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PubMedDate not supplied

Statistical mechanical treatment of protein conformation. I. Conformational properties of amino acids in proteins.

A statistical mechanical (one-dimensional Ising model) treatment, based on the dominance of short-range interactions, is developed in this series of papers; it is intended as an improvement over empirical prediction schemes for obtaining approximate initial conformations of proteins (to be used to try to deduce the native conformation by subsequent energy minimization). In the present paper, the statistical weights for a two-state model (alpha-helical and other conformations) and for a three-state model (alpha-helical, extended, and other conformations) are evaluated from x-ray data on 16 native proteins. The method for evaluating the statistical weights is presented. Asymmetric alpha-helical nucleation parameters are also evaluated for the 20 naturally occurring amino acids. On the basis of these statistical weights, the conformational properties of the twenty naturally occurring amino acids are discussed. The statistical weights evaluated from x-ray data are also discussed in comparison with experimental results on the helix--coil transition in polyamino acids in solution. The predominant role of short-range interactions, and some possible long-range effects in determining the statistical weights, are discussed in conjunction with the mechanism of protein folding.

Amino Acids↗
PubMed2002

The use of dedicated methodology and statistical reviewers for peer review: a content analysis of comments to authors made by methodology and regular reviewers.

STUDY OBJECTIVES: In 1997, Annals of Emergency Medicine initiated a protocol by which every original research article, in addition to each regular review, was concurrently evaluated by 1 of 2 methodology and statistical reviewers. We characterized and contrasted comments made by the methodology and regular peer reviewers. METHODS: After pilot testing, interrater reliability assessment, and revision, we finalized a 99-item taxonomy of reviewer comments organized in 8 categories. Two authors, uninvolved in the writing of reviews, classified each comment from a random sample of methodology reviews from 1999. For 30 of these reviews (15 for each methodology reviewer), the 2 authors also scored all (range 2 to 5) regular reviews. RESULTS: Sixty-five reviews by methodologist A, 60 by methodologist B, and 68 by regular reviewers were analyzed. Comments by methodologist A most frequently concerned the presentation of results (33% of all comments) and methods (17%). Methodologist B commented most frequently on presentation of results (28%) and statistical methods (16%). Regular reviewers most frequently made non-methodology/statistical comments (45%) and comments on presentation of results (18%). Of note, comments made by methodology and regular reviewers about methods issues were often contradictory. CONCLUSION: The distributions of comments made by the 2 methodology and statistical reviewers were similar, although reviewer A emphasized presentation and reviewer B stressed statistical issues. The regular reviewers (most of whom were unaware that a dedicated methodology and statistical reviewer would be reviewing the article) paid much less attention to methodology issues. The 2 dedicated methodology and statistical reviewers created reviews that were similarly focused and emphasized methodology issues that were distinct from the issues raised by regular reviewers.

Peer Review, Research↗
PubMed2002

Statistical methodology in general psychiatric journals.

Development of psychiatric research methods requires systematic review of their status. This study describes the frequency with which various statistical research designs and methods are reported in general psychiatric journals. All original research articles in four psychiatric journals in 1996 were reviewed: The American Journal of Psychiatry (AJP), The Archives of General Psychiatry (AGP), The British Journal of Psychiatry (BJP) and the Nordic Journal of Psychiatry (NJP). Evaluation included 448 regular articles, which reported original research findings based on systematic collection and statistical analysis of research data. Aspects measured were research design, statistical methodology, description of procedures and presentation of results. Percentage frequencies of reported statistical procedures were compared between the journals. The policy of determining statistical significance was still the most generally used method of conducting research. Compared to earlier reviews, readers of psychiatric reports in 1996 more frequently encountered computer-dependent multivariate techniques. There were differences in the utilization and reporting of statistical procedures among the journals. The authors of psychiatric journals might apply these results in designing their psychiatric research to present intelligible and compact analysis combined with a high quality presentation technique, thus being in line with the policy and presentation of the leading psychiatric journals.

Cross-Sectional Studies↗
PubMed1994

ODS_BOOTSTRAP: assessing the statistical reliability of physical maps by bootstrap resampling.

