Development of a variational scheme for model inversion of multi-area model of brain. Part II: VBEM method

In Part I and Part II of these two companion papers (henceforth called Part I and Part II), we develop and evaluate a variational Bayesian expectation maximization (VBEM) method for model inversion of our multi-area extended neural mass model (MEN). In this paper, we develop the VBEM method to estimate posterior distributions of parameters of MEN. We choose suitable prior distributions for the model parameters in order to use properties of a conjugate-exponential model in implementing VBEM. Consequently, VBEM leads to analytically tractable forms. The proposed VBEM algorithm starts with initialization and consists of repeated iterations of a variational Bayesian expectation step (VB E-step) and a variational Bayesian maximization step (VB M-step). Posterior distributions of the model parameters are updated in the VB M-step. Distribution of the hidden state is updated in the VB E-step. We develop a variational extended Kalman smoother (VEKS) to infer the distribution of the hidden state in the VB E-step and derive the forward and backward passes of VEKS, analogous to the Kalman smoother. In Part I, we evaluate and validate the VBEM method using simulation studies.     

Dynamic rheology of agar gels: theory and experiments. Part I. Development of a rheological model

A theoretical rheological model for agar gels is proposed, based on the bead and spring model for linear flexible random coils and the model for crosslinked polymers. The model introduces the concept of a temperature dependence of the monomeric friction coefficient, ζ₀, of the agar molecule. The model has a random coil-like behavior at high temperatures (close to 373 K), and contributions from a three-dimensional network at low temperatures (close to 273 K). A proposed temperature dependence of the net association rate allows the calculation of the fraction of associated molecules as a function of time and temperature. The proposed model predicts the gelation behavior of agar gels utilizing time–temperature data (cooling curves).     

A simulation study of population interaction between the greenhouse whitefly,Trialeurodes vaporariorum Westwood (Homoptera: Aleyrodidae), and the parasitoidEncarsia formosa gahan (Hymenoptera: Aphelinidae) I. Description of the model

A simple simulation model was developed to simulate the population dynamics of the system of the greenhouse whitefly (Trialeurodes vaporariorumWestwood ) and the parasitoid Encarsia formosaGahan . On the assumption that temperature is constant, the whitefly population was described as theLeslie Matrix model. Parasitization and host feeding by the parasitoid population were modelled by means of a modified disc equation. The validity of the model was demonstrated by comparing the predictions of the model with the observed values obtained in greenhouse experiments.     

Development of a multienzyme reactor for dopamine synthesis: II. Reactor engineering and simulation

Aspects of reaction engineering associated with multienzyme reactions have been studied in a system where dopamine is produced from catechol, pyruvate and ammonium by sequential enzymatic reactions catalyzed by tyrosine phenol lyase (TPL) and tyrosine decarboxylase (TDC). Microbial cells containing TPL activity (Erwinia herbicola) and TDC activity (Streptococcus faecalis) were coimmobilized in glutaraldehyde cross-linked porcine gelatin beads with a mean diameter of 2.8 mm for use in the reactions. Measurement of the transport properties in the beads indicate that the gelatin matrix does not significantly increase the diffusion resistance and that dopamine partitions into the matrix (K = 2). A packed-bed reactor containing the coimmobilized cell beads successfully produced dopamine, although with a low conversion. Using computer simultaneous it is shown that separate, sequential TPL and TDC, rather than simultaneous, reactions, would require smaller reactors overall for the same conversion. (c) 1992 John Wiley & Sons, Inc.     

An interfacial equilibria model for the electrokinetic properties of a fat emulsion. Part III: A predictive computer model

Abstract

The semi-empirical thermodynamic model for the binding of metal ions to an emulsion (intralipid 20%) reported previously (Hall et al., 1991 ; Gaskin et al., 1993) is incorporated into a thermodynamic computer model. This permits the zeta potential and emulsion stability together with precipitate formation to be estimated for any intravenous nutrition regimen. A regimen frequently used in the intravenous nutrition of patients is considered in this modeling study. The effect of solution pH and calcium on the zeta potential of the emulsion is predicted. Calcium and magnesium are the only metal cations which are predicted to be of importance when considering stability of this emulsion.     

