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PubMed1992

Statistical methods for short-term tests in genetic toxicology: the first fifteen years.

Short-term tests (STTs) for detecting and assessing genotoxic or mutagenic effects have catalyzed the development of biostatistical methods for more than one decade. Most notably, the Ames Salmonella/microsome assay created statistical methodology with a range of applications going beyond genotoxicity. Early approaches with parametric statistical methods appeared to be insufficient and have been replaced by non-parametric ones requiring less restrictive distributional assumptions. There have also been successful attempts to use biomathematical models for establishing dose-response relationships. Overdispersion has been recognized as a major problem for the evaluation of mutagenic count data and methods to cope with it have became available. A theory of generalized linear modelling is emerging to combine dose-response modeling with much less restrictive distributional assumptions, while allowing the inclusion of concomitant factors arising from the experimental conditions. The methodological survey below reviews the present state of this development and is intended to promote further research into biostatistical issues and methods of analysis. Appropriate methods for the design and analysis of STTs are discussed. The progress for the Ames assay was only partially transmitted to the analysis of the large number of other short-term assays. Several such assays are reviewed with respect to their present state of statistical evaluation.

Animals↗
PubMed2005

EEG nonstationarity during intracranially recorded seizures: statistical and dynamical analysis.

OBJECTIVE: The investigation of nonstationarity in complex, multivariable signals, such as electroencephalographic (EEG) recordings, requires the application of different and novel approaches to analysis. In this study, we have divided the EEG recordings during epileptic seizures into sequential stages using spectral and statistical analysis, and have as well reconstructed discrete-time models (maps) that reflect dynamical (deterministic) properties of the EEG voltage time series. METHODS: Intracranial human EEG recordings with epileptic seizures from three different subjects with medically intractable temporal lobe epilepsy were studied. The methods of statistical (power spectra, wavelet spectra, and one-dimensional probability distribution functions) and dynamical (comparison of dynamical models) nonstationarity analysis were applied. RESULTS: Dynamical nonstationarity analysis revealed more detailed inner structure within the seizures than the statistical analysis. Three or four stages with different dynamics are typically present within seizures. The difference between interictal activity and seizure events was also more evident through dynamical analysis. CONCLUSIONS: Nonstationarity analysis can reveal temporal structure within an epileptic seizure, which could further understanding of how seizures evolve. The method could also be used for identification of seizure onset. SIGNIFICANCE: Our approach reveals new information about the temporal structure of seizures, which is inaccessible using conventional methods.

Electroencephalography↗
PubMed2006

Establishing a statistic model for recognition of steroid hormone response elements.

Identification of hormone response elements (HREs) is essential for understanding the mechanism of hormone-regulated gene expression. To date, there has been a lack of effective bioinformatics tools for recognition of specific HRE such as Progesterone Response Elements (PRE). In this paper, a comprehensive survey and comparison of in silico methods is conducted for establishing a more accurate statistic model. Homogeneity of steroid HRE is analyzed and a reliable training dataset is constructed through extensive searching for experimentally validated response elements from more than 150 literature sources. Based on the observation that the verified HREs carry di-nucleotide preservation in comparison with uniform nucleotide distributions, both mono and di-nucleotide Position Weight Matrices are computed to extract the statistic pattern of the positions. It is followed by the sequence transition pattern recognition using a specifically designed profile Hidden Markov Model. Reciprocal combination of the statistic and transition patterns significantly improves the performance of the model in terms of higher sensitivity and specificity. Upon acquisition of the putative response elements in the promoter areas of vertebrate genes, a qualitative scheme is applied to assess the probability for each gene to be a hormone primary target. Using >650 records of experimentally validated steroid hormone response elements, a high sensitivity level of 73% and high specificity level of one prediction per 8.24 kb is reached, allowing this model to be used for further prediction of primary target genes through the analysis of their upstream promoters, for human or other vertebrate genomes of interest. Additional documents, supplementary data and the web-based program developed for response elements prediction are freely available for academic research at . Submission of putative gene promoter regions for recognition of potential regulatory PREs can be as long as 5 kb.

Animals↗
PubMed2006

An investigation of the validity of the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition avoidant personality disorder construct as a prototype category and the psychometric properties of the diagnostic criteria.

