Applications of the Poly-K Statistical Test to Life-Time Cancer Bioassay Studies

The statistical analysis of cancer bioassay data has historically depended on the pathological determination of the experimental animal's cause of death. The poly-k statistical test has provided a method of statistical analysis of animal bioassay data without the need for cause of death information. The test has been shown to have good statistical properties in the typical 2-year cancer bioassay. However, while the poly-k test has been applied to chronic lifetime animal studies, it has not been formally evaluated with respect to the operating characteristics of this statistical test when applied to such studies. Thus, our objective is to assess the performance of the poly-k test for lifetime studies and to make comparisons with other tests. We observed in one recent lifetime study of the gasoline additive methyl tertiary butyl ether (MTBE) that the application of the poly-k test was not statistically robust. Simulation studies were subsequently conducted for a limited number of scenarios of lifetime cancer bioassays. These simulations showed that the poly-k test is not statistically robust for testing effect of increasing dose in some lifetime cancer studies.     

The Knox method and other tests for space-time interaction

The Knox method, as well as other tests for space-time interaction, are biased when there are geographical population shifts, i.e., when there are different percent population growths in different regions. In this paper, the size of the population shift bias is investigated for the Knox test, and it is shown that it can be a considerable problem. A Monte Carlo method for constructing unbiased space-time interaction tests is then presented and illustrated on the Knox test as well as for a combined Knox test. Practical implications are discussed in terms of the interpretation of past results and the design of future studies.     

A comparison of likelihood ratio tests and Rao's score test for three separable covariance matrix structures

The problem of testing the separability of a covariance matrix against an unstructured variance‐covariance matrix is studied in the context of multivariate repeated measures data using Rao's score test (RST). The RST statistic is developed with the first component of the separable structure as a first‐order autoregressive (AR(1)) correlation matrix or an unstructured (UN) covariance matrix under the assumption of multivariate normality. It is shown that the distribution of the RST statistic under the null hypothesis of any separability does not depend on the true values of the mean or the unstructured components of the separable structure. A significant advantage of the RST is that it can be performed for small samples, even smaller than the dimension of the data, where the likelihood ratio test (LRT) cannot be used, and it outperforms the standard LRT in a number of contexts. Monte Carlo simulations are then used to study the comparative behavior of the null distribution of the RST statistic, as well as that of the LRT statistic, in terms of sample size considerations, and for the estimation of the empirical percentiles. Our findings are compared with existing results where the first component of the separable structure is a compound symmetry (CS) correlation matrix. It is also shown by simulations that the empirical null distribution of the RST statistic converges faster than the empirical null distribution of the LRT statistic to the limiting χ² distribution. The tests are implemented on a real dataset from medical studies.     

Adjusting O'Brien's test to control type I error for the generalized nonparametric Behrens-Fisher problem

O'Brien (1984, Biometrics 40, 1079-1087) introduced a simple nonparametric test procedure for testing whether multiple outcomes in one treatment group have consistently larger values than outcomes in the other treatment group. We first explore the theoretical properties of O'Brien's test. We then extend it to the general nonparametric Behrens-Fisher hypothesis problem when no assumption is made regarding the shape of the distributions. We provide conditions when O'Brien's test controls its error probability asymptotically and when it fails. We also provide adjusted tests when the conditions do not hold. Throughout this article, we do not assume that all outcomes are continuous. Simulations are performed to compare the adjusted tests to O'Brien's test. The difference is also illustrated using data from a Parkinson's disease clinical trial.     

A Note on the Bias of O'Brien's OLS Test

O'Brien's Ordinary Least Squares (OLS) test is a well known procedure for testing the multivariate one-sided hypothesis when the covariance matrix is unknown. Simulation results have been reported where the actual test level exceeds the nominal one. Here it is shown analytically that the actual level is always larger than the nominal one if the covariance matrix is nonnegative.     

