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At least 1,495 records · Page 83Linked to original sources
PubMed2006

A biological interpretation of transient anomalous subdiffusion. I. Qualitative model.

Anomalous subdiffusion has been reported for two-dimensional diffusion in the plasma membrane and three-dimensional diffusion in the nucleus and cytoplasm. If a particle diffuses in a suitable infinite hierarchy of binding sites, diffusion is well known to be anomalous at all times. But if the hierarchy is finite, diffusion is anomalous at short times and normal at long times. For a prescribed set of binding sites, Monte Carlo calculations yield the anomalous diffusion exponent and the average time over which diffusion is anomalous. If even a single binding site is present, there is a very short, almost artifactual, period of anomalous subdiffusion, but a hierarchy of binding sites extends the anomalous regime considerably. As is well known, an essential requirement for anomalous subdiffusion due to binding is that the diffusing particle cannot be in thermal equilibrium with the binding sites; an equilibrated particle diffuses normally at all times. Anomalous subdiffusion due to barriers, however, still occurs at thermal equilibrium, and anomalous subdiffusion due to a combination of binding sites and barriers is reduced but not eliminated on equilibration. This physical model is translated directly into a plausible biological model testable by single-particle tracking.

Binding Sites↗
PubMed1987

Deficit of the "primacy effect" in parkinsonians interpreted by means of the working memory model.

29 Parkinsonians and 29 controls matched for age and schooling were tested for memory by means of a free recall test (serial position curve) and two spans (verbal and non-verbal). The free recall test yields three measures: primacy (item 1); secondary memory (items 2-7) and recency (items 8-12). The Parkinsonians displayed a selective deficit of primacy, which is taken to be evidence of defective functioning of the Central Executive in the Working Memory model.

Aged↗
PubMed2000

The role of interpretation processes and parental discussion in the media's effects on adolescents' use of alcohol.

OBJECTIVE: The process that connects media use with alcohol-related beliefs and behaviors has not been well documented. To address this issue, we examined adolescents' viewing patterns, beliefs about alcohol and media messages, and parental discussion of media messages in the context of a theoretical model of message interpretation processes. Measures included the degree to which adolescents found portrayals desirable, realistic, and similar to their own lives; the degree to which they wanted to be like (identify with) the portrayals; and the degree to which they associated positive outcomes with drinking alcohol (expectancies). DESIGN: Cross-sectional survey. SETTING: Two public high schools in the California central coastal area that include a diverse population in terms of ethnic origin, income level, and education level. PARTICIPANTS: Ninth-grade students (n = 252) and 12th-grade students (n = 326). OUTCOME MEASURES: Students reported the number of days within the past week watching various genres of television content, along with perceptions of realism of content, desirability of portrayals, identification with portrayals, expectancies toward alcohol use, personal norms for alcohol use, desire for products with alcohol logos, current alcohol use, frequency of parental reinforcement, and counter-reinforcement of television messages. Associations were examined via hierarchical multiple regression analysis. RESULTS: Effects of media exposure on drinking behavior, controlling for grade level, ethnicity, gender, household income, and education levels were primarily positive and indirect, operating through a number of intervening beliefs, especially expectancies (beta =.59; r(2) =.33). Direct associations, primarily with exposure to late-night talk shows (beta =.12; r(2) =.01), were small. Parental discussion also affected behavior indirectly, operating through expectancies, identification, and perceived realism. The appeal of products with alcohol logos, which was higher among the younger students (t = 3.44) and predicted by expectancies (beta =. 37; r(2) =.13), sports viewing (beta =.17; r(2) =.03) and late-night talk shows (beta =.10; r(2) =.01), predicted actual drinking behavior (beta =.22; r(2) =.04). Drinking behavior was higher among the older students (t = -2.515). CONCLUSIONS: Adolescents make drinking decisions using a progressive, logical decision-making process that can be overwhelmed by wishful thinking. The potential risk of frequent exposure to persuasive alcohol portrayals via late-night talk shows, sports, music videos, and prime-time television for underage drinking is moderated by parental reinforcement and counter-reinforcement of messages. Interventions need to acknowledge and counter the appeal of desirable and seemingly realistic alcohol portrayals in the media and alert parents to their potential for unintended adverse effects.

