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PubMed2003

Application of 3D-Jury, GRDB, and Verify3D in fold recognition.

In CASP5, the BioInfo.PL group has used the structure prediction Meta Server and the associated newly developed flexible meta-predictor, called 3D-Jury, as the main structure prediction tools. The most important feature of the meta-predictor is a high (86%) correlation between the reported confidence score and the quality of the selected model. The Gene Relational Database (GRDB) was used to confirm the fold recognition results by selecting distant homologues and subsequent structure prediction with the Meta Server. A fragment-splicing procedure was performed as a final processing step with large fragments extracted from selected models using model quality control provided by Verify3D. The comparison of submitted models with the native structure conducted after the CASP meeting showed that the GRDB-supported structure prediction led to a satisfactory template fold selection, whereas the fragment-splicing procedure must be improved in the future.

Amino Acid Sequence↗
PubMed1976

Further evidence for a phycobilisome model from selective dissociation, fluorescence emission, immunoprecipitation, and electron microscopy.

Phycobilisomes, isolated in 500 mM Sorensen's phosphate buffer pH 6.8 from the red alga, Porphyridium cruetum, were analyzed by selective dissociation at various phosphate concentrations. The results are consistent with a structural model consisting of an allophycocyanin core, surrounding by a hemispherical layer of R-phycocyanin, with phycoerythrin being on the periphery. Such a structure also allows maximum energy transfer. Intact phycobilisomes transfer excitation energy ultimately to a pigment with a fluorescence emission maximum at 675 nm. This pigment is presumed to be allophycocyanin in an aggreagated state. Uncoupling of energy transfer among the pigments, and physical release of the phycobiliproteins from the phycobilisome follow a parallel time-course; phycoerythrin is released first, followed by R-phycocyanin, and then allophycocyanin. In 55 mM phosphate buffer, the times at which 50% of each phycobiliprotein has dissociated are: phycoerythrin 40 min, R-phycocyanin 75 min, and allophycocyanin 140 min. The proposed arrangement of phycobiliproteins within phycobilisomes is also consistent with the results from precipitation reactions with monospecific antisera on intact and dissociated phycobilisomes. Anti-phycoertythrin reacts almost immediately with intact phycobilisomes, but reactivity with anti-R-phycocyanin and anti-allophycocyanin is considerably delayed, suggesting that the antigens are not accessible until a loosening of the phycobilsome structure occurs. Reaction wbilisomes, but is much more rapid in phycobilisomes of Nostoc sp. which contains 6-8 times more allophycocyanin. It is proposed that allophycocyanin is partially exposed on the base of isolated intact phycobilisomes of both algae, but that in P. cruentum there are too few accessible sites to permit a rapid formation of a precipitate with anti-allophyocyanin.

Energy Transfer↗
PubMed1984

[A statistical approach to measure fitness by PWC170].

This paper discusses measurements of physical work capacity. When the sample size is small, its model selection problem is difficult in the multiple regression analysis. Although the development of model selection may be correct, it is not always useful for practical data. Since the number of the parameters is large compared with the sample size, we shall discretize continuous data into categorical data and shall use the CATDAP program.

Computers↗
PubMedDate not supplied

[The use of the perfused rat heart as a model for selecting antihypoxic compounds].

The test system for selection of antihypoxic compounds was developed and approved on the basis of the model of the perfused rat heart. It was found that the hypoxic state of the moderate degree of severity simulated on the myocardium is optimal for the assessment of the studied antihypoxic compounds. Taking into consideration the fact that at the early stages of hypoxia the electron transport is disordered at the level of the first enzymatic complex of the respiration chain, the protective actions of the agents (menadione and hydroquinone) being able of shunting the respiration chain to bypass the damaged area were studied. It was found that under hypoxia these compounds improve the energy-dependent contractile properties of the myocardium, that is, show up the antihypoxic effects.