In the program ODS_BOOTSTRAP we provide a methodology for quickly ordering clones in a genomic library into a physical map and for applying a statistical tool known as the bootstrap to assess the statistical reliability of a clonal ordering. Each clone is assigned a binary fingerprint by one of a variety of experimental approaches to physical mapping. For example, the binary fingerprints might be generated by hybridizing a panel of m probes to a library of n clones. The resulting n x m binary data matrix, X, is input to ODS_BOOTSTRAP, which utilizes the similarity in binary fingerprints of clones to construct a physical map. Under this particular implementation of bootstrap resampling, the m probes (or columns of the data matrix) are sampled randomly with replacement in the computer to generate a new n x m data matrix, X*, from which a second physical map is constructed. The resampling process is repeated 100 or more times to generate 100 or more X* matrices. The resulting 100 or more physical maps are compared with the original physical map based on the original data matrix X by counting how often links in the original physical map reappear. Three confidence statistics are introduced for each link in a physical map. The statistic C1 is defined as the percentage of time two neighboring clones on the original map reappear as neighbors under resampling. The statistic C2 is defined as the percentage of time that two neighboring clones i and j on the original map reappear as neighbors or that a clone with an identical binary fingerprint to clone i reappears as a neighbor to clone j. The statistic C3 is defined as the percentage of time that two neighboring clones on the original map reappear in the same contig under resampling.

Algorithms↗
PubMed1991

Statistical analysis in dBASE-compatible databases.

Database management in clinical and experimental research often requires statistical analysis of the data in addition to the usual functions for storing, organizing, manipulating and reporting. With most database systems, transfer of data to a dedicated statistics package is a relatively simple task. However, many statistics programs lack the powerful features found in database management software. dBASE IV and compatible programs are currently among the most widely used database management programs. d4STAT is a utility program for dBASE, containing a collection of statistical functions and tests for data stored in the dBASE file format. By using d4STAT, statistical calculations may be performed directly on the data stored in the database without having to exit dBASE IV or export data. Record selection and variable transformations are performed in memory, thus obviating the need for creating new variables or data files. The current version of the program contains routines for descriptive statistics, paired and unpaired t-tests, correlation, linear regression, frequency tables, Mann-Whitney U-test, Wilcoxon signed rank test, a time-saving procedure for counting observations according to user specified selection criteria, survival analysis (product limit estimate analysis, log-rank test, and graphics), and normal t and chi-squared distribution functions.

Database Management Systems↗
PubMed2003

Improved statistical power of the multilinear reference tissue approach to the quantification of neuroreceptor ligand binding by regularization.

A multilinear reference tissue approach has been widely used recently for the assessment of neuroreceptor-ligand interactions with positron emission tomography. The authors analyzed this "multilinear method" with respect to its sensitivity to statistical noise, and propose regularization procedures that reduce the effects of statistical noise. Computer simulations and singular value decomposition of its operational equation were used to investigate the sensitivity of the multilinear method to statistical noise. Regularization was performed by truncated singular value decomposition, Tikhonov-Phillips regularization, and by imposing boundary constraints on the rate constants. There was a significant underestimation of distribution volume ratios. Singular value decomposition showed that the bias was caused by statistical noise. The regularization procedures significantly increased the test-retest stability. The bias could be reduced by applying linear constraints on the rate constants based on their normal range. Underestimation of distribution volume ratios by the multilinear method is caused by its sensitivity to statistical noise. Statistical power in the discrimination of different groups of subjects can be significantly improved by regularization procedures without introducing additional bias. Correct distribution volume ratios can be obtained by imposing physiologic constraints on the rate constants.

Brain Chemistry↗
PubMed2004

Prediction of permeability for porous media reconstructed using multiple-point statistics.

To predict multiphase flow through geologically realistic porous media, it is necessary to have a three-dimensional (3D) representation of the pore space. We use multiple-point statistics based on two-dimensional (2D) thin sections as training images to generate geologically realistic 3D pore-space representations. Thin-section images can provide multiple-point statistics, which describe the statistical relation between multiple spatial locations and use the probability of occurrence of particular patterns. Assuming that the medium is isotropic, a 3D image can be generated that preserves typical patterns of the void space seen in the thin sections. The method is tested on Berea sandstone for which a 3D image from micro-CT (Computerized Tomography) scanning is available and shows that the use of multiple-point statistics allows the long-range connectivity of the structure to be preserved, in contrast to two-point statistics methods that tend to underestimate the connectivity. Furthermore, a high-resolution 2D thin-section image of a carbonate reservoir rock is used to reconstruct 3D structures by the proposed method. The permeabilities of the statistical images are computed using the lattice-Boltzmann method (LBM). The results are similar to the measured values, to the permeability directly computed on the micro-CT image for Berea and to predictions using analysis of the 2D images and the effective medium approximation.

