Bayesian Bootstrap Clones for Censored Markov Chains

In this article, we consider r observations from a non‐homogeneous censored Markov chain, with transition probability matrix P. For the product estimator of P proposed by Aalen and Johansen (1978) and Phelan (1988), we investigate the behavior of Bayesian bootstrap clones to approximate the sampling distribution of , and then construct approximate confidence interval. It is shown that the approximation based on the random‐weighted distribution is first‐order consistent. The performance of the Bayesian bootstrap clones (BBC) is also discussed by small sample simulation. Finally, we illustrate the BBC procedure in the application to the WHO malaria survey data (cf. Singer and Cohen 1970).     

Inhibition of osteoclast formation and function by bicarbonate: Role of soluble adenylyl cyclase

High inhibits and low stimulates bone resorption, which mediates part of the effect of chronic acidosis or acid feeding on bone. Soluble adenylyl cyclase (sAC) is a bicarbonate sensor that can potentially mediate the effect of bicarbonate on osteoclasts. Osteoclasts were incubated in 0, 12, and 24 mM at pH 7.4 for 7–8 days and assayed for tartrate‐resistant acid phosphatase (TRAP) and vacuolar‐ATPase expression, and H⁺ accumulation. Total number and area of TRAP (+) multinucleated osteoclasts was decreased by in a dose‐dependent manner. V‐ATPase expression and H⁺ accumulation normalized to cell cross‐sectional area or protein were not significantly changed. The ‐induced inhibition of osteoclast growth and differentiation was blocked by either 2‐hydroxyestradiol, an inhibitor of sAC or sAC knockdown by sAC specific siRNA. The model of inhibiting osteoclast via sAC was further supported by the fact that the dose‐response on osteoclasts is flat when cells were saturated with 8‐bromo‐cAMP, a permeant cAMP analog downstream from sAC thus simulating sAC activation. To confirm our in vitro findings in intact bone, we developed a 1‐week mouse calvaria culture system where osteoclasts were shown to be viable. Bone volume density (BV/TV) determined by micro‐computed tomography (µCT), was higher in 24 mM compared to 12 mM treated calvaria. This effect on BV/TV was blocked by 2‐hydroxyestradiol. In summary, sAC mediates the inhibition of osteoclast function by , by acting as a sensor. J. Cell. Physiol. 220: 332–340, 2009. © 2009 Wiley‐Liss, Inc.     

Enhancement of neutral lipid productivity in the microalga Isochrysis affinis Galbana (T-Iso) by a mutation-selection procedure

Microalgae offer a high potential for energetic lipid storage as well as high growth rates. They are therefore considered promising candidates for biofuel production, with the selection of high lipid‐producing strains a major objective in projects on the development of this technology. We developed a mutation‐selection method aimed at increasing microalgae neutral lipid productivity. A two step method, based on UVc irradiation followed by flow cytometry selection, was applied to a set of strains that had an initial high lipid content and improvement was assessed by means of Nile‐red fluorescence measurements. The method was first tested on Isochrysis affinis galbana (T‐Iso). Following a first round of mutation‐selection, the total fatty acid content had not increased significantly, being for the wild type (WT) and for the selected population (S1M1). Conversely, fatty acid distribution among the lipid classes was affected by the process, resulting in a 20% increase for the fatty acids in the neutral lipids and a 40% decrease in the phospholipids. After a second mutation‐selection step (S2M2), the total fatty acid content reached with a fatty acid distribution similar to the S1M1 population. Growth rate remained unaffected by the process, resulting in a 80% increase for neutral lipid productivity. Biotechnol. Bioeng. 2012; 109: 2737–2745. © 2012 Wiley Periodicals, Inc.     

The Hyper-Negative Binomial Distribution

A generalized family of the negative binomial distribution is introduced in a paper by Srivastava, Yousry and Ahmed (1986). It is a solution of the difference equation and is called the hyper-negative binomial distribution. Certain properties including the moments of the distribution are presented. Moment estimators of the parameters are obtained and goodness of fit is illustrated for chromatid aberration data.     

