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PubMed2000

Phenomenological glass model for vibratory granular compaction

A model for weakly excited granular media is derived by combining the free volume argument of Nowak et al. [Phys. Rev. E 57, 1971 (1998)] and the phenomenological model for supercooled liquids of Adam and Gibbs [J. Chem. Phys. 43, 139 (1965)]. This is made possible by relating the granular excitation parameter Gamma, defined as the peak acceleration of the driving pulse scaled by gravity, to a temperaturelike parameter eta(Gamma). The resulting master equation is formally identical to that of Bouchaud's trap model for glasses [J. Phys. I 2, 1705 (1992)]. Analytic and simulation results are shown to compare favorably with a range of known experimental behavior. This includes the logarithmic densification and power spectrum of fluctuations under constant eta, the annealing curve when eta is varied cyclically in time, and memory effects observed for a discontinuous shift in eta. Finally, we discuss the physical interpretation of the model parameters and suggest further experiments for this class of systems.

Journal Article↗
PubMed2004

Multimedia persistence as an indicator of potential for population-level intake of environmental contaminants.

Although intuitively it is apparent that population-level exposure to contaminants dispersed in the environment must be related to the persistence of the contaminant, there has been little effort to quantify this link formally. In this paper we investigate the relationship between overall persistence and/or overall residence time in a multimedia exposure environment and the population-level intake of contaminants as expressed by intake fraction (iF), the cumulative fraction of chemical emitted to the environment that is taken up by members of the population. We demonstrate that for any given contaminant and emission scenario the definition of iF implies that it is directly proportional to the overall multimedia persistence (Pov), or the overall multimedia residence time (Tov). The proportionality constant has dimensions of time and represents the characteristic time for population intake (CTI) of the chemical from the environment. We then apply the CalTOX fate and exposure model to explore how Tov and CTI combine to determine the magnitude of iF We find that CTI has a narrow range of possible values relative to Tov across multiple chemicals and emissions scenarios. We use data from the Canadian Environmental Protection Act Priority Substance List (PSL1) Assessments and multimedia Pov to show that exposure assessments based on empirical observation are consistent with interpretations from the model. Results indicate that Pov derived from screening-level assessments of persistence, bioaccumulation potential, and toxicity (PBT) is a useful indicator of the potential for population-level exposure.

Environmental Exposure↗
PubMed1989

Giving wellness a spiritual workout. Two model programs emphasize the development of self-reliance.

Many hospitals, corporations, and communities have developed wellness programs to help people maintain a healthy life-style. Today's wellness doctrine reflects modern medical thinking that, to achieve optimal human potential, a person must enjoy physical, mental, emotional, and spiritual well-being. Most wellness programs, however, concentrate on the physical; few take into account spiritual well-being. Wellness programs developed by the Boulder County YMCA, Longmont, CO, and the University of Maryland, College Park, were based on an interpretation of a model suggested by Carl Jung that defines spirituality as the development of self-reliance. According to Jung, the constituents of self-reliance include awareness, inner faith, self-worth, humility, patience, acceptance, and self-confidence. He suggested that the absence of any one of these could cause a breakdown in a person's belief system and lead to a spiritual crisis. These programs trained participants to recognize the importance of their spiritual well-being and to find practical ways to improve it. Key components were a stress management course; workshops in confidence building and values clarification; and classes, lectures, and workshops that emphasize the integration of spiritual and physical well-being.

Colorado↗
PubMed1993

bpshape wk4: a computer program that implements a physiological model for analyzing the shape of blood pressure waveforms.