This study investigated several aspects of the validity of the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition avoidant personality disorder (APD) construct, with emphasis on the psychometric properties of the diagnostic criteria and the prototype nature of the construct. A sample of 1,058 patients from the Norwegian Network of Psychotherapeutic Day Hospitals was examined by means of exploratory factor analysis, correlation, and diagnostic efficiency statistics, chi(2) analysis, and frequency distribution. The results indicated that APD is a 1-dimensional construct with good internal consistency. The criteria had acceptable diagnostic efficiency; criterion 3 performed poorest. Number of APD criteria showed no distinct threshold between No-APD and patients with APD. Sixty-two different combinations of any 4 APD criteria occurred. It can be concluded that the prototype model fitted the data well and that the APD diagnostic criteria perform well in the current classification system. The Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition hierarchy of criteria was not supported.

Adult↗
PubMed2006

Statistical methods for estimating usual intake of nutrients and foods: a review of the theory.

Although 24-hour recalls are frequently used in dietary assessment, intake on a single day is a poor estimator of long-term usual intake. Statistical modeling mitigates this limitation more effectively than averaging multiple 24-hour recalls per respondent. In this article, we describe the statistical theory that underlies the four major modeling methods developed to date, then review the strengths and limitations of each method. We focus on the problem of estimating the distribution of usual intake for a population from 24-hour recall data, giving special attention to the problems inherent in modeling usual intake for foods or food groups that a proportion of the population does not consume every day (ie, episodically consumed foods). All four statistical methods share a common framework. Differences between the methods arise from different assumptions about the measurement characteristics of 24-hour recalls and from the fact that more recently developed methods build upon their predecessor(s). These differences can result in estimated usual intake distributions that differ from one another. We also demonstrate the need for an improved method for estimating usual intake distributions for episodically consumed foods.

Data Interpretation, Statistical↗
PubMed2006

A statistical method for comparing viral growth curves.

Viral replication is often analyzed by growth curves, in which viral multiplication in the presence of host cells is measured as a function of time. Comparing growth curves is one of the most sensitive ways of comparing viral growth under different conditions or for comparing replication of different viral mutants. However, such experiments are rarely analyzed in a statistically rigorous fashion. Here a statistical method is described for comparing curves, using replication of HIV in the presence of an integrase inhibitor as an example. A complication in the analysis arises due to the fact that sequential measurements of virus accumulation are not independent, which constrains the choice of statistical method. In the recommended approach, the values for virus accumulation over time are fitted to an exponential equation, then the means of the extracted growth rates compared using a nonparametric test, either the Mann-Whitney U-test for two samples or the Kruskal-Wallis test for multiple samples. A web-based tutorial for implementing this method is available at http://microb230.med.upenn.edu/tutorials/wangTutorial.

Data Interpretation, Statistical↗
PubMed2004

Cancer death statistics: analogy between epidemiology and critical systems in physics.

The determination of risk factors in carcinogenesis is said to be an essential step towards the understanding of this disease. Most mathematical models describing the evolution of mortality figures use the concept of death probability (or "force of mortality" or "hazard of death"). When summarizing the death statistics through this unique parameter, one implicitly makes the assumption that the death events are independent from one individual to another. In this paper, we show that this hypothesis has profound consequences as it implies a "gaussian" behavior of the death statistics fluctuations. In order to verify the validity of this assumption, French cancer death statistics between the years 1978-1996 are examined. Their fluctuations, for every age bracket, are computed and then compared to the expected gaussian fluctuations that should emerge from a model of death probability. We show that the observed fluctuations are in close agreement with a gaussian model up to 35-40 years. After 40 years, the fluctuations are much higher and cannot be explained by a model where every individual would have a given "probability of death". These observations may produce a new insight into old-age cancer mortality. It suggests that there could exist a major difference between cancers in young or older organisms: cancer developed in young organisms are the consequence of a specific attack against an organ (essentially originated from a single cause, like a virus or a genetic deficiency). On the other hand, older organism are closer to a "critical state" and, as such, the outcome of a cancer in a given organ could be the consequence of a chain of "malfunctions" (analogous to an avalanche in physical systems) in the entire organism.

Adolescent↗
PubMed2006

A confirmation of Rexed's laminar hypothesis using the Sholl linear method complemented by nonparametric statistics.

