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PubMed1992

An extended version of a novel method for the estimation of partition coefficients.

Using the semi-empirical AM1 method, 302 compounds have been studied and equilibrium properties calculated. Functions based on linear combinations of subsets of calculated properties have been fit to the 1-octanol-water partition coefficients. The best such semi-empirical approach function has 18 parameters, has a standard deviation of 0.306, and seems to describe the partition coefficients of the 302 compounds. The predictive power of the function was tested and found to be good. Since this new version is based on a much larger number of, and structurally more varied, compounds and uses an improved, new function, we expect it to be a very useful method to predict partition properties of a wide variety of compounds.

Chemistry, Physical↗
PubMed2007

Variance of estimated DTI-derived parameters via first-order perturbation methods.

In typical applications of diffusion tensor imaging (DTI), DT-derived quantities are used to make a diagnostic, therapeutic, or scientific determination. In such cases it is essential to characterize the variability of these tensor-derived quantities. Parametric and empirical methods have been proposed to estimate the variance of the estimated DT, and quantities derived from it. However, the former method cannot be generalized since a parametric distribution cannot be found for all DT-derived quantities. Although powerful empirical methods, such as the bootstrap, are available, they require oversampling of the diffusion-weighted imaging (DWI) data. Statistical perturbation methods represent a hybrid between parametric and empirical approaches, and can overcome the primary limitations of both methods. In this study we used a first-order perturbation method to obtain analytic expressions for the variance of DT-derived quantities, such as the trace, fractional anisotropy (FA), eigenvalues, and eigenvectors, for a given experimental design. We performed Monte Carlo (MC) simulations of DTI experiments to test and validate these formulae, and to determine their range of applicability for different experimental design parameters, including the signal-to-noise ratio (SNR), diffusion gradient sampling scheme, and number of DWI acquisitions. This information should be useful for designing DTI studies and assessing the quality of inferences drawn from them.

Algorithms↗
PubMed2002

Potential of mean force for protein-protein interaction studies.

Calculating protein-protein interaction energies is crucial for understanding protein-protein associations. On the basis of the methodology of mean-field potential, we have developed an empirical approach to estimate binding free energy for protein-protein interactions. This knowledge-based approach has been used to derive distance-dependent free energies of protein complexes from a nonredundant training set in the Protein Data Bank (PDB), with a careful treatment of homology. We calculate atom pair potentials for 16 pair interactions, which can reflect the importance of hydrophobic interactions and specific hydrogen-bonding interactions. The derived potentials for hydrogen-bonding interactions show a valley of favorable interactions at a distance of approximately 3 A, corresponding to that of an established hydrogen bond. For the test set of 28 protein complexes, the calculated energies have a correlation coefficient of 0.75 compared with experimental binding free energies. The performance of the method in ranking the binding energies of different protein-protein complexes shows that the energy estimation can be applied to value binding free energies for protein-protein associations.

Databases, Protein↗
PubMed1991

Estimation of the design effect in community intervention studies.

This paper considers the estimation of the variance of a mortality rate in community intervention studies with little or no replication of intervention regimens. Our approach in estimation of this cluster sampling variance is to determine the variance for simple random sampling and multiply it by a design effect which we calculate with use of information obtained from other sources. When the county is the unit of randomization and the outcome is mortality, we calculate the design effect as the ratio of the age adjusted mortality rates for single stage cluster sampling relative to simple random sampling; we use information from all counties in a state in the calculations. We apply this approach empirically for breast cancer mortality. We found that these design effects were dependent on length of time for accumulation of deaths (1.1 for one year up to 3.5 for eight years) and were quite consistent for the three states and nine years considered in the investigation. We present a model that accounts for the time dependence of the design effect and we show it provides a good representation of the observed relationship.

Adult↗
PubMed2001

Correlation coefficient estimation involving a left censored laboratory assay variable.

