The geometry of the phosphodiester backbone was analyzed for 7739 dinucleotides from 447 selected crystal structures of naked and complexed DNA. Ten torsion angles of a near-dinucleotide unit have been studied by combining Fourier averaging and clustering. Besides the known variants of the A-, B- and Z-DNA forms, we have also identified combined A + B backbone-deformed conformers, e.g. with α/γ switches, and a few conformers with a syn orientation of bases occurring e.g. in G-quadruplex structures. A plethora of A- and B-like conformers show a close relationship between the A- and B-form double helices. A comparison of the populations of the conformers occurring in naked and complexed DNA has revealed a significant broadening of the DNA conformational space in the complexes, but the conformers still remain within the limits defined by the A- and B- forms. Possible sequence preferences, important for sequence-dependent recognition, have been assessed for the main A and B conformers by means of statistical goodness-of-fit tests. The structural properties of the backbone in quadruplexes, junctions and histone-core particles are discussed in further detail.

Although unbiasedness is a basic property of a good test, many tests on vector parameters or scalar parameters against two-sided alternatives are not finite-sample unbiased. This was already noticed by Sugiura [Ann. Inst. Statist. Math. 17 (1965) 261--263]; he found an alternative against which the Wilcoxon test is not unbiased. The problem is even more serious in multivariate models. When testing the hypothesis against an alternative which fits well with the experiment, it should be verified whether the power of the test under this alternative cannot be smaller than the significance level. Surprisingly, this serious problem is not frequently considered in the literature. The present paper considers the two-sample multivariate testing problem. We construct several rank tests which are finite-sample unbiased against a broad class of location/scale alternatives and are finite-sample distribution-free under the hypothesis and alternatives. Each of them is locally most powerful against a specific alternative of the Lehmann type. Their powers against some alternatives are numerically compared with each other and with other rank and classical tests. The question of affine invariance of two-sample multivariate tests is also discussed.Comment: Published in at http://dx.doi.org/10.3150/10-BEJ326 the Bernoulli (http://isi.cbs.nl/bernoulli/) by the International Statistical Institute/Bernoulli Society (http://isi.cbs.nl/BS/bshome.htm

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Background: Myocardial infarction and stroke represent a major public health problem in most developing countries. This study explores genetic predisposition of acute myocardial infarction in the Czech population. Methods and Results: Genome-wide expression study used matched case-control design. Peripheral blood samples of the controls were matched to those of cases based on gender, age, status of diabetes mellitus and smoking status. Six months cardiovascular survival status of the cases was used to identify two distinct subgroups among the cases. Linear models for microarray data were employed to identify differential gene expression. Shrunken centroids technique helped in identifying the subsets of differentially expressed genes with predictive properties in independent samples. Predictive properties were evaluated using bootstrap sampling. Sixty transcripts were found to be both clinically and statistically differentially expressed among the cases not surviving the six months follow-up period relative to controls, while no such transcripts were observed among other surviving cases.The two subgroups of cases exhibited fourteen differentially expressed transcripts. Predictive modeling indicated sixteen out of sixty transcripts to best discriminate between the controls and cases that died during the follow-up period from cardiovascular causes, while for the surviving cases the already non-significant set of transcripts could not be further reduced. Eleven out of fourteen transcripts were found to best discriminate between the two groups of cases using shrunken centroids. Conclusions: The study identified genes associated with excess genetic risk of acute myocardial infarction, including those associated with the six months fatality of the cases.

We consider the likelihood ratio test of a simple null hypothesis (with density f 0 ) against a simple alternative hypothesis (with density g 0 ) in the situation that observations X i are mismeasured due to the presence of measurement errors. Thus instead of X i for i = 1 , … , n , we observe Z i = X i + δ V i with unobservable parameter δ and unobservable random variable V i . When we ignore the presence of measurement errors and perform the original test, the probability of type I error becomes different from the nominal value, but the test is still the most powerful among all tests on the modified level. Further, we derive the minimax test of some families of misspecified hypotheses and alternatives. The test exploits the concept of pseudo-capacities elaborated by Huber and Strassen (1973) and Buja (1986). A numerical experiment illustrates the principles and performance of the novel test.