The Wald Statistic in Proportional Hazards Hypothesis Testing

In survivorship modelling using the proportional hazards model of Cox (1972, Journal of the Royal Statistical Society, Series B, 34, 187–220), it is often desired to test a subset of the vector of unknown regression parameters β in the expression for the hazard rate at time t. The likelihood ratio test statistic is well behaved in most situations but may be expensive to calculate. The Wald (1943, Transactions of the American Mathematical Society 54, 426–482) test statistic is easier to calculate, but has some drawbacks. In testing a single parameter in a binomial logit model, Hauck and Donner (1977, Journal of the American Statistical Association 72, 851–853) show that the Wald statistic decreases to zero the further the parameter estimate is from the null and that the asymptotic power of the test decreases to the significance level. The Wald statistic is extensively used in statistical software packages for survivorship modelling and it is therefore important to understand its behavior. The present work examines empirically the behavior of the Wald statistic under various departures from the null hypothesis and under the presence of Type I censoring and covariates in the model. It is shown via examples that the Wald statistic's behavior is not as aberrant as found for the logistic model. For the single parameter case, the asymptotic non-null distribution of the Wald statistic is examined.     

Comparison of properties of tests for assessing tumor clonality

SUMMARY: In a recent article Begg et al. (2007, Biometrics 63, 522-530) proposed a statistical test to determine whether or not a diagnosed second primary tumor is biologically independent of the original primary tumor, by comparing patterns of allelic losses at candidate genetic loci. The proposed concordant mutations test is a conditional test, an adaptation of Fisher's exact test, that requires no knowledge of the marginal mutation probabilities. The test was shown to have generally good properties, but is susceptible to anticonservative bias if there is wide variation in mutation probabilities between loci, or if the individual mutation probabilities of the parental alleles for individual patients differ substantially from each other. In this article, a likelihood ratio test is derived in an effort to address these validity issues. This test requires prespecification of the marginal mutation probabilities at each locus, parameters for which some information will typically be available in the literature. In simulations this test is shown to be valid, but to be considerably less efficient than the concordant mutations test for sample sizes (numbers of informative loci) typical of this problem. Much of the efficiency deficit can be recovered, however, by restricting the allelic imbalance parameter estimate to a prespecified range, assuming that this parameter is in the prespecified range.     

Age-adjusted exact trend tests in the event of rare occurrences

Preclinical animal carcinogenicity studies are usually concerned with testing the statistical significance of a dose-response relationship. When the response consists of a rare event such as the development of a certain type of tumor, exact statistical methods are often employed. The exact randomization trend test based on the multivariate hypergeometric distribution is less powerful in the presence of treatment-related risks other than the specified response. Particularly, the loss of power becomes more pronounced when competing risks cause progressively higher mortality rates with increasing dose, which is usual in practice. An age-adjusted form of the randomization test is proposed to adjust for this effect. Permutational distribution for Peto's cause-of-death (COD) test is also explored and compared with its asymptotic counterpart by simulation. The use of COD information has been a controversial issue due to the subjectivity in the pathologists' determinations as well as for economic reasons. The proposed age-adjusted exact test does not require COD, and it is shown to compare favorably to the COD tests via an extensive Monte Carlo simulation. Applications of the methods to two real data sets are included.     

Small Vaccination Experiments with Binary Outcome: The Paradox of Increasing Power with Decreasing Sample Size and/or Increasing Imbalance

In animal vaccination experiments with binary outcome (diseased/non diseased), the comparison of the vaccinated and control group is often based on the Fisher exact test. A tool for the evaluation of different designs is proposed, based on the expected power of the Fisher exact test. The expected power can sometimes unexpectedly increase with decreasing sample size and/or increasing imbalance. The reasons for these peculiar results are explained and compared to the results of two other types of tests: the unconditional test and the randomisation test. In a vaccination experiment with a restricted number of animals it is shown to be important to consider expected power in order to choose the most appropriate design.     