When assessing a correlation between two exposure or biological marker variables, one sometimes encounters the problem of indeterminate values for one of the variables due to an assay detection limit. In this event, investigators often report correlation coefficients computed after removing the pairs involving non-detectable values, or after substituting some small constant for those values. These ad hoc practices can lead to bias in both point and confidence interval estimates of the true correlation coefficient. To address this issue, we consider two parametric techniques for estimating the correlation in the presence of left censoring for one of the variables. The first is a maximum likelihood approach, and the second is an adaptation of multiple imputation motivated primarily by potential benefits in confidence interval coverage. Both of the estimators studied reduce to the standard Pearson's correlation coefficient in the event of no censoring, and hence are valid in cases where this measure would be appropriate for the complete data. We assess these approaches empirically and contrast them with ad hoc methods for estimating the correlation between cervicovaginal human immunodeficiency virus (HIV) viral load measurements and CD4+ lymphocyte counts from HIV positive women enrolled in a clinical trial conducted in Bangkok, Thailand.

Anti-HIV Agents↗
PubMed2002

Model-based estimation of vaccine effects from community vaccine trials.

Community vaccine trials are becoming increasingly important to assess both the direct and indirect community level effects of vaccination. In this paper, we present statistical methods to analyse such trials, using a design with several matched pairs of communities. The communities are matched on similarities in infection transmission as reflected through the basic reproduction number. Two methods of analysis are presented and compared. The first is simple empirical estimation of vaccine effects. Summary measures of these effects are constructed by reciprocal variance weighted averages across the community pairs. The second is likelihood-based where we derive a mixed effects epidemic model. This model takes the intercommunity variability into account through a random effect on the basic reproduction number. With this model, we derive a distribution-free estimator for the variance of the random effect. We use simulated epidemics to explore the performance of the two estimation methods for different numbers of community pairs and different levels of inter-pair variability. Both methods provide acceptable estimates in terms of bias and precision under reasonable conditions. Although the empirical approach involves fewer assumptions than the model-based approach, the resulting vaccine effectiveness estimates are only applicable to the vaccination fraction tested in the trial. In contrast, the model-based approach can be used to predict the vaccine effectiveness at vaccination fractions other than those used in the trial. Thus, it can be used as a public health policy tool for predicting the community level effects of vaccination. We demonstrate such use by predicting total vaccine effectiveness for the whole range of vaccination fractions.

Computer Simulation↗
PubMed2002

Copper sorption on a straw lignin: experiments and EPR characterization.

Spectroscopic and physicochemical data, X-ray photoelectron spectroscopy (XPS), solid-state (13)C cross-polarization magic-angle-spinning NMR, GC/MS, specific surface area, site density, and surface acidity constants have been recorded or determined for a ligno-cellulosic substrate (LS) extracted from straw. Its copper(II)-bound ability has also been studied. The LS solid that exhibits two types of binding sites, carboxylic and phenolic groups, has a great affinity for copper(II), with a maximum of adsorption at around 4 mg g(-1) as early as the pH reaches 6. The structural characterization of the Cu(II) surface complexes has been investigated using EPR spectroscopy. The CuO(4) chromophore of the inner-sphere surface complexes is a slightly distorted square. A surface oxidation occurred simultaneously, which leads to semiquinonic radicals. Furthermore, our empirical approach, which used a correlation between thermodynamics data and EPR parameters, has led to a surface complexation constant log beta equal to 12.6. This indicates that copper(II) surface complexes are relatively stable.

Journal Article↗
PubMed2000

Protein crystallization by design: chymotrypsinogen without precipitants.

