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Results for “Model interpretability”

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At least 739 records · Page 41Linked to original sources

PubMed2002

Optimizing imaging time for improved performance in oncology PET studies.

PURPOSE: The potential for improving the diagnostic performance of static positron imaging tomography (PET) by judiciously choosing optimum post-injection imaging times is investigated. PROCEDURES: Dynamic and whole-body scan data, from 2-deoxy-2-[18F]fluoro-D-glucose (FDG) oncological studies, are analyzed for changing standardized uptake value (SUV) behavior with increasing post-injection times at either single- or multiple-bed positions. Model-based interpretations address d(SUV)/dt, shown to correlate with SUV, and the contrast ratio for a tumor and its surroundings. A method for correcting measurements to a standardized time is given. RESULTS: Both data and model-based equations suggest that starting data acquisition later than the average 55 +/- 15 (SD) minutes post-injection reported in the FDG literature can improve contrast ratios. Considerations for choosing an optimum time from a clinical standpoint are listed. CONCLUSIONS: It is concluded that the appropriate time for each particular protocol can be found with the aid of the information presented here. True optimization, however, remains a complex issue.

Journal Article↗

PubMed2002

Validation of a kinetic model for the reactions in RIA.

The goal of this work was to check the validity of a model previously described for the study of kinetics of the processes taking place during the immuno-analytical measurement of insulin. The antibody was immobilized on the suface wall of the reaction tube. Tracer and insulin concentration, temperature, viscosity and ionic strength in the reaction medium were taken as independent variables. Biexponential kinetics depending on the concentration was observed. The results of the viscosity study show a clear negative influence of this parameter on the direct reaction velocity. Ionic strength had a slight effect, which suggests that the observed variation due to the addition of glycerol is not induced by the influence of the dielectric constant of the solution used. The effect of the temperature shows activation parameters similar to water flow-viscosity energy, which suggests a diffusion control for the reaction. The proposed model correctly interprets the influence of the studied variables.

Antibodies↗

PubMed2002

A strategy to enhance the usability of the minimal model as used with the intravenous glucose tolerance test in diabetes research and clinical management.

The Minimal Model method of determining Insulin Sensitivity from the Intravenous glucose Tolerance Test is a valuable tool for the Diabetes research community. However the Minimal Model algorithm itself is not readily available in a user-friendly modem windows environment to the clinical researcher in many research departments. In addition use of the model often requires intervention by an experienced "modeller" to interpret the results produced by the method. This paper proposes a more readily available and usable version of the program and discusses the issues which surround the use of the program by clinical researchers without computer mathematical modelling experience.

Algorithms↗

PubMed1975

[Psychoanalytic interpretation of sleep-disturbances. Model of a structural-theoretical classification (author's transl)].

In psychoanalytic literature anxiety, guilt-feelings and unconscious hostility are assumed to be the most common causes of spleeplessness. The author attempts to ascribe these emotions to conflicts between the instances of the psychoanalytic personality model as a structure-theoretical classification of sleep-disturbances. Three large groups emerge: Neurotic disturbances of sleep with internalized conflicts (these correspond essentially to what are generally understood to be neurotic sleep-disturbances), neurotic disturbances of sleep with externalized conflicts (these are more common in childhood) and non-neurotic sleep disturbances. Within these groups the relative parts of effectiveness of the instances of the psychoanalytic personality-model - ego, super-ego, id and reality - are discussed.

Aggression↗

PubMed2005

Light scattering from intact cells reports oxidative-stress-induced mitochondrial swelling.

Angularly resolved light scattering measurements were performed on suspensions of EMT6 cells and on mitochondria isolated from rabbit liver. Mie theory analysis of the scattering from intact cells indicated that mitochondrial-sized organelles dominated scattering in the range 5-90 degrees . This interpretation was supported by the analysis of scattering from isolated mitochondria. Intact cells were subjected to oxidative stress by photodynamic insult. After 3 h of incubation in the heme precursor aminolevulinic acid hexylester, EMT6 cells accumulated abundant protoporphyrin IX, an endogenous photosensitizer formed in mitochondria. Irradiation of aminolevulinic acid/protoporphyrin IX-sensitized cells with 10 J cm(-2) of 514 nm light led to pronounced changes in angularly resolved light scattering consistent with mitochondrial swelling. Electron microscopy of similarly treated EMT6 cell monolayers showed significant changes in mitochondrial morphology, which included distension of the outer unit membrane and bloating of the internal mitochondrial compartment. Informed by these electron microscopy results, we implemented a coated sphere model to interpret the scattering from intact cells subjected to oxidative stress. The coated sphere interpretation was compatible with the scattering measurements from these cells, whereas simpler Mie theory models based on homogenous swelling were dramatically unsuccessful. Thus, in this system, angularly resolved light scattering reports oxidative-stress-induced changes in mitochondrial morphology.

