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PubMed2005

Modeling of the hysteresis phenomena in finite-sized slitlike nanopores. Revision of the recent results by rigorous numerical analysis.

The systematic investigation of the hysteresis phenomena in finite-sized slitlike nanopores via the Aranovich-Donohue (AD) lattice density functional theory (LDFT) is presented. The new reliable quantitative modeling of the adsorption and desorption branch of the hysteresis loop, through the formation and movement of the curved meniscus, is formulated. As a result, we find that our proposal, which closely mimics the experimental findings, can reproduce a rounded shape of the desorption branch of the hysteresis loop. On the basis of the exhausted commutations, we proved that the hysteresis loop obtained in the considered finite-sized slitlike geometry is of the H1 type of the IUPAC classification. This fundamental result and the other most important results do not confirm the results of the recent studies of Sangwichien et al., whereas they fully agree with the recent lattice studies due to Monson et al. We recognize that the nature of the hysteresis loops (i.e. position, width, shape, and the multiple steps) mainly depends on the value of the energy of both the adsorbate-adsorbate and adsorbate-adsorbent interactions; however, the first one is critical for the appearance of hysteresis. Thus, for relatively small adsorbate-adsorbate interactions, the adsorption-desorption process is fully reversible in the whole region of the bulk density. We show that the strong adsorbate-adsorbent interactions produce (also observed experimentally) multiple steps within hysteresis loops. Contrary to the other studies of the hysteresis phenomena in confined geometry via the LDFT formalism, we constructed both ascending and descending scanning curves, which are known from the experimental observations. Additionally, we consider the problem of the stability of both the obtained adsorption and desorption branches of the computed hysteresis loop in finite-sized slitlike nanopores.

Journal Article↗
PubMed1978

Model for the incidence of embryonal cancers: application to retinoblastoma.

The two-mutation theory of cancer initiation hypothesizes that some cancers originate after two successive mutations, of which the second mutation is always somatic and the first mutation may be germinal (hereditary cases) or somatic (nonhereditary cases). A quantitative model using the Poisson distribution is developed for ages at diagnosis for hereditary and nonhereditary cases. This model relates age-specific incidence data explicitly to the number of divisions of embryonal cells and to rates of somatic mutations per cell division. A good fit is obtained when the model is applied to data on ages at diagnosis for one such embryonal tumor, retinoblastoma.

Age Factors↗
PubMed1995

DNA staining changes associated with apoptosis and necrosis in blood lymphocytes of individuals with HIV infection.

We used flow cytometry to quantitate cells that die by apoptosis or necrosis. The method uses low concentrations of two DNA binding dyes that allow one to establish selective regions for live, apoptotic, and necrotic cells in a rat thymocytes model. Quantitative analysis of blood lymphocyte death in individuals with HIV infection by this technique shows the presence of nonviable cells that exhibit a spectrum of changes in staining by DNA binding dyes. These changes range from typical features of cells undergoing programmed cell death or apoptosis to changes observed in cells that die by accidental death or necrosis. The proportion of cells exhibiting these lethal changes increases significantly in patients who progress to AIDS, but, although cells with staining features associated with apoptosis and necrosis were both found to be increased in in vitro-activated cells from AIDS patients, spontaneous in vivo activation preferentially leads to apoptotic changes without a significant increase of cells exhibiting the staining changes associated with necrosis.

Animals↗
PubMed2006

A model for immunological correlates of protection.

Immunological assays measure characteristics of the immune system, such as antibody levels, specific to certain diseases. High assay values are often associated with protection from disease. A question of interest is how the relationship between assay values and subsequent development of disease should be quantitatively modelled. Existing approaches successfully model the relationship for high assay values, where the probability of developing disease is low. However at low assay values, the probability of developing disease is more closely associated with factors such as disease prevalence rates and an individual's chance of exposure to infection; these are less well captured by existing models. This paper presents a model that accommodates both assay values and factors independent of assay values, enabling protection from disease to be modelled over the whole range of assay values and proposing a method for predicting the efficacy of a vaccine from the assays of vaccinees and non-vaccinees.

