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PubMedDate not supplied

A milestone in ribosomal crystallography: the construction of preliminary electron density maps at intermediate resolution.

Preliminary electron density maps of the large and the small ribosomal particles from halophilic and thermophilic sources, phased by the isomorphous replacement method, have been constructed at intermediate resolution. These maps contain features comparable in size with what is expected for the corresponding particles, and their packing arrangements are in accord with the schemes obtained by ab-initio procedures as well as with the motifs observed in thin sections of the crystals by electron microscopy. To phase higher resolution data, procedures are being developed for derivatization by specific labeling of the ribosomal particles at selected locations with rather small and dense clusters. Potential binding sites are being inserted either by site directed mutagenesis or by chemical modifications to facilitate cluster binding on the surface of the halophilic large and the thermophilic small ribosomal particles, which yield the crystals diffracting to highest resolution (2.9 and 7.3 A (1 A = 0.1 nm), respectively). For this purpose, the surface of these ribosomal particles is being characterized and procedures are being developed for quantitative detachment of selected ribosomal proteins and for their incorporation into core particles. The genes of these proteins are being cloned, sequenced, mutated to introduce reactive side groups, mainly cysteines, and overexpressed. In parallel, two in situ small and stable complexes were isolated from the halophilic ribosome. Procedures for their crystal production in large quantities are currently being developed. Models, reconstructed at low resolution from crystalline arrays of ribosomes and their large subunits, are being used for initial low-resolution phasing of the X-ray amplitudes. The interpretation of these models stimulated the design and the crystallization of complexes mimicking defined functional states of a higher quality than those obtained for isolated ribosomes. These models also inspired modelling experiments according to results of functional studies, performed elsewhere, focusing on the progression of nascent proteins.

Base Sequence↗
PubMedDate not supplied

Effect of apolipoprotein E variants on plasma lipids and apolipoproteins in the Orang Asli ('aborigines') of Malaysia.

Members of the Semai group of Orang Asli ('aborigines') in peninsular Malaysia were examined for apolipoprotein E (apo E) variants in relation to plasma total cholesterol (TC), high density lipoprotein cholesterol, low density lipoprotein cholesterol (LDLC), triglycerides (TG), apolipoprotein AI and apolipoprotein B (apo B). The e2 and e4 alleles were found to be higher than in most other groups as reported. The sample as a whole was normotriglyceridaemic (mean plasma TG, 1.5 mmol/l) and very markedly hypocholesterolaemic (mean plasma TC 1.7 mmol/l). The distribution of apo E variants was not related to any of the plasma lipids or apolipoprotein fractions using results from all subjects, but if a distinctly hypertriglyceridaemic sub-section was omitted (TG > 1.7 mmol/l) then apo E variants were determinants of plasma TC, LDLC, and apo B concentrations, the lower values of these being associated with the 2-2 and 2-3 genotypes, and the higher with 3-4, and 4-4.

Alleles↗
PubMed2002

Automated signal generation in prescription-event monitoring.

Signal generation is a method of highlighting potential safety issues in a drug that then need to be investigated further. Previously automated signal generation has mainly been applied to spontaneous reporting systems. The Drug Safety Research Unit (DSRU) performs observational postmarketing studies on selected newly marketed medicines in England using a method known as prescription-event monitoring (PEM). The DSRU has investigated automated procedures for the generation of signals using the event data from PEM studies. Proportional reporting ratios (PRRs) and incidence rate ratios (IRRs) were studied as possible tools for signal generation in PEM data. The PEM database contains 78 completed studies of drugs prescribed in primary care from a variety of therapeutic classes. Retrospective studies were carried out to identify the implications of changing the comparator group of drugs, along with analysing the results at different levels in the DSRU's hierarchical dictionary and performing signal generation after 30 and 180 days of observation since starting the drug. Automated signal generation is a useful hypothesis generating method that is likely to prove to be useful both in clinical trials and postmarketing studies. PRRs are simple to apply and do not require a denominator. IRRs take into account the time subjects were exposed to the drug prior to the event of interest, and offers a useful, and more in depth look into the data. However, with both methods it is important to perform signal generation at multiple levels in the dictionary and with careful selection of the comparator group.

Adverse Drug Reaction Reporting Systems↗
PubMed2004

[A review of statistical analysis methods in measurement data].

Enumeration data is consisted of categorical variable. It is obtained by counting the frequency of the inhomogeneous data. In clinical research, the collected data cover quite of categorical variables. Composed of those categorical variables, the enumeration data had to be correspondingly analyzed with special statistical methods on the ground of their design methods. The statistical methods of measurement data include descriptive statistics and inferential statistics. Descriptive statistics is mainly used to measure the relative number such as rate, proportion and ratio. Inferential statistics is mainly employed to estimate the confidence limit such as estimating the 95% confidence interval of rate and to have the hypothesis testing in the example of having chi-square test etc. By highlighting the specific statistical methods of enumeration data, this review intends to help the clinicians and researchers select correct statistical methods in accordance with enumeration data.