Characterization of a pilot plant airlift tower loop bioreactor. I: evaluation of the phase properties with model media

Investigations were carried out in a 9 m high, 4 m(3) volume, pilot plant airlift tower loop bioreactor with a draft tube. The reactor was characterized by measuring residence time distributions of the gas phase using pseudostochastic tracer signals and a mass spectrometer and by evaluating the mixing in the liquid phase with single-pulse tracer inputs. The local gas holdup and the bubble size (piercing length) were measured with two-channel electrical conductivity probes. The mean residence times and the intensities of the axial mixing in the riser and downcomer and the circulation times of the phases as well as the fraction of the recirculated gas phase were evaluated. The gas holdup in the riser is nearly uniform along the reactor. In the downcomer, it diminishes from top to bottom. The liquid phase dispersion coefficients, D(L), are smaller than those measured in the corresponding bubble columns. In the pilot plant with tap water the following relationship was found: D(Lr) = cw(SG) (n); with c = 203.4; n = 0.5;D(Lr)(cm(2) s(-1);) and W(SG)(cm s(-1)) where D(Lr) is the longitudinal dispersion coefficient in the riser and W(SG) is the superficial gas velocity. The gas phase dispersion coefficients in the riser of the pilot plant, D(Gr), are also enlarged with increasing superficial gas velocity, W(SG), however, no simple relationship exists. Parameter D(Gr) is the highest in the presence of antifoam agents, intermediate in tap water, and the smallest in ethanol solution.     

Development of a multienzyme reactor for dopamine synthesis: I. enzymology and kinetics

The enzymology and kinetics of tyrosine phenol lyase (TPL) from Erwinia herbicola, and tyrosine decarboxylase (TDC) from Streptococcus faecalis have been investigated for potential use in a coimmobilized multienzyme biocatalytic system for the production of dopamine. In this multienzyme biotransformation using whole cells optimized for each of the respective enzymes, TPL catalyzes the production of 3,4-dihydroxyphenyl-L-alanine (L-dopa) from catechol, pyruvate, and ammonium, and this is subsequently decarboxylated by TDC to produce dopamine. Performing the reactions simultaneously, thereby removing L-dopa, is one option for overcoming the TPL equilibrium constraints. The enzymes have different optimal pH values, so the reaction kinetics at a compromise pH of 7.1, where both enzymes could be operated simultaneously, were investigated. For the concentration range investigated, TPL followed pseudo-first-order kinetics with respect to catechol, pyruvate, and ammonium. TDC exhibited significant product inhibition as well as inhibition by combinations of catechol and pyruvate.     

The kinetoplastida endocytic apparatus. Part I: a dynamic system for nutrition and evasion of host defences

The endocytic system of kinetoplastid parasites is a highly polarized membrane network focused on the flagellar pocket localized at one end of the cell. When first characterized, the endosomal network was envisioned as a simple system for uptake of extracellular material by fluid-phase or receptor-mediated mechanisms. Subsequently, it has become clear that the kinetoplastid endosomal system has an active and vital role in avoiding the host immune system and virulence, as well as providing the basic functions to fulfil cellular nutritional requirements. In two reviews, recent advances in the definition and comprehension of kinetoplastida endocytosis are discussed and, in Trypanosoma brucei in particular as the more developed experimental system. In Part 1, the endocytic system is considered in context of the surface molecules and their potential roles in virulence.     

Modeling lipid accumulation in oleaginous fungi in chemostat cultures: I. Development and validation of a chemostat model for Umbelopsis isabellina

Lipid-accumulating fungi may be able to produce biodiesel precursors from agricultural wastes. As a first step in understanding and evaluating their potential, a mathematical model was developed to describe growth, lipid accumulation and substrate consumption of the oleaginous fungus Umbelopsis isabellina (also known as Mortierella isabellina) in submerged chemostat cultures. Key points of the model are: (1) if the C-source supply rate is limited, maintenance has a higher priority than growth, which has a higher priority than lipid production; (2) the maximum specific lipid production rate of the fungus is independent of the actual specific growth rate. Model parameters were obtained from chemostat cultures of U. isabellina grown on mineral media with glucose and NH₄ ⁺. The model describes the results of chemostat cultures well for D > 0.04 h⁻¹, but it has not been validated for lower dilution rates because of practical problems with the filamentous fungus. Further validation using literature data for oleaginous yeasts is described in part II of this paper. Our model shows that not only the C/N-ratio of the feed, but also the dilution rate highly influences the lipid yield in chemostat cultures.     