Antibodies, Bacterial↗
PubMed1994

Track structure, chromosome geometry and chromosome aberrations.

The joint role of radiation track structure and chromosome geometry in determining yields of chromosome aberrations is discussed. Ideally, the geometric models of chromosomes used for analyzing aberration yields should have the same degree of realism as track structure models. However, observed chromosome aberrations are produced by processes on comparatively large scales, e.g., misrepair involving two DSB located on different chromosomes or two DSB separated by millions of base pairs on one chromosome, and quantitative models for chromatin on such large scales have to date almost never been attempted. We survey some recent data on large-scale chromosome geometry, mainly results obtained with fluorescence in situ hybridization ("chromosome painting") techniques. Using two chromosome models suggested by the data, we interpret the relative yields, at low and high LET, of inter-chromosomal aberrations compared to intra-chromosomal, inter-arm aberrations. The models consider each chromosome confined within its own "chromosome localization sphere," either as a random cloud of points in one model or as a confined Gaussian polymer in the other. In agreement with other approaches, our results indicate that at any given time during the G0/G1 part of the cell cycle a chromosome is largely confined to a sub-volume comprising less than 10% of the volume of the cell nucleus. The possible significance of the ratio of inter-chromosomal aberrations to intra-chromosomal, inter-arm aberrations as an indicator of previous exposure to high LET radiation is outlined.

Cell Cycle↗
PubMed2000

Extra-pair paternity as the result of reproductive transactions between paired mates.

Transactional ('optimal skew' or concessions') models of social evolution emphasize that dominant members of society can be favoured for donating parcels of reproduction to same-sexed subordinates in return for cooperation by the latter. We developed a mathematically similar model in which extra-pair paternity in broods receiving biparental care is viewed as emerging from a reproductive transaction between the paired mates. The model quantitatively predicted the maximum paternity that a male mate can demand before its female mate is favoured to break the pair bond and caring solitarily for a brood sired entirely by a neighbouring male. The model predicts that extra-pair paternity results when the neighbouring male is of sufficiently higher quality than the male mate. In such cases, the exact amount of extra-pair paternity will vary directly with the difference in quality between the two males and inversely with the value (fitness impact) of the male mate's parental care. Importantly, the transactional model provided a unified explanation for experimental and observational evidence that extra-pair paternity rises with decreasing quality of the male mate, increasing genetic variability among breeding males, increasing breeding density, increasing availability of food and decreasing involvement of the male mate in parental care.

Animals↗
PubMedDate not supplied

From concept to practice: including the social determinants of health in environmental assessments.

The present paper examines the historical evolution of health impact assessments as part of the environmental assessment process. The development of a coherent public health framework must be based on the model of determinants of health, integrating toxic and infectious risks and social impacts of projects. The integration of common concepts, processes and methodologies from the area of public health and social impact assessment challenges the quantitative model approach to risk assessment. The expert-driven risk assessment is transformed into a social learning process where local knowledge and scientific input foster a dialogue among stakeholders. The issue-oriented, iterative and participative assessment process may be applied to the health impact assessment of public policies. Sustainable development with its social objectives of empowerment, participation, equity, poverty alleviation, social cohesion, population stability and institutional development is an appropriate framework for conducting health impact assessments.

Canada↗
PubMedDate not supplied

The development of cytogenetically normal, abnormal and mosaic embryos: a theoretical model.