Protein crystals are usually obtained by an empirical approach based on extensive screening to identify suitable crystallization conditions. In contrast, we have used a systematic predictive procedure to produce data-quality crystals of bovine chymotrypsinogen A and used them to obtain a refined X-ray structure to 3 A resolution. Measurements of the osmotic second virial coefficient of chymotrypsinogen solutions were used to identify suitable solvent conditions, following which crystals were grown for approximately 30 hours by ultracentrifugal crystallization, without the use of any precipitants. Existing structures of chymotrypsinogen were obtained in solutions including 10-30 % ethanol, whereas simple buffered NaCl solutions were used here. The protein crystallized in the tetragonal space group P4(1)2(1)2, with one molecule per asymmetric unit. The quality of the refined map was very high throughout, with the main-chain atoms of all but four residues clearly defined and with nearly all side-chains also defined. Although only minor differences are seen compared to the structures previously reported, they indicate the possibility of structural changes due to the crystallization conditions used in those studies. Our results show that more systematic crystallization of proteins is possible, and that the procedure can expand the range of conditions under which crystals can be grown successfully and can make new crystal forms available.

Animals↗
PubMed1999

Comparison of filtering methods for fMRI datasets.

When studying complex cognitive tasks using functional magnetic resonance imaging (fMRI) one often encounters weak signal responses. These weak responses are corrupted by noise and artifacts of various sources. Preprocessing of the raw data before the application of test statistics helps to extract the signal and can vastly improve signal detection. Artifact sources and algorithms to handle them are discussed. In an empirical approach targeted to yield an optimal recovery of the hemodynamic response, we implemented a test bed for baseline correction and noise-filtering methods. A known signal is modulated onto foreground patches obtained from event-related fMRI experiments. Quantitative performance measures are defined to optimize the characteristics of a given filter and to compare their results. Marked improvements in the sensitivity and selectivity are achieved by optimized filtering. Examples using real data underline the usefulness of this preprocessing sequence.

Algorithms↗
PubMed1988

Nonresponsiveness to antianginal therapy--a frequent problem?

Nonresponsiveness to anginal treatment varies greatly and may be due to either the pathophysiology of the patients or the special pharmacology of different antianginal drugs. Therefore, individualized therapy, taking all aspects of patient and drug into account to improve responsiveness, seems desirable. Patients may vary--thus influencing the outcome of antianginal therapy--with respect to the severity of the disease, vasospastic components, and the pattern of organic vessel involvement. Drugs differ with respect to the ease of dose-finding, tolerance, the extent of spasmolytic activity, side effects, and paradoxical effects. In no patient with coronary artery disease is the outcome to treatment predictable, even if a full diagnostic evaluation of the patient has been performed. For example, the individual relevance of angiographically documented vasospastic components in patients with underlying organic multivessel disease can hardly be predicted, and therefore the appropriate choice of an antianginal drug is difficult. In addition, a full invasive evaluation of all coronary patients, only to find arguments for the optimal drug therapy, is not feasible. Therefore, the empiric approach is recommended for daily routine. Drugs are preferred that usually provide a high response rate and the smallest cause for concern.

Angina Pectoris↗
PubMed1992

A comparison of five methods for estimating general glaucomatous visual field depression.

The separation of local and diffuse visual field loss is important for evaluating the nature and extent of glaucomatous visual field damage. Here, five automated methods for estimating diffuse loss in glaucomatous visual fields (as measured with the Octopus G1 program) are compared. Four are taken from the published literature, and one is introduced in this investigation. It is shown that the new index (here called diffuse loss) provides the best agreement with a value determined using a more empirical approach.

Glaucoma↗
PubMed1986

The clinical relevance of locally produced carcinoembryonic antigen in cerebrospinal fluid.

Sixteen out of eighteen meningeal carcinomas (89%) secreted carcinoembryonic antigen (CEA) into the cerebrospinal fluid, where it could be quantified separately from the portion originating from the circulating blood. The discrimination of both fractions was performed according to an empirical approach analogous to the immunoglobulins. Only 47% of the intraparenchymal carcinomas released CEA into the CSF compartment and it is possible that the extra-cellular space of these tumour sites does not communicate with the free CSF space. Extradural metastases may cause an impairment of the blood-CSF barrier via restrictions of the CSF fluid turnover, but the dura remains impermeable for the tumour marker. Seven out of 54 primary brain tumours (13%) released carcinoembryonic antigen into the cerebrospinal fluid.