Adolescent↗
PubMed2005

QSAR analysis of phenolic antioxidants using MOLMAP descriptors of local properties.

Molecular maps of atom-level properties (MOLMAPs) were developed to represent the diversity of chemical bonds existing in a molecule. Chemical reactivity, being related to the ability for bond breaking and bond making, is primarily determined by the properties of bonds available in a molecule. In order to use physicochemical properties of individual bonds for an entire molecule, and at the same time having a fixed-length molecular representation, all the bonds of a molecule are mapped into a fixed-size 2D self-organizing map (MOLMAP). This article illustrates the application of MOLMAP descriptors to QSAR, with a study of the radical scavenging activity of 47 naturally occurring phenolic antioxidants. Counterpropagation neural networks (CPG NNs) were trained with MOLMAP descriptors selected using genetic algorithms to predict antioxidant activity. The model was subsequently validated by the leave-one-out (LOO) procedure obtaining a q(2) of 0.71. Random Forests were grown with the entire set of MOLMAP descriptors giving 70% of correct classifications as potent, active or inactive in a LOO experiment. Interpretations of both models in terms of discriminant variables were concordant and allowed identifying bonds and substructures that are mostly responsible for antioxidant activity. This work shows how MOLMAPs can be used for data mining of structural and biological activity data, leading to the extraction of relationships between local properties and activity.

Algorithms↗
PubMed2003

Electrophysiological evidence for serial sentence processing: a comparison between non-preferred and ungrammatical continuations.

Event-related potentials (ERPs) were used to address a much debated issue in sentence processing research, namely whether one or multiple interpretations are pursued in case of syntactic ambiguities. For example in the syntactically ambiguous fragment "The man is painting the house and the garage...", 'and' either connects 'the house' and 'the garage', or conjoins two clauses (e.g., "The man is painting the house and the garage is already finished"). According to serial models, only one syntactic interpretation (the simplest) is pursued first (the first interpretation in the example). If this interpretation is incompatible with subsequently incoming words, the syntactic analysis of the preceding sentence fragment is revised. In contrast, parallel models propose that multiple interpretations of the ambiguity are pursued simultaneously. The two models were tested by comparing ERPs to words that were either ungrammatical, or grammatical but non-preferred continuations of the preceding sentence fragment. In a serial model, these two are not distinguished until after initial revision; in a parallel model, a distinction can be made at an early stage. The results supported a serial model: both with an acceptability judgment and a passive reading task a left lateralized negativity was found for ungrammatical and non-preferred continuations relative to unambiguous grammatical continuations, which indicates that ungrammatical and non-preferred continuations were initially processed in the same way. However, in later time intervals, the ERPs to the ungrammatical continuation showed a posterior positivity (P600), whereas the ERPs to the non-preferred continuation had a more anterior focus, which indicates that they were processed differently.

Adolescent↗
PubMed2001

Comparative binding energy (COMBINE) analysis of human neutrophil elastase inhibition by pyridone-containing trifluoromethylketones.

The complexes of human neutrophil elastase with a series of 40 N3-substituted trifluoromethylketone-based pyridone inhibitors have been modelled. The series spans three orders of magnitude in inhibition constants despite the fact that it was originally developed in an attempt to improve the oral activity of a lead compound. Ligand-receptor interaction energies calculated using molecular mechanics did not correlate well with the experimental activities. A good correlation with activity was found, however, when a COMBINE analysis of the same data was carried out, which allowed a quantitative interpretation of the modelled complexes. The essence of this method is to partition the ligand-receptor interaction energies into individual residue-based van der Waals and electrostatic contributions, and to subject the resulting energy matrix to partial least squares analysis. Incorporation of two additional descriptors representing the electrostatic energy contributions to the partial desolvation of both the receptor and the ligands improved the QSAR model, as did the replacement of the distance-dependent electrostatic contributions with solvent-screened electrostatic interactions calculated by numerically solving the Poisson-Boltzmann equation. The model was validated both internally (cross-validation) and externally, using a set of twelve 6-phenyl-pyridopyrimidine analogs. The analysis reveals the subtle interplay of binding forces which occurs within the enzyme active site and provides objective information that can be interpreted in the light of the receptor structure. This information, gained from a series of real compounds, can be easily translated into 3D real or virtual database queries in the search for more active derivatives.