Construction of Prediction Intervals in Location-Scale Families

Let x₁ ≤x₂ ≤x₃ … ≤x_r be the r smallest observations out of n observations from a location-scale family with density $ \frac{1}{\sigma}f\left({\frac{{x - \mu}}{\sigma}} \right) $ where μ and σ are the location and the scale parameters respectively. The goal is to construct a prediction interval of the form $ \left({\hat \mu + k_1 \hat \sigma,\,\hat \mu + k_2 \hat \sigma} \right) $ for a location-scale invariant function, T(Y) = T(Y₁, …, Y_m), of m future observations from the same distribution. Given any invariant estimators $ \hat \mu $ and $ \hat \sigma $, we have developed a general procedure for how to compute the values of k₁ and k₂. The two attractive features of the procedure are that it does not require any distributional knowledge of the joint distribution of the estimators beyond their first two raw moments and $ \hat \mu $ and $ \hat \sigma $ can be any invariant estimators of μ and σ. Examples with real data have been given and extensive simulation study showing the performance of the procedure is also offered.     

Effects of temperature on microbial ethanol production. III. The influence of the temperature on the relation existing between the specific ethanol formation rate of the yeast Saccharomyces cerevisiae Sc 5 and the ethanol concentration in the culture medium

The ethanol-inhibitory behaviour of the yeast Saccharomyces cerevisiae Sc 5 was found to be characterized by a continual-linear relation between the specific ethanol formation rate and the ethanol concentration. Therefore the simple equation could be applied for it. It is shown that this model is correct only then, if all of the process parameters are in their optimum. Out of the optimum temperature range the characteristics of the function ν = f(P) change in such a way that in regard to the ethanol concentration P twc linear relations exist for each suboptimum temperature: and a non-linear equation is current for each superoptimum temperature: where b_T is also a function of the temperature and always less than 1. Taking as a basis these equations the specific ethanol formation rate of the used strain can be calculated for the whole biokinetic P/T-sphere of ethanol production.     

Adaptation of the rat cardiac proteome in response to intensity‐controlled endurance exercise

Endurance training improves cardiac function and protects against heart disease. The rodent intensity‐controlled running model replicates endurance exercise in humans and can be used to investigate molecular adaptations in the heart. Rats (n = 6, 280 ± 3 g) performed exercise tests to measure their peak oxygen uptake ( ) and training was prescribed at 70–75% for 30 min, 4 days/wk. Hearts were isolated 4 h after a final test and left ventricle proteomes compared to weight‐matched control animals (n = 6, 330 ± 2 g) using differential analysis of 2‐D gels. Proteins were identified by searching MS and MS/MS spectra against Swiss‐Prot using MASCOT (www.matrixscience.com). Average increased 23% (p = 0.008) over the 6‐week regimen and 23 gel spots differed (p<0.05) between exercised and control hearts. Expression of myofibrillar proteins (e.g. α‐myosin heavy chain and cardiac α‐actin) and proteins associated with fatty acid metabolism (e.g. heart fatty acid binding protein, acetyl coenzyme A dehydrogenase and mitochondrial thioesterase‐1) increased. In addition, this work discovered a novel increase in phosphorylation of heat shock protein 20 at serine 16. Previously this modification has been associated with improved cardiomyocyte contractility and protection against apoptosis.     

