Statistical issues arising in the Women's Health Initiative

A brief overview of the design of the Women's Health Initiative (WHI) clinical trial and observational study is provided along with a summary of results from the postmenopausal hormone therapy clinical trial components. Since its inception in 1992, the WHI has encountered a number of statistical issues where further methodology developments are needed. These include measurement error modeling and analysis procedures for dietary and physical activity assessment; clinical trial monitoring methods when treatments may affect multiple clinical outcomes, either beneficially or adversely; study design and analysis procedures for high-dimensional genomic and proteomic data; and failure time data analysis procedures when treatment group hazard ratios are time dependent. This final topic seems important in resolving the discrepancy between WHI clinical trial and observational study results on postmenopausal hormone therapy and cardiovascular disease.     

Statistical issues with microarrays: processing and analysis

The study of gene expression with printed arrays and prefabricated chips is evolving from a qualitative to a quantitative science. Statistical procedures for determining quality control, differential expression, and reproducibility of findings are a natural consequence of this evolution. However, problems inherent to the technologies have raised important issues of how to apply adequate statistical tests. As a consequence, statistical approaches to microarray research are not yet as routine as they are in other sciences. Statistical methods, tailored to microarrays, continue to be adapted and developed. We present an overview of these methods and of outstanding issues in their use and validation.     

Statistical issues in the analysis of quantitative traits in combined crosses.

We consider some practical statistical issues in QTL analysis where several crosses originate in multiple inbred parents. Our results show that ignoring background polygenic variation in different crosses may lead to biased interval mapping estimates of QTL effects or loss of efficiency. Threshold and power approximations are derived by extending earlier results based on the Ornstein-Uhlenbeck diffusion process. The results are useful in the design and analysis of genome screen experiments. Several common designs are evaluated in terms of their power to detect QTL.     

Regulatory issues in the use of insect-cell culture

Conclusion The insect cell as host for protein production is relative new. Therefore few data are available. This creates a vicious circle because it makes the choice of insect cells as basis for a pharmaceutical process less attractive. There are three main issues when comparing insect-cells to traditional systems as mammalian and bacterial cells. First, since the expression vector is not incorporated in the cells, a virus stock similar to the cell bank system has to be laid down and tested. This will cost time and money. Secondly the vector is subject to mutation and therefore the decrease in infectivity has to be characterized and validated. Third, the post-translational modification of the protein may differ. None of the mentioned issues, however, forms an obstacle that can not be overcome.     

The use of glyoxylic acid for the fluorescence histochemical demonstration of peripheral stores of noradrenaline and 5-hydroxytryptamine in whole mounts.

The reactions of glyoxylic acid with peripheral stores of noradrenaline and 5-hydroxytryptamine to provide a fluorescence histochemical method for their localization have been investigated. Incubation in glyoxylic acid, followed by drying and heating of whole mount preparations gives an intense and well localized reaction. For incubation, a concentration of 2% glyoxylic acid, buffered to pH 7 at room temperature for 30 minutes gives ideal results. The method is equally good if the pH is varied in the range 6 to 9 or if the tissue is stored in the incubation mixture for up to 6 hours. Ideal development of the fluorophore requires an initial excess of moisture in the tissue, that this moisture is driven off during development, and that the tissue is protected from further moistening. A suitable method of achieving these ends is to heat partially dried tissue at 100 degrees C for 4 minutes and then cover it with paraffin oil. 5-hydroxytryptamine can be readily distinguished from noradrenaline because it forms a fluorophore after reaction at pH 3.5, whereas noradrenaline does not. Both amines can be visualized after incubation at neutral pH. Comparison with the formaldehyde vapour technique reveals three main advantages (and no disadvantages) of the glyoxylic acid method: (1) it gives a finer localization with higher fluorescence yield, (2) the glyoxylic acid method is less susceptible to variations in procedure and, (3) it is both simpler and quicker to apply.     

Animal care and use issues in movement disorder research

Animal models of movement disorders can present special challenges for the research institutions that use them. Such models often affect the animals' ability to ambulate and perform normal body functions, and these potential effects on health and well-being mandate additional steps to ensure humane animal care and use. Indeed, the appropriate level of care for these models may call for actions that go beyond what is required or considered standard for other protocols. A proactive team approach to animal use protocol development and animal management is important. Through the commitment and involvement of the entire team-researchers, facility personnel, and institutional animal care and use committee members--institutions that use these valuable models can ensure both the fulfillment of research objectives and the implementation of the best practices for animal care. Among the most commonly used animal models of movement disorder are models of stroke, brain and spinal cord injury, dystonia, Parkinson's disease, and Huntington's disease. Despite their relatively wide use, there is very little in the literature that describes the specific needs of individual models and the challenges those needs may present in today's regulatory environment. In this article, we discuss animal use considerations and provide the available animal care information on specific models. Interested readers are also referred to the additional information in the accompanying articles in this issue of ILAR Journal.     

Germination and outgrowth of Bacillus popilliae in hemolymph slide mounts

Cabbage looper hemolymph induced rapid germination and outgrowth of spores of Bacillus popilliae. Spores germinated within sporangia but outgrowth occurred from free released spores as well as from spores retained in sporangia. With 37°C, an alkaline pH, and tyrosinase, outgrowth resulted in 1 hr. Of six strains of milky disease bacteria tested, hemolymph mediated germination and outgrowth of only those which are infective perorally for European chafer larvae, indicating a potential use as a screening tool to assess virulence for the chafer.     