Humans↗
PubMed1969

Ion exchange properties of the canine carotid artery.

Properties of the ion exchange mechanisms in the arterial wall were investigated by comparing water and electrolyte contents, and by measuring the steady-state entry of (22)Na, (42)K, and (26)Cl under similar in vitro conditions. Overnight incubation of freshly dissected slices at 2 degrees C resulted in an accumulation of sodium, chloride, and water and a loss of potassium. Subsequent incubation at 37 degrees C in a physiological solution resulted in a reversal of these processes. Loss of water, sodium, and chloride at 37 degrees C could also take place into a potassium-free solution. Under all conditions studied the quantity of fast exchanging electrolyte (half time less than 3 min) exceeded that contained in the inulin and sucrose spaces. The excess could not be attributed to connective tissue adsorption. A kinetic model was applied to the flux data which incorporated two simultaneous processes: bulk diffusion and a reversible reaction. The assumption that the cell membrane behaved as a discrete barrier for the exchange of all cell electrolyte was relaxed in this approach. A theory based upon the physicochemical properties of proteins, ions, and water in biological systems provided a physical basis for the kinetic model, and for interpreting the ion exchange properties of the vascular wall.

Animals↗
PubMed2002

Theoretical descriptors for the quantitative rationalisation of plastocyanin mutant functional propertiess.

A quantitative rationalisation of the effect of specific amino acids on the recognition process and redox characteristics of plastocyanin towards cytochrome f, as determined by point mutation experiments, has been attempted in this study. To achieve this goal we derived theoretical descriptors directly from the three-dimensional structure of the plastocyanin mutants, in the same manner as it is usually done for small drug-like molecules. The protein descriptors computed can be related to: (a) the electrostatic and dipole-dipole interactions, effective at long distance; (b) polar interactions whose features are encoded by charged partial surface area descriptors; (c) the propensity of the surface residues to form hydrogen bonding interactions; and (d) dispersion and repulsive interactions. Moreover, an estimation of mutation-dependent variation of redox potential observed has been obtained by electrostatic free energy calculations. The quantitative structure-activity relationship (QSAR) models offer structural interpretation of the point mutation experiment responses and can be of help in the design of new protein engineering experiments.

Models, Molecular↗
PubMed2006

A mathematical model for the evaluation of amplitude of hemoglobin fluctuations in elderly anemic patients affected by myelodysplastic syndromes: correlation with quality of life and fatigue.

Therapy with RBC transfusions and rHuEPO for management of anemia in patients with myelodysplastic syndromes causes recurrent fluctuations in hemoglobin levels. The purpose of this study was to elaborate a mathematical model for the interpretation of hemoglobin fluctuations and to correlate the resulting numerical parameter (Variaglobin Index) with quality of life and fatigue. In 32 myelodysplastic patients, lower amplitude of the Variaglobin Index was found significantly correlated with a better quality of life and less fatigue. The mathematical model proposed here makes it easy to monitor anemia in myelodysplastic patients and to adjust therapy accordingly.

Aged↗
PubMedDate not supplied

Fragmental approach in QSPR.