Solution conformation of a tetradecapeptide stabilized by two di‐n‐propyl glycine residues

The solution conformation of a designed tetradecapeptide Boc‐Val‐Ala‐Leu‐Dpg‐Val‐Ala‐Leu‐Val‐Ala‐Leu‐Dpg‐Val‐Ala‐Leu‐OMe (Dpg‐14) containing two di‐n‐propyl glycine (Dpg) residues has been investigated by ¹H NMR and circular dichroism in organic solvents. The peptide aggregates formed at a concentration of 3 mM in the apolar solvent CDCl₃ were broken by the addition of 12% v/v of the more polar solvent DMSO‐d₆. Successive N_iH N_i+1H NOEs observed over the entire length of the sequence in this solvent mixture together with the observation of several characteristic medium‐range NOEs support a major population of continuous helical conformations for Dpg‐14. Majority of the observed coupling constants ( ) also support ? values in the helical conformation. Circular dichroism spectra recorded in methanol and propan‐2‐ol give further support in favor of helical conformation for Dpg‐14 and the stability of the helix at higher temperature. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.     

Inhibition-threshold substrate concentrations

A proposed substrate inhibition model (M. C. Tseng and M. Wayman, Can. J. Microbiol., 21 , 994 (1975)), ((1)) ((2)) derived from yeast growth rates has been applied to data for bacterial growth: Pseudomonas methanica grown on methanol and Arthrobacter AK19 grown on n-butanol. The model represents the experimental data very well.     

Effect of cell lysates on retroviral transduction efficiency of cells in suspension culture

Recombinant retroviruses are effective vectors able to integrate transgenes into the target cell's genome to achieve longer‐term expression. This study investigates the effect of cell lysis products, a common cell culture by‐product, on the transduction of suspension cells by gammaretroviral vectors. Cell lysates derived from human and murine suspension cell lines significantly increased the transduction of human TF‐1 and K‐562 cell lines by gibbon ape leukemia virus‐pseudotyped retroviral vectors without altering tropism. The transduction efficiency of TF‐1 cells increased as a function of lysate concentration and decreased with increasing target cell concentrations. This was adequately predicted using a saturation equation based on the lysed‐to‐target cell concentration ratio, R, where: Lysate completely masked the effects of fibronectin when the two were added in combination. With protamine sulfate, the transduction efficiency was increased by lysate to 58% from 20% for protamine sulfate alone. Overall, the presence of cell lysate significantly influenced the outcome of the transduction process, either alone or in the presence of protamine sulfate or fibronectin. Biotechnol. Bioeng. 2010;105: 1168–1177. © 2009 Wiley Periodicals, Inc.     

Removal of nitrate and hexavalent uranium from groundwater by sequential treatment in bioreactors packed with elemental sulfur and zero‐valent iron

The bioreduction of soluble hexavalent uranium (U^VI) to insoluble tetravalent uranium (U^IV) is an attractive bioremediation strategy for the clean‐up of contaminated groundwater. High levels of the common occurring co‐contaminant, nitrate ( ), can potentially interfere with uranium bioremediation. In this study, treatment of a synthetic groundwater containing a mixture of and U^VI was investigated in a sulfur–limestone autotrophic denitrifying (SLAD) bioreactor that was coupled in series with a bioreactor packed with zero‐valent iron (Fe⁰, ZVI) and sand. An additional aim of the study was to explore the possible role of biological activity in enhancing the reduction of U^VI by Fe⁰. The SLAD reactor removed efficiently (99.8%) at loadings of up to 20 mmol L d^?1, with near stoichiometric conversion to benign dinitrogen gas (N₂). The ZVI bioreactor subsequently removed uranium (99.8%) at high (0.22 mM) and low (0.02 mM) influent concentrations of the radionuclide. Aqueous uranium was reliably eliminated to below the maximum contaminant level of 30 µg L^?1 (0.13 µM) when the ZVI reactor was operated at average empty bed hydraulic retention times as low as 2.3 h, demonstrating the feasibility of the sequential treatment strategy in packed bed bioreactors. Sequential extraction of the ZVI reactor packing confirmed that uranium was immobilized as U^IV. Uranium removal was enhanced by microbial activity as confirmed by the increased rate of uranium removal in batch assays inoculated with effluent from the ZVI bioreactor and spiked with Fe⁰ compared to abiotic controls. Biotechnol. Bioeng. 2010;107: 933–942. © 2010 Wiley Periodicals, Inc.     