We describe the theory and computer implementation of a newly-derived mathematical model for analyzing the shape of blood pressure waveforms. Input to the program consists of an ECG signal, plus a single continuous channel of peripheral blood pressure, which is often obtained invasively from an indwelling catheter during intensive-care monitoring or non-invasively from a tonometer. Output from the program includes a set of parameter estimates, made for every heart beat. Parameters of the model can be interpreted in terms of the capacitance of large arteries, the capacitance of peripheral arteries, the inertance of blood flow, the peripheral resistance, and arterial pressure due to basal vascular tone. Aortic flow due to contraction of the left ventricle is represented by a forcing function in the form of a descending ramp, the area under which represents the stroke volume. Differential equations describing the model are solved by the method of Laplace transforms, permitting rapid parameter estimation by the Levenberg-Marquardt algorithm. Parameter estimates and their confidence intervals are given in six examples, which are chosen to represent a variety of pressure waveforms that are observed during intensive-care monitoring. The examples demonstrate that some of the parameters may fluctuate markedly from beat to beat. Our program will find application in projects that are intended to correlate the details of the blood pressure waveform with other physiological variables, pathological conditions, and the effects of interventions.

Animals↗
PubMed1997

An overview of a multimedia benchmarking analysis for three risk assessment models: RESRAD, MMSOILS, and MEPAS.

Multimedia modelers from the United States Environmental Protection Agency (EPA) and the United States Department of Energy (DOE) collaborated to conduct a detailed and quantitative benchmarking analysis of three multimedia models. The three models--RESRAD (DOE), MMSOILS (EPA), and MEPAS (DOE)--represent analytically-based tools that are used by the respective agencies for performing human exposure and health risk assessments. The study is performed by individuals who participate directly in the ongoing design, development, and application of the models. Model form and function are compared by applying the models to a series of hypothetical problems, first isolating individual modules (e.g., atmospheric, surface water, groundwater) and then simulating multimedia-based risk resulting from contaminant release from a single source to multiple environmental media. Study results show that the models differ with respect to environmental processes included (i.e., model features) and the mathematical formulation and assumptions related to the implementation of solutions. Depending on the application, numerical estimates resulting from the models may vary over several orders-of-magnitude. On the other hand, two or more differences may offset each other such that model predictions are virtually equal. The conclusion from these results is that multimedia models are complex due to the integration of the many components of a risk assessment and this complexity must be fully appreciated during each step of the modeling process (i.e., model selection, problem conceptualization, model application, and interpretation of results).

Air Pollutants↗
PubMed1989

A cautionary note on the use of autoregressive models in analysis of longitudinal data.

Rosner et al. presented a simple, easily implemented modelling method for retaining time order relationships in analyses of longitudinal data when successive measures are correlated. Evaluation of time order is particularly useful in epidemiologic studies concerned with exposure to potentially toxic substances and subsequent outcome, but may also have use in more traditional growth studies that relate intake to subsequent development. The analysis allows for unequally spaced measures and missing data. The estimation method permits varying numbers of observations per subject and, with measures equally spaced, one can fit the model with use of ordinary least squares regression software. We report on a potential false association that can result when both exposure and outcome are related to time. We illustrate this problem with a small scale simulation and example. We also note a more serious problem with Rosner's approach in interpreting parameters. Although the model may be useful for prediction, parameters depend on the autocorrelation and are not readily interpretable. We recommend alternative modelling strategies be used when autocorrelation of errors is suspected.

Age Factors↗
PubMedDate not supplied

Modeling relationships between various domains of hearing aid provision.

Various inventories have been developed to quantify the success of hearing aid provision. Though numerous parameters including initial measures (hearing disability, handicap) or 'outcome measures' (e.g. benefit, satisfaction and usage) are recorded, relationships and interactions among them are still unclear. A study applying a questionnaire addressing 11 domains relevant to amplification was conducted in order to generate different psychometric models with the AMOS software package for structural equation modeling. The models expose easily interpretable interactions and are helpful in understanding effects occurring with commonly used outcome measures: benefit reflects the difference between the aided and unaided condition but additionally comprises the importance of the hearing aid within a specific situation. Satisfaction is highly reliant on benefit. Usage is strongly dependent on the severity of hearing problems and therefore not appropriate in assessing the success of amplification. Moreover, the models help to predict the outcome of clinically used inventories (i.e. the Glasgow Hearing Aid Benefit Profile).

