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Interpretation of fluorescence decays using a power-like model.

A power-like decay function, characterized by the mean excited-state lifetime and relative variance of lifetime fluctuation around the mean value, was applied in analysis of fluorescence decays measured with the aid of time-correlated single photon counting. We have examined the fluorescence decay, in neutral aqueous medium, of tyrosine (L-tyrosine and N-acetyl-L-tyrosinamide), and of the tyrosine residues in a tryptophan-free protein, the enzyme purine nucleoside phosphorylase from Escherichia coli in a complex with formycin A (an inhibitor), and orthophosphate (a co-substrate). Tryptophan fluorescence decay was examined in neutral aqueous medium for L-tryptophan, N-acetyl-L-tryptophanamide, and for two tryptophan residues in horse liver alcohol dehydrogenase. To detect solvent effect, fluorescence decay of Nz-acetyl-L-tryptophanamide in aqueous medium was compared with that in dioxan. Hitherto, complex fluorescence decays have usually been analyzed with the aid of a multiexponential model, but interpretation of the individual exponential terms (i.e., pre-exponential amplitudes and fluorescence lifetimes), has not been adequately characterized. In such cases the intensity decays were also analyzed in terms of the lifetime distribution as a consequence of an interaction of fluorophore with environment. We show that the power-like decay function, which can be directly obtained from the gamma distribution of fluorescence lifetimes, is simpler and provides good fits to highly complex fluorescence decays as well as to a purely single-exponential decay. Possible interpretation of the power-like model is discussed.

Computer Simulation↗

Automatic buffer capacity model building for advanced interpretation of titration curves.

An automatic buffer capacity model building algorithm was developed. The objective of this algorithm is to characterize multiple buffer systems from experimental titration curves. Starting from a simple mathematical model that incorporates the available prior knowledge on the buffer system, the model is sequentially extended by incorporating additional monoprotic buffer equations. To select the most appropriate model from the resulting set of automatically built models, a model structure selection technique was constructed from existing methods.

Algorithms↗

Shape model for the molecular interpretation of the flexoelectric effect.

A mean-field model for the flexoelectric polarization in nematics is presented, based on a continuous description of director deformations coupled to the molecular degrees of freedom via surface interactions. In such a framework, a consistent picture of the flexoelectric effect is obtained, including both dipolar and quadrupolar contributions, with a realistic account of the molecular characteristics of shape and charge distribution. The method is aimed at establishing a quantitative link between chemical structure and flexoelectric response. It provides numerical estimates of the effect and its temperature dependence and allows the recognition of the relevant molecular features for its emergence. Application to some representative systems, comprising mesogenic molecules and photoisomerizable dopants, is considered; it is shown that simple interpretative schemes can be misleading and a comparison with experimental data is reported.

Journal Article↗

Interpretation of linear regression models that include transformations or interaction terms.

In linear regression analyses, we must often transform the dependent variable to meet the statistical assumptions of normality, variance stability, or linearity. Transformations, however, can complicate the interpretation of results because they change the scale on which the dependent variable is measured. In this setting, the inclusion of product terms or the transformation of some independent (or predictor) variables may further complicate interpretation. In this article, we present some interpretations of linear models that include transformations or product terms. We illustrate these interpretations using regression analyses designed to study determinants of serum testosterone levels. These examples show how one can present results using simple measures, such as medians, and interpret regression parameters.

Epidemiologic Methods↗

[Dynamic psychiatric interpretation of a disease model of trichotillomania].

Every patient's "communal existence" allows to interpret deviations of behavior such as trichotillomania as a disturbance of interaction. When the child begins to wangle out of the dual union between mother and child it needs ways to delimitate itself, If the mother does not concede this demarcation (f. i. because she does not want to release the child from the symbiosis and therefore is "overprotecting") the child often becomes a victim of despair and, later on, of perplexity. At last it uses the own body as "Vis-a-vis". The accumulated aggressiveness is then worked off motorically by means of trichotillomania. In this way despair and perplexity in the field of interaction are passed on so to speak "atmospherically" to the mother, who in turn, having arranged treatment, transfers them on to the doctor. It is discussed how the area of irritation can be dissolved.