Studies on the dynamic properties of terrestrial ecosystems based on a simulation model I. Critical light conditions for stability of a tropical rainforest ecosystem

By employing a microcomputer model developed in a previous study (Oikawa, 1985), the stability of a tropical rainforest ecosystem composed of three strata was analyzed in relation to incident light flux density. Surplus production (P _s ), calculated as a function of the leaf area index and light attenuation coefficient, was remarkably affected by the maximum illuminance at noon (I _{0, max}). Simulation experiments for a period of 100 years demonstrated that the upper stratum was able to reach a steady state at about 50 years and thereafter, when a value ofI _{0, max} equal to or greater than 80 klux was assigned to the upper stratum, where the higher the value ofI _{0, max} , the greater the biomasses and the carbon fluxes at the steady state as a result of enhanced productivity. WhenI _{0, max} was assigned a value of 70 klux, on the other hand, this experiment predicted a failure of the upper stratum to maintain stability due to deficiency of surplus productivity. Moreover, it was also suggested that excessive luxuriance of the upper stratum due toI _{0, max} elevation may have a detrimental effect upon the survival of the middle stratum, since increasingI _{0, max} decreases the light energy available for the middle stratum even in absolute terms, resulting in disappearance of this stratum whenI _{0, max} is equal to or greater than 120 klux. These simulation experiments suggested that a tropical rainforest ecosystem composed of three strata is able to exist within a narrow range ofI _{0, max} between 80 and 110 klux, light conditions which are much higher than the light compensation point for canopy photosynthesis This article is dedicated to Professor Toshiro Saeki, University of Tokyo, in appreciation of the sincere encouragement he has given to the author.     

Some introductory formalizations on the affine Hilbert spaces model of the origin of life. I. On quantum mechanical measurement and the origin of the genetic code: a general physical framework theory

A physical (affine Hilbert spaces) frame is developed for the discussion of the interdependence of the problem of the origin (symbolic assignment) of the genetic code and a possible endophysical (a kind of "internal") quantum measurement in an explicite way, following the general considerations of Balázs (Balázs, A., 2003. BioSystems 70, 43-54; Balázs, A., 2004a. BioSystems 73, 1-11). Using the Everett (a dynamic) interpretation of quantum mechanics, both the individual code assignment and the concatenated linear symbolism is discussed. It is concluded that there arises a skewed quantal probability field, with a natural dynamic non-linearity in codon assignment within the physical model adopted (essentially corresponding to a much discussed biochemical frame of self-catalyzed binding (charging) of t RNA like proto RNAs (ribozymes) with amino acids). This dynamic specific molecular complex assumption of individual code assignment, and the divergence of the code in relation to symbol concatenation, are discussed: our frame supports the former and interpret the latter as single-type codon (triplet), also unambiguous and extended assignment, selection in molecular evolution, corresponding to converging towards the fixedpoint of the internal dynamics of measurement, either in a protein- or RNA-world. In this respect, the general physical consequence is the introduction of a fourth rank semidiagonal energy tensor (see also Part II) ruling the internal dynamics as a non-linear in principle second-order one. It is inferred, as a summary, that if the problem under discussion could be expressed by the concepts of the Copenhagen interpretation of quantum mechanics in some yet not quite specified way, the matter would be particularly interesting with respect to both the origin of life and quantum mechanics, as a dynamically supported natural measurement-theoretical split between matter ("hardware") and (internal) symbolism ("software") aspects of living matter.     

A structured model for simulation of cultures of the cyanobacterium Spirulina platensis in photobioreactors: I. Coupling between light transfer and growth kinetics

The study of the interactions between physical limitation by light and biological limitations in photobioreactors leads to very complex partial differential equations. Modeling of light transfer and kinetics and the assessment of radiant energy absorded in photoreactors require an equation including two parameters for light absorption and scattering in the culture medium. In this article, a simple model based on the simplified, monodimensional equation of Schuster for radiative transfer is discussed. This approach provides a simple way to determine a working illuminated volume in which growth occurs, therefore allowing indentification of kinetic parameters. These parameters might then be extended to the analysis of more complex geometries such as cylindrical reactors. Moreover, this model allows the behavior of batch or continuous cultures of cyanobacteria under light and mineral limitations to be predicted. (c) 1992 John Wiley & Sons, Inc.     

The pronghorn (Antilocapra americana): A review as a model for development of a “Species Management Plan” format,Part I

A format is suggested for a “Species Management Plan”; the model for this presentation is the pronghorn (Antilocapra americana). By using the Species Management Plan format, the captive maintenance of pronghorn is analyzed in relation to habitat and microhabitat needs, behavioral requirements, and nutritional needs. A strategy for captive maintenance of pronghorn in relatively wet climates is presented. It is suggested that development of a Species Management Plan is necessary before any new species is acquired for captive maintenance and reproduction.     