昆虫种群数据分析及在SPSS软件上的实现

选择合适的统计分析方法对昆虫种群分析至关重要。本文以昆虫种群数据常用的分析方法为基础,介绍了单因素方差分析、多因素方差分析、重复测量方差分析和回归分析等多种分析方法的基本原理,强调了各种分析方法的应用前提,避免误用方法导致结果判读产生偏差,并结合SPSS软件的使用,实现相应的分析,旨在为昆虫种群数据分析提供方法论的参考。     

Statistical issues in quality control of proteomic analyses: good experimental design and planning

Quality control is becoming increasingly important in proteomic investigations as experiments become more multivariate and quantitative. Quality control applies to all stages of an investigation and statistics can play a key role. In this review, the role of statistical ideas in the design and planning of an investigation is described. This involves the design of unbiased experiments using key concepts from statistical experimental design, the understanding of the biological and analytical variation in a system using variance components analysis and the determination of a required sample size to perform a statistically powerful investigation. These concepts are described through simple examples and an example data set from a 2-D DIGE pilot experiment. Each of these concepts can prove useful in producing better and more reproducible data.     

土地利用/景观生态学研究中的马尔可夫链统计性质分析

马尔可夫链在土地利用和景观生态学研究中得到了广泛应用,而应用中通常假设土地利用变化为满足马尔可夫性的一阶时齐马尔可夫链,对马尔可夫链的统计性质是否成立却很少进行检验.本文以北京市土地利用变化监测数据为算例,提出了马尔可夫链统计性质的皮尔逊χ² 拟合优度检验方法.检验结果表明,土地利用研究中通常假设的时齐性和马尔可夫性(一阶性)在统计学上并不成立,即北京土地利用演变过程为非时齐的高阶马尔可夫链.相对于马尔可夫统计性质的似然比检验中转移概率大于零的要求,皮尔逊χ²检验对转移概率的要求相对宽松,允许转移概率为零,所以应用的范围较似然比检验更为广泛.     

Surgical issues surrounding use of aromatase inhibitors

There are important surgical issues related to the use of the third generation aromatase inhibitors in both the neoadjuvant and adjuvant settings. Neoadjuvant hormone therapy is effective at downstaging tumours, particularly large tumours initially thought to be inoperable or requiring mastectomy. Randomised trials have shown that the newer aromatase inhibitors letrozole and anastrozole increase the numbers of women who are suitable for breast-conservation compared with tamoxifen, and that letrozole is superior to tamoxifen in terms of clinical response.

Aromatase inhibitors are most effective in ER-rich tumours and are clinically and biologically effective in both HER2 positive and negative tumours, whereas HER2 positive tumours show a level of resistance to tamoxifen.

In neoadjuvant studies comparing aromatase inhibitors with tamoxifen, the duration of use has been 3–4 months, by which time any response is usually evident but longer treatment periods produce continued shrinkage and response. The re-excision rate following breast conservation surgery after neoadjuvant hormone therapy is favourable compared with the rates following immediate wide local excision. Local recurrence rates are acceptable in patients undergoing neoadjuvant therapy and breast-conserving surgery providing post-operative radiotherapy is given.

Adjuvant aromatase inhibitors, as well as having an effect on metastatic disease and survival, reduce local and regional recurrence.     

Statistical evaluation of the regulatory guidelines for use of furosemide in race horses

The pharmacokinetic behavior of furosemide concentrations in performance horses is of great interest to the equine industry and equine researchers. Specifically, such information is useful for the evaluation of the existing guidelines in several racing jurisdictions and for the possible development of new guidelines for varying time periods after administration. We studied several approaches within the framework of nonlinear mixed effects models to increase the accuracy of evaluating these guidelines. Theoretical properties of the proposed methods were examined and the variances of the resulting estimators compared. Their numerical performances were further evaluated through simulations. Finally, we applied these methods to a furosemide concentration profile data set and used our findings to address certain important practical issues.     

Statistical sampling of bacterial strains and its use in bacterial diversity measurement

The cultural bacterial strains of two sediment samples, i.e., 260 strains, were submitted to numerical taxonomy to determine ecological profiles. From these profiles several calculations of bacterial diversity were done with increasing number of strains (between 10 and 130). Studying 20–30 strains was sufficient to obtain a diversity of bacterial community.Number of tests could be reduced from 62 to 30 without any influence on bacterial diversity. Similarity between studied tests was shown by using numerical taxonomy.     

Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer

With the proliferation of related microarray studies by independent groups, a natural step in the analysis of these gene expression data is to combine the results across these studies. However, this raises a variety of issues in the analysis of such data. In this article, we discuss the statistical issues of combining data from multiple gene expression studies. This leads to more complications than those in standard meta-analyses, including different experimental platforms, duplicate spots and complex data structures. We illustrate these ideas using data from four prostate cancer profiling studies. In addition, we develop a simple approach for assessing differential expression using the LASSO method. A combination of the results and the pathway databases are then used to generate candidate biological pathways for cancer.