Abundance trends of American martens in Michigan based on statistical population reconstruction

Estimating the dynamics of furbearer populations is challenging because their elusive behavior and low densities make observations difficult. Statistical population reconstruction is a flexible approach to demographic assessment for harvested populations, but the technique has not been applied to furbearers. We extended this approach to furbearers and analyzed 8 yr of age-at-harvest data for American marten (Martes americana) in the Upper Peninsula of Michigan. Marten abundance estimates showed a general downward trend from an estimate of = 1,733.3 animals in 2000 to = 1,163.9 in 2007. The harvest probability of martens increased nearly 5-fold from 0.0542 in 2000 to 0.2637 in 2007, which corresponded to a 5-fold increase in trap-nights. Continued monitoring of martens in the Upper Peninsula, Michigan, and a reassessment of current harvest regulations are necessary given the estimated decreases. Moreover, we do not encourage the use of harvest indices as the sole technique to assess the status and trends of marten and fisher populations. Auxiliary studies in the Upper Peninsula, Michigan, will allow for continued use and improvement in the application of these models. © 2011 The Wildlife Society.     

A kinetic study of the alcoholic fermentation of grape juice

The alcoholic fermentation of grape juice by a wine yeast was studied batchwise at pH 3.6 and 4.05 to develop kinetic equations relating cell concentration, N, to product concentration, P. In the exponential growth phase where A, B, and C are constants, and μ is the specific growth rate. In the stationary phase, where the cell population is constant, was found to apply. This equation, which incorporates a stoichiometric constant, P_m, predicted correctly the operation of a continuous fermentor at pH 3.6 and at 4.05. To study more fully the effect of alcohol concentration on yeast growth, a continuous fermentor was used in which the grape juice feed was supplemented with pure alcohol. At pH 3.6 the specific growth rate varied as, There was no growth inhibition below an alcohol concentration of 2.6 g./100 cc., but inhibition was complete above 6.85 g./100 cc. This is a modified form of the relation suggested by Hinshelwood.¹ The data suggest that growth in batch culture was limited not only by alcohol but also by some other factor, probably a nutritional deficiency.     

Antioxidant Activities of Aqueous Extract from Agrimonia pilosa Ledeb and Its Fractions

Agrimonia pilosa Ledeb is used as the tonic for asthenia and fatigue in China. Considering that the energizing effect might be correlated with antioxidant properties, we investigated the antioxidant activities of aqueous extract (AE) from Agrimonia pilosa Ledeb by assessing radical‐scavenging and anti‐lipid‐peroxidation abilities. We found that AE shows a moderate antioxidant activity to scavenge DPPH^., O , and ^.OH and inhibit β‐carotene bleaching with IC₅₀ values of 13.0, 33.2, 351, and 11.9 μg/ml, respectively, while its AcOEt‐soluble fraction (ESF) and BuOH soluble fraction (BSF) exhibit remarkable efficiencies. The ESF's IC₅₀ values of scavenging DPPH^., O , and ^.OH, and inhibiting β‐carotene bleaching are 5.6, 5.8, 171, and 7.6 μg/ml, respectively, and those of BSF are 7.5, 8.4, 82.0, and 6.2 μg/ml, respectively. In addition, we found that there is a significant correlation between total phenol content and the antioxidant activity determined by O and ^.OH scavenging, and β‐carotene‐bleaching assays. Furthermore, HPLC analysis revealed the presence of quercetin, hyperoside, quercitrin, taxifoliol, luteolin‐7‐O‐β‐D ‐glucopyranoside, and rutin in Agrimonia pilosa Ledeb . Thus, we suggest that the extracts from Agrimonia pilosa Ledeb , could be considered as natural antioxidant sources and dietary nutritional supplements to prevent oxidation‐related diseases.     

