₅ subtypes. The D₁ and D₅ dopamine receptors are genetically distinct, sharing >80% sequence homology within the highly conserved seven transmembrane spanning domains, but displaying only 50% overall homology at the amino acid level. When expressed in transfected GH₄C₁ rat pituitary cells, both D₁ and D₅ receptors stimulate adenylyl cyclase and have identical affinities toward dopaminergic agonists and antagonists. In order to analyze specific signaling pathways mediated by activation of either D₁ or D₅ receptors, we have identified the G proteins that are coupled to these receptors. Through functional analyses and competition binding studies, and from immunoprecipitation techniques, using antisera against the various α subunits of G proteins, we have established that both D₁ and D₅ receptors couple to G_sα. In addition, D₁ receptors are also coupled to G_oα. Since G_oα has been implicated in the regulation of Ca²⁺, K⁺, and Na⁺ channels, this finding would suggest that D₁ receptors can mediate the functional activity of these ion channels. There is also evidence to indicate that D₅ receptors couple to G_zα, a novel G protein abundantly expressed in neurons. Thus, despite similar pharmacological properties, such differential coupling of D₁ and D₅ receptors to G proteins other than G_sα, indicates that dopamine can transduce varied signaling responses upon the simultaneous stimulation of both these receptors.     

Exploring the foraging environment of a natural enemy of Callosobruchus maculatus: Spatial egg distribution in stored cowpea

Knowledge of the spatial distribution of stored product insects may reduce the dependency on chemicals for control of these insects. Biological control, for instance, could be improved based on such knowledge. In this paper we describe the three-dimensional spatial oviposition pattern of Callosobruchus maculatus in stored cowpea. Individual C. maculatus females oviposited in clusters of 70±15 (SD) eggs. These clusters were variable in shape. In any cluster 90 to 95% of the eggs fitted into a volume of 19.1±3.5 cm³. The egg density was highest (0.6 eggs bean^–1) at the center of a cluster and decreased towards the periphery. A statistically significant relationship existed between the number of eggs n in a cluster and the cluster volume, V(cm³): V=11.5+0.11n. We also investigated the spatial egg distribution of beetles which emerged from egg clusters such as those produced by individual females. Their oviposition was not confined to one specific area but was scattered throughout the bean mass. A point pattern analysis showed that the density of the `parent' cluster had no effect on the spatial egg pattern. These results give insight into the foraging environment which the egg parasitoid Uscana lariophaga, a promising candidate for biological control of C. maculatus, is facing. We argue that the probability p of encountering at least one other bean with eggs after a parasitization is a function of the number n of beans that are visited: p=1–0.42 (0.37)^(n–1).     

Theoretical study on small clusters of BaTiO3 using DFT calculations

Using density functional theory with the generalised gradient approximation, the structural and electronic properties of small (BaTiO₃)_n (n = 1–4) clusters have been studied. All the analysed growth modes were observed to consist of the same unit block, which in turn is similar to the well-known (TiO₂)₂ cluster. The BaTiO₃ and (BaTiO₃)₂ systems were observed to adopt analogous geometries to the ground state of (TiO₂)_n clusters with C_s and D_2h symmetries, respectively. The calculated value of the energy gap for the studied (BaTiO₃)_n clusters tends to approach that observed for its tetragonal bulk BaTiO₃ counterpart when n ≥ 3 is considered; the same tendency is observed for the Ba–Ba, Ba–Ti, Ti–O and Ba–Ti interatomic distances. For all the (BaTiO₃)_n clusters, the structural characteristics of their respective isomers were explored.     

Incubation of Metanephroi with Vitamin D3 Increases Numbers of Glomeruli

To characterize actions of vitamin D3 on metanephroi transplanted from rat embryos to adult recipients, we incubated metanephroi with or without 0.01, 0.1 or 1 ug/ml vitamin D3, 25-hydroxyvitamin D₃ [25(OH)D₃] or 1, 25-hydroxyvitamin D₃ [1,25(OH)2D₃] prior to implantation. The number of glomeruli in developed metanephroi three weeks post-transplantation that had been incubated with 1.0 ug/ml vitamin D₃ was increased relative to the number in metanephroi that were not incubated with vitamin D₃ (control), an effect that was not recapitulated by administration of vitamin D₃ directly to hosts at the time of transplantation. Incubation of metanephroi with 1.0 ug/ml vitamin D₃ also enhanced inulin clearances of metanephroi measured at 12 weeks post-transplantation. The hydroxylated derivative of vitamin D₃, 25(OH)D₃, increased glomerulus number when applied at 0.01 ug/ml but not at higher concentrations, while the twice-hydroxylated derivative 1,25(OH)₂D₃, failed to increase glomerulus number at any concentration tested. We conclude that incubation with vitamin D₃ prior to implantation enhances inulin clearance possibly by increasing the number of glomeruli that develop post-transplantation.