Data Interpretation, Statistical↗
PubMed1994

Application of 3-dimensional homology modeling of cytochrome P450 2B1 for interpretation of site-directed mutagenesis results.

Three-dimensional structures of cytochrome P450 2B1 were modeled based on the crystallographic structure of P450cam. The effect of the alignment, loop choice, and minimization with or without water was assessed. Although final models were similar in overall structure, the identity of active site residues depended upon the alignment. An example is Phe-206, which may or may not form part of the active site. The choice of the loop conformation had a lesser effect, while including water in the final minimization step was essential for preserving the shape and size of the active site. The best model (model 2) was in good agreement with the data from site-directed mutagenesis studies, and correctly predicted the effect of substitutions at 9 out of 10 amino acid positions. Thus, residues important for P450 2B1 activity, such as Ile-114, Phe-206, Ile-290, Thr-302, Val-363, and Gly-478, constitute part of the active site and are able to interact with the substrate androstenedione through hydrophobic interactions. On the other hand, Ser-303, Ser-360 and Lys-473 are far from the active site and/or cannot interact with the substrate, in agreement with experimental data. The model indicates other residues likely to be important for enzyme function, such as Tyr-111, Leu-209, Ile-477, and Ile-480, which can be tested experimentally. The substrate may assume numerous binding orientations consistent with observed patterns of hydroxylation at C15 and C16. The replacement in the model of certain amino acid residues to mimic residue substitutions from site-directed mutagenesis studies and docking of the substrate into the modified active site allowed a plausible explanation for alterations in regio- and stereospecificities of some mutants of P450 2B1, such as Gly-478-->Ala or Val-363-->Ala.

Amino Acid Sequence↗
PubMed2006

Analysis of the stochastic variation in LTQ single scan mass spectra.

A better understanding of the scan-to-scan signal intensity variation can lead to more sophisticated algorithms for database searching and de novo peptide sequencing using single scan mass spectra. In this study, we systematically studied the variation in relative intensity of m/z values in the single scan product ion mass spectra (MS2) derived from five representative precursor ions (MS1) collected using an LTQ linear ion trap under constant flow direct infusion conditions with peptide concentrations held constant. We applied a matching algorithm based on a pair hidden Markov model to align the peaks from each scan belonging to the same m/z value prior to assessing the signal intensity variation. The most significant single contributor to scan-to-scan signal intensity variation for high abundance ions was centroider error. Our study also showed that the variation in signal intensity is higher than what would be expected if the ion statistics derived from the dual geometry electron multiplier detector followed a Poisson distribution.

Algorithms↗
PubMed2004

Can improved software facilitate the wider use of ambulatory blood pressure measurement in clinical practice?

BACKGROUND: 24-h ambulatory blood pressure measurement (ABPM) is now recognized as being indispensable in the diagnosis and management of hypertension. The technique must, therefore, be made available in primary care, but in doing so it must be recognized that unfamiliarity with the technique may lead to misinterpretation of data. OBJECTIVE: To facilitate the wider application of ABPM, especially in primary care, we examined the features that would facilitate the development of a standardized user-friendly software program for the presentation, analysis and interpretation of data. METHODS AND RESULTS: The following features were considered essential to any software program for ABPM: standardized plots of 24-h profiles; computer interpretation of ABPM data and patterns; a user-friendly one-page report, flexible statistical analysis, and the facility to group data and to export data for audit and research analysis. The dabl ABPM program incorporating these features was introduced into the Blood Pressure Unit, Beaumont Hospital in 2000 and has been used in over 15 000 ABPM recordings. The program is now being used widely in general practice and specialized centres. CONCLUSIONS: It is feasible to design a software program to provide a standardized plotting format for ABPM, a basic analysis of data for day-to-day clinical work, or elaborate analyses for research, and an interpretative report to assist diagnosis and to provide an educational process for doctors and nurses not familiar with the technique.

Blood Pressure Monitoring, Ambulatory↗
PubMed1996

An exact McNemar test for paired binary Markov chains.

A straightforward extension of the McNemar test for paired binary data yields an exact test for the equality of the limiting marginal distributions for bivariate binary Markov chains. The exact distribution of the test statistics under the null hypothesis of equal marginals depends on the classical cell occupancy statistics for the Bose-Einstein model. Exact p-values are computed for the one-sided test, and the mean and variance of the test statistic are found. The power of the Markov-McNemar test is found to be close to the power of the classical McNemar test for independent paired observations when the independence assumption holds. The method is applied to the comparison of ribosomal DNA sequences.

Animals↗
PubMed1993

The analysis and interpretation of method comparison studies in rehabilitation research.