Images of Golgi-impregnated neurons from laminae I to VI in the dorsal horn of the cat spinal cord were subjected to the linear Sholl analysis of concentric circles to support Rexed's hypothesis on the laminar organization of spinal gray matter in mammals. Since Rexed's determination of the laminae is based upon size, location, and grouping of cell bodies, neglecting one of the principal morphologic attributes of the neuron-the dendritic tree, the purpose of the present study was to evaluate Rexed's hypothesis testing the structure of dendritic arborization patterns of neurons. The differences in the complexity of dendritic trees between the groups of neurons from different laminae were evaluated by nonparametric statistics. Data obtained using Sholl's method is not always subjected to complete statistical analysis. The problem becomes particularly apparent in the quantitative examination of dendritic structures. Our aim was also to perform a careful analysis of our data for normality, in order to choose the appropriate statistical method for data processing. In the linear Sholl analysis, it is important to properly represent and interpret the frequency functions. The objective of this study was also to investigate the problems of determining the frequency functions, plotting the corresponding lines of regression, and measuring the degree of fluctuation of experimental data points around these lines. The main result of our testing is a confirmation of Rexed's laminar scheme: we have proved that there are 6 out of 10 possible pairs of samples where one member significantly differs from the other, i.e. one lamina is significantly distinguishable from the other.

Algorithms↗
PubMed2005

Assessing statistical precision, power, and robustness of alternative experimental designs for two color microarray platforms based on mixed effects models.

Recommendations on experimental designs for two color microarray systems have been generally conflicting as they pertain to the general choice between reference and non-reference loop designs. This conflict may currently exist because many previously published assessments may not have effectively connected design layout with the level of biological relative to technical replication. We reassess various reference and non-reference designs for statistical efficiency in terms of standard errors of mean differences, power of test, and robustness using recently developed mixed model software tools. In minimally replicated cases (n = 2), it appears that the reference design outperforms the classical loop design whereby a sample from each animal is used for only one particular array hybridization. Alternatively, the reference design was consistently inferior to those connected loop designs in which a sample from each animal is used in two different hybridizations. Nevertheless, the gap in power between these two designs diminished as the biological to residual variance ratio increased. The statistical efficiency of a single large classical loop design for the comparison of many treatments was demonstrated to be highly sensitive to missing arrays relative to a common reference design (n = 2). However, the use of two loops within an interwoven loop design was shown to be substantially more robust to missing arrays and statistically more efficient relative to a common reference design. Furthermore, the use of more than one loop leads to less disparity in precision and power comparisons between any two treatments.

Animals↗
PubMed1996

Statistical methods for cost-effectiveness analyses.

A statistical framework is presented for examining cost and effect data on competing interventions obtained from an RCT or from an observational study. Parameters of the join distribution of costs and effects or a regression function linking costs and effects are used to define cost-effectiveness (c-e) measures. Several new c-e measures are proposed that utilize the linkage between costs and effects on the patient level. These measures reflect perspectives that are different from those of the commonly used measures, such as the ratio of expected cost to expected effect, and they can lead to different relative rankings of the interventions. The cost-effectiveness of interventions are assessed statistically in a two stage procedure that first eliminates clearly inferior interventions. Members of the remaining admissible set are then rank ordered according to a c-e preference measure. Statistical techniques, particularly in the multivariate normal case, are given for several commonly used c-e measures. These techniques provide methods for obtaining confidence intervals, for testing the hypothesis of admissibility and for the equality of interventions, and for ranking interventions. The ideas are illustrated for a hypothetical clinical trial of antipsychotic agents for community-based persons with mental illness.

Antipsychotic Agents↗
PubMed1999

Tutorial: survival analysis--a statistic for clinical, efficacy, and theoretical applications.

Current demands for increased research attention to therapeutic efficacy, efficiency, and also for improved developmental models call for analysis of longitudinal outcome data. Statistical treatment of longitudinal speech and language data is difficult, but there is a family of statistical techniques in common use in medicine, actuarial science, manufacturing, and sociology that has not been used in speech or language research. Survival analysis is introduced as a method that avoids many of the statistical problems of other techniques because it treats time as the outcome. In survival analysis, probabilities are calculated not just for groups but also for individuals in a group. This is a major advantage for clinical work. This paper provides a basic introduction to nonparametric and semiparametric survival analysis using speech outcomes as examples. A brief discussion of potential conflicts between actuarial analysis and clinical intuition is also provided.

Child↗
PubMedDate not supplied

Performance improvement of the SPIHT coder based on statistics of medical ultrasound images in the wavelet domain.