Aminolevulinic Acid↗

PubMedDate not supplied

Lesion spectra: radiation signatures and biological gateways.

We describe an integrative approach to the modeling of biophysical radiation effects. The model takes aim at practical applications of the knowledge provided by molecular studies of radiation-matter interactions in DNA. The central proposition is the idea that the distribution of molecular lesions (i.e., a molecular lesion spectrum, MLS) generated in DNA by exposure to a particular radiation is a characteristic of that causal radiation (i.e., is a radiation signature, RS). We have found that adaptive neural networks (ANN's) provide an efficient way to validate that proposition and that ANN's are also likely to be invaluable in any attempt to correlate cancers with radiation types (i.e., with RS's), to use RS's for evaluating individual carcinogenic susceptibilities, and to develop a low-dose personalized monitoring capability. Although efforts to identify products of radiation that are specific to radiation type and to link those with biological responses are almost a century old, the RS concept has provided the first quantitative confirmation of such causal relations. That is, RS's and radiation markers have been identified for various types of radiation, electromagnetic (EM) and particulate, and these signatures and markers may constitute a new way for fast radiation exposure estimates, risk assessment, and cumulative low-dose evaluation. In this work, while we will present a short review of the concepts and methods related to both RS's and markers, almost the entire effort will relate to the modeling and interpretation of RS's using ANN processing.

Biomarkers↗

PubMed1994

Complex dynamic order in ventricular fibrillation.

Self-sustained circus movement of excitation has long been discussed as the underlying mechanism of ventricular fibrillation. This concept now appears to have found general acceptance. Mapping studies are very expensive and do not permit observations to be isolated from varying external influences. The authors have therefore used a simple cellular automation for studying the basic principles of excitation spreading during ventricular fibrillation under various conditions. Highly ordered spiral waves, described in other computer models, previously interpreted as fibrillation were encountered. Comparisons of pseudo-electrocardiograms created by the cellular automaton with original electrocardiographic recordings showed similarity in the time series and in fast Fouriér transformation. Modulation of refractory times often led to the termination of model fibrillation. Clinical evidence suggests that maintenance of the 1/f (RR-variability) variations produced by the autonomic nervous system exerts a protective effect on the evolution of ventricular fibrillation.

Computer Simulation↗

PubMed1988

The electrical potential produced by a strand of cardiac muscle: a bidomain analysis.

Analytic expressions are derived relating the transmembrane potential to the intracellular, interstitial and external potentials in a cylindrical strand of cardiac muscle lying in a saline bath. The bidomain model is used to account for the anisotropy and interstitial space in the tissue. The implications of this model for interpreting potential data from strands of cardiac muscle are discussed.

Action Potentials↗

PubMedDate not supplied

Modeling vitellogenesis in female fish exposed to environmental stressors: predicting the effects of endocrine disturbance due to exposure to a PCB mixture and cadmium.

A wide variety of chemical and physical environmental stressors have been shown to alter the reproductive processes in fish by interfering with endocrine function. Most endocrine indicators or biomarkers are static measures from dynamic hormonally-mediated processes, and often do not directly relate to reproductive endpoints of ecological significance. Adequate production of the yolk precursor protein, vitellogenin, is critical for the survival and normal development of the sensitive egg and yolk-sac larval fish life stages. We developed a model that simulates vitellogenesis in a mature female sciaenid fish. The model simulates the major biochemical reactions over a 6-month period from the secretion of gonadotropin (GtH) into the blood to the production of vitellogenin. We simulated the effects of two endocrine disrupting chemicals (EDCs) that have different actions on vitellogenin production: a PCB mixture and cadmium. Predicted changes in steroid concentrations and cumulative vitellogenin production compared favorably with changes reported in laboratory experiments. Simulations illustrate the potential utility of our model for interpreting reproductive endocrine biomarkers measured in fish collected from degraded environments.

