Confidence intervals following group sequential tests in clinical trials

Tsiatis, Rosner, and Mehta (1984, Biometrics 40, 797-803) proposed a procedure for constructing confidence intervals following group sequential tests of a normal mean. This method is first extended for group sequential tests for which the sample sizes between interim analyses are not identical or the times are not equally spaced. Then properties of this confidence interval estimation procedure are studied by simulation. The extension accommodates the flexible procedure by Lan and DeMets (1983, Biometrika 70, 659-663) for constructing discrete group sequential boundaries to form a structure for monitoring and estimation following a class of group sequential tests. Finally, it is demonstrated how to combine the procedures by Lan and DeMets and by Tsiatis, Rosner, and Mehta using a FORTRAN program.     

Experimental tests of the cellular tensegrity hypothesis

The tensegrity model depicts the cytoskeleton (CSK) as a prestressed network of interconnected filaments. The prestress is generated by the CSK contractile apparatus and is partly balanced by traction at the cell-substrate interface and partly by CSK internal compression elements such as microtubules (MTs). A key feature of tensegrity is that the shear modulus (G) must increase in proportion with the prestress. Here we have tested that prediction as well as the idea that compression of MTs balance a portion of the cell prestress. Airway smooth muscle cells were studied. Traction microscopy was used to calculate traction. Because traction must be balanced by the stress within the cell, the prestress could be computed. Cell G was measured by oscillatory magnetic cytometry. The prestress was modulated using graded concentrations of contracting (histamine) or relaxing (isoproterenol) agonists and by disrupting MTs by colchicine. It was found that G increased in proportion with the prestress and that compression of MTs balanced a significant, but a relatively small fraction of the prestress. Taken together, these results do not disprove other models of cell deformability, nor they prove tensegrity. However, they do support a priori predictions of tensegrity. As such, it may not be necessary to invoke more complex mechanisms to explain these central features of cell deformability.     

Robust hypothesis tests for independence in community assembly

The extent to which competition affects the distributions of species at large spatial scales is unclear. To evaluate this question, hypothesis tests that do not depend on parametric assumptions are needed. Here, we develop a broadly applicable test that requires only one parametric assumption. Letting i and j denote the ith and jth colonists to arrive at a site, respectively, and [i j] the event that i and j belong to the same "unit" (e.g., functional group, genus), we show how colonists will be partitioned into units if for all i and j, [i j] is independent of whether i and j share unit membership with the other colonists, conditional on other information about shared units. Our distribution of partitions is useful for inferring competitive effects, because these effects predict that for at least one i and j, P ([i j]) will be less when i and j share unit membership than when they do not.     

Global gene expression analysis of developing neocortex using SAGE

The mammalian brain is estimated to contain about a hundred billion neurons, making it the most complex biological structure on earth. Trying to understand the assembly and function of this elaborate organ is a formidable task. Yet the information to build a brain is encoded by no more than a subset of the 80,000 genes present in the genome, a more manageable number. This review describes the use of SAGE technology (Serial Analysis of Gene Expression) to decode the genetic repertoire of genes that are differentially expressed in time and in space during development of the neocortex, the part of the mammalian brain responsible for complex traits. We demonstrate that SAGE is not only powerful for generating comprehensive molecular portraits from the developing cortex but can also assist in discovering new genes.     

Comparison of family-based association tests in chromosome regions selected by linkage-based confidence intervals

We use the Genetic Analysis Workshop 14 simulated data to explore the effectiveness of a two-stage strategy for mapping complex disease loci consisting of an initial genome scan with confidence interval construction for gene location, followed by fine mapping with family-based tests of association on a dense set of single-nucleotide polymorphisms. We considered four types of intervals: the 1-LOD interval, a basic percentile bootstrap confidence interval based on the position of the maximum Zlr score, and asymptotic and bootstrap confidence intervals based on a generalized estimating equations method. For fine mapping we considered two family-based tests of association: a test based on a likelihood ratio statistic and a transmission-disequilibrium-type test implemented in the software FBAT. In two of the simulation replicates, we found that the bootstrap confidence intervals based on the peak Zlr and the 1-LOD support interval always contained the true disease loci and that the likelihood ratio test provided further strong confirmatory evidence of the presence of disease loci in these regions.     

The adaptive bleaching hypothesis: experimental tests of critical assumptions

Coral bleaching, the loss of color due to loss of symbiotic zooxanthellae or their pigment, appears to be increasing in intensity and geographic extent, perhaps related to increasing sea surface temperatures. The adaptive bleaching hypothesis (ABH) posits that when environmental circumstances change, the loss of one or more kinds of zooxanthellae is rapidly, sometimes unnoticeably, followed by formation of a new symbiotic consortium with different zooxanthellae that are more suited to the new conditions in the host's habitat. Fundamental assumptions of the ABH include (1) different types of zooxanthellae respond differently to environmental conditions, specifically temperature, and (2) bleached adults can secondarily acquire zooxanthellae from the environment. We present simple tests of these assumptions and show that (1) genetically different strains of zooxanthellae exhibit different responses to elevated temperature, (2) bleached adult hosts can acquire algal symbionts with an apparently dose-dependent relationship between the concentration of zooxanthellae and the rate of establishment of the symbiosis, (3) and finally, bleached adult hosts can acquire symbionts from the water column.     

Serial analysis of gene expression: rapid RT-PCR analysis of unknown SAGE tags.

In a pilot study on SAGE on Reed-Sternberg cells we have sequenced 1055 tags representing 701 genes. Screening of the GenBank database resulted in the identification of a corresponding gene or EST for 490 of them. For 211 of the tags no homology could be detected. A major problem of the serial analysis of gene expression (SAGE) approach is how to further analyse the unknown tags. We have developed an RT-PCR-based method, rapid analysis of unknown SAGE tags (RAST-PCR), to analyse the expression of the corresponding genes. This approach can be used as a screening method to investigate whether or not the gene is differentially expressed between several cell types of interest.     

Comparison of microarray and SAGE techniques in gene expression analysis of human glioblastoma

To enhance glioblastoma (GB) marker discovery, we compared gene expression in GB with human normal brain (NB) by accessing the SAGE Genie web site and compared the results with published data. Nine GB and five NB SAGE libraries were analyzed using the Digital Gene Expression Displayer (DGED); the results of DGED were tested by Northern blot analysis and RT-PCR of arbitrarily selected genes. Review of available data from the articles on gene expression profiling by microarray-based hybridization showed as few as 35 overlapped genes with increased expression in GB. Some of them were identified in four articles, but most genes were identified in three or even in two investigations. Some differences were also found between SAGE results of GB analysis. The Digital Gene Expression Displayer approach revealed 676 genes differentially expressed in GB vs. NB with cutoff ratio: twofold change and P ≤ 05. Differential expression of selected genes obtained by DGED was confirmed by Northern analysis and RT-PCR. Altogether, only 105 of 955 genes presented in published investigations were among the genes obtained by DGED. Comparison of the results obtained by microarrays and SAGE is very complicated because the authors present only the most prominent differentially expressed genes. However, even available data give quite poor overlapping of genes revealed by microarrays. Some differences between results obtained by SAGE in different investigations can be explained by high dependence on the statistical methods used. As for now, the best solution to search for molecular tumor markers is to compare all available results and to select only those genes where significant expression in tumors combined with very low expression in normal tissues was reproduced in several articles. One hundred five differentially expressed genes, common to both methods, can be included in the list of candidates for the molecular typing of GBs. Some genes, encoded cell surface or extracellular proteins may be useful for targeting gliomas with antibody-based therapy. The text was submitted by the authors in English.