Objective bayesian analysis of the Yule–Simon distribution with applications

The Yule–Simon distribution is usually employed in the analysis of frequency data. As the Bayesian literature, so far, has ignored this distribution, here we show the derivation of two objective priors for the parameter of the Yule–Simon distribution. In particular, we discuss the Jeffreys prior and a loss-based prior, which has recently appeared in the literature. We illustrate the performance of the derived priors through a simulation study and the analysis of real datasets.     

Local time and Tanaka formula for a multitype Dawson–Watanabe superprocess

In [3] Dynkin defined the local time of a continuous superprocess as a stochastic integral and gave a criterion for existence of local time. Here we prove that the conditions in Dynkin's existence criterion are satisfied by the multitype Dawson–Watanabe superprocess, and give a Tanaka formula‐like representation of the local time which is used to show that the occupation measure of the multitype superprocess is absolutely continuous with respect to an appropriate reference measure, and that the corresponding density coincides a.s. with the local time. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Gut microbiota, diet, and heart disease

Modulation of the gut microbiota is an area of growing interest, particularly for its link to improving and maintaining the systemic health of the host. It has been suggested to have potential to reduce risk factors associated with chronic diseases, such as elevated cholesterol levels in coronary heart disease (CHD). Diets of our evolutionary ancestors were largely based on plant foods, high in dietary fiber and fermentable substrate, and our gut microbiota has evolved against a background of such diets. Therapeutic diets that mimic plant-based diets from the early phases of human evolution may result in drug-like cholesterol reductions. In contrast, typical Western diets low in dietary fiber and fermentable substrate, and high in saturated and trans fatty acids, are likely contributors to the increased need for pharmacological agents for cholesterol reduction. The gut microbiota of those consuming a Western diet are likely underutilized and depleted of metabolic fuels, resulting in a less than optimal gut microbial profile. As a result, this diet is mismatched to our archaic gut microbiota and, therefore, to our genome, which has changed relatively little since humans first appeared. While the exact mechanism by which the gut microbiota may modulate cholesterol levels still remains uncertain, end products of bacterial fermentation, particularly the short chain fatty acids (i.e., propionate), have been suggested as potential candidates. While more research is required to clarify the potential link between gut microbiota and CHD risk reduction, consuming a therapeutic diet rich in plant foods, dietary fiber, and fermentable substrate would be a useful strategy for improving systemic health, possibly by altering the gut microbiota.     

Understanding binding affinity: a combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin

The binding of a series of p-alkylbenzamidinium chloride inhibitors to the serine proteinase trypsin over a range of temperatures has been studied using isothermal titration (micro)calorimetry and molecular dynamics simulation techniques. The inhibitors have small structural variations at the para position of the benzamidinium ion. They show small differences in relative binding affinity but large compensating differences in enthalpy and entropy. Binding affinity decreases with increased branching at the first carbon but increases with increasing the length of a linear alkyl substituent, suggesting that steric hindrance and hydrophobic interactions play dominant roles in binding. Structural analysis showed that the backbone of the enzyme was unaffected by the change of the para substituent. In addition, binding does not correlate strongly with octanol/water partition data. To further characterize this system, the change in the heat capacity on binding, the change in solvent-accessible surface area on binding, the effect of inhibitor binding on the hydration of the active site, the pK(a) of His57, and interactions within the catalytic triad have been investigated. Although the changes in inhibitor structure are small, it is demonstrated that simple concepts such as steric hindrance, hydrophobicity, and buried surface area are insufficient to explain the binding data. Other factors, such as access to the binding site and the cost of dehydration of the active site, are of equal or greater importance.     

Synthesis and Ruthenium-Catalyzed Enantioselective Hydrogenation of 3-O-Substituted 1,3-Dihydroxypropan-2-ones. Part 2

A number of 3-O-substituted 1,3-dihydroxypropan-2-ones have been synthesized in view of their potential use as prochiral precursors of optically active glycerols. Indeed, the oxo-ethers have been reduced to the corresponding 3-O-substituted glycerols via chiral Ru complexes derived from (S)-binap, ( =(?)-(S)-2,2′-bis(diphenylphosphino)-1,1′-binaphthalene) with enantiomeric excesses up to 93%. The steric course of the catalytic reduction appears to be essentially dependent on the steric encumbrance of the substituents; indeed, a dramatic increase of the enantiomeric excess is observed when the bulky trityl group is substituted by the less encumbering benzyl or octadecyl groups.     

The solute-solvent system: solvent constraints on the conformational dynamics of acetylcholine

The objective of this study was to determine if and how a solvent influences internal motions in a solute molecule. Acetylcholine was chosen as the object of study given its interesting molecular structure and major biological significance. Molecular dynamics simulations were carried out in the vacuum (10 ns), water (5 ns), methanol (5 ns), and octanol (1.5 ns). Seven clusters of conformers were identified, namely, +g+g, -g-g, +gt, -gt, t+g, t-g, and tt, where the gauche and trans labels refer to the dihedral angles tau(2) and tau(3), respectively. As expected, the relative proportion of these conformational clusters was highly solvent-dependent and corresponded to a progressive loss of conformational freedom with increasing molecular weight of the solvent. More importantly, the conformational clusters were used to calculate instantaneous and median angular velocity (omega and omega(M), respectively) and instantaneous and median angular acceleration (alpha and alpha(M), respectively). Angular velocity and angular acceleration were both found to decrease markedly with increasing molecular weight of the solvent, i.e., vacuum (epsilon = 1) > water > methanol > octanol. The decrease from the vacuum to octanol was approximately 40% for tau(2) and approximately 60% for tau(3). Such solvent-dependent constraints on a solute's internal motions may be biologically and pharmacologically relevant.     

Influence of Cyclodextrins on the Kinetics of Oxidation of Amino Acids and BSA by Hydrazyl Radicals

The kinetics of oxidation of amino acids (Arg, His, Lys, Phe, Thr and Tyr), a dipeptide (Gly-His), and BSA (bovine serum albumin) by two persistent water soluble free radicals of the hydrazyl type has been studied.The rate decreases in the order Arg>Lys>Tyr>Thr>HisBSAPheGly-His with bothfree radicals. Addition to the reaction mixture of - and -cyclodextrin decreases the oxidation rate, probably due to amino acidencapsulation in the cyclodextrin cavity. -Cyclodextrin protects more efficiently against oxidation than -cyclodextrin.     

High-performance liquid chromatography-electrospray ionization mass spectrometry and multiple mass spectrometry studies of hyperforin degradation products

The alcoholic extract of the aerial parts of Hypericum perforatum L. finds wide application because of its antidepressant activity. The extract contains a number of constituents with documented biological activity including chlorogenic acid, a broad range of flavonoids, naphthodianthrones and phloroglucinols. Hyperforin and adhyperforin are the major phloroglucinol constituents found in the lipophilic fraction of the extracts. Since the stability of hyperforin has been shown to be limited, an investigation of the hyperforin degradation products using HPLC-electrospray ionization mass spectrometry and multiple mass spectrometry was undertaken.