Animals↗
PubMed2001

Using artificial evolution and selection to model insect navigation.

BACKGROUND: An animal's behavioral strategies are often constrained by its evolutionary history and the resources available to it. Artificial evolution allows one to manipulate such constraints and explore how they influence evolved strategies. Here we compare the navigational strategies of flying insects with those of artificially evolved "animats" endowed with various motor architectures. Using evolutionary algorithms, we generated artificial neural networks that controlled a virtual animat's navigation within a 2D, simulated world. Like a flying insect, the animat possessed motors that generated thrust and torque, a compass, and visual sensors. Some animats were limited to forward motion, while others could also move sideways. Animats were selected for the precision with which they reached a target specified by a visual landmark. RESULTS: Animats given sideways motors could alter flight direction without changing body orientation and evolved strategies similar to those of flying bees or wasps performing the same task. Both animats and insects first aimed at the landmark. In the last phase, both adopted a fixed body orientation and adjusted their position to keep the landmark at a fixed retinal location. Animats unable to uncouple flight direction and body orientation evolved subtly different strategies and performed less robustly. CONCLUSIONS: This convergence between the navigational strategies of animals and animats suggests that the insect's strategies are primarily an adaptation to the demands of using visual information and compass direction to reach a position in space and that they are not significantly compromised by the insect's evolutionary history.

Animals↗
PubMed2003

A model to select regimens for phase III trials for patients with advanced-stage non-small cell lung cancer.

PURPOSE: Historical data from pilot, Phase II, and Phase III studies for patients with advanced-stage non-small cell lung cancer (NSCLC) were used to evaluate a statistical model developed to provide assistance in selecting regimens from pilot studies for subsequent use in larger Phase III randomized studies. EXPERIMENTAL DESIGN: Information from 33 Phase III trials for patients with advanced-stage NSCLC performed from 1973 and 1994 in the United States and Canada was collected. The data from antecedent pilot or Phase II and subsequent Phase III trials were analyzed using a predictive statistical model. This model uses the number of patients in the pilot/Phase II study, the median survival of patients in the pilot, and the number of deaths observed, to estimate the statistical likelihood that the pilot regimen will be shown superior to standard therapy in a subsequent Phase III trial. RESULTS: Ten pilot/Phase II studies were identified that preceded eleven subsequent Phase III studies. The three pilot regimens associated with Phase III trials, revealing statistically significant longer survival, had an expected power of 0.69, 0.85, and 0.94 respectively. The regimens from the seven other pilot studies for which the median power expected was 0.38 (range, 0.07-0.80) showed no difference when compared with standard treatment in a Phase III trial. CONCLUSION: The use of the expected power model provides an important enhancement to the screening of new therapies. Regimens with an expected power of >0.55 may be good candidates for testing in Phase III trials.

Carcinoma, Non-Small-Cell Lung↗
PubMed2001

Efficient screening of covariates in population models using Wald's approximation to the likelihood ratio test.

We propose an efficient algorithm for screening covariates in population model building using Wald's approximation to the likelihood ratio test (LRT) statistic in conjunction with Schwarz's Bayesian criterion. The algorithm can be applied to a full model fit of k covariate parameters to calculate the approximate LRT for all 2k - 1 possible restricted models. The algorithm's efficiency also permits internal validation of the model selection process via bootstrap methods. We illustrate the use of this algorithm for both model selection and validation with data from a Daypro pediatric study. The algorithm is easily implemented using standard statistical software such as SAS/IML and S-Plus. A SAS/IML macro to perform the algorithm is provided.

Adult↗
PubMed2005

Inference of nested variance components in a longitudinal myopia intervention trial.