Methodological problems of using fragmental descriptors for construction of QSAR/QSPR equations are considered, and the main achievements in this field are summarized and discussed. If a structure-property data set is sufficiently large to allow building statistically significant models, then any topological index can be replaced with a set of fragmental descriptors. Several examples of using the fragmental approach for predicting retention indices and the normal boiling points of organic compounds are considered. Advantages of using fragmental descriptors, namely a "transparency" and interpretability of QSAR/QSPR models, are exemplified.

Databases, Factual↗
PubMed2003

Spectroscopic and photophysical properties of hexanuclear rhenium(III) chalcogenide clusters.

The electronic, vibrational, and excited-state properties of hexanuclear rhenium(III) chalcogenide clusters based on the [Re(6)(mu(3)-Q)(8)](2+) (Q = S, Se) core have been investigated by spectroscopic and theoretical methods. Ultraviolet or visible excitation of [Re(6)Q(8)](2+) clusters produces luminescence with ranges in maxima of 12 500-15 100 cm(-)(1), emission quantum yields of 1-24%, and emission lifetimes of 2.6-22.4 microseconds. Nonradiative decay rate constants and the luminescence maxima follow the trend predicted by the energy gap law (EGL). Examination of 24 clusters in solution and 14 in the solid phase establish that exocluster ligands engender the observed EGL behavior; clusters with oxygen- or nitrogen-based apical ligands achieve maximal quantum yields and the longest lifetimes. The excited-state decay mechanism was investigated by applying nonradiative decay models to temperature-dependent emission experiments. Solid-state Raman spectra were recorded to identify vibrational contributions to excited-state deactivation; spectral assignments were enabled by normal coordinate analysis afforded from Hartree-Fock and DFT calculations. Excited-state decay is interpreted with a model where normal modes largely centered on the [Re(6)Q(8)](2+) core induce nonradiative relaxation. Hartree-Fock and DFT calculations of the electronic structure of the hexarhenium family of compounds support such a model. These experimental and theoretical studies of [Re(6)Q(8)](2+) luminescence provide a framework for elaborating a variety of luminescence-based applications of the largest series of isoelectronic clusters yet discovered.

Journal Article↗
PubMed2004

Exploring protein-folding ensembles: a variable-barrier model for the analysis of equilibrium unfolding experiments.

Recent theoretical and experimental results point to the existence of small barriers to protein folding. These barriers can even be absent altogether, resulting in a continuous folding transition (i.e., downhill folding). With small barriers, the detailed properties of folding ensembles may become accessible to equilibrium experiments. However, further progress is hampered because folding experiments are interpreted with chemical models (e.g., the two-state model), which assume the existence of well defined macrostates separated by arbitrarily high barriers. Here we introduce a phenomenological model based on the classical Landau theory for critical transitions. In this physical model the height of the thermodynamic free energy barrier and the general properties of the folding ensemble are directly obtained from the experimental data. From the analysis of differential scanning calorimetry data alone, our model identifies the presence of a significant (>35 kJ/mol) barrier for the two-state protein thioredoxin and the absence of a barrier for BBL, a previously characterized downhill folding protein. These results illustrate the potential of our approach for extracting the general features of protein ensembles from equilibrium folding experiments.

Calorimetry, Differential Scanning↗
PubMed2001

A model of consolation.

Consolation is needed when a human being suffers (i.e. feels alienated from him- or herself, from other people, from the world or from his or her ultimate source of meaning). The aim of this study was to illuminate the meaning of consolation. Tape-recorded narrative interviews were carried out with 18 professionals from various spheres. The transcribed interviews were interpreted hermeneutically. A model of consolation is outlined in a drawing. It states that the mediator and the receiver of consolation must become ready for consolation before it can take place. To be ready means to be present and available. Availability means expressing suffering and listening respectively, and thereby opening up for communion and consoling dialogue. Communion brings about contact with the sacred dimension that human beings share and thus with goodness, light, joy, beauty and life. Consolation involves a shift of perspective and an experience of meaning in spite of suffering.

Adult↗
PubMed1996

Depressive thinking: changes in schematic mental models of self and world.