Journal Article↗
PubMed2005

Problems in using statistical analysis of replacement and silent mutations in antibody genes for determining antigen-driven affinity selection.

The analysis of molecular signatures of antigen-driven affinity selection of B cells is of immense use in studies on normal and abnormal B cell development. Most of the published literature compares the expected and observed frequencies of replacement (R) and silent (S) mutations in the complementarity-determining regions (CDRs) and the framework regions (FRs) of antibody genes to identify the signature of antigenic selection. The basic assumption of this statistical method is that antigenic selection creates a bias for R mutations in the CDRs and for S mutations in the FRs. However, it has been argued that the differences in intrinsic mutability among different regions of an antibody gene can generate a statistically significant bias even in the absence of any antigenic selection. We have modified the existing statistical method to include the effects of intrinsic mutability of different regions of an antibody gene. We used this method to analyse sequences of several B cell-derived monoclonals against T-dependent antigens, T-independent antigens, clones derived from lymphoma and amyloidogenic clones. Our sequence analysis indicates that even after correcting for the intrinsic mutability of antibody genes, statistical parameters fail to reflect the role of antigen-driven affinity selection in maturation of many clones. We suggest that, contrary to the basic assumption of such statistical methods, selection can act both for and against R mutations in the CDR as well as in the FR regions. In addition we have identified different methodological difficulties in the current uses of such statistical analysis of antibody genes.

Animals↗
PubMed1998

Statistical methodology: IV. Analysis of variance, analysis of covariance, and multivariate analysis of variance.

Medical research frequently involves the statistical comparison of >2 groups, often using data obtained through the application of complex experimental designs. Fortunately, inferential statistical methodologies exist to address these situations. Analysis of variance (ANOVA) in its many forms is used to simultaneously test the equality of all groups in a study. One-way (with 1 independent variable), 2-way (with 2 independent variables), and repeated-measures (patients serve as their own controls) ANOVAs are forms of this technique. Each form has been developed to analyze data from a specific experimental design. Analysis of covariance (ANCOVA) allows the researcher to control for confounding variables that may influence the response of the dependent variable. Finally, multivariate analysis of variance (MANOVA) evaluates the simultaneous responses of multiple dependent variables to > or = 1 independent variable. Whereas ANOVA is the correct alternative to statistically inappropriate multiple t-tests, MANOVA is the correct alternative to statistically inappropriate multiple univariate ANOVA calculations. Use of each of these statistical methods requires an appropriate experimental design and data meeting a number of assumptions. When used properly, each of these methods provides a powerful statistical analysis technique.

Analysis of Variance↗
PubMed1998

Underregistration of neonatal deaths: an empirical study of the accuracy of infantile vital statistics in Taiwan.

STUDY OBJECTIVE: The accuracy of the official statistic on infant deaths in Taiwan has been questioned. This study aimed to survey infant deaths nationwide, to measure associated vital statistics, and compare them with the official statistics to assess accuracy. DESIGN AND PARTICIPANTS: A nationwide survey of all gestational outcomes occurring at > or = 20 weeks' gestation over a three day study period (15-17 May 1989) was conducted to collect data from 23 counties and cities nationwide using a two stage data collection procedure. MAIN RESULTS: The survey derived infant death rate was 9.72 per 1000 live births, which was higher than the reported official statistic of 5.71 per 1000 live births. A more detailed examination of data on infant deaths showed that the estimated neonatal death rate of 6.68 per 1000 live births (95% confidence intervals: 3.33, 11.96 per 1000 live births) was significantly higher than the published official statistic of 1.94 per 1000 live births, while the postneonatal mortality of 3.04 per 1000 live births was comparable to the reported statistic of 3.37 per 1000 live births. CONCLUSIONS: This study empirically documented the underregistration of infant deaths in Taiwan, particularly those occurring during the first 27 days of life.