This paper proposes some modifications to the state-of-the-art Set Partitioning In Hierarchical Trees (SPIHT) image coder based on statistical analysis of the wavelet coefficients across various subbands and scales, in a medical ultrasound (US) image. The original SPIHT algorithm codes all the subbands with same precision irrespective of their significance, whereas the modified algorithm processes significant subbands with more precision and ignores the least significant subbands. The statistical analysis shows that most of the image energy in ultrasound images lies in the coefficients of vertical detail subbands while diagonal subbands contribute negligibly towards total image energy. Based on these statistical observations, this work presents a new modified SPIHT algorithm, which codes the vertical subbands with more precision while neglecting the diagonal subbands. This modification speeds up the coding/decoding process as well as improving the quality of the reconstructed medical image at low bit rates. The experimental results show that the proposed method outperforms the original SPIHT on average by 1.4 dB at the matching bit rates when tested on a series of medical ultrasound images. Further, the proposed algorithm needs 33% less memory as compared to the original SPIHT algorithm.

Algorithms↗
PubMedDate not supplied

Improving the process quality using statistical design of experiments: a case study.

A technique known as Statistical design of experiments is a powerful technique for process characterization, optimization, and modeling. It has been widely accepted in manufacturing industry for improving product performance and reliability, process capability, and yield. This article illustrates the application of statistical design of experiments based on the Taguchi approach in a certain company that manufactures electromagnetic clutch coils. The objective of the study was to improve the quality of the existing process and thereby achieve heightened customer satisfaction for the product. An eight-trial experiment was conducted with the aim of reducing the number of rejects from the process. The expected savings per month was estimated to be over $11,500. The results of the study have provided a greater stimulus for the wider application of statistical design of experiments in other core processes within the company.

Analysis of Variance↗
PubMed2003

Statistical issues on objective, design, and analysis of noninferiority active-controlled clinical trial.

In practice, "noninferiority" active-controlled trials have been designed for three different objectives: establishing evidence of efficacy over placebo, preserving a specific percentage of the effect size of the active control, or demonstrating the test treatment is "not much inferior" to the active control. All three objectives can be represented by the same set of statistical hypotheses with the parameters defined differently. The various designs and statistical analysis procedures for active-controlled trials proposed in the literature can be group into two basic types: the historical-controlled trial approach and the cross-study comparison approach. These approaches require some unverifiable constancy assumptions. Under the constancy assumptions, the cross-study comparison uses the estimate effect of active-control treatment as the unbiased estimate of the active/placebo difference in the current noninferiority trial. A normalized Z-statistic is used to test the hypotheses. On the other hand, the historical controlled trial approach uses a conservative confidence limit as if it were a constant to replace the active/placebo difference in the current trial. The two approaches may lead to consistent conclusions only when the constancy assumptions can be supported by a large number of historical studies giving a consistent active-control treatment effect over placebo and that the active-control effect does not change over time.

Controlled Clinical Trials as Topic↗
PubMed2004

Calcium regulation of single ryanodine receptor channel gating analyzed using HMM/MCMC statistical methods.

Type-II ryanodine receptor channels (RYRs) play a fundamental role in intracellular Ca(2+) dynamics in heart. The processes of activation, inactivation, and regulation of these channels have been the subject of intensive research and the focus of recent debates. Typically, approaches to understand these processes involve statistical analysis of single RYRs, involving signal restoration, model estimation, and selection. These tasks are usually performed by following rather phenomenological criteria that turn models into self-fulfilling prophecies. Here, a thorough statistical treatment is applied by modeling single RYRs using aggregated hidden Markov models. Inferences are made using Bayesian statistics and stochastic search methods known as Markov chain Monte Carlo. These methods allow extension of the temporal resolution of the analysis far beyond the limits of previous approaches and provide a direct measure of the uncertainties associated with every estimation step, together with a direct assessment of why and where a particular model fails. Analyses of single RYRs at several Ca(2+) concentrations are made by considering 16 models, some of them previously reported in the literature. Results clearly show that single RYRs have Ca(2+)-dependent gating modes. Moreover, our results demonstrate that single RYRs responding to a sudden change in Ca(2+) display adaptation kinetics. Interestingly, best ranked models predict microscopic reversibility when monovalent cations are used as the main permeating species. Finally, the extended bandwidth revealed the existence of novel fast buzz-mode at low Ca(2+) concentrations.

Algorithms↗
PubMed1957

The statistical detection of threshold signals in the retina.