Buoyant densities of natural and synthetic DNA's in CsCl and Cs2SO4 considered as sequence-dependent properties

The buoyant densities of natural and synthetic DNA's can be accurately interrelated if second-neighbor influences are taken into account. We derive the following expressions, based partly on the buoyant densities of six synthetic DNA's, for the buoyant densities ρ (g/cm³) of DNA's having random sequences. In CsCl, and in Cs₂SO₄, . In these equations, H_G is the mole fraction of G : C base pairs in the DNA and the buoyant densities are calculated relative to densities for E. coli DNA of 1.703 and 1.426 (g/cm³) in CsCl and Cs₂SO₄, respectively.     

Occupancy and abundance of wintering birds in a dynamic agricultural landscape

Assessing wildlife management action requires monitoring populations, and abundance often is the parameter monitored. Recent methodological advances have enabled estimation of mean abundance within a habitat using presence–absence or count data obtained via repeated visits to a sample of sites. These methods assume populations are closed and intuitively assume habitats within sites change little during a field season. However, many habitats are highly variable over short periods. We developed a variation of existing occupancy and abundance models that allows for extreme spatio-temporal differences in habitat, and resulting changes in wildlife abundance, among sites and among visits to a site within a field season. We conducted our study in sugarcane habitat within the Everglades Agricultural Area southeast of Lake Okeechobee in south Florida. We counted wintering birds, primarily passerines, within 245 sites usually 5 times at each site during December 2006–March 2007. We estimated occupancy and mean abundance of birds in 6 vegetation states during the sugarcane harvest and allowed these parameters to vary temporally or spatially within a vegetation state. Occupancy and mean abundance of the common yellowthroat (Geothlypis trichas) was affected by structure of sugarcane and uncultivated edge vegetation (occupancy = 1.00 [ = 0.96–1.00] and mean abundance = 7.9 [ = 3.2–19.5] in tall sugarcane with tall edge vegetation versus 0.20 [ = 0.04–0.71] and 0.22 [ = 0.04–1.2], respectively, in short sugarcane with short edge vegetation in one half of the study area). Occupancy and mean abundance of palm warblers (Dendroica palmarum) were constant (occupancy = 1.00, = 0.69–1.00; mean abundance = 18, = 1–270). Our model may enable wildlife managers to assess rigorously effects of future edge habitat management on avian distribution and abundance within agricultural landscapes during winter or the breeding season. The model may also help wildlife managers make similar management decisions involving other dynamic habitats such as wetlands, prairies, and even forested areas if forest management or fires occur during the field season. © 2011 The Wildlife Society.     

A Novel Monoterpene?Stilbene Adduct with a 4,4‐Dimethyl‐2,3‐diphenylchromane Skeleton from Artocarpus xanthocarpus

Artoxanthochromane ( 1 ), a Diels? Alder‐type conjugation product of 4‐isopropenylresorcinol and oxyresveratrol, was isolated from the heartwood of Artocarpus xanthocarpus and characterized. The structure of 1 was elucidated as 2‐(2,4‐dihydroxyphenyl)‐3‐(3,5‐dihydroxyphenyl)‐7‐hydroxy‐4,4‐dimethylchromane by 1D‐ and 2D‐NMR spectroscopy, and other spectral evidences. A plausible metabolic mechanism was proposed to illustrate the biosynthetic pathway of artoxanthochromane. This compound exhibited mild mushroom tyrosinase inhibitory, and weak free radical‐scavenging activities on ABTS^+. and superoxide anion (O ) free radicals.     