Use of a structured kinetic model of antibody synthesis and secretion for optimization of antibody production systems: I. Steady-state analysis

Steady-state simulations using our previously developed structured kinetic model of antibody synthesis and secretion by hybridoma cells are used here in conjunction with factorial design analysis to identify intracellular parameters important in determining the specific antibody secretion rate and predict the dependence of this rate on cell specific growth rate. Simulation results suggest that the specific growth rate, the assembly rate of the heavy and light chains and the heavy- and -chain gene dosage can significantly affect the rate of antibody secretion. Based on these results, environmental and/or genetic manipulation approaches are proposed for maximizing the specific antibody secretion rate and the antibody volumetric productivity in large-scale antibody production systems.     

Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor.

Although aqueous simulations with periodic boundary conditions more accurately describe protein dynamics than in vacuo simulations, these are computationally intensive for most proteins. Trp repressor dynamic simulations with a small water shell surrounding the starting model yield protein trajectories that are markedly improved over gas phase, yet computationally efficient. Explicit water in molecular dynamics simulations maintains surface exposure of protein hydrophilic atoms and burial of hydrophobic atoms by opposing the otherwise asymmetric protein-protein forces. This properly orients protein surface side chains, reduces protein fluctuations, and lowers the overall root mean square deviation from the crystal structure. For simulations with crystallographic waters only, a linear or sigmoidal distance-dependent dielectric yields a much better trajectory than does a constant dielectric model. As more water is added to the starting model, the differences between using distance-dependent and constant dielectric models becomes smaller, although the linear distance-dependent dielectric yields an average structure closer to the crystal structure than does a constant dielectric model. Multiplicative constants greater than one, for the linear distance-dependent dielectric simulations, produced trajectories that are progressively worse in describing trp repressor dynamics. Simulations of bovine pancreatic trypsin were used to ensure that the trp repressor results were not protein dependent and to explore the effect of the nonbonded cutoff on the distance-dependent and constant dielectric simulation models. The nonbonded cutoff markedly affected the constant but not distance-dependent dielectric bovine pancreatic trypsin inhibitor simulations. As with trp repressor, the distance-dependent dielectric model with a shell of water surrounding the protein produced a trajectory in better agreement with the crystal structure than a constant dielectric model, and the physical properties of the trajectory average structure, both with and without a nonbonded cutoff, were comparable.     

Process analytical technology case study: Part II. Development and validation of quantitative near-infrared calibrations in support of a process analytical technology application for real-time release

This article is the second of a series of articles detailing the development of near-infrared (NIR) methods for solid dosage-form analysis. Experiments were conducted at the Duquesne University Center for Pharmaceutical Technology to demonstrate a method for developing and validating NIR models for the analysis of active pharmaceutical ingredient (API) content and hardness of a solid dosage form. Robustness and cross-validation testing were used to optimize the API content and hardness models. For the API content calibration, the optimal model was determined as multiplicative scatter correction with Savitsky-Golay first-derivative preprocessing followed by partial least-squares (PLS) regression including 4 latent variables. API content calibration achieved root mean squared error (RMSE) and root mean square error of cross validation (RMSECV) of 1.48 and 1.80 mg, respectively. PLS regression and baseline-fit calibration models were compared for the prediction of tablet hardness. Based on robustness testing, PLS regression was selected for the final hardness model, with RMSE and RMSECV of 8.1 and 8.8 N, respectively. Validation testing indicated that API content and hardness of production-scale tablets is predicted with root mean square error of prediction of 1.04 mg and 8.5 N, respectively. Explicit robustness testing for high-flux noise and wavelength uncertainty demonstrated the robustness of the API concentration calibration model with respect to normal instrument operating conditions. Published: October 6, 2005 The views presented in this article do not necessarily reflect those of the Food and Drug Administration.     

Development of a novel stall design for dairy cattle: Part II. The effect of minimal stall partitioning on lying behavior,rumination, stall cleanliness,and preference