Aggression↗

Catch in the primary spines of the sea urchin Eucidaris tribuloides: a brief review and a new interpretation.

Previous models of reversible catch in echinoid spines, as a property of muscle or of collagen, are briefly reviewed and discussed. This brief review offers a new interpretation of catch in primary spines of Eucidaris tribuloides, viewing the collagen and small muscles of the catch ligament working together as a variable-length tendon. In the model presented, changes in ligament length when out of catch are accommodated by sliding of discontinuous, interdigitating and cross-link-stabilized columns of collagen fibrils, the muscle layer external to the ligament effecting spine movement. Catch is viewed as a consequence of contraction of small muscles inserted on the collagen columns within the ligament. Ligament shortening tightens the profuse (ca. 30,000/mm2) and highly ordered collagen insertion loops within the stereoms of the spine base and test, and catch results from the multiplicative effect of these friction sites in series. New data are presented on novel structural cross-links between collagen fibrils. The cross-links stabilize the ligament columns. The central ligament in Eucidaris plays a purely passive mechanical role in maintaining the alignment of the spine-test articulation. It contains no muscle and neither contracts nor undergoes catch; its insertions are simple, unlike the complex stereom insertions of the main ligament.

Animals↗

Interpreting a medium-resolution model of tubulin: comparison of zinc-sheet and microtubule structure.

We previously used electron crystallography of zinc-induced two-dimensional crystalline sheets of tubulin to construct a medium-resolution three dimensional (3-D) reconstruction (at 6.5 A) of this protein. Here we present an improved model, and extend the interpretation to correlate it to microtubule structure. Secondary sequence predictions and projection density maps of subtilisin-cleaved tubulin provide information on the location of the C-terminal portion, which has been suggested to be involved in the binding of microtubule-associated proteins. The zinc-sheet tubulin model is compared to microtubules in two ways; comparison of electron diffraction from the zinc-sheets to electron diffraction from microtubules, and by docking the zinc-sheet protofilament 3-D model into a helical reconstruction from ice-embedded microtubules. By correlating the zinc-sheet protofilament to a reconstruction of axonemal protofilaments, we assigned polarity to the protofilament in our model. The polarity assignment together with our model for dimer boundaries and the assignment of alpha- and beta-monomers in our reconstruction, provides a microtubule model where the alpha-monomer crowns the plus- (or fast-growing) end of the microtubule and contact is made in the centrosome with gamma-tubulin via the beta-monomer.

Amino Acid Sequence↗

An approach to the interpretation of backpropagation neural network models in QSAR studies.

An approach to the interpretation of backpropagation neural network models for quantitative structure-activity and structure-property relationships (QSAR/QSPR) studies is proposed. The method is based on analyzing the first and second moments of distribution of the values of the first and the second partial derivatives of neural network outputs with respect to inputs calculated at data points. The use of such statistics makes it possible not only to obtain actually the same characteristics as for the case of traditional "interpretable" statistical methods, such as the linear regression analysis, but also to reveal important additional information regarding the non-linear character of QSAR/QSPR relationships. The approach is illustrated by an example of interpreting a backpropagation neural network model for predicting position of the long-wave absorption band of cyane dyes.

Adsorption↗

The random transition model of the cell cycle. A critical review.

The random transition model of the cell cycle has received much attention in recent years in attempts to describe and explain variations in cell cycle times. In this review we suggest statistical procedures for fitting the model to experimental data in place of the invalid techniques currently used. However, we also argue that there have been misconceptions about criteria for quality of fit of the model, and consequent biological interpretations. Other models fit just as well, and the analyses we describe do not provide evidence for any particular biological mechanism.

Animals↗

A diffusion model of early visual search: theoretical analysis and experimental results.

