Bayesian clustering of farm types using the mixtures model

A Bayesian method of classifying observations that are assumed to come from a number of distinct subpopulations is outlined. The method is illustrated with simulated data and applied to the classification of farms according to their level and variability of income. The resultant classification shows a greater diversity of technical charactersitics within farm types than is conventionally the case. The range of mean farm income between groups in the new classification is wider than that of the conventional method and the variability of income within groups is narrower. Results show that the highest income group in 2000 included large specialist dairy farmers and pig and poultry producers, whilst in 2001 it included large and small specialist dairy farms and large mixed dairy and arable farms. In both years the lowest income group is dominated by non-milk producing livestock farms.

Estimating the hidden number of scrapie affected holdings in great Britain using a simple, truncated count model allowing for heterogeneity

None of the current surveillance streams monitoring the presence of scrapie in Great Britain provide a comprehensive and unbiased estimate of the prevalence of the disease at the holding level. Previous work to estimate the under-ascertainment adjusted prevalence of scrapie in Great Britain applied multiple-list capture-recapture methods. The enforcement of new control measures on scrapie-affected holdings in 2004 has stopped the overlapping between surveillance sources and, hence, the application of multiple-list capture-recapture models. Alternative methods, still under the capture-recapture methodology, relying on repeated entries in one single list have been suggested in these situations. In this article, we apply one-list capture-recapture approaches to data held on the Scrapie Notifications Database to estimate the undetected population of scrapie-affected holdings with clinical disease in Great Britain for the years 2002, 2003, and 2004. For doing so, we develop a new diagnostic tool for indication of heterogeneity as well as a new understanding of the Zelterman and Chao's lower bound estimators to account for potential unobserved heterogeneity. We demonstrate that the Zelterman estimator can be viewed as a maximum likelihood estimator for a special, locally truncated Poisson likelihood equivalent to a binomial likelihood. This understanding allows the extension of the Zelterman approach by means of logistic regression to include observed heterogeneity in the form of covariates-in case studied here, the holding size and country of origin. Our results confirm the presence of substantial unobserved heterogeneity supporting the application of our two estimators. The total scrapie-affected holding population in Great Britain is around 300 holdings per year. None of the covariates appear to inform the model significantly.

Design and analysis of climate model experiments for the efficient estimation of anthropogenic signals

Presented herein is an experimental design that allows the effects of several radiative forcing factors on climate to be estimated as precisely as possible from a limited suite of atmosphere-only general circulation model (GCM) integrations. The forcings include the combined effect of observed changes in sea surface temperatures, sea ice extent, stratospheric (volcanic) aerosols, and solar output, plus the individual effects of several anthropogenic forcings. A single linear statistical model is used to estimate the forcing effects, each of which is represented by its global mean radiative forcing. The strong colinearity in time between the various anthropogenic forcings provides a technical problem that is overcome through the design of the experiment. This design uses every combination of anthropogenic forcing rather than having a few highly replicated ensembles, which is more commonly used in climate studies. Not only is this design highly efficient for a given number of integrations, but it also allows the estimation of (nonadditive) interactions between pairs of anthropogenic forcings. The simulated land surface air temperature changes since 1871 have been analyzed. The changes in natural and oceanic forcing, which itself contains some forcing from anthropogenic and natural influences, have the most influence. For the global mean, increasing greenhouse gases and the indirect aerosol effect had the largest anthropogenic effects. It was also found that an interaction between these two anthropogenic effects in the atmosphere-only GCM exists. This interaction is similar in magnitude to the individual effects of changing tropospheric and stratospheric ozone concentrations or to the direct (sulfate) aerosol effect. Various diagnostics are used to evaluate the fit of the statistical model. For the global mean, this shows that the land temperature response is proportional to the global mean radiative forcing, reinforcing the use of radiative forcing as a measure of climate change. The diagnostic tests also show that the linear model was suitable for analyses of land surface air temperature at each GCM grid point. Therefore, the linear model provides precise estimates of the space time signals for all forcing factors under consideration. For simulated 50-hPa temperatures, results show that tropospheric ozone increases have contributed to stratospheric cooling over the twentieth century almost as much as changes in well-mixed greenhouse gases.