Adolescent↗
PubMed1976

Electronic state of heme in cytochrome oxidase. I. Magnetic circular dichroism of the isolated enzyme and its derivatives.

Magnetic circular dichroism (MCD) spectra have been recorded for beef heart cytochrome oxidase and a number of its inhibitor complexes. The resting enzyme exhibits a derivate shape Faraday C term in the Soret region, characteristic of low spin ferric heme, which accounts for 50% of the total oxidase heme a. The remaining heme a (50%) is assigned to the high spin state. MCD temperature studies, comparison with the MCD spectra of heme a-imidazole model compounds, and ligand binding (cyanide, formate) studies are consistent with these spin state assignments in the oxidized enzyme. Furthermore, the ligand binding properties and correlations between optical and MCD parameters indicate that in the resting enzyme the low spin heme a is due solely to cytochrome a3+ and the high spin heme a to cytochrome a33+. The Soret MCD of the reduced protein is interpreted as th sum of two MCD curves: an intense, asymmetric MCD band very similar to that exhibited by deoxymyoglobin which we assign to paramagnetic high spin cytochrome a3(2+) and a weaker, more symmetric MCD contribution, which is attributed to diamagnetic low spin cytochrome a2+. Temperature studies of the Soret MCD intensity support this proposed spin state heterogeneity. Ligand binding (CO, CN-) to the reduced protein eliminates the intense MCD associated with high spin cytochrome a3(2+); however, the band associated with cytochrome a2+ is observed under these conditions as well as in a number of inhibitor complexes (cyanide, formate, sulfide, azide) of the partially reduced protein. The MCD spectra of oxidized, reduced, and inhibitor-complexed cytochrome oxidase show no evidence for heme-heme interaction via spectral parameters. This conclusion is used in conjunction with the fact that ferric, high spin heme exhibits weak MCD intensity to calculate the MCD spectra for the individual cytochromes of the oxidase as well as the spectra for some inhibitor complexes of cytochrome a3. The results are most simply interpreted using the model we have recently proposed to account for the electronic and magnetic properties of cytochrome (Palmer, G., Babcock, F.T., and Vcikery, L.E. (1976) Proc. Natl. Acad. Sci. U. S. A. 73, 2206-2210).

Animals↗
PubMed1991

Analysis of rat lens 45Ca2+ fluxes: evidence for Na(+)-Ca2+ exchange.

The influx and efflux kinetics of 45Ca2+ were studied in the rat lens in vitro. Both data sets could be fitted by a multi-compartment mathematical model and were interpreted in terms of extracellular, cytosolic and slowly-exchanging (bound) components. At the end of a 16-hr influx period, when uptake into the extracellular and cytosolic compartments is complete, the 45Ca2+ exchanged fraction is less than 20% of the total calcium determined by atomic absorption. The bound compartment is therefore by far the largest in the lens. The efflux rate constant determined from the model for the cytosolic compartment was approximately 8 x 10(-3) min-1 and its origin was confirmed by its sensitivity to temperature, absence of external sodium and presence of the amiloride-analogue, dichlorobenzamil. A 55% reduction in efflux was obtained in sodium-free solution, indicating that Na(+)-Ca2+ exchange is responsible for a large proportion of calcium movement from the lens against its electrochemical gradient. This was confirmed in influx studies where, reduction of the lens sodium gradient by either exposure to sodium-free medium or 0.1 mM ouabain significantly elevated the 45Ca2+ content of the lens relative to the control level. Exposure to sodium-free conditions also rendered the lens opaque, which did not occur in the absence of external calcium. These experiments suggest a critical role for Na(+)-Ca2+ exchange in maintaining a low internal Ca2+ and hence transparency.

Amiloride↗
PubMed2004

Optimal parasite infection strategies: a state-dependent approach.

