A generalized Markov sampler

A recent development of the Markov chain Monte Carlo (MCMC) technique is the emergence of MCMC samplers that allow transitions between different models. Such samplers make possible a range of computational tasks involving models, including model selection, model evaluation, model averaging and hypothesis testing. An example of this type of sampler is the reversible jump MCMC sampler, which is a generalization of the Metropolis-Hastings algorithm. Here, we present a new MCMC sampler of this type. The new sampler is a generalization of the Gibbs sampler, but somewhat surprisingly, it also turns out to encompass as particular cases all of the well-known MCMC samplers, including those of Metropolis, Barker, and Hastings. Moreover, the new sampler generalizes the reversible jump MCMC. It therefore appears to be a very general framework for MCMC sampling. This paper describes the new sampler and illustrates its use in three applications in Computational Biology, specifically determination of consensus sequences, phylogenetic inference and delineation of isochores via multiple change-point analysis.

Lysine requirements of pre-lay broiler breeder pullets: Determination by indicator amino acid oxidation

The indicator amino acid oxidation (IAAO) method allows the determination of amino acid requirements under conditions of low growth rate as found in pre-laying broiler breeder pullets. Cobb 500 breeder pullets (20 wk old; 2290 +/- 280 g, n = 4) were adapted (6 d) to a pelleted, purified control diet containing all nutrients at greater than or equal to 110% of NRC recommendations. After recovery from surgery for implantation of a jugular catheter, each bird was fed, in random order, test diets containing one of nine levels of lysine (0.48, 0.96, 1.92, 2.88, 3.84, 4.80, 7.68, 9.60 and 14.40 g/kg of diet). Indicator oxidation was determined during 4-h primed (74 kBq/kg body), constant infusions (44 kBq (.) h(-1) (.) kg body(-1)) of L-[1-C-14]phenylalanine. Using the breakpoint of a one-slope broken-line model, the lysine requirement was determined to be 4.88 +/- 0.96 g/kg of diet or 366 +/- 72 mg (.) hen(-1) (.) d(-1) with an upper 95% Cl of 6.40 g/kg of diet or 480 mg (.) hen(-1) (.) d(-1). IAAO allows determination of individual bird amino acid requirements for specific ages and types of birds over short periods of time and enables more accurate broiler breeder pullet diet formulation.

Electrochemical deposition of cupric ions for the determination of mass transfer rates to a stepped rotating cylinder electrode

The stepped rotating cylinder electrode (SRCE) geometry has been developed as a simple aid to the practical study of the flow-enhanced corrosion and applied electrochemistry problems commonly observed under conditions of disturbed, turbulent flow. The electrodeposition of cupric ions from an acid sulphate plating bath has been used to characterise differential rates of mass transfer to the SRCE. The variation in thickness of electrodeposited copperfilms has allowed the mapping of local rates of mass transfer over the active surface of this geometry. Both optical and scanning electron microscopy were used for the examination of metallographic sections to provide a high resolution evaluation of the distribution of mass transfer coefficient. Results are also discussed using the convective-diffusion model in combination with the existing direct numerical flow simulation (DNS) data for this geometry.

Molecular analysis of the pathway for the synthesis of thiol tripeptides in the model legume Lotus japonicus

The thiol tripeptides, glutathione (GSH) and homoglutathione (hGSH), perform multiple roles in legumes, including protection against toxicity of free radicals and heavy metals. The three genes involved in the synthesis of GSH and hGSH in the model legume, Lotus japonicus, have been fully characterized and appear to be present as single copies in the genome. The gamma-glutamylcysteine synthetase (gammaecs) gene was mapped on the long arm of chromosome 4 (70.0 centimorgans [cM]) and consists of 15 exons, whereas the glutathione synthetase (gshs) and homoglutathione synthetase (hgshs) genes were mapped on the long arm of chromosome 1 (81.3 cM) and found to be arranged in tandem, with a separation of approximately 8 kb. Both genes consist of 12 exons of exactly the same size (except exon 1, which is similar). Two types of transcripts were detected for the gshs gene, which putatively encode proteins localized in the plastids and cytosol. Promoter regions contain cis-acting regulatory elements that may be involved in the plant's response to light, hormones, and stress. Determination of transcript levels, enzyme activities, and thiol contents in nodules, roots, and leaves revealed that gammaecs and hgshs are expressed in all three plant organs, whereas gshs is significantly functional only in nodules. This strongly suggests an important role of GSH in the rhizobia-legume symbiosis.

Optimal price regulation in a growth model with monopolistic suppliers of intermediate goods

In this paper we investigate the trade-off faced by regulators who must set a price for an intermediate good somewhere between the marginal cost and the monopoly price. We utilize a growth model with monopolistic suppliers of intermediate goods. Investment in innovation is required to produce a new intermediate good. Marginal cost pricing deters innovation, while monopoly pricing maximizes innovation and economic growth at the cost of some static inefficiency. We demonstrate the existence of a second-best price above the marginal cost but below the monopoly price, which maximizes consumer welfare. Simulation results suggest that substantial reductions in consumption, production, growth, and welfare occur where regulators focus on static efficiency issues by setting prices at or near marginal cost.