Blood-Brain Barrier↗
PubMed1980

Concentration profile for the dissolution of drug tablets undergoing simultaneous degradation.

An empirical approach to the concentration-time history of a dissolving drug has resulted in a cube-root equation in which the characteristic constant of the equation embodies the important physical variables of the system. This expression has been used to study the dissolution of a drug that degrades simultaneously in the test solution. An alternative representation of the dissolution process is first-order kinetics. These two approaches are compared by fitting the experimental data of the dissolution of digoxin and melphalan tablets in various media, and a new method for the proper analysis of data for the dissolution of tablets that simultaneously degrade in the test solution is presented.

Chemistry, Pharmaceutical↗
PubMed1995

Vaccination today and tomorrow.

The vaccines against infectious diseases in use today are, with few exceptions, prepared from the causal agents themselves, either by inactivating them with a chemical such as formaldehyde or by attenuating them so that they grow and thus evoke an immune response in the natural host but cause no disease. These empirical approaches have produced many highly successful vaccines. Increasing knowledge at the molecular level of the agents and of the immune response to protein antigent is now providing us with the opportunity to design vaccines that will elicit protective responses without the need to use the agents themselves. The critical issue is to identify the immune responses that correlate with protection.

Animals↗
PubMed1990

Critical issues in the residential care of people with autism.

There is an ever-growing need to expand both the number and range of residential services for individuals with autism while developing strategies for assuring the quality of these programs. Future program development will be facilitated by an empirical approach to the critical elements that have been identified throughout the articles in this issue.

Autistic Disorder↗
PubMed1990

Benzodiazepine anti-conflict effects in Maudsley reactive (MR/Har) and non-reactive (MNRA/Har) rats.

The Maudsley Reactive (MR/Har) and Non-Reactive (MNRA/Har) rat strains, bred originally by Broadhurst for differences in Open Field Defecation, also differ in their control (i.e., non-drug) behavior in the Conditioned Suppression of Drinking (CSD) conflict procedure, a second "model" behavior for the study of anxiety and/or emotionality in rats. The present studies compared the effects of diazepam and alprazolam on CSD behavior in these two strains of rats. In daily 10-min sessions, water-deprived rats were trained to drink from a tube that was occasionally electrified (0.2-0.5 mA), electrification being signaled by a tone. Both diazepam and alprazolam increased punished responding in a dose-related manner. The per cent increase in punished responding (for diazepam only) was comparable in the two strains; however, both statistical and empirical approaches indicated that the magnitude of the anti-conflict effect of benzodiazepines in MNRA/Har versus MR/Har rats was not related to differences in baseline (i.e., non-drug) punished responding. Based on the absolute change in shocks received, rats of the MNRA/Har strain exhibited a significantly greater anti-conflict effect following diazepam or alprazolam treatment than did rats of the MR/Har strain. These findings further the hypothesis that the behavioral differences exhibited by Maudsley MR/Har and MNRA/Har rat strains may constitute a genetically-based "animal model" for the study of emotionality and/or anxiety.

Alprazolam↗
PubMed1996

Determination of pulmonary mean transit time and cardiac output using a one-dimensional model.

In this work, we show that a one-dimensional model of the blood flow across the lungs can reproduce the evolution of a bolus versus the time. Solving the differential equation governing the bolus concentration in the framework of this model, we determine the solution which fulfills Gaussian initial boundary conditions. An effective parameter related to the ratio of a diffusion coefficient to the square of the mean speed of the flow is defined. The determination of its numerical values following a semi-empirical approach enables us to know accurately the mean transit time and the cardiac output. The results have been compared to other methods, and were found in good agreement. Such an approach could be of interest in all studies where the knowledge of flow--including micro-circulation--is needed.

Analysis of Variance↗