Animals↗

PubMed1996

Nonlinear control of movement distance at the human elbow.

The kinematic, kinetic, and electromyographic (EMG) patterns observed during fast, single-joint flexion movement have been widely studied as a paradigm for understanding voluntary movement. Several patterns have been described that depend upon the movement task (e.g., distance, speed, and load). A previous model that interpreted differences in EMG patterns in terms of pulse-height or pulse-width modulation of rectangular pulses of motoneuron pool excitation cannot explain all the EMG patterns reported in the literature. We proposed a more general version of that model, consisting of a set of four equations, which specify the parameters of the excitation pulses for a wide variety of movement tasks. Here we report experiments in which subjects performed fast elbow flexions over a range of distances from 2.8 degrees to 45 degrees. The EMG patterns that we observe are consistent with this more general model. We conclude that this model is sufficient to specify muscle excitation patterns that will launch a movement toward and stop it in the neighborhood of a target. This model operates on the basis of prior knowledge about the task rather than feedback received during the task.

Adult↗

PubMed2004

Applying data mining techniques to library design, lead generation and lead optimization.

Many data mining techniques have been applied to activity and ADMET datasets and the resulting models are being used to understand quantitative structure-activity relationships and design new libraries. This review summarizes data mining concepts and discuss their application to library design, lead generation (particularly for sequential screening) and lead optimization (specifically for generating and interpreting QSAR models). Also, this review discusses recent comparative studies between data mining techniques and draws some conclusions about the patterns emerging in the drug discovery data mining field.

Algorithms↗

PubMed2006

Metabolic networks in motion: 13C-based flux analysis.

Many properties of complex networks cannot be understood from monitoring the components--not even when comprehensively monitoring all protein or metabolite concentrations--unless such information is connected and integrated through mathematical models. The reason is that static component concentrations, albeit extremely informative, do not contain functional information per se. The functional behavior of a network emerges only through the nonlinear gene, protein, and metabolite interactions across multiple metabolic and regulatory layers. I argue here that intracellular reaction rates are the functional end points of these interactions in metabolic networks, hence are highly relevant for systems biology. Methods for experimental determination of metabolic fluxes differ fundamentally from component concentration measurements; that is, intracellular reaction rates cannot be detected directly, but must be estimated through computer model-based interpretation of stable isotope patterns in products of metabolism.

Animals↗

PubMedDate not supplied

Using temperature to test models of flow near Yucca Mountain, Nevada.

Ground water temperatures in the fractured volcanic aquifer near Yucca Mountain, Nevada, have previously been shown to have significant spatial variability with regions of elevated temperatures coinciding roughly with near-vertical north-south trending faults. Using insights gained from one-dimensional models, previous investigators have suggested upwelling along faults from an underlying aquifer as a likely explanation for this ground water temperature pattern. Using a three-dimensional coupled flow and heat-transport model, we show that the thermal high coinciding with the Paintbrush fault zone can be explained without significant upwelling from the underlying aquifer. Instead, the thermal anomaly is consistent with thermal conduction enhanced slightly by vertical ground water movement within the volcanic aquifer sequence. If more than approximately 400 m3/day of water enters the volcanic aquifer from below along a 10 km fault zone, the calculated temperatures at the water table are significantly greater than the measured temperatures. These results illustrate the potential limitations in using one-dimensional models to interpret ground water temperature data, and underscore the value in combining temperature data with fully coupled three-dimensional simulations.

Environmental Monitoring↗

PubMedDate not supplied

Human sexuality in biological perspective: theoretical and methodological considerations.

An increasing number of observers are claiming that a biological model is more appropriate to an understanding of human sexuality than the conventional social-learning one. Such claims have prompted a perusal of the biological literature to ascertain whether the relevant evidence is convincing. The results of this review suggest that claims for the biological model are questionable since the evidence for that model either derives from animal studies (and is thus not generally applicable to human behavior) or is inconclusive, contradictory, or methodologically deficient. It is concluded, therefore, that behavioral scientists are at present on firm ground in using a social-learning, in preference to a biological, model to interpret most aspects of human sexual behavior.

Adolescent↗

PubMed1982

Epidemiological models of poliomyelitis and measles and their application in the planning of immunization programmes.