Assisted reproduction and preimplantation genetic diagnosis (PGD) involve various complicated techniques, each of them with its own problems. However, the greatest problem with PGD for chromosome abnormalities is not of a technical nature but is a biological phenomenon: chromosomal mosaicism in the cleavage stage embryo. Here, we present a hypothetical, quantitative model for the development of chromosomally normal, abnormal and mosaic embryos. The arising of mosaicism in 2-8-cell embryos was described by a binomial probability model on the occurrence of mitotic events inducing chromosomal changes in the blastomeres. This model converted the 'mean' rate of mosaicism found in cross-sectional studies (60%) into an equal rate of mosaic embryos at arrival at the 8-cell stage (59.8%). The disappearance of > 90% of the mosaic embryos or the mosaicism itself from surviving embryos during the morula stage was explained by mitotic arrest of most of the mitotically changed cells under increasing cell cycle control. In our model, 25.9 and 14.3% of the embryos at the 8-cell stage are normal and abnormal respectively. The remaining 59.8% of the embryo shows mosaicism: 34.6% of abnormal/normal cells and 25.2% of abnormal/abnormal cells. The high proportion of abnormal and mosaic embryos together explains the high rate of abnormal laboratory findings in PGD for chromosomal abnormalities and aneuploidy screening. The poor representation of a 1- or 2-cell biopsy for the 7- or 6-cell post-biopsy embryo in the case of mosaicism explains the high rate of false-negative and false-positive results.

Chromosome Aberrations↗
PubMed2004

Angiogenesis in an in vivo model of adipose tissue development.

Obesity is associated with an increased risk for cardiovascular disease and cancer. Angiogenesis is a critical component of these pathological processes, and expanding adipose tissue represents one of the few sites of active angiogenesis in the adult. Despite the potential importance of angiogenesis in obesity, little is known about underlying mechanisms. This problem is magnified by the absence of useful quantitative model systems. In this report, we examine the angiogenic process using the 3T3-F442A model of adipose tissue development. In this model, 3T3-F442A preadipocytes are implanted subcutaneously into athymic Balb/c nude mice. We show that these cells develop into highly vascularized fat pads over the next 14-21 days, and that these fat pads are morphologically similar to normal subcutaneous adipose tissue. Histological studies demonstrate that a new microvasculature is evident as early as 5 days after cell implantation, and real-time quantitative RT-PCR analyses show that the expression of endothelial cell markers and adipogenesis markers increase in parallel during fat pad development. Finally, these preliminary studies suggest that the neovasculature originates by sprouting from larger, host-derived blood vessels that run parallel to peripheral nerves and that endothelial progenitor cells play little, if any, role in this process.

3T3-L1 Cells↗
PubMed1989

Mechanics and control of the cytoskeleton in Amoeba proteus.

Many models of the cytoskeletal motility of Amoeba proteus can be formulated in terms of the theory of reactive interpenetrating flow (Dembo and Harlow, 1986). We have devised numerical methodology for testing such models against the phenomenon of steady axisymmetric fountain flow. The simplest workable scheme revealed by such tests (the minimal model) is the main preoccupation of this study. All parameters of the minimal model are determined from available data. Using these parameters the model quantitatively accounts for the self assembly of the cytoskeleton of A. proteus: for the formation and detailed morphology of the endoplasmic channel, the ectoplasmic tube, the uropod, the plasma gel sheet, and the hyaline cap. The model accounts for the kinematics of the cytoskeleton: the detailed velocity field of the forward flow of the endoplasm, the contraction of the ectoplasmic tube, and the inversion of the flow in the fountain zone. The model also gives a satisfactory account of measurements of pressure gradients, measurements of heat dissipation, and measurements of the output of useful work by amoeba. Finally, the model suggests a very promising (but still hypothetical) continuum formulation of the free boundary problem of amoeboid motion. by balancing normal forces on the plasma membrane as closely as possible, the minimal model is able to predict the turgor pressure and surface tension of A. proteus. Several dynamical factors are crucial to the success of the minimal model and are likely to be general features of cytoskeletal mechanics and control in amoeboid cells. These are: a constitutive law for the viscosity of the contractile network that includes an automatic process of gelation as the network density gets large; a very vigorous cycle of network polymerization and depolymerization (in the case of A. proteus, the time constant for this reaction is approximately 12 s); control of network contractility by a diffusible factor (probably calcium ion); and control of the adhesive interaction between the cytoskeleton and the inner surface of the plasma membrane.

Amoeba↗
PubMed2002

Adhesion, friction, and mechanical properties of functionalized alkanethiol self-assembled monolayers.