Data Collection↗
PubMed2004

A survey of statistics in three UK general practice journal.

BACKGROUND: Many medical specialities have reviewed the statistical content of their journals. To our knowledge this has not been done in general practice. Given the main role of a general practitioner as a diagnostician we thought it would be of interest to see whether the statistical methods reported reflect the diagnostic process. METHODS: Hand search of three UK journals of general practice namely the British Medical Journal (general practice section), British Journal of General Practice and Family Practice over a one-year period (1 January to 31 December 2000). RESULTS: A wide variety of statistical techniques were used. The most common methods included t-tests and Chi-squared tests. There were few articles reporting likelihood ratios and other useful diagnostic methods. There was evidence that the journals with the more thorough statistical review process reported a more complex and wider variety of statistical techniques. CONCLUSIONS: The BMJ had a wider range and greater diversity of statistical methods than the other two journals. However, in all three journals there was a dearth of papers reflecting the diagnostic process. Across all three journals there were relatively few papers describing randomised controlled trials thus recognising the difficulty of implementing this design in general practice.

Bibliometrics↗
PubMed2004

Statistical inference and Aristotle's Rhetoric.

Formal logic operates in a closed system where all the information relevant to any conclusion is present, whereas this is not the case when one reasons about events and states of the world. Pollard and Richardson drew attention to the fact that the reasoning behind statistical tests does not lead to logically justifiable conclusions. In this paper statistical inferences are defended not by logic but by the standards of everyday reasoning. Aristotle invented formal logic, but argued that people mostly get at the truth with the aid of enthymemes--incomplete syllogisms which include arguing from examples, analogies and signs. It is proposed that statistical tests work in the same way--in that they are based on examples, invoke the analogy of a model and use the size of the effect under test as a sign that the chance hypothesis is unlikely. Of existing theories of statistical inference only a weak version of Fisher's takes this into account. Aristotle anticipated Fisher by producing an argument of the form that there were too many cases in which an outcome went in a particular direction for that direction to be plausibly attributed to chance. We can therefore conclude that Aristotle would have approved of statistical inference and there is a good reason for calling this form of statistical inference classical.

Bayes Theorem↗
PubMed2006

Statistical description of the free-space propagation of highly aberrated optical beams.

The free-space propagation of initially aberrated optical beams is considered with an emphasis on aero-optical applications. An exact statistical solution of the paraxial wave equation is derived that can be used to obtain statistics of the beam such as beam center, spread, and higher-order statistics as algebraic functions of propagation distance, wavelength, and statistics of the initial wavefront. Correlations between the proposed description and intensity-based statistics, such as the Strehl ratio, are investigated. It is found that the root-mean-square (rms) of the gradient of the wavefront plays an important role in causing coherence degradation and that the rms of the wavefront error is not always an appropriate measure of the degradation. To illustrate the use of this statistical tool, index of refraction data from a numerical simulation of compressible flow over a cylinder are employed to perform an aero-optical analysis.

Journal Article↗
PubMed2006

Statistical epistasis is a generic feature of gene regulatory networks.

Functional dependencies between genes are a defining characteristic of gene networks underlying quantitative traits. However, recent studies show that the proportion of the genetic variation that can be attributed to statistical epistasis varies from almost zero to very high. It is thus of fundamental as well as instrumental importance to better understand whether different functional dependency patterns among polymorphic genes give rise to distinct statistical interaction patterns or not. Here we address this issue by combining a quantitative genetic model approach with genotype-phenotype models capable of translating allelic variation and regulatory principles into phenotypic variation at the level of gene expression. We show that gene regulatory networks with and without feedback motifs can exhibit a wide range of possible statistical genetic architectures with regard to both type of effect explaining phenotypic variance and number of apparent loci underlying the observed phenotypic effect. Although all motifs are capable of harboring significant interactions, positive feedback gives rise to higher amounts and more types of statistical epistasis. The results also suggest that the inclusion of statistical interaction terms in genetic models will increase the chance to detect additional QTL as well as functional dependencies between genetic loci over a broad range of regulatory regimes. This article illustrates how statistical genetic methods can fruitfully be combined with nonlinear systems dynamics to elucidate biological issues beyond reach of each methodology in isolation.