Many macroparasites spend a crucial phase of their life-cycle as free-living infective stages. Despite their importance, however, little theoretical work has considered how evolution may shape the behaviour of these stages. Here, we develop what we believe to be the first stochastic dynamic programming model of parasite life-history strategies to investigate how a trade-off between resource depletion and host encounter rate may shape the optimal infection strategy of a macroparasite. The optimal strategy depends strongly on the probability of host contact and, depending on the relative costs and benefits, macroparasites should adopt either a passive 'ambushing' (sit-and-wait) strategy, an active 'cruising' strategy or a mixed strategy with an initial cruising phase, followed by a switch to ambushing when energy reserves fall to a threshold level. Under no circumstances does the model predict ambush-then-cruise. We use our model to help interpret previously published data on entomopathogenic nematode foraging behaviour, showing how this framework could facilitate our understanding of macroparasite behaviour during this key stage of the life-cycle.

Animals↗
PubMed2003

3D-MEDNEs: an alternative "in silico" technique for chemical research in toxicology. 1. prediction of chemically induced agranulocytosis.

A novel approach to molecular negentropy from the point of view of Markov models is introduced. Stochastic negentropies (MEDNEs) are used to develop a linear discriminant analysis. The discriminant analysis produced a set of two discriminant functions, which gave rise to a very good separation of 93.38% of 151 chemicals (training series) into two groups. The total predictability (86.67%, i.e., 52 compounds out of 60) was tested by means of an external validation set. Randić's orthogonalization procedures allowed interpretation of the model while avoiding collinearity descriptors. On the other hand, factor analysis was used to suggest the relation of MEDNEs with other molecular descriptors and properties into a property space. Three principal factors (related to three orthogonal MEDNEs) can be used to explain approximately 90% of the variance of different molecular parameters of halobenzenes including bulk, energetic, dipolar, molecular surface-related, and hydrophobic parameters. Finally, preliminary experimental results coincide with a theoretical prediction when agranulocytosis induction by G-1, a novel microcidal that presents Z/E isomerism, is not detected.

Agranulocytosis↗
PubMedDate not supplied

U.S. physician workforce forecasting: a tale of two states.

Physician workforce forecasting in the U.S. has returned to preeminence in the recent past. With the publication of the federal Council on Graduate Medical Education's Sixteenth Report: Physician Workforce Policy Guidelines for the United States, 2000-2020, efforts have begun to examine specialty- and geography-specific forecasts to determine the extent to which the projected national shortage of physicians will affect particular specialties and populations in particular areas. This article begins with a brief history of physician workforce forecasting in the U.S. over the past 25 years and summarizes the findings of two state-specific attempts to forecast physician supply and demand in the coming years. Discussions of the findings from the two studies as well as a brief commentary on how particular model assumptions obfuscate interpretation of the forecasts are provided. Finally, a brief discussion of how the forecasts were used by stakeholders in each state is presented.

California↗
PubMed2005

Collapsing mechanistic models: an application to dose selection for proof of concept of a selective irreversible antagonist.

When data fail to support fully mechanistic models, alternative modeling strategies must be pursued. Simpler, more empirical models or the fixing of various rate constants are necessary to avoid over-parameterization. Fitting empirical models can dilute information, limit interpretation, and cloud inference. Fixing rate constants requires external, relevant, and reliable information on the mechanism and can introduce subjectivity as well as complicate determining the validity of model extrapolation. Furthermore, both these methods ignore the possibility that failure of the data to support the mechanistic model could contain information about the pharmacodynamic process. If the pathway has processes with "fast" dynamics, these steps could collapse yielding parametrically simpler classes of models. The collapsed models would retain the mechanistic interpretation of the full model, which is crucial for performing substantive inference, while reducing the number of parameters to be estimated. These concepts are illustrated through their manifestations on the dose-effect relationship and ensuing dose selection for a proof of concept study. Specifically, a mechanistic model for a selective irreversible antagonist was posited and candidate classes of models were derived utilizing "fast dynamics" assumptions. Model assessment determined the rate-limiting step facilitating pertinent inference with respect to the mechanism. For comparison, inference using a more empirical modeling strategy is also presented. A general solution for the collapse of the typical PK-PD model differential equations is provided in Appendix A.