Determination of lifter design, speed and filling effects in AG mills by 3D DEM

The power required to operate large gyratory mills often exceeds 10 MW. Hence, optimisation of the power consumption will have a significant impact on the overall economic performance and environmental impact of the mineral processing plant. In most of the published models of tumbling mills (e.g. [Morrell, S., 1996. Power draw of wet tumbling mills and its relationship to charge dynamics, Part 2: An empirical approach to modelling of mill power draw. Trans. Inst. Mining Metall. (Section C: Mineral Processing Ext. Metall.) 105, C54-C62. Austin, L.G., 1990. A mill power equation for SAG mills. Miner. Metall. Process. 57-62]), the effect of lifter design and its interaction with mill speed and filling are not incorporated. Recent experience suggests that there is an opportunity for improving grinding efficiency by choosing the appropriate combination of these variables. However, it is difficult to experimentally determine the interactions of these variables in a full scale mill. Although some work has recently been published using DEM simulations, it was basically. limited to 2D. The discrete element code, Particle Flow Code 3D (PFC3D), has been used in this work to model the effects of lifter height (525 cm) and mill speed (50-90% of critical) on the power draw and frequency distribution of specific energy (J/kg) of normal impacts in a 5 m diameter autogenous (AG) mill. It was found that the distribution of the impact energy is affected by the number of lifters, lifter height, mill speed and mill filling. Interactions of lifter design, mill speed and mill filling are demonstrated through three dimensional distinct element methods (3D DEM) modelling. The intensity of the induced stresses (shear and normal) on lifters, and hence the lifter wear, is also simulated. (C) 2004 Elsevier Ltd. All rights reserved.

The current account, fiscal policy, and medium-run income determination

This article presents a new framework for analyzing the simultaneous determination of current account imbalances and the path of national income. Using standard macroeconomic behavioral relationships, it first examines how and why current account deficits matter by investigating links between domestic consumption, government spending, output, saving, investment, interest rates, and capital flows. Central to the model is the distinction between aggregate output and expenditure that enables dissection of the effects of discretionary fiscal change on the current account and national income. The framework yields results relevant to the twin deficits hypothesis that are contrary to those of standard models.

Determination of domain sizes in blends of poly(ethylene) and poly(styrene) formed in the presence of supercritical carbon dioxide

Well-mixed blends of poly(ethylene) and poly(styrene) have been synthesized using supercritical carbon dioxide as a solvent. The morphology of the blends has been conclusively characterized using differential scanning calorimetry (DSC), small-angle X-ray scattering (SAXS), Raman microprobe microscopy, and C-13 solid-state cross-polarization magic angle spinning NMR (C-13 CPMAS NMR). DSC measurements demonstrate that poly(styrene) in the blends resides solely in the amorphous regions of the poly(ethylene) matrix; however, corroborative evidence from the SAXS experiments shows that poly(styrene) resides within the interlamellar spaces. The existence of nanometer-sized domains of poly(styrene) was shown within a blend of poly(styrene) and poly(ethylene) when formed in supercritical carbon dioxide using Raman microprobe microscopy and C-13 CPMAS NMR spectroscopy coupled with a spin diffusion model. This contrasts with blends formed at ambient pressure in the absence of solvent, in which domains of poly(styrene) in the micrometer size range are formed. This apparent improved miscibility of the two components was attributed to better penetration of the monomer prior to polymerization and increased swelling of the polymer substrate by the supercritical carbon dioxide solvent.

Determination of alpha-conotoxin binding modes on neuronal nicotinic acetylcholine receptors

alpha-Conotoxins, from cone snails, and alpha-neurotoxins, from snakes, are competitive inhibitors of nicotinic acetylcholine receptors (nAChRs) that have overlapping binding sites in the ACh binding pocket. These disulphide-rich peptides are used extensively as tools to localize and pharmacologically characterize specific nAChRs subtypes. Recently, a homology model based on the high-resolution structure of an ACh binding protein (AChBP) allowed the three-fingered alpha-neurotoxins to be docked onto the alpha7 nAChR. To investigate if alpha-conotoxins interact with the nAChR in a similar manner, we built homology models of human alpha7 and alpha3beta2 nAChRs, and performed docking simulations of alpha-conotoxins ImI, PnIB, PnIA and MII using the program GOLD. Docking revealed that alpha-conotoxins have a different mode of interaction compared with alpha-neurotoxins, with surprisingly few nAChR residues in common between their overlapping binding sites. These docking experiments show that Imi and PnIB bind to the ACh binding pocket via a small cavity located above the beta9/beta10 hairpin of the (+)alpha7 nAChR subunit. Interestingly, PnIB, PnIA and MII were found to bind in a similar location on alpha7 or alpha3beta2 receptors mostly through hydrophobic interactions, while ImI bound further from the ACh binding pocket, mostly through electrostatic interactions. These findings, which distinguish alpha-conotoxin and alpha-neurotoxin binding modes, have implications for the rational design of selective nAChR antagonists. Copyright (C) 2004 John Wiley Sons, Ltd.