Epistasis, Genetic↗
PubMed2005

Use of statistical procedures in Brazilian and international dental journals.

A descriptive survey was performed in order to assess the statistical content and quality of Brazilian and international dental journals, and compare their evolution throughout the last decades. The authors identified the reporting and accuracy of statistical techniques in 1000 papers published from 1970 to 2000 in seven dental journals: three Brazilian (Brazilian Dental Journal, Revista de Odontologia da Universidade de Sao Paulo and Revista de Odontologia da UNESP) and four international journals (Journal of the American Dental Association, Journal of Dental Research, Caries Research and Journal of Periodontology). Papers were divided into two time periods: from 1970 to 1989, and from 1990 to 2000. A slight increase in the number of articles that presented some form of statistical technique was noticed for Brazilian journals (from 61.0 to 66.7%), whereas for international journals, a significant increase was observed (65.8 to 92.6%). In addition, a decrease in the number of statistical errors was verified. The most commonly used statistical tests as well as the most frequent errors found in dental journals were assessed. Hopefully, this investigation will encourage dental educators to better plan the teaching of biostatistics, and to improve the statistical quality of submitted manuscripts.

Bibliometrics↗
PubMed2004

Likelihood ratios: a simple and flexible statistic for empirical psychologists.

Empirical studies in psychology typically employ null hypothesis significance testing to draw statistical inferences. We propose that likelihood ratios are a more straightforward alternative to this approach. Likelihood ratios provide a measure of the fit of two competing models; the statistic represents a direct comparison of the relative likelihood of the data, given the best fit of the two models. Likelihood ratios offer an intuitive, easily interpretable statistic that allows the researcher great flexibility in framing empirical arguments. In support of this position, we report the results of a survey of empirical articles in psychology, in which the common uses of statistics by empirical psychologists is examined. From the results of this survey, we show that likelihood ratios are able to serve all the important statistical needs of researchers in empirical psychology in a format that is more straightforward and easier to interpret than traditional inferential statistics.

Empirical Research↗
PubMed2003

[Estimation of glandular content rate and statistical analysis of the influence of age group and compressed breast thickness on the estimated value].

Because the glandular content rate is an important factor in evaluating breast cancer detection and average glandular dose, it is important in mammography research to estimate and analyze this rate. The purpose of this study was to obtain a formula for statistical estimation of the glandular content rate, to clarify statistically the influence of age group and compressed breast thickness (CBT) on estimating the glandular content rate, and to show statistically the general relation between glandular content rate and the factors of age and CBT. The subjects were 740 Japanese women aged 20-91 years (mean+/-SD: 48.3+/-12.8 years) who had undergone mammography. In our study, the glandular content rate was statistically estimated from age group, mAs-value, and CBT when subjects underwent mammography, from a phantom simulation, and from MR images of the breast. In addition, multivariate analysis was carried to examine statistically the influence of age group and CBT on glandular content rate. The mean glandular content rate as estimated by age group was as follows: 35.6% for those in their 20s, 33.4% in the 30s, 27.5% in the 40s, 23.8% in the 50s, and 21.8% in those 60 and over. The rate for the subjects as a whole was 27.1%. This study indicated that overestimation occurred if the estimated value of the glandular content rate was not corrected in the 3D-measurement by MRI. In addition, this study showed that the statistical influence on glandular content rate was significantly larger for CBT than age.

Adult↗
PubMed2000

Report and summary of the major conclusions from statistics in genotoxicity testing working group from the International Workshop on Genotoxicity Test Procedures (IWGTP), March 1999.

A working group of five statisticians experienced in the use of statistical methods in mutagenicity reviewed aspects of the statistical analysis of genotoxicity test procedures. Issues discussed included methods for integrating biological importance and statistical significance, the relationship of the experimental unit to the experimental design, and the impact of new developments in statistics and computing. Three major recommendations were made relating to the need for: (1) the effective use of statistical advice in designing interlaboratory and intralaboratory investigations; (2) the development of appropriate experimental designs for new assays; and (3) education and training in the use of statistical methodology in mutagenicity testing. Environ. Mol. Mutagen. 35:260-263, 2000 Published 2000 Wiley-Liss, Inc.

Guidelines as Topic↗