Equations of substrate-limited growth: the case for blackman kinetics

A simplified model of cell metabolism, consisting of a series of linked reversible enzymatic reactions dependent on the concentration of a single external substrate has been developed. The general mathematical solution for this system of reactions is presented. This general solution confirms the concept of a rate-limiting step, or “master reaction”, in biological systems as first proposed by Blackman. The maximum rate of such a process is determined by, and equal to, the maximum rate of the slowest forward reaction in the series. Of practical interest in modeling the growth rate of cells are three cases developed from the general model. The simplest special case results in the Monod equation when the maximum forward rate of one enzymatic reaction in the cell is much less than the maximum forward rate of any other enzymatic reactions. More realistic is the case where the maximum forward rates of more than one enzymatic reaction are slow. When two slow enzymatic reactions are separated from each other by any number of fast reactions that overall can be described by a large equilibrium constant, the Blackman form results: and A third case is that in which two slow enzymatic steps are separated by an equilibrium constant that is not large. Unlike the Monod and Blackman forms, which contain only two arbitrary constants, this model contains three arbitrary constants: The Monod and Blackman forms are special cases of this three constant form. In comparing equations with two arbitrary constants the Monod equation gave poorer fit of the data in most cases than the Blackman form. It is concluded that workers modeling the growth of microorganisms should give a t least as much consideration to the Blackman form as is given to the Monod equation.     

Neuronal influences are necessary to produce mitochondrial co‐localization with glutamate transporters in astrocytes

Recent evidence suggests that the predominant astrocyte glutamate transporter, GLT‐1/ Excitatory Amino Acid Transporter 2 (EAAT2) is associated with mitochondria. We used primary cultures of mouse astrocytes to assess co‐localization of GLT‐1 with mitochondria, and tested whether the interaction was dependent on neurons, actin polymerization or the kinesin adaptor, TRAK2. Mouse primary astrocytes were transfected with constructs expressing V5‐tagged GLT‐1, pDsRed1‐Mito with and without dominant negative TRAK2. Astrocytes were visualized using confocal microscopy and co‐localization was quantified using Volocity software. Image analysis of confocal z‐stacks revealed no co‐localization between mitochondria and GLT‐1 in pure astrocyte cultures. Co‐culture of astrocytes with primary mouse cortical neurons revealed more mitochondria in processes and a positive correlation between mitochondria and GLT‐1. This co‐localization was not further enhanced after neuronal depolarization induced by 1 h treatment with 15 mM K⁺. In pure astrocytes, a rho kinase inhibitor, Y27632 caused the distribution of mitochondria to astrocyte processes without enhancing GLT‐1/mitochondrial co‐localization, however, in co‐cultures, Y27632 abolished mitochondrial:GLT‐1 co‐localization. Disrupting potential mitochondrial: kinesin interactions using dominant negative TRAK2 did not alter GLT‐1 distribution or GLT‐1: mitochondrial co‐localization. We conclude that the association between GLT‐1 and mitochondria is modest, is driven by synaptic activity and dependent on polymerized actin filaments.

     

Challenging a paradigm: Theoretical calculations of the protonation state of the Cys25‐His159 catalytic diad in free papain

A central mechanistic paradigm of cysteine proteases is that the His–Cys catalytic diad forms an ion‐pair NH(+)/S(?) already in the catalytically active free enzyme. Most molecular modeling studies of cysteine proteases refer to this paradigm as their starting point. Nevertheless, several recent kinetics and X‐ray crystallography studies of viral and bacterial cysteine proteases depart from the ion‐pair mechanism, suggesting general base catalysis. We challenge the postulate of the ion‐pair formation in free papain. Applying our QM/SCRF(VS) molecular modeling approach, we analyzed all protonation states of the catalytic diad in free papain and its SMe derivative, comparing the predicted and experimental pK_a data. We conclude that the His–Cys catalytic diad in free papain is fully protonated, NH(+)/SH. The experimental pK_a = 8.62 of His159 imidazole in free papain, obtained by NMR‐controlled titration and originally interpreted as the NH(+)/S(?) ? N/S(?) equilibrium, is now assigned to the NH(+)/SH ? N/SH equilibrium. Proteins 2009. © 2009 Wiley‐Liss, Inc.