Administration, Oral↗
PubMed1998

Crystallographic studies of casein kinase I delta toward a structural understanding of auto-inhibition.

A recombinant form of mammalian casein kinase I delta (CKIdelta) containing the catalytic domain and an auto-inhibitory domain was expressed in Escherichia coli, purified and crystallized. X-ray data were collected to 2.4 A resolution, and the crystals belong to space group C2221. Molecular replacement using the structure of the catalytic domain of CKIdelta yielded strong electron density for residues in the model, but no interpretable density was found for the inhibitory domain. A conserved intermolecular contact suggests the formation of dimers which would inhibit the activity of this protein kinase.

Casein Kinases↗
PubMed1979

Cognitive influences on perceptual processing.

These experiments investigate the influence of frequency of occurrence of a visual stimulus (stimulus probability) on encoding processes, in an attempt to discover what sorts of mechanisms allow cognitive processes to modify perceptual processes. Experiments 1 and 2 show that frequently occurring visual letters do not facilitate encoding of visually similar letters. This implies that stimulus probability does not directly affect the feature detectors used in encoding the letters. Four more experiments provide evidence that stimulus probability has its effect on the availability of an abstract code that is generated by the encoding process from the visual input. Results from the experiments with letter stimuli could be interpreted using a model similar to the logogen model of Morton. Experiments with nonsense forms suggest that subjects use abstract codes in dealing with the forms only when the stimuli are constructed from a set of orthogonal features. A secondary finding was that visual quality has an effect that extends past the feature analysis stage and into a stage in which the visual input activities an abstract code. This result calls into question the common practice of interpreting the interaction of a factor with visual quality as evidence that the factor affects visual feature analysis.

Cognition↗
PubMedDate not supplied

[A model of the biological oscillator as the basis for the coordination of motor activity].

System mechanisms, that underlied motor activity coordinations were investigated on the model of biological oscillator. It has been shown how the value of phase resettings induced by single stimuli sequences depends on the stimulation location in the cycle. The time of reaction to the stimulus has been determined as the function of stimulus location. In addition, the character of transitional process, after which the parameters of initial rhythmic activity completely become normal, has been determined. The data obtained have been interpreted for the model of temporal motor control, which was suggested by A. Wing and A. Kristofferson.

Acoustic Stimulation↗
PubMed2026

In silico analysis and comparison of the metabolic capabilities of different organisms by reducing metabolic complexity.

BACKGROUND: Understanding how metabolic capabilities diverge across microbial species is essential for deciphering community function, ecological interactions, and the design of synthetic microbiomes. Despite shared core pathways, microbial phenotypes can differ markedly due to evolutionary adaptations and metabolic specialization. Genome-scale metabolic models (GEMs) provide a systems-level framework to explore these differences; however, their complexity hinders direct comparison. RESULTS: We introduce NIS (Neidhardt-Ingraham-Schaechter), a computational workflow that integrates the redGEM, lumpGEM, and redGEMX algorithms to systematically reduce genome-scale models into biologically interpretable modules. This approach enables direct, quantitative comparison of fueling pathways, biomass biosynthetic routes, and environmental exchange processes while retaining essential metabolic information. We first demonstrate the utility of NIS by analyzing Escherichia coli and Saccharomyces cerevisiae, which revealed both conserved and divergent strategies in central metabolism, biosynthetic cost, and substrate utilization. We then applied NIS to the core honeybee gut microbiome, uncovering distinct metabolic traits, functional redundancy, and complementarity that help explain auxotrophy, cross-feeding interactions, and microbial coexistence. CONCLUSIONS: NIS provides an automated, scalable, and reproducible framework for dissecting microbial metabolic networks beyond gene content or taxonomy. By linking metabolism to ecological function, NIS offers new opportunities to interpret microbial community dynamics and to support the rational design of microbiomes in health, agriculture, and environmental applications. Video Abstract.

Metabolic Networks and Pathways↗