THE POWER OF SENSORY DISCRIMINATION METHODS USED IN REPLICATED DIFFERENCE AND PREFERENCE TESTS

Research on the power of discrimination methods in difference and preference tests has both theoretical and practical significance. Power is important to evaluate the sensitivities of tests and determine sample size. Ennis and Bi (1998, 1999) proposed the beta-binomial distribution to model replicated difference and preference tests with inter-trial variation and analyzed in general the power of the tests. In this paper, the power of discrimination methods for replicated difference and preference tests is discussed further. The equations for calculating power for methods based on the BB model are given. Examples with tables and charts for calculating and comparing the power of the methods are also given.     

Codominant scoring of AFLP in association panels

A study on the codominant scoring of AFLP markers in association panels without prior knowledge on genotype probabilities is described. Bands are scored codominantly by fitting normal mixture models to band intensities, illustrating and optimizing existing methodology, which employs the EM-algorithm. We study features that improve the performance of the algorithm, and the unmixing in general, like parameter initialization, restrictions on parameters, data transformation, and outlier removal. Parameter restrictions include equal component variances, equal or nearly equal distances between component means, and mixing probabilities according to Hardy–Weinberg Equilibrium. Histogram visualization of band intensities with superimposed normal densities, and optional classification scores and other grouping information, assists further in the codominant scoring. We find empirical evidence favoring the square root transformation of the band intensity, as was found in segregating populations. Our approach provides posterior genotype probabilities for marker loci. These probabilities can form the basis for association mapping and are more useful than the standard scoring categories A, H, B, C, D. They can also be used to calculate predictors for additive and dominance effects. Diagnostics for data quality of AFLP markers are described: preference for three-component mixture model, good separation between component means, and lack of singletons for the component with highest mean. Software has been developed in R, containing the models for normal mixtures with facilitating features, and visualizations. The methods are applied to an association panel in tomato, comprising 1,175 polymorphic markers on 94 tomato hybrids, as part of a larger study within the Dutch Centre for BioSystems Genomics.     

Whisker-mediated plant transformation: An alternative technology

A number of different methods, involving direct DNA delivery are now available for plant transformation. Here we review the most recently developed technique which involves the mixing of silicon carbide whiskers with plant cells and plasmid DNA. Fertile transgenic plants have now been produced using whisker-mediated transformation, and this method can now be considered as a simple, inexpensive alternative for plant transformation. A brief review on transformation of animal cells andChlamydomonas using whiskers technology is also included.     

A log-linear modeling framework for selective mixing.

Nonrandom mixing can significantly alter the diffusion path of an infectious disease such as AIDS that requires intimate contact. Recent attempts to model this effect have sought a general framework capable of representing both simple and arbitrarily complicated mixing structures, and of solving the balancing problem in a nonequilibrium multigroup population. Log-linear models are proposed here as a general framework for solving the first problem. This approach offers several additional benefits: The parameters used to govern the mixing have a simple, intuitive interpretation, the framework provides a statistically sound basis for the estimation of these parameters from mixing-matrix data, and the resulting estimates are easily integrated into compartmental models for diffusion. A modified selection model is proposed to solve the second problem of generalizing the selection process to nonequilibrium populations. The distribution of contacts under this model is derived and is found to satisfy the assumptions of statistical inference for log-linear models. Together these techniques provide an integrated and flexible framework for modeling the role of selective mixing in the spread of disease.     

CFD simulation of mixing in anaerobic digesters

A three-dimensional CFD model incorporating the rheological properties of sludge was developed and applied to quantify mixing in a full-scale anaerobic digester. The results of the model were found to be in good agreement with experimental tracer response curve. In order to predict the dynamics of mixing, a new parameter, UI (uniformity index) was defined. The visual patterns of tracer mixing in simulation were well reflected in the dynamic variation in the value of UI. The developed model and methods were applied to determine the required time for complete mixing in a full-scale digester at different solid concentrations. This information on mixing time is considered to be useful in optimizing the feeding cycles for better digester performance.     

COMPARISON OF METHODS FOR ANALYZING REPLICATED PREFERENCE TESTS

Preference testing is commonly used in consumer sensory evaluation. Traditionally, it is done without replication, effectively leading to a single 0/1 (binary) measurement on each panelist. However, to understand the nature of the preference, replicated preference tests are a better approach, resulting in binomial counts of preferences on each panelist. Variability among panelists then leads to overdispersion of the counts when the binomial model is used and to an inflated Type I error rate for statistical tests of preference. Overdispersion can be adjusted by Pearson correction or by other models such as correlated binomial or beta‐binomial. Several methods are suggested or reviewed in this study for analyzing replicated preference tests and their Type I error rates and power are compared. Simulation studies show that all methods have reasonable Type I error rates and similar power. Among them, the binomial model with Pearson adjustment is probably the safest way to analyze replicated preference tests, while a normal model in which the binomial distribution is not assumed is the easiest.     