Meinecke (1989, Exp. 1, cond. HO) showed that the detectability of a visual target embedded in a linear noise array decreases with increasing retinal eccentricity, while the reaction time (RT) of the hits increases. One of the most interesting features of her results was that the RT of the correct rejections is consistently larger than the RT for signals presented near the fovea. This finding suggests that initially visual attention is concentrated near the fixation point and then diffuses across the stimulus array to perform a serial, exhaustive search. We present a diffusion model of early visual-search processes that quantitatively describes this evolution of attention in time and space; in contrast to most previous conceptions, it is based on a genuine relation between the spatial and temporal dimensions of the search processes performed. The model predicts quantitatively both detection performance and RT. We conducted an experiment similar to that of Meinecke (1989), but with an additional variation of the presentation time. All the main features of the 189 predictions could be explained by the model. The interpretation of the four model's parameters is discussed in some detail and compared with previous estimates of the microscopic search speed derived from alternative models. Finally, we consider some possible modifications related to results of Kehrer (1987, 1989), and some generalizations to multi target detection and two-dimensional stimulus arrays.

Adult↗

Modelling variability in lymphatic filariasis: macrofilarial dynamics in the Brugia pahangi--cat model.

A striking feature of lymphatic filariasis is the considerable heterogeneity in infection burden observed between hosts, which greatly complicates the analysis of the population dynamics of the disease. Here, we describe the first application of the moment closure equation approach to model the sources and the impact of this heterogeneity for macrofilarial population dynamics. The analysis is based on the closest laboratory equivalent of the life cycle and immunology of infection in humans--cats chronically infected with the filarial nematode Brugia pahangi. Two sets of long-term experiments are analysed: hosts given either single primary infections or given repeat infections. We begin by quantifying changes in the mean and aggregation of adult parasites (inversely measured by the negative binomial parameter, kappa in cohorts of hosts using generalized linear models. We then apply simple stochastic models to interpret observed patterns. The models and empirical data indicate that parasite aggregation tracks the decline in the mean burden with host age in primary infections. Conversely, in repeat infections, aggregation increases as the worm burden declines with experience of infection. The results show that the primary infection variability is consistent with heterogeneities in parasite survival between hosts. By contrast, the models indicate that the reduction in parasite variability with time in repeat infections is most likely due to the 'filtering' effect of a strong, acquired immune response, which gradually acts to remove the initial variability generated by heterogeneities in larval mortality. We discuss this result in terms of the homogenizing effect of host immunity-driven density-dependence on macrofilarial burden in older hosts.

Animals↗

Comparative two- and three-dimensional finite element modelling techniques for tibial fractures.

Often the choice of a two-dimensional modelling approach over a three-dimensional approach is made on the basis of available resources, and not on task appropriateness. In the case of simulating the mechanical behaviour of irregular anatomical structures in biomedical engineering, the authenticity of two-dimensional model behaviour and the interpretation of model solutions is of particular concern since little comparable two-dimensional and three-dimensional data have been published. As part of a research programme, a comparison was made between two-dimensional and three-dimensional finite element models (FEMs) that examine the stress-strain environment of a clinical bone fracture and callus. In comparison with the three-dimensional model, the two-dimensional model substantially underestimated peak compressive principal stresses in the callus tissue and peak equivalent strains. This was a consequence of geometrical and structural asymmetry in a plane perpendicular to the two-dimensional model. However, the two-dimensional model predicted similar patterns of stress and strain distribution to the corresponding mid-longitudinal plane of the three-dimensional model, and underestimates of peak stress and strain were much reduced. This confirmed that despite the irregular geometry and structure of the subject, the two-dimensional model provided a valid mechanical simulation in the plane of the fracture that it represented.

Biomechanical Phenomena↗

A haemodynamic model for the physiological interpretation of in vivo measurements of the concentration and oxygen saturation of haemoglobin.