This report describes the construction and application of epidemiological models of measles and poliomyelitis. In these models, epidemiological classes and their age structure have been based on the natural history of these diseases in the population aged 0 - 19 years. The flow of the population through the classes has been expressed as an equation system suitable for computer interpretation. The models have been used to simulate both the natural course of the diseases and the effect of various immunization schemes. The models were also used to explore prospects for control and eradication of these diseases with specific immunization programmes, and their relative effectiveness and cost-effectiveness are discussed.

Adolescent↗

PubMed2004

Positional entropy during pigeon homing II: navigational interpretation of Bayesian latent state models.

In these two companion papers we introduce a new approach to the analysis of bird navigation which brings together several novel mathematical and technical applications. Miniaturized GPS logging devices provide track data of sufficiently high spatial and temporal resolution that considerable variation in flight behaviour can be observed remotely from the form of the track alone. We analyse a fundamental measure of bird flight track complexity, spatio-temporal entropy, and explore its state-like structure using a probabilistic hidden Markov model. The emergence of a robust three-state structure proves that the technique has analytical power, since this structure was not obvious in the tracks alone. We propose the hypothesis that positional entropy is indicative of underlying navigational uncertainty, and that familiar area navigation may break down into three states of navigational confidence. By interpreting the relationship between these putative states and features on the map, we are able to propose a number of hypothetical navigational strategies feeding into these states. The first of these two papers details the novel technical developments associated with this work and the second paper contains a navigational interpretation of the results particularly with respect to visual features of the landscape.

Animals↗

PubMed2003

Epidemiological transition: model or illusion? A look at the problem of health in Mexico.

This paper discusses the validity of the epidemiological transition model to interpret changes in the structure of mortality and morbidity. Epistemological and political questions are posed. The case of Mexico is used to illustrate the limitations its use imposes on understanding the constellation of components explaining the epidemiological profile, and the problems involved in designing a public health policy on the basis of this sort of misinterpretation. It is suggested that the illusory certainty of a pre-determined destiny distorts the prospective that would enable to construct scenarios; what is actually happening remains hidden by the model and health policies are designed without adequate parameters for evaluating their effective impact. We conclude with some remarks on the usefulness of constructing alternative forms of interpretation for understanding changes in the epidemiological profile, one of the most important inputs for designing better policies to face the challenges posed by health care and dealing with illness in modern-day societies.

Causality↗

PubMed1993

Inhibition of spinach D-glyceraldehyde 3-phosphate: NADP+ oxidoreductase (nonphosphorylating) by adenylate compounds: the effect of dead-end inhibitors on a steady state random reaction mechanism.

D-Glyceraldehyde 3-phosphate: NADP+ oxidoreductase, nonphosphorylating (GNR; EC 1.2.1.9) purified from spinach leaves was investigated by initial velocity analysis. The hyperbolic saturation curves became nonhyperbolic when NADP+ was varied at elevated D-glyceraldehyde 3-phosphate (G3P) concentrations (sigmoidicity) or when G3P was varied at low NADP+ concentrations (pseudo-substrate inhibition), suggesting a random bi bi mechanism (Scagliarini et al. Plant Physiol. 94, 1337-1344, 1990). Free ATP was a linear competitive inhibitor of both NADP+ with KI 0.5 +/- 0.2 mM (SD) and G3P with KI 3.2 +/- 0.2 mM as determined by data in the hyperbolic range of responses when the nonvaried substrate was saturating. Similarly ADP inhibited competitively with KI 1.9 +/- 0.4 mM (NADP+) and 3.5 +/- 0.5 mM (G3P). Inhibition was mixed-type when the nonvaried substrate was below saturation. ATP, but not ADP, tended to enhance the nonhyperbolic behavior of GNR, resulting in potentiated inhibition at high [G3P]/[NADP+] ratios. The Mg-chelated form of ATP was less effective. The rate equation of a steady state random bi bi reaction mechanism in the presence of a dead-end inhibitor was derived. Suitable values of the rate constants were chosen to fit the kinetic data for the uninhibited enzyme. These values and the measured inhibition constants inserted in the rate equation can satisfactorily account for the nonhyperbolic inhibition patterns of ATP and ADP. The generalized model represents a possible alternative to allosteric models in interpreting nonlinear kinetics and dead-end inhibition of two-substrate enzymes.

Adenosine Diphosphate↗