We have used interfacial force microscopy to study the adhesion, friction, and mechanical properties of molecular monolayers self-assembled on Au surfaces. This quantitative and stable scanning-probe technique permits detailed studies of these factors. By systematic variation of the chemical nature of the end groups on the monolayers and utilization of standard and intuitive contact-mechanics models, quantitative results are presented of inter- and intrafilm bonding strength as well as the relationship between mechanical behavior and the lateral friction force.

Journal Article↗
PubMed1982

Thermodynamic analysis of human hemoglobins in terms of the Perutz mechanism: extensions of the Szabo--Karplus model to include subunit assembly.

The stereochemical postulates of Perutz for the mechanism of hemoglobin [Perutz, M. F. (1970) Nature (London) 228, 726--739] have been formulated into a statistical thermodynamic model. The model is based on that of Szabo and Karplus [Szabo, A., & Karplus, M. (1972) J. Mol. Biol 72, 163--197] but has been extended to include the properties of dissociated dimers in equilibrium with tetramers. The dissociation eliminates the alpha 1 beta 2 intersubunit contact which is the major site of ligand-linked structure change. The model quantitatively describes the coupling between binding of oxygen and protons in dimers and tetramers, the change in quaternary structure, and the breaking of salt bridges which are assumed to stabilize the deoxy quaternary structure. The extended model has been tested against an extensive series of recent experimental data from our laboratory and elsewhere on the ligand-linked dimer-tetramer assembly in normal human hemoglobin A and in the variant hemoglobin Kansas (beta 102 Asp leads to Asn). Two versions of the model were used which differ in the properties of the dissociated dimers. For both hemoglobins, the models were found capable of simultaneously describing the data on the ligand-linked dimer-tetramer assembly and predicting the tetramer Bohr effect. However, neither model predicted reasonable values for the tetramer Bohr effect without simultaneously predicting unreasonable values for the affinities of individual chains. Both models incorrectly predict preferential binding of oxygen to the alpha or beta chains within the tetramer. These results argue against the Perutz mechanism for the molecular processes of hemoglobin.

Hemoglobin A↗
PubMed2006

A neural model of surface perception: lightness, anchoring, and filling-in.

A neural model is proposed of how the visual system processes natural images under variable illumination conditions to generate surface lightness percepts. Previous models clarify how the brain can compute relative contrast. The anchored Filling-In Lightness Model (aFILM) clarifies how the brain 'anchors' lightness percepts to determine an absolute lightness scale that uses the full dynamic range of neurons. The model quantitatively simulates lightness anchoring properties (Articulation, Insulation, Configuration, Area Effect) and other lightness data (discounting the illuminant, the double brilliant illusion, lightness constancy and contrast, Mondrian contrast constancy, Craik-O'Brien-Cornsweet illusion). The model clarifies how retinal processing stages achieve light adaptation and spatial contrast adaptation, and how cortical processing stages fill-in surface lightness using long-range horizontal connections that are gated by boundary signals. The new filling-in mechanism runs 1000 times faster than diffusion mechanisms of previous filling-in models.

Adaptation, Ocular↗
PubMed1984

Choice in a self-control paradigm: Quantification of experience-based differences.

Previous quantitative models of choice in a self-control paradigm (choice between a larger, more-delayed reinforcer and a smaller, less-delayed reinforcer) have not described individual differences. Two experiments are reported that provide additional quantitative data on experience-based differences in choice between reinforcers of varying sizes and delays. In Experiment 1, seven pigeons in a self-control paradigm were exposed to a fading procedure that increased choices of the larger, more-delayed reinforcer through gradually decreasing the delay to the smaller of two equally delayed reinforcers. Three control subjects, exposed to each of the small-reinforcer delays to which the experimental subjects were exposed, but for fewer sessions, demonstrated that lengthy exposure to each of the conditions in the fading procedure may be necessary in order for the increase to occur. In Experiment 2, pigeons with and without fading-procedure exposure chose between reinforcers of varying sizes and delays scheduled according to a concurrent variable-interval variable-interval schedule. In both experiments, pigeons with fading-procedure exposure were more sensitive to variations in reinforcer size than reinforcer delay when compared with pigeons without this exposure. The data were described by the generalized matching law when the relative size of its exponents, representing subjects' relative sensitivity to reinforcer size and delay, were grouped according to subjects' experience.