EOQ, JIT and fixed costs in the Ready-mixed concrete industry

The successful implementation of just-in-time (JIT) purchasing policy in many industries has prompted many companies that still use the economic order quantity (EOQ) purchasing policy to ponder if they should switch to the JIT purchasing policy. Despite existing studies that directly compare the costs between the EOQ and JIT purchasing systems, this decision is, however, still difficult to be made, especially when price discount has to be considered. JIT purchasing may not always be successful even though plants that adopted JIT operations have experienced or can take advantage of physical space reduction. Hence, the objective of this study is to expand on a classical EOQ with a price discount model to derive the EOQ–JIT cost indifference point. The objective was tested and achieved through a survey and case study conducted in the ready-mixed concrete industry in Singapore.

A novel repair model for imperfect maintenance

Commonly used repair rate models for repairable systems in the reliability literature are renewal processes, generalised renewal processes or non-homogeneous Poisson processes. In addition to these models, geometric processes (GP) are studied occasionally. The GP, however, can only model systems with monotonously changing (increasing, decreasing or constant) failure intensities. This paper deals with the reliability modelling of failure processes for repairable systems where the failure intensity shows a bathtub-type non-monotonic behaviour. A new stochastic process, i.e. an extended Poisson process, is introduced in this paper. Reliability indices are presented, and the parameters of the new process are estimated. Experimental results on a data set demonstrate the validity of the new process.

A novel repair model for imperfect maintenance

The basic repair rate models for repairable systems may be homogeneous Poisson processes, renewal processes or nonhomogeneous Poisson processes. In addition to these models, geometric processes are studied occasionally. Geometric processes, however, can only model systems with monotonously changing (increasing, decreasing or constant) failure intensity. This paper deals with the reliability modelling of the failure process of repairable systems when the failure intensity shows a bathtub type non-monotonic behaviour. A new stochastic process, an extended Poisson process, is introduced. Reliability indices and parameter estimation are presented. A comparison of this model with other repair models based on a dataset is made.

In vitro fermentation of chitosan derivatives by mixed cultures of human faecal bacteria

Stirred, pH controlled batch cultures were carried out with faecal inocula and various chitosans to investigate the fermentation of chitosan derivatives by the human gut flora. Changes in bacterial levels and short chain fatty acids were measured over time. Low, medium and high molecular weight chitosan caused a decrease in bacteroides, bifidobacteria, clostridia and lactobacilli. A similar pattern was seen with chitosan oligosaccharide (COS). Butyrate levels also decreased. A three-stage fermentation model of the human colon was used for investigation of the metabolism of COS. In a region representing the proximal colon, clostridia decreased while lactobacilli increased. In the region representing the transverse colon, bacteroides and clostridia increased. Distally a small increase in bacteroides occurred. Butyrate levels increased. Under the highly competitive conditions of the human colon, many members of the microflora, are unable to compete for chitosans of low, medium or high molecular weight. COS were more easily utilised and when added to an in vitro colonic model led to increased production of butyrate, but some populations of potentially detrimental bacteria also increased. (c) 2005 Elsevier Ltd. All rights reserved.

A two-stage continuous culture system to study the effect of supplemental alpha-lactalbumin and glycomacropeptide on mixed cultures of human gut bacteria challenged with enteropathogenic Escherichia coli and Salmonella serotype Typhimurium

Aims: Certain milk factors may promote the growth of a gastrointestinal microflora predominated by bifidobacteria and may aid in overcoming enteric infections. This may explain why breast-fed infants experience fewer intestinal infections than their formula-fed counterparts. The effect of formula supplementation with two such factors was investigated in this study. Methods and Results: Infant faecal specimens were used to ferment formulae supplemented with glycomacropeptide (GMP) and alpha-lactalbumin (alpha-la) in a two-stage compound continuous culture model. At steady state, all fermenter vessels were inoculated with 5 ml of 0.1 M phosphate-buffered saline (pH 7.2) containing 10(8) CFU ml(-1) of either enteropathogenic Escherichia coli 2348/69 (O127:H6) or Salmonella serotype Typhimurium (DSMZ 5569). Bacteriology was determined by independent fluorescence in situ hybridization. Vessels that contained breast milk (BM), as well as alpha-la and GMP supplemented formula had stable total counts of bifidobacteria while lactobacilli increased significantly only in vessels with breast milk. Bacteroides, clostridia and E. coli decreased significantly in all three groups prior to pathogen addition. Escherichia coli counts decreased in vessels containing BM and alpha-la while Salmonella decreased significantly in all vessels containing BM, alpha-la and GMP. Acetate was the predominant acid. Significance and Impact of the Study: Supplementation of infant formulae with appropriate milk proteins may be useful in mimicking the beneficial bacteriological effects of breast milk.