A three-dimensional general circulation model of the surface layers of Lake Baikal

A three-dimensional general circulation model has been developed to investigate mixing processes in Lake Baikal, Siberia. Emphasis is placed on the 4–5-month period when the lake is completely ice-covered, a time of particular importance to the re-population of the lake by diatoms. The model represents the top 250 m and includes a new mixing scheme developed specifically for the investigation of under-ice flows. The effects of spatial patterns of snow and ice transparency on circulation and temperature are investigated. In general, temperature profiles provide an indication of the extent and depth of mixing and are highly sensitive to the presence of snow and to the transparency of ice. Generated profiles agree well with in situ measurements, which are difficult to obtain during this period. The model is shown to be particularly successful in simulating mixing processes in Lake Baikal. The surface heat fluxes that are required for a model of this type were estimated using satellite data, which provide complete coverage of the lake within one image. An increase in albedo values of 20% has no significant impact on the development of the temperature profile. Finally, density driven currents generated in the model were investigated. The magnitudes of the model currents compared to observations suggest that the background flow under ice in the lake may be density driven.     

A general method for polyethylene-glycol-induced genetic transformation of bacteria and yeast

Polyethylene glycol (PEG) can induce genetic transformation in both bacteria (Escherichia coli) and yeast (Saccharomyces cerevisiae) without cell wall removal. PEG-mediated transformation of E. coli is technically simple and yields transformants with an efficiency of 10(6)-10(7) transformants/microgram DNA. Detailed analysis of the parameters involved in PEG-mediated transformation of E. coli reveals basic differences between the PEG and standard CaCl2 methods for transformation of E. coli. PEG-mediated transformation of yeast is far simpler than existing protoplast methods and is comparable in efficiency. The new methods described here for PEG-mediated genetic transformation may prove to be of general utility in performing genetic transformation in a wide variety of organisms.     

What Makes Eco‐Transformation of Industrial Parks Take Off in China?

This article focuses on the effects of policy instruments for developing viable eco‐industrial parks (EIPs) in China. We analyzed the root of China's national EIP program and inventoried the general instruments available to local authorities to shape and promote eco‐industrial development. Empirical research conducted in Tianjin Economic‐technological Development Area and Dalian Development Area led to the activities and actions conducted by local authorities. A quantitative method, technique for order of preference by similarity to ideal solution, was adopted to reveal the effects of policy instruments for comparative analysis. We conclude that the planned EIP model is useful in the early stage of EIP development, and, subsequently, it should be combined with a facilitated model to achieve long‐term goals for eco‐transformation. To this end, the policy package of economic, regulatory, and voluntary instruments should be integrated and tailored in alignment with the local situation.     

An efficient multivariate approach for estimating preference when individual observations are dependent

1. We discuss aspects of resource selection based on observing a given vector of resource variables for different individuals at discrete time steps. A new technique for estimating preference of habitat characteristics, applicable when there are multiple individual observations, is proposed. 2. We first show how to estimate preference on the population and individual level when only a single site- or resource component is observed. A variance component model based on normal scores in used to estimate mean preference for the population as well as the heterogeneity among individuals defined by the intra-class correlation. 3. Next, a general technique is proposed for time series of observations of a vector with several components, correcting for the effect of correlations between these. The preference of each single component is analyzed under the assumption of arbitrarily complex selection of the other components. This approach is based on the theory for conditional distributions in the multi-normal model. 4. The method is demonstrated using a data set of radio-tagged dispersing juvenile goshawks and their site characteristics, and can be used as a general tool in resource or habitat selection analysis.     

Endemic disease in environments with spatially heterogeneous host populations

The main interest in epidemic models stems from their use in uncovering certain qualitative features of epidemic processes. A deterministic model of a general epidemic in a population with an arbitrary number of separate population centers is presented. The mixing within each center is assumed to be homogeneous, and the usual threshold theorem holds for each population. The mixing between centers is nonhomogeneous. This model is used to identify the necessary and sufficient conditions under which a disease will become endemic in the general population when each population center is below the threshold required for establishment of the disease and does not mix with other centers. These conditions depend critically on the concavity of the infection rate function with respect to the length of exposure time. The application of these results to host-vector models is discussed.     

Structural instability of models of sexual selection

Models for sexual selection by the coevolution of female preference and a male trait have as a generic feature the existence of a neutrally stable line of equilibria up and down which the system can drift at random. However, this feature is structurally unstable since it is destroyed by introducing either mutation or weak direct selection on female preference into the model, to be replaced by a single equilibrium (or a finite set of disconnected equilibria). This process is investigated in detail under a simple but general population genetic model. It is concluded that the level of female preference is determined by mutation, selection, and genetic drift acting directly on it, and drags the male trait along with it along the line of equilibria. More attention should be paid to selective forces acting directly on female preference.     