Estimation of water retention curve from mercury intrusion porosimetry and van Genuchten model

The water retention curve (WRC) is a hydraulic characteristic of concrete required for advanced modeling of water (and thus solute) transport in variably saturated, heterogeneous concrete. Unfortunately, determination by a direct experimental method (for example, measuring equilibrium moisture levels of large samples stored in constant humidity cells) is a lengthy process, taking over 2 years for large samples. A surrogate approach is presented in which the WRC is conveniently estimated from mercury intrusion porosimetry (MIP) and validated by water sorption isotherms: The well-known Barrett, Joyner and Halenda (BJH) method of estimating the pore size distribution (PSD) from the water sorption isotherm is shown to complement the PSD derived from conventional MIP. This provides a basis for predicting the complete WRC from MIP data alone. The van Genuchten equation is used to model the combined water sorption and MIP results. It is a convenient tool for describing water retention characteristics over the full moisture content range. The van Genuchten parameter estimation based solely on MIP is shown to give a satisfactory approximation to the WRC, with a simple restriction on one. of the parameters.

Determination of chromophore charge states in the low pH color transition of the fluorescent protein Rtms5(H146S) via time-dependent DFT

The red fluorescent protein Rtms5H146S displays a transition from blue (absorbance λmax 590 nm) to yellow (absorbance λmax not, vert, similar453 nm) upon titration to low pH. The pKa of the reaction depends on the concentration of halide, offering promise for new expressible halide sensors. The protonation state involved in the low pH form of the chromophore remains, however, ambiguous. We report calculated excitation energies of different protonation states of an RFP chromophore model. These suggest that the relevant titration site is the phenoxy moiety of the chromophore, and the relevant base and conjugate acid are anionic and neutral chromophore species, respectively.

Determination of Cole parameters in multiple frequency bioelectrical impedance analysis using only the measurement of impedances

Conventional bioimpedance spectrometers measure resistance and reactance over a range of frequencies and, by application of a mathematical model for an equivalent circuit (the Cole model), estimate resistance at zero and infinite frequencies. Fitting of the experimental data to the model is accomplished by iterative, nonlinear curve fitting. An alternative fitting method is described that uses only the magnitude of the measured impedances at four selected frequencies. The two methods showed excellent agreement when compared using data obtained both from measurements of equivalent circuits and of humans. These results suggest that operational equivalence to a technically complex, frequency-scanning, phase-sensitive BIS analyser could be achieved from a simple four-frequency, impedance-only analyser.

Leading coordinate analysis of reaction pathways in proton chain transfer: Application to a two-proton transfer model for the green fluorescent protein

The ‘leading coordinate’ approach to computing an approximate reaction pathway, with subsequent determination of the true minimum energy profile, is applied to a two-proton chain transfer model based on the chromophore and its surrounding moieties within the green fluorescent protein (GFP). Using an ab initio quantum chemical method, a number of different relaxed energy profiles are found for several plausible guesses at leading coordinates. The results obtained for different trial leading coordinates are rationalized through the calculation of a two-dimensional relaxed potential energy surface (PES) for the system. Analysis of the 2-D relaxed PES reveals that two of the trial pathways are entirely spurious, while two others contain useful information and can be used to furnish starting points for successful saddle-point searches. Implications for selection of trial leading coordinates in this class of proton chain transfer reactions are discussed, and a simple diagnostic function is proposed for revealing whether or not a relaxed pathway based on a trial leading coordinate is likely to furnish useful information.

On labour market dualism in the Lewis model: A comment

In a special issue of this journal commemorating the 50th anniversary of W. Arthur Lewis's (The Manchester School, Vol. 28 (1954), No. 2, pp. 139-191) seminal paper, the Lewis model is treated as a model of labour market dualism (Fields, The Manchester School, Vol. 72 (2004), No. 6, pp. 724-735). This interpretation is flawed for a number of reasons. First, it overemphasizes the role ascribed by Lewis to intersectoral earnings differentials in his original model. Second, it fails to acknowledge that a major shortcoming of the model was its inability to account for the widening intersectoral earnings differential observed across a wide range of developing economies. For Lewis himself this was one of the 'major theoretical puzzles of the period' (1979, p. 150). Third, it ignores Lewis's subsequent revision of the model (Lewis, The Manchester School, Vol. 47 (1979), No. 3, pp. 211-229) that, ironically, incorporates a dual labour market to resolve this puzzle. However, for Lewis the critical issue was dualism within the modern sector, not, as Fields understands it, labour market dualism between the modern and traditional sectors. Fields's appreciation of the contribution of the Lewis model to understanding the process of wage determination in developing economies is therefore misplaced.