Journal Article↗
PubMed2004

A relative signalling model for the formation of a topographic neural map.

The highly ordered wiring of retinal ganglion cell (RGC) neurons in the eye to their synaptic targets in the superior colliculus of the midbrain has long served as the dominant experimental system for the analysis of topographic neural maps. Here we describe a quantitative model for the development of one arm of this map--the wiring of the nasal-temporal axis of the retina to the caudal-rostral axis of the superior colliculus. The model is based on RGC-RGC competition that is governed by comparisons of EphA receptor signalling intensity, which are made using ratios of, rather than absolute differences in, EphA signalling between RGCs. Molecular genetic experiments, exploiting a combinatorial series of EphA receptor knock-in and knockout mice, confirm the salient predictions of the model, and show that it both describes and predicts topographic mapping.

Animals↗
PubMed2003

Deteriorating beta-cell function in type 2 diabetes: a long-term model.

BACKGROUND: Type 2 diabetes is characterized by insulin resistance and the progressive loss of islet beta-cell function. Although the former is already established at diagnosis and changes little thereafter, beta-cell function continues to decline, leading to secondary failure of anti-hyperglycaemic therapies. AIM: To develop a quantitative model of the process of beta-cell function decay over time, using trial data. DESIGN: Re-analysis of published data. METHODS: The results of the Belfast Diet Study were re-analysed. Assuming patients are diagnosed at different stages in the disease process, time displacement of data was used to obtain a bi-partite spline model describing loss of insulin secretion over a 6-year period. RESULTS: The model was developed combining two phases, in which a long slow gradual loss of beta-cell function leads to a crisis in metabolic regulation, precipitating a much more rapid decay phase. This paradigm was consistent with a previous non-linear model of beta-cell mass regulation. DISCUSSION: This model may have important implications for targeting appropriate therapy to patients in each phase: delaying or avoiding full clinical type 2 diabetes in the first phase; and preventing the development of diabetic complications in the second phase.

Adolescent↗
PubMed2000

Serial control of phonology in speech production: a hierarchical model.

A dynamic oscillator-based model of the sequencing of phonemes in speech production (OSCAR) is described. An analysis of phoneme movement errors (anticipations, perseverations, and exchanges) from a large naturalistic speech error corpus provides a new set of data suitable for quantitative modeling and is used to derive a set of constraints that any speech-production model must address. The new computational model is shown to account for error type proportions, movement error distance gradients, the syllable-position effect, and phonological similarity effects. The model provides an alternative to frame-based accounts, serial buffer accounts, and associative chaining theories of serial order processing in speech.

Humans↗
PubMed1995

Health risk assessment of chemical mixtures from a research perspective.

Human exposures to chemicals in the environment and workplace typically involve chemical mixtures. One of the key risk assessment issues for mixtures is that of extrapolation from high to low dose. Observation of an interaction among chemicals in a mixture at high concentrations in animals does not necessarily mean that the same effect, in type or magnitude, will be significant in humans exposed to lower concentrations of the mixture. Physiologically based toxicokinetic (PBTK) models can be used to assist in the extrapolation from high to low dose. Mechanisms observed in animals such as competitive inhibition of xenobiotic metabolism (e.g., butadiene and styrene or benzene and toluene) can be incorporated into PBTK models. The models can then be used to predict the magnitude of the interactive effects at high and low exposure concentrations. The most relevant predictions can then be tested using selected experiments. A research strategy involving hypothesis generation through quantitative modeling and testing through laboratory-based experiments may be the most effective strategy for addressing the complex issue of human health risks from exposures to chemical mixtures.

Animals↗