Outer surface modification of synthetic multifunctional pores

The characteristics of pores formed by p-octiphenyl beta-barrels with LWV triads at the outer surface are reported in comparison with the conventional rigid-rod beta-barrels with all-L outer surface. Maintained multifunctionality of tetrameric pores with external LWV triads (inversion of ion selectivity, molecular recognition and transformation) is implicative for intact barrel interior. Increased pore activity supports dominance of high bilayer affinity for W over low affinity for V. Transmembrane p-octiphenyl orientation (from fluorescence depth quenching) supports barrel-stave (rather than toroidal) pores and dominance of transmembrane preference of rigid rods over interfacial preference of W. Destabilization of beta-barrel pores in membranes (from short single-channel lifetimes) and in the media (from 4th-power dependence on monomer concentration) by LWV triads supports dominance of low beta-propensity for W over high beta-propensity for V. The relation between the stability of supramolecular (pre)pores and dependence of activity on monomer concentration is discussed in a more general context.     

On the relation between extended forms of the sinusoidal perfusion and of the convection-dispersion models of hepatic elimination

Two models of hepatic elimination, the distributed sinusoidal perfusion model, and the convection-dispersion model, are extended and then compared for first order kinetics in the steady-state. The sinusoidal perfusion model is extended by the inclusion of intrahepatic sites of mixing between sinusoids. The degree of such mixing is estimated for taurocholate elimination by isolated perfused rat livers by a comparison of anatomical and kinetic estimates of uptake heterogeneity, using previously published data. The dispersion model is generalized by the inclusion of distributions of enzyme activity along the flow. Direct comparison of the two models in the limit in which the degree of dispersion is small, allows the flow-dependence of the dispersion coefficient to be determined, thereby greatly extending the explanatory power of the convection-dispersion model. Finally, the effect of intrahepatic mixing sites on uptake by Michaelis-Menten kinetics is quantified in terms of the distributed sinusoidal perfusion model, with results which may be applicable to capillary beds in general.     

Runaway sexual selection when female preferences are directly selected

We introduce models for the runaway coevolution of female mating preferences and male display traits. The models generalize earlier results by allowing for direct natural selection on the preference, arbitrary forms of mate choice, and fairly general assumptions about the underlying genetics. Results show that a runaway is less likely when there is direct selection on the preference, but that it is still possible if there is a sufficiently large phenotypic correlation between the female's preference and the male's trait among mated pairs. Comparison of three preference functions introduced by Lande (1981) shows that open-ended preferences are particularly prone to a runaway, and that absolute preferences require very large differences between females in their preferences. We analyze the causes of the runaway seen in a model developed by Iwasa and Pomiankowski (1995).     

Observations Relating to the Efficiency of Mixing in Rapid Reaction Flow Devices

The principle of dimensional analysis of liquid flow has been applied to the problem of rapid mixing in flow apparatus. A model of the Hartridge-Roughton mixing chamber and observation tube has been scaled approximately 1/1.000 so that the times after mixing are approximately 6 s, the flow velocities are the order of 2 cm/s, and the distance from mixing to observation is 120 mm. Visual observation is employed to observe the end point of the mixing of acid-base with a color indicator, thymol blue. Quantitative estimates of the effect of the number of jets, the effect of screens placed in the flow stream, and the angle of jets, one with respect to another, lead to quantitative evaluations of these parameters for the scale model. The extent to which these parameters apply to the full-scale apparatus at faster flow velocities suggest that the general principles employed in the scale model are valid, although more emphasis is placed upon turbulence generation at the low flow velocities employed in this experiment than at the faster flow velocities employed in the full-scale apparatus.     

Degradation of Phenol Compounds by Microbial Communities of the Amur Estuary

The microbiological transformation of various phenol compounds and their origin in the mixing zone of the Amur Estuary is considered. The results of the model experiments on the decomposition and transformation of phenol compounds by microbial communities and bacteria are reported. Self-depuration of the Amur Estuary depends on the mechanisms of the transformation of aromatic compounds in the presence of cosubstrates, the enzymatic activity of microbial communities, and the temperature. In winter, the ecological risk of pollution by aromatic compounds increases.     

Fluidized-bed fermenters: A steady-state analysis

A new mathematical model is presented model is presented for use in the design and optimization of fluidized-bed fermenters. Unlike previous models, the biomass particle size is not a required input parameter, but is predicted as a consequence of the process by which the fermenter reaches a steady state. Both tower fermenters and supported-film bioreactors are included in the analysis. The differences between them are explained as a consequence of the different effects of added biomass on the particle settling velocity and the tendency of a fluidized bed to stratify. A detailed qualitative treatment of solids mixing allows the model to predict the varying biomass concentration through a tower fermenter and the more constant concentration in the supported film reactor. Other features of this analysis are the inclusion of an axial dispersion term to allow for different liquid mixing conditions, and the introduction of a variable transformation that eliminates the need for a computer solution. A sample design problem is included.