This paper was motivated by a double-blind randomized clinical trial of myopia intervention. In addition to the primary goal of comparing treatment effects, we are concerned with the modelling of correlation that may come from two possible sources, one among the longitudinal observations and the other between measurements taken from both eyes per subject. The data are nested repeated measurements. We suggest three models for analysis. Each one expresses the correlation differently in various covariance structures. We articulate their differences and describe the implementations in estimation using commercial statistical software. The computer output can be further utilized to perform model selection with Schwarz criterion. Simulation studies are conducted to evaluate the performance under each model. Data of the myopia intervention trial are reanalysed with these models for illustration. The results indicate that atropine is more effective in reducing the progression rate, the rates are homogeneous across subjects, and, among the suggested models, the one with independent random effects of two eyes fits best. We conclude that model selection is a crucial step before making inference with estimates; otherwise the correlation may be attributed incorrectly to a different mechanism. The same conclusion applies to other variance components as well.

Analysis of Variance↗
PubMed2005

Estimation of age-specific sensitivity and sojourn time in breast cancer screening studies.

This study investigates statistical approaches to quantitatively describing the age effect on screening sensitivity and sojourn time distribution in breast cancer screening studies. Such an investigation is directly motivated by the need to understand the inherent relationships between age and these important quantities. We incorporate the age effect through generalized linear models under a progressive disease modelling framework and obtain the corresponding parameter estimators using the maximum likelihood method. Among a set of potential models, we use Akeike's information criterion and likelihood ratio test in model selection and inferences. Extensive simulation studies show that the estimators have reasonable accuracy and the model selection criterion works well. The proposed methods are illustrated using data from two large breast cancer screening trials. The results show that the screening sensitivity increases with age at screening examinations based on these two trials.

Adult↗
PubMed2007

Comparison of multivariate calibration models for glucose, urea, and lactate from near-infrared and Raman spectra.

Partial least-squares (PLS) calibration models have been generated from a series of near-infrared (near-IR) and Raman spectra acquired separately from sixty different mixed solutions of glucose, lactate, and urea in aqueous phosphate buffer. Independent PLS models were prepared and compared for glucose, lactate, and urea. Near-IR and Raman spectral features differed substantially for these solutes, with Raman spectra enabling greater distinction with less spectral overlap than features in the near-IR spectra. Despite this, PLS models derived from near-IR spectra outperformed those from Raman spectra. Standard errors of prediction were 0.24, 0.11, and 0.14 mmol L(-1) for glucose, lactate, and urea, respectively, from near-IR spectra and 0.40, 0.42, and 0.36 mmol L(-1) for glucose, lactate, and urea, respectively, from Raman spectra. Differences between instrumental signal-to-noise ratios were responsible for the better performance of the near-IR models. The chemical basis of model selectivity was examined for each model by using a pure component selectivity analysis combined with analysis of the net analyte signal for each solute. This selectivity analysis showed that models based on either near-IR or Raman spectra had excellent selectivity for the targeted analyte. The net analyte signal analysis also revealed that analytical sensitivity was higher for the models generated from near-IR spectra. This is consistent with the lower standard errors of prediction.

Calibration↗
PubMed2003

Analysis of multilocus models of association.

It is increasingly recognized that multiple genetic variants, within the same or different genes, combine to affect liability for many common diseases. Indeed, the variants may interact among themselves and with environmental factors. Thus realistic genetic/statistical models can include an extremely large number of parameters, and it is by no means obvious how to find the variants contributing to liability. For models of multiple candidate genes and their interactions, we prove that statistical inference can be based on controlling the false discovery rate (FDR), which is defined as the expected number of false rejections divided by the number of rejections. Controlling the FDR automatically controls the overall error rate in the special case that all the null hypotheses are true. So do more standard methods such as Bonferroni correction. However, when some null hypotheses are false, the goals of Bonferroni and FDR differ, and FDR will have better power. Model selection procedures, such as forward stepwise regression, are often used to choose important predictors for complex models. By analysis of simulations of such models, we compare a computationally efficient form of forward stepwise regression against the FDR methods. We show that model selection includes numerous genetic variants having no impact on the trait, whereas FDR maintains a false-positive rate very close to the nominal rate. With good control over false positives and better power than Bonferroni, the FDR-based methods we introduce present a viable means of evaluating complex, multivariate genetic models. Naturally, as for any method seeking to explore complex genetic models, the power of the methods is limited by sample size and model complexity.