Alternative explanations for the changes in thinking associated with depression were examined. Depressive thinking could reflect a generalized increase in accessibility of negative constructs and memories, previously associated with depression. Alternatively, depressive thinking could reflect changes at a more generic level of cognitive representation, related to schematic mental models. To investigate contrasting predictions from these two explanations, depressed patients and non-depressed controls completed sentence stems involving social approval or personal achievement e.g. 'If I could always be right then others would-me'. Construct accessibility views predict that depression will be associated with more negative completions (e.g. 'dislike'). By contrast, the schematic model view predicts patients may give more positive completions (e.g. 'like'). This is because schematic models reflect inter-relationships between constructs, and, it is suggested, depression is associated with use of schematic mental models that imply closer dependence of personal worth/acceptance on success/approval than the models used in the non-depressed state. Predictions from the schematic model view were supported, confirming previous findings. Results suggest that depressive thinking reflects changes in the high level mental models used to interpret experience.

Adolescent↗
PubMed2001

Role of lateral acceleration in curve driving: driver model and experiments on a real vehicle and a driving simulator.

Experimental studies show that automobile drivers adjust their speed in curves so that maximum vehicle lateral accelerations decrease at high speeds. This pattern of lateral accelerations is described by a new driver model, assuming drivers control a variable safety margin of perceived lateral acceleration according to their anticipated steering deviations. Compared with a minimum time-to-lane-crossing (H. Godthelp, 1986) speed modulation strategy, this model, based on nonvisual cues, predicts that extreme values of lateral acceleration in curves decrease quadratically with speed, in accordance with experimental data obtained in a vehicle driven on a test track and in a motion-based driving simulator. Variations of model parameters can characterize "normal" or "fast" driving styles on the test track. On the simulator, it was found that the upper limits of lateral acceleration decreased less steeply when the motion cuing system was deactivated, although drivers maintained a consistent driving style. This is interpreted per the model as an underestimation of curvilinear speed due to the lack of inertial stimuli. Actual or potential applications of this research include a method to assess driving simulators as well as to identify driving styles for on-board driver aid systems.

Acceleration↗
PubMed1996

Indices for performance evaluation of predictive models in food microbiology.

Two complementary measures are proposed as simple indices of the performance of models in predictive food microbiology. The indices assess the level of confidence one can have in the predictions of the model and whether the model displays any bias which could lead to 'fail-dangerous' predictions. The use of the indices is demonstrated using data collated from independent and published literature. This analysis supports previous reports that evaluation of predictive models by comparison to published microbial growth rate data may be inappropriate because of limitations in that data. The indices may fail to reveal some forms of systematic deviation between observed and predicted behaviour. It is concluded, however, that the indices provide an objective and readily interpreted summary of model performance and may serve as a first step towards the development of an objective and useful definition of the term 'validated model' in predictive food microbiology.

Evaluation Studies as Topic↗
PubMed2003

An assessment of the phototoxic hazard of a personal product ingredient using in vitro assays.

Where substances are intended for use in personal products applied to the skin an assessment of potential phototoxic hazard is required. This report describes a tiered testing strategy involving in vitro assays used for the phototoxic hazard assessment of a personal product ingredient (Ingredient X). The initial assay was measurement of a UV/visible absorption spectrum to identify absorption at relevant wavelengths. This was followed by in vitro assays for phototoxicity (3T3 cell neutral red uptake phototoxicity test) and photoallergy (photobinding to human serum albumin). These in vitro screens gave equivocal results for Ingredient X which appeared to suggest a weak phototoxic reaction. To further evaluate the phototoxic hazard of Ingredient X to human skin, a phototoxicity assay using a 3-D human skin model was conducted. Ingredient X did not cause phototoxicity in this assay. Overall conclusions from these studies were that although Ingredient X showed slight intrinsic potential for photoactivation, it was unlikely to present a hazard to human skin. This report illustrates the value in a step-wise strategy of the use of human skin models to help interpret the results of other in vitro phototoxicity assays.

3T3 Cells↗