Rehabilitation researchers are frequently interested in comparing the results of two tests that measure the same function. There are practical as well as financial advantages to having more than one method of assessing a particular component of function. Investigations examining the results of two tests are referred to as method comparison studies and commonly analyzed using the Pearson product-moment correlation coefficient (r). Several researchers have argued that the Pearson r is a measure of linear association (co-variation) between variables and does not provide accurate estimates of direct agreement. We compared several commonly used quantitative methods to establish agreement and have demonstrated that the Pearson r is not appropriate for use in studies where the purpose is to determine whether two instruments are interchangeable. An alternative to the Pearson r for analyzing data from method comparison studies is presented. The new procedure, referred to as the limits of agreement method, is easy to compute and emphasizes the clinical comparability of two instruments (or raters) instead of focusing solely on the statistical relationship.

Data Interpretation, Statistical↗
PubMed2004

[The importance of the sample design effect].

INTRODUCTION: Sample selection through a complex design influences the subsequent statistical analysis. MATERIAL AND METHOD: The different means of sample selection may result in bias and greater variance of estimators; simple randomized sampling is the reference design. Diverse examples are provided, illustrating how the various sampling strategies can result in bias and increase variance. RESULTS: The inclusion of different weighting techniques reduces bias. Evaluation of the effect of design enables measurement of the degree of variance distortion due to the sampling design used and therefore provides a direct evaluation of the alteration in the confidence intervals estimated when the sampling design deviates from simple randomized sampling. CONCLUSIONS: We recommend measurement of the effect of the design on analysis of the data obtained by sampling and inclusion of weighting techniques in statistical analyses.

Data Collection↗
PubMed2005

SeqState: primer design and sequence statistics for phylogenetic DNA datasets.

Choosing and designing primers based on available DNA sequence data and statistical contrasting of domains or structural features is a common routine among molecular biologists. Currently available, free software tools were found to lack desirable features related to these tasks. This was the motivation for developing a new program, SeqState. SeqState locates regions that remain to be sequenced in phylogenetic DNA datasets, evaluates user-provided primers and selects primers best suited to fill gaps in the sequences. If the primers provided by the user are unsuitable, new primers are designed. Primers can be loaded from a primer database, be supplied as part of the alignment or be entered manually. The position of internal primers is automatically localised in the loaded data file. Primers can be edited, and changes and new primers can be saved to the database. Primer sheets allow the user to view internal dimers, complements to a second primer, mismatches to all loaded sequences, and other primer characteristics. Calculation of various sequence statistics can be requested for the whole dataset or parts thereof (character sets), with standard errors estimated by bootstrapping. Insertion-deletion events can be evaluated statistically and encoded for subsequent phylogenetic analysis according to several published coding principles.

Algorithms↗
PubMed1999

Statistical inference by confidence intervals: issues of interpretation and utilization.

This article examines the role of the confidence interval (CI) in statistical inference and its advantages over conventional hypothesis testing, particularly when data are applied in the context of clinical practice. A CI provides a range of population values with which a sample statistic is consistent at a given level of confidence (usually 95%). Conventional hypothesis testing serves to either reject or retain a null hypothesis. A CI, while also functioning as a hypothesis test, provides additional information on the variability of an observed sample statistic (ie, its precision) and on its probable relationship to the value of this statistic in the population from which the sample was drawn (ie, its accuracy). Thus, the CI focuses attention on the magnitude and the probability of a treatment or other effect. It thereby assists in determining the clinical usefulness and importance of, as well as the statistical significance of, findings. The CI is appropriate for both parametric and nonparametric analyses and for both individual studies and aggregated data in meta-analyses. It is recommended that, when inferential statistical analysis is performed, CIs should accompany point estimates and conventional hypothesis tests wherever possible.

Bias↗
PubMed2004

Distribution-based criteria for change in health-related quality of life in Parkinson's disease.

BACKGROUND AND OBJECTIVE: To be useful, results from health-related quality of life (HRQoL) measures must be interpretable. The objective of this article is to examine statistical (distributional) approaches to interpretability. The standard error of measurement (SEM) and the standard error of the difference (S(diff)) are used in data on individuals with Parkinson's disease to calculate the minimum change scores required to be statistically meaningful for each dimension of an instrument to assess HRQoL in Parkinson's disease, the PDQ-39. METHODS: Data was collected from both a community and a clinic study; in both studies the PDQ-39 was administered at baseline and follow-up. RESULTS: The patterns of SEMs and S(diff)s were similar both across time periods and between samples, for all dimensions except Social Support. CONCLUSIONS: The results suggest that, for example, six points change on a 0-100 transformed scoring of the Mobility dimension may be considered on distributional grounds a minimum meaningful change. The demonstrated consistency across occasions and types of sample of SEMs and S(diff) for the majority of the dimensions of the PDQ-39, is evidence of the theoretically claimed advantage of this measure of sample independence, and supports use of this distributional approach to minimum meaningful change.

Adult↗