The Relationship Between Two Statistical Tests for the Comparison of Two Exponential Distributions

To compare two exponential distributions with or without censoring, two different statistics are often used; one is the F test proposed by COX (1953) and the other is based on the efficient score procedure. In this paper, the relationship between these tests is investigated and it is shown that the efficient score test is a large-sample approximation of the F test.     

逆转录-聚合酶链反应在乙型脑炎减毒活疫苗生物反应罐清洁验证中的应用

为了对乙型脑炎减毒活疫苗生物反应罐清洁后乙型脑炎病毒(JEV)检测方法进行探讨,从GenBank中收录的乙型脑炎病毒的E蛋白基因序列设计一对引物,以乙型脑炎减毒株SA14-14-2培养物提取RNA作为模板,进行逆转录和PCR扩增。结果表明乙型脑炎减毒株SA14-14-2扩增出预期的特异性条带,阴性对照没有扩增出任何条带。聚合酶链反应与血吸附试验比较,有灵敏、快速、稳定性的特点,可用于生物反应罐清洁后乙型脑炎残留病毒的检测。     

Transferrin secretion and hepatocyte ploidy: analysis at the single cell level using a semi-automatic image analysis method

In a previous work it was shown that transferrin (Tf) secretion is directly related to the membrane surface area of hepatocytes (Péchinot D. et al. [31]). The aim of the present work was to search for a possible relationship between Tf secretion and hepatocytic ploidy using a semi-automatic image analysis method. A determination of Tf secretion by isolated normal adult hepatocytes was achieved at the single cell level, using a modified reverse hemolytic plaque test. A Feulgen reaction was also performed on these hepatocytes. It allowed the evaluation, for each secreting hepatocyte, of the quantity of Tf secreted and its nuclear characteristics. Discrimination between diploid (2c) and tetraploid (4c and 2c2c) hepatocytes was performed and the amount of Tf secreted by each subpopulation determined. It appeared that a 2-fold secretion ratio was not found between tetraploid and diploid hepatocytes. These results suggest, as Tf production is not directly proportional to the degree of ploidy of hepatocytes, that some not yet elucidated regulatory mechanisms may act on Tf gene expression.     

A note on permutation tests for variance components in multilevel generalized linear mixed models

In many applications of generalized linear mixed models to multilevel data, it is of interest to test whether a random effects variance component is zero. It is well known that the usual asymptotic chi-square distribution of the likelihood ratio and score statistics under the null does not necessarily hold. In this note we propose a permutation test, based on randomly permuting the indices associated with a given level of the model, that has the correct Type I error rate under the null. Results from a simulation study suggest that it is more powerful than tests based on mixtures of chi-square distributions. The proposed test is illustrated using data on the familial aggregation of sleep disturbance.     

Superiority inferences on individual endpoints following noninferiority testing in clinical trials

We consider the problem of drawing superiority inferences on individual endpoints following non-inferiority testing. R?hmel et al. (2006) pointed out this as an important problem which had not been addressed by the previous procedures that only tested for global superiority. R?hmel et al. objected to incorporating the non-inferiority tests in the assessment of the global superiority test by exploiting the relationship between the two, since the results of the latter test then depend on the non-inferiority margins specified for the former test. We argue that this is justified, besides the fact that it enhances the power of the global superiority test. We provide a closed testing formulation which generalizes the three-step procedure proposed by R?hmel et al. for two endpoints. For the global superiority test, R?hmel et al. suggest using the L?uter (1996) test which is modified to make it monotone. The resulting test not only is complicated to use, but the modification does not readily extend to more than two endpoints, and it is less powerful in general than several of its competitors. This is verified in a simulation study. Instead, we suggest applying the one-sided likelihood ratio test used by Perlman and Wu (2004) or the union-intersection t(max) test used by Tamhane and Logan (2004).     