Chromosome Mapping↗
PubMed2001

Methods for conducting sensitivity analysis of trials with potentially nonignorable competing causes of censoring.

We consider inference for the treatment-arm mean difference of an outcome that would have been measured at the end of a randomized follow-up study if, during the course of the study, patients had not initiated a nonrandomized therapy or dropped out. We argue that the treatment-arm mean difference is not identified unless unverifiable assumptions are made. We describe identifying assumptions that are tantamount to postulating relationships between the components of a pattern-mixture model but that can also be interpreted as imposing restrictions on the cause-specific censoring probabilities of a selection model. We then argue that, although sufficient for identification, these assumptions are insufficient for inference due to the curse of dimensionality. We propose reducing dimensionality by specifying semiparametric cause-specific selection models. These models are useful for conducting a sensitivity analysis to examine how inference for the treatment-arm mean difference changes as one varies the magnitude of the cause-specific selection bias over a plausible range. We provide methodology for conducting such sensitivity analysis and illustrate our methods with an analysis of data from the AIDS Clinical Trial Group (ACTG) study 002.

Acquired Immunodeficiency Syndrome↗
PubMed1984

Some pitfalls in selecting descriptive pharmacokinetic models.

Some pitfalls in selecting pharmacokinetic models are enumerated. To calculate the pharmacokinetic parameters of a drug that exhibits a biphasic convex plasma concentration-time curve, a two-compartment model does not automatically have to be applied. When only the parent drug in plasma is considered, a two-compartment model seems to be most appropriate. However, when the kinetic behavior of the metabolite has to be taken into account, and when a metabolic equilibrium underlies the metabolic elimination, the two-compartment model may not be appropriate. Also, when calculating the kinetic parameters of a drug with a concave biphasic plasma concentration-time curve, a capacity-limited metabolic conversion is not the automatic explanation for this observation. Limitations in renal excretion and bioavailability may be the reasons for this behavior. Convex and concave biphasic plasma concentration-time curves are illustrated, using sulfonamides as test compounds.

Crystallization↗
PubMed1987

Propagating depolarization in anisotropic human and canine cardiac muscle: apparent directional differences in membrane capacitance. A simplified model for selective directional effects of modifying the sodium conductance on Vmax, tau foot, and the propagation safety factor.

As yet there is no model or simulation that accounts for the anisotropic difference in the shape of the upstroke and safety factor of propagating cardiac action potentials: fast upstrokes occur with slow transverse propagation and slow upstrokes occur with fast longitudinal propagation. The purpose of this paper is to demonstrate, however, that a simplified cable model based on directional differences in the effective membrane capacitance predicts in detail the experimentally measured directionally dependent behavior of the upstroke in response to modification of the sodium conductance. Quinidine and lidocaine produced greater relative decreases in Vmax and conduction velocity with longitudinal propagation than with transverse propagation, as predicted on the basis that the shape differences should produce an anisotropic distribution in the membrane uptake of sodium channel binding drugs. The simulation predictions of the effects of positive shifts of the take-off potential due to premature action potentials were also confirmed experimentally: there was a greater relative decrease in conduction velocity, Vmax, and Vamp with a greater increase in tau foot during longitudinal propagation than with transverse propagation. The major anisotropic differences in shape occurred when the take-off potential approached the least negative value that produced a propagated response. The extensive experimental verification of the results of a simplified model based on directional differences of effective membrane capacitance, combined with directional differences in effective axial resistivity, provides an initial quantitative basis for the anisotropic behavior of propagating depolarization in response to modification of the sodium conductance in cardiac muscle.

Action Potentials↗