1. Photographic records of impulses from single ganglion cells in the cat's retina were made while the retina was stimulated by flashes occurring once a second. Ten flashes at each of several intensities near threshold were used. 2. For the purpose of statistical analysis, the number of impulses (x) falling within a critical period following each flash was used as an index of the response. Histograms of x were plotted and used to calculate rates of transfer of information by the ganglion cell for the case of an ideal experiment, the yes-no choice, in which flashes of intensity I and blanks are to be distinguished. 3. The information rate increased (a) with increasing stimulus intensity and (b) with the number of identical flashes or blanks presented successively in a block. The intensity chosen as threshold by the experimenter, who observed the impulses visually and aurally, corresponded to an average information rate for single flashes of 0.7 bit/flash, compared to the maximum possible rate of 1 bit/flash. A threshold intensity giving 0.4 or more bit/flash, if presented in blocks of six identical flashes, corresponded to 0.95 or more bit/block, or near certainty. Thus the calculation of information rates using the index x provides an estimate of threshold at least as sensitive as those obtained during an experiment, which were made only after observing the responses to five to ten flashes of the same intensity. 4. The index x has statistical properties similar to those of the "index of neural activity" used by Tanner and Swets (1954) in their statistical model of human vision, and represents a possible physical interpretation of their index. However, x gave values (0.5 to 1.5) of the parameter called the slope which were consistently smaller than their values (2.1 to 3.1).

Animals↗
PubMed2004

Statistical pixelwise inference models for planar data analysis: an application to gamma-camera uniformity monitoring.

In this paper two tests based on statistical models are presented and used to assess, quantify and provide positional information of the existence of bias and/or variations between planar images acquired at different times but under similar conditions. In the first test a linear regression model is fitted to the data in a pixelwise fashion, using three mathematical operators. In the second test a comparison using z-scoring is used based on the assumption that Poisson statistics are valid. For both tests the underlying assumptions are as simple and few as possible. The results are presented as parametric maps of either the three operators or the z-score. The z-score maps can then be thresholded to show the parts of the images which demonstrate change. Three different thresholding methods (naive, adaptive and multiple) are presented: together they cover almost all the needs for separating the signal from the background in the z-score maps. Where the expected size of the signal is known or can be estimated, a spatial correction technique (referred to as the reef correction) can be applied. These tests were applied to flood images used for the quality control of gamma camera uniformity. Simulated data were used to check the validity of the methods. Real data were acquired from four different cameras from two different institutions using a variety of acquisition parameters. The regression model found the bias in all five simulated cases and it also found patterns of unstable regions in real data where visual inspection of the flood images did not show any problems. In comparison the z-map revealed the differences in the simulated images from as low as 1.8 standard deviations from the mean, corresponding to a differential uniformity of 2.2% over the central field of view. In all cases studied, the reef correction increased significantly the sensitivity of the method and in most cases the specificity as well. The two proposed tests can be used either separately or in combination and are capable of showing trends and/or the magnitude of difference between images acquired under similar conditions with high positional and statistical precision. In addition to gamma camera quality control, they could be applied to any pair (or set) of registered planar images to detect subtle changes, e.g. a set of scintigrams or conventional radiographs of a patient before, during and after treatment.

Computer Simulation↗
PubMed2005

Relations of gestational length and timing and type of incomplete pregnancy to ovarian cancer risk.

While the protective nature of parity with respect to ovarian cancer has been well documented, whether a history of incomplete pregnancy affects ovarian cancer risk is uncertain. Data collected from 739 epithelial ovarian cancer cases and 1,313 community controls in the Delaware Valley from 1994 to 1998 were used to evaluate the relation between gestational length and timing of first induced or spontaneous abortion and ovarian cancer risk. Incomplete pregnancy was not associated with ovarian cancer among nulliparous women or among ever-pregnant women either before or after adjustment for relevant confounders (for nulliparous women, odds ratio (OR) = 1.12, 95% confidence interval (CI): 0.66, 1.89; for ever-pregnant women, OR = 0.95, 95% CI: 0.76, 1.18). Among unigravid women, one full-term pregnancy was more protective than an incomplete pregnancy (adjusted OR = 0.29, 95% CI: 0.15, 0.57). These results were independent of the type of pregnancy loss. Among ever-pregnant women, a spontaneous abortion before a first birth provided significant protection (adjusted OR = 0.47, 95% CI: 0.30, 0.75), while no significant effect was found for an induced abortion prior to a first birth (adjusted OR = 0.80, 95% CI: 0.44, 1.47). These data do not support an independent association between incomplete pregnancies, either spontaneous or induced, and ovarian cancer risk.

Abortion, Induced↗