P-values For Discrete Test Statistics

This paper considered the relative merits of the P-value and the mid-P-value. It is shown that inference based on the mid-P-value is in a certain sense on firmer ground. In particular the expected mid-P-value does not change under an irrelevant breakup in the test statistic.     

Two different genetic strains of stalked-Ulva (Ulvales, Chlorophyta) grow on intertidal rocky shores in Ebisujima, central Japan

Stalked‐Ulva has been recognized as an ecologic form of Ulva pertusa Kjellman with narrow and extensive stipes that grows on rocky shores with strong wave action. However, it is possible that stalked‐Ulva includes more than two taxa, because it has been shown previously that some isolates of stalked‐Ulva did not cross with U. pertusa. Therefore, further crossing tests, observations of swarmer behavior, culture studies and comparison of DNA sequences were made to clarify whether or not all stalked‐Ulva are included within U. pertusa. Crossing tests showed that stalked‐Ulva contained two different types, one that crossed with U. pertusa (Up strain) and one (N strain) that did not. The biflagellate swarmers of N strains showed negative phototaxis and were slightly larger than male and female gametes of Up strains. Thalli cultured from the swarmers of N strains released the same type of swarmers again. The N strains have an asexual life history, reproducing solely by biflagellate swarmers. Internal transcriber spacer sequence analysis indicated that these two entities are U. pertusa (Up strain) and U. fasciata Delile (N strain). In culture both strains differ morphologically from wild thalli with stipes; it seems that the two different taxa both show a petiolate morphology when growing under the same environmental conditions.     

杂交油菜种子纯度的RAPD检测研究

在简化油菜DNA提取方法的基础上,建立了适用于杂交油菜种子纯度检测的RAPD技术分析系统,从814条随机引物中筛选获得了2条可同时稳定区分CMS杂交油菜品种秦优7号及其亲本的引物,经过大量的不同来源油菜个体的验证,证明了该方法具有很好的重复性,准确性和可靠性,与酯酶同工酶法比较,发现利用RAPD技术能够检测酯酶同工酶法难以鉴别的杂交种及其亲本系,因此,选择合适引物,建立良好的反应体系,简化DNA提取程序,降低分析成本等,可使RAPD技术实用化。     

Effect of zinc administration on thyrotropin releasing hormone-stimulated prolactinemia in healthy men

Previous in vitro studies have demonstrated zinc (Zn⁺⁺) inhibition of basal and of potassium (K⁺) or thyrotropin-releasing hormone (TRH)-stimulated prolactin (PRL) secretion, in a selective, reversible, and dose-dependent manner. Thus, Zn⁺⁺ may regulate physiologically pituitary PRL secretion. Furthermore, studies with patients with uremia, cirrhosis or prolactinoma, have shown the coexistence of hypozincemia and hyperprolactinemia and zinc supplementation did not correct hyperprolactinemia in these patients. In normal individuals Zn⁺⁺ administration produced controversial results on PRL secretion. Here, we investigated whether zinc administration affects TRH-stimulated PRL in healthy men. We found that Zn⁺⁺ administration does not change the TRH-stimulated PRL. Therefore, in normal conditions, Zn⁺⁺ does not inhibit TRH-stimulated prolactinemia. In addition, we found that acute increases of blood PRL and TRH do not alter blood Zn⁺⁺ levels.     

On the exact null distribution of the generalised likelihood ratio test for analysing unreplicated factorial designs

Al-Shiha and Yang (1999) proposed a multistage procedure for analysing unreplicated factorial experiments, which is based on the statistic that is derived from the generalised likelihood ratio test statistic under the assumption of normality. It was shown by their simulation study that the method is quite competitive with Lenth's (1989) method. In their paper, because of the difficulty of determining the null distribution analytically, the quantiles of the null distribution were empirically simulated. In this paper, we give the exact null distribution of their test statistic, which makes it possible to calculate the critical values of the test.