Crystal structures of [PhLi center dot(-)-sparteine](2), [PhOLi center dot(-)-sparteine](2), and the mixed aggregate [PhLi center dot PhOLi center dot 2(-)-sparteine]

Crystal structure determination of adducts of sparteine and PhLi, (-)-sparteine and PhOLi and of sparteine and PhLi/PhOLi reveal a four-membered ring with two lithium centers, each capped by a (-)-sparteine ligand, as central motif of all structure. Quantum-chemical calculations show that the mixed aggregate [PhLi center dot PhOLi center dot 2(-)-sparteine] is energetically more favorable than the model system {1/2[PhLi center dot(-)-sparteine](2) + 1/2[PhOLi center dot(-)-sparteine](2)}.

Mixed initial-boundary value problem in particle modeling of microelectronic devices

The Boltzmann equation in presence of boundary and initial conditions, which describes the general case of carrier transport in microelectronic devices is analysed in terms of Monte Carlo theory. The classical Ensemble Monte Carlo algorithm which has been devised by merely phenomenological considerations of the initial and boundary carrier contributions is now derived in a formal way. The approach allows to suggest a set of event-biasing algorithms for statistical enhancement as an alternative of the population control technique, which is virtually the only algorithm currently used in particle simulators. The scheme of the self-consistent coupling of Boltzmann and Poisson equation is considered for the case of weighted particles. It is shown that particles survive the successive iteration steps.

A bagging-based correction for the mixture model estimator of population size

Estimation of a population size by means of capture-recapture techniques is an important problem occurring in many areas of life and social sciences. We consider the frequencies of frequencies situation, where a count variable is used to summarize how often a unit has been identified in the target population of interest. The distribution of this count variable is zero-truncated since zero identifications do not occur in the sample. As an application we consider the surveillance of scrapie in Great Britain. In this case study holdings with scrapie that are not identified (zero counts) do not enter the surveillance database. The count variable of interest is the number of scrapie cases per holding. For count distributions a common model is the Poisson distribution and, to adjust for potential heterogeneity, a discrete mixture of Poisson distributions is used. Mixtures of Poissons usually provide an excellent fit as will be demonstrated in the application of interest. However, as it has been recently demonstrated, mixtures also suffer under the so-called boundary problem, resulting in overestimation of population size. It is suggested here to select the mixture model on the basis of the Bayesian Information Criterion. This strategy is further refined by employing a bagging procedure leading to a series of estimates of population size. Using the median of this series, highly influential size estimates are avoided. In limited simulation studies it is shown that the procedure leads to estimates with remarkable small bias.

A refined LEED analysis of water on Ru{0001}: an experimental test of the partial dissociation model

Despite a number of earlier studies which seemed to confirm molecular adsorption of water on close-packed surfaces of late transition metals, new controversy has arisen over a recent theoretical work by Feibelman, according to which partial dissociation occurs on the Ru{0001} surface leading to a mixed (H2O + OH + H) superstructure. Here, we present a refined LEED-IV analysis of the (root3 x root3)R30degrees-D2O-Ru{0001} structure, testing explicitly this new model by Feibelman. Our results favour the model proposed earlier by Held and Menzel assuming intact water molecules with almost coplanar oxygen atoms and out-of-plane hydrogen atoms atop the slightly higher oxygen atoms. The partially dissociated model with an almost identical arrangement of oxygen atoms can, however, not unambiguously be excluded, especially when the single hydrogen atoms are not present in the surface unit cell. In contrast to the earlier LEED-IV analysis, we can, however, clearly exclude a buckled geometry of oxygen atoms.