We present a model that describes the effect of physiological parameters such as the speed of blood flow, local oxygen consumption, capillary recruitment, and vascular dilation/constriction on the concentration and oxygen saturation of haemoglobin in tissue. This model can be used to guide the physiological interpretation of haemodynamic and oximetric data collected in vivo with techniques such as optical imaging, near-infrared spectroscopy and functional magnetic resonance imaging. In addition to providing a formal description of well-established results (exercise-induced hyperemia, reperfusion hyperoxia, decrease in the concentration of deoxyhaemoglobin induced by brain activity, measurement of arterial saturation by pulse oximetry, etc.), this model suggests that the superposition of asynchronous contributions from the arterial, capillary and venous haemoglobin compartments may be at the origin of observed out-of-phase oscillations of the oxyhaemoglobin and deoxyhaemoglobin concentrations in tissue.

Hemodynamics↗

Model selection for the interpretation of protein side chain methyl dynamics.

A number of different dynamics models are considered for fitting (13)C and (2)H side chain methyl relaxation rates. It is shown that in cases where nanosecond time scale dynamics are present the extended Lipari-Szabo model which is explicitly parameterized to include the effects of slow motions can produce wide distributions of fitting parameters even in cases where the errors are relatively small and large numbers of relaxation rates are considered. In contrast, fits of (15)N backbone dynamics using this model are far more robust. The origin of this difference is analyzed and can be explained by the different functional forms of the spectral density in these two cases. The utility of a number of models for the analysis of methyl side chain dynamics is presented.

Amino Acids↗

A model for multisystem evaluation, interpretation, and treatment of individuals with neurologic dysfunction.

We have presented a model that can be used to organize current concepts of neuroanatomy, neurophysiology, and motor control theory into a clinically relevant context. This model can be used to postulate the causal relationship among pathology, impairments, and disabilities. Knowledge of the insult often provides predictive information regarding stability of the disability, progression of the disease, and possibly recovery. Knowledge of neuropathology should guide the clinician regarding the types of impairments that are expected. Thus, by knowing the type and location of the lesion, the clinician already has a perspective regarding which evaluative tests should be emphasized and what treatment strategies will be most effective. In the absence of known pathology, knowledge of motor control theory, neuroanatomy, and neuropathology can still help the clinician make educated judgments regarding the interrelationship of the patient's impairments. In this model, we separate impairments that result directly from neuropathology and those that arise indirectly to help the clinician keep the total patient in perspective and to focus intervention. This separation emphasizes the applicability and limitations of motor control theories in the treatment of neurologically impaired individuals. Motor control theory helps to identify the relationship between direct impairments and their likely consequences; motor control theory does not address the very real issue of impairments that arise indirectly in systems such as the musculoskeletal and cardiopulmonary systems. Impairments that occur as a composite effect of multiple causes are identified as a separate category. Some of the causes of these impairments can often be addressed by physical therapy intervention, and some cannot.(ABSTRACT TRUNCATED AT 250 WORDS)

Cerebrovascular Disorders↗

From heart attacks to melanoma: do common sense models of somatization influence symptom interpretation for female victims?

Common sense models regarding gender and stress influenced how laypeople responded to information about symptoms in 3 experiments. In Study 1, medical intervention was perceived to be less important for female targets reporting chest pain and stressful events than for male targets experiencing identical symptoms and stressors. In addition, chest pain was less likely to be attributed to cardiac causes for female targets. This gender-based stress-discounting effect was replicated for symptoms of gallstones and melanoma in Study 2, where participants again were less likely to recommend medical care for female than for male targets. Recognition memory for information about a somatizing target was tested in Study 3; results suggested that laypeople hold stereotypes associating somatization with female gender. The authors' findings provide insight into the naive theories that shape symptom interpretation and self-referral behavior.

Adolescent↗

Improved methods for building protein models in electron density maps and the location of errors in these models.

Map interpretation remains a critical step in solving the structure of a macromolecule. Errors introduced at this early stage may persist throughout crystallographic refinement and result in an incorrect structure. The normally quoted crystallographic residual is often a poor description for the quality of the model. Strategies and tools are described that help to alleviate this problem. These simplify the model-building process, quantify the goodness of fit of the model on a per-residue basis and locate possible errors in peptide and side-chain conformations.

Chemical Phenomena↗