Free-stalls for dairy cows promote cleanliness, provide cows with a defined space to lie down, and decrease labor and bedding required for maintenance. However, current stall features can restrict behavior and reduce stall use. The objective of this study was to assess the short-term effect of a novel free-stall design (flexible single-bar partition, no neck rail, increased slope) on stall cleanliness and the lying behavior, rumination, milk production, and preferences of dairy cows in comparison to standard free-stalls (metal loop partitions, neck rail). In the first experiment, 60 Holstein cows were randomly divided into two groups and switched between standard and novel stalls in a replicated crossover design with four 7-day periods. Lying behavior and rumination were recorded continuously. Milk yields were recorded 2x/day, and stall cleanliness scores were collected on the last four days of weeks 3 and 4. The second experiment was a 6-day preference test where 14 cows from experiment 1 were given free access to 16 standard and 16 novel stalls. Lying behavior was recorded continuously. On day 6, standing, perching, and intention, lying, and rising movements were recorded. In experiment 1, cows spent 12 min less time lying down (14.1 vs 14.3 ± 0.48 h/d), had one fewer lying bouts (8.8 vs 9.8 ± 0.23 bouts/d), and had longer lying bouts by 6 min (1.4 vs 1.5 ± 0.05 h/bout) in novel stalls. Rumination time (547.3 vs 548.9 ± 4.66 min/d) and milk yield (35.0 vs 35.2 ± 0.51 kg/d) did not differ between stall types. However, novel stalls were more than twice as soiled as standard stalls (32.8 vs 14.2 ± 1.38% of rear half soiled). In experiment 2, the cows most recently housed in the novel stalls showed a clear preference for lying down in those stalls, whereas cows most recently housed in standard stalls showed no preference. Intention and lying down movements were longer in standard stalls when other cows were present in diagonally opposite stalls, but were similar between stall types when not occupied. All cows preferred standing in novel stalls. Novel stalls may have improved stall use compared to standard free-stalls, and the design requires further development to address cleanliness concerns. Future work is required to provide comfortable stalls without sacrificing cleanliness.     

Development of a synthetic plant volatile-based attracticide for female noctuid moths. I. Potential sources of volatiles attractive to Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae)

This paper is the first of a series which will describe the development of a synthetic plant volatile-based attracticide for noctuid moths. It discusses potential sources of volatiles attractive to the cotton bollworm, Helicoverpa armigera (Hübner), and an approach to the combination of these volatiles in synthetic blends. We screened a number of known host and non-host (for larval development) plants for attractiveness to unmated male and female moths of this species, using a two-choice olfactometer system. Out of 38 plants tested, 33 were significantly attractive to both sexes. There was a strong correlation between attractiveness of plants to males and females. The Australian natives, Angophora floribunda and several Eucalyptu s species were the most attractive plants. These plants have not been recorded either as larval or oviposition hosts of Helicoverpa spp., suggesting that attraction in the olfactometer might have been as nectar foraging rather than as oviposition sources. To identify potential compounds that might be useful in developing moth attractants, especially for females, collections of volatiles were made from plants that were attractive to moths in the olfactometer. Green leaf volatiles, floral volatiles, aromatic compounds, monoterpenes and sesquiterpenes were found. We propose an approach to developing synthetic attractants, here termed 'super-blending', in which compounds from all these classes, which are in common between attractive plants, might be combined in blends which do not mimic any particular attractive plant.     

Application of Markov Chain Model to Calculate the Average Number of Times of Use of a Material in Society. An Allocation Methodology for Open-Loop Recycling. Part 1: Methodology Development (7 pp)

- Preamble. In this series of two papers, a methodology to calculate the average number of times a material is used in a society from cradle to grave is presented and applied to allocation of environmental impact of virgin material. Part 1 focuses on methodology development and shows how the methodology works with hypothetical examples of material flows. Part 2 presents case studies for steel recycling in Japan, in which the methodology is applied and allocation of environmental impact of virgin steel is conducted. - Abstract Goal, Scope and Background. It has been recognized that LCA has a limitation in assessing open cycle recycling of materials because of inevitable subjective judgments in setting system boundary. According with the enforcement of recycling laws, there has been a rapid increase in recycling ratio of materials at the end-of-life of products in many industrialized countries. So, materials' life cycle is getting more complicated, which makes it difficult to quantify the environmental impacts of materials used in a product in an appropriate way. The purpose of this paper is to develop a methodology to calculate the average number of times a material is used in a society from cradle to grave. The method developed in this paper derives the average number of times material is used; this value could be used for allocation of environmental burdens of virgin material as well as an indicator for assessing the state of material use in a certain year, based on material flow of material in that year. Main Features Our methodology is based on Markov chain model using matrix-based numerical analysis. A major feature of this method is that it creates transition probability matrices for a material from the way in which the material is produced, consumed, and recycled, making it possible to simply elicit indicators that assess the status of material use in products in society. Our methodology could be an alternative method to derive the average number of times material is used, which could be used for allocation of environmental burdens of virgin material. Results and Discussions The methodology was applied to hypothetical examples of material flows, in which a virgin material was produced and used in products, recycled and finally landfilled. In some cases, closed loop and open loop recycling of materials existed. The transition probability matrix was created for each material flow, and how many times a virgin material is used in products until all of the elements are ultimately landfilled. Conclusions This methodology is applicable to a complicated material flow if the status of residence of a material and its flow in a society can be figured out. All the necessary data are the amount of virgin material production, amount of the material used in products, recycling rate of the material at the end of life of each product, the amount of scrap of the material that are used for products. In Part 2 of this paper, case studies for steel were conducted.