Use of a reduced Schiff-Base ligand to prepare novel chloro-bridged chains of rare Cu(II) trinuclear complexes with mixed azido/oxo and chloro/oxo bridges

Two mixed bridged one-dimensional (1D) polynuclear complexes, [Cu3L2(mu(1,1)-N-3)(2)(mu-Cl)Cl](n) (1) and {[Cu3L2(mu-Cl)(3)Cl]center dot 0.46CH(3)OH}(n), (2), have been synthesized using the tridentate reduced Schiff-base ligand HL (2-[(2-dimethylamino-ethylamino)-methyl]-phenol). The complexes have been characterized by X-ray structural analyses and variable-temperature magnetic susceptibility measurements. In both complexes the basic trinuclear angular units are joined together by weak chloro bridges to form a 1D chain. The trinuclear structure of 1 is composed of two terminal square planar [Cu(L)(mu(1,1)-N-3)] units connected by a central Cu(II) atom through bridging nitrogen atoms of end-on azido ligands and the phenoxo oxygen atom of the tridentate ligand. These four coordinating atoms along with a chloride ion form a distorted trigonal bipyramidal geometry around the central Cu(II). The structure of 2 is similar; the only difference being a Cl bridge replacing the mu(1,1)-N-3 bridge in the trinuclear unit. The magnetic properties of both trinuclear complexes can be very well reproduced with a simple linear symmetrical trimer model (H = JS(i)S(i+1)) with only one intracluster exchange coupling (J) including a weak intertrimer interaction (.j) reproduced with the molecular field approximation. This model provides very satisfactory fits for both complexes in the whole temperature range with the following parameters: g = 2.136(3), J = 93.9(3) cm(-1) and zj= -0.90(3) cm(-1) (z = 2) for 1 and g = 2.073(7), J = -44.9(4) cm(-1) and zJ = -1.26(6) cm(-1) (z = 2) for 2.

Climate model calculations of the impact of aerosols from road transport and shipping

Road transport and shipping are copious sources of aerosols, which exert a 9 significant radiative forcing, compared to, for example, the CO2 emitted by these sectors. An 10 advanced atmospheric general circulation model, coupled to a mixed-layer ocean, is used to 11 calculate the climate response to the direct radiative forcing from such aerosols. The cases 12 considered include imposed distributions of black carbon and sulphate aerosols from road 13 transport, and sulphate aerosols from shipping; these are compared to the climate response 14 due to CO2 increases. The difficulties in calculating the climate response due to small 15 forcings are discussed, as the actual forcings have to be scaled by large amounts to enable a 16 climate response to be easily detected. Despite the much greater geographical inhomogeneity 17 in the sulphate forcing, the patterns of zonal and annual-mean surface temperature response 18 (although opposite in sign) closely resembles that resulting from homogeneous changes in 19 CO2. The surface temperature response to black carbon aerosols from road transport is shown 20 to be notably non-linear in scaling applied, probably due to the semi-direct response of clouds 21 to these aerosols. For the aerosol forcings considered here, the most widespread method of 22 calculating radiative forcing significantly overestimates their effect, relative to CO2, 23 compared to surface temperature changes calculated using the climate model.

Wind-driven mixing below the oceanic mixed layer

This study describes the turbulent processes in the upper ocean boundary layer forced by a constant surface stress in the absence of the Coriolis force using large-eddy simulation. The boundary layer that develops has a two-layer structure, a well-mixed layer above a stratified shear layer. The depth of the mixed layer is approximately constant, whereas the depth of the shear layer increases with time. The turbulent momentum flux varies approximately linearly from the surface to the base of the shear layer. There is a maximum in the production of turbulence through shear at the base of the mixed layer. The magnitude of the shear production increases with time. The increase is mainly a result of the increase in the turbulent momentum flux at the base of the mixed layer due to the increase in the depth of the boundary layer. The length scale for the shear turbulence is the boundary layer depth. A simple scaling is proposed for the magnitude of the shear production that depends on the surface forcing and the average mixed layer current. The scaling can be interpreted in terms of the divergence of a mean kinetic energy flux. A simple bulk model of the boundary layer is developed to obtain equations describing the variation of the mixed layer and boundary layer depths with time. The model shows that the rate at which the boundary layer deepens does not depend on the stratification of the thermocline. The bulk model shows that the variation in the mixed layer depth is small as long as the surface buoyancy flux is small.