Our findings suggest the vitamin D₃ effect is mediated locally.     

Stomatal behaviour in a beech canopy: an analysis of Bowen ratio measurements compared with porometer data

On the basis of measurements or stand transpiration and microclimate, the bulk stomatal or bulk leaf conductance (g_L) of a beech forest in northern Germany was calculated for periods in which leaves were fully expanded and the canopy was dry. This conductance depends strongly on light and humidity conditions above the forest. During periods with photosynthetic photon flux densities Q > 1200 μmol m^?2s^?1, g_L was reduced from 1500mmol m^?2s^?1 at a vapour pressure deficit D= 0.5kPa to 500 mmol m^?2s^?1 at D= 2kPa. Light saturation of g_L was not reached until Q= 1200 μmol m^?2s^?1 at low D, or until even higher Q at higher D. The dependence of g_L, on Q and D was described mathematically by a non-linear equation that requires two empirical parameters. Values for g_L as simulated by this equation provided a satisfactory agreement with independent porometer data collected on single leaves and scaled up to the canopy. A comparison of stomatal and aerodynamic conductances showed a strong coupling between the forest canopy and the atmosphere, indicating that transpiration of the beech forest is controlled mainly by the stomata.     

Incubation of Metanephroi with Vitamin D3 Increases Numbers of Glomeruli

To characterize actions of vitamin D3 on metanephroi transplanted from rat embryos to adult recipients, we incubated metanephroi with or without 0.01, 0.1 or 1 ug/ml vitamin D3, 25-hydroxyvitamin D₃ [25(OH)D₃] or 1, 25-hydroxyvitamin D₃ [1,25(OH)2D₃] prior to implantation. The number of glomeruli in developed metanephroi three weeks post-transplantation that had been incubated with 1.0 ug/ml vitamin D₃ was increased relative to the number in metanephroi that were not incubated with vitamin D₃ (control), an effect that was not recapitulated by administration of vitamin D₃ directly to hosts at the time of transplantation. Incubation of metanephroi with 1.0 ug/ml vitamin D₃ also enhanced inulin clearances of metanephroi measured at 12 weeks post-transplantation. The hydroxylated derivative of vitamin D₃, 25(OH)D₃, increased glomerulus number when applied at 0.01 ug/ml but not at higher concentrations, while the twice-hydroxylated derivative 1,25(OH)₂D₃, failed to increase glomerulus number at any concentration tested. We conclude that incubation with vitamin D₃ prior to implantation enhances inulin clearance possibly by increasing the number of glomeruli that develop post-transplantation.Our findings suggest the vitamin D₃ effect is mediated locally.Key Words: kidney, organogenesis, transplantation     

Stomatal conductance and photosynthesis vary linearly with plant hydraulic conductance in ponderosa pine

Recent work has shown that stomatal conductance (g_s) and assimilation (A) are responsive to changes in the hydraulic conductance of the soil to leaf pathway (K_L), but no study has quantitatively described this relationship under controlled conditions where steady‐state flow is promoted. Under steady‐state conditions, the relationship between g_s, water potential (Ψ) and K_L can be assumed to follow the Ohm's law analogy for fluid flow. When boundary layer conductance is large relative to g_s, the Ohm's law analogy leads to g_s = K_L (Ψ_soil?Ψ_leaf)/D, where D is the vapour pressure deficit. Consequently, if stomata regulate Ψ_leaf and limit A, a reduction in K_L will cause g_s and A to decline. We evaluated the regulation of Ψ_leaf and A in response to changes in K_L in well‐watered ponderosa pine seedlings (Pinus ponderosa). To vary K_L, we systematically reduced stem hydraulic conductivity (k) using an air injection technique to induce cavitation while simultaneously measuring Ψ_leaf and canopy gas exchange in the laboratory under constant light and D. Short‐statured seedlings (< 1 m tall) and hour‐long equilibration times promoted steady‐state flow conditions. We found that Ψ_leaf remained constant near ? 1·5 MPa except at the extreme 99% reduction of k when Ψ_leaf fell to ? 2·1 MPa. Transpiration, g_s, A and K_L all declined with decreasing k (P < 0·001). As a result of the near homeostasis in bulk Ψ_leaf, g_s and A were directly proportional to K_L (R² > 0·90), indicating that changes in K_L may affect plant carbon gain.