Efficiency in the Use of Hotellings T2

Alternative scale models are compared with regard to the Pitman efficiency of Hotelling's T² in tests for means. A basic decomposition identifies subspaces of the parameters in which one model is more efficient than another, or the two models have equal efficiency. Local and global bounds for relative Pitman efficiencies are given with reference to these subspaces. Applications include efficiency comparisons of marginal and conditional tests in a given model, and a comparison of the sensitivities of selected T² tests regarding psychological profiles in treated and control groups of children.     

Multiple Comparisons of Polynomial Distributions

Asymptotically correct 90 and 95 percentage points are given for multiple comparisons with control and for all pair comparisons of several independent samples of equal size from polynomial distributions. Test statistics are the maxima of the X²-statistics for single comparisons. For only two categories the asymptotic distributions of these test statistics result from DUNNETT'S many-one tests and TUKEY'S range test (cf. MILLER, 1981). The percentage points for comparisons with control are computed from the limit distribution of the test statistic under the overall hypothesis H₀. To some extent the applicability of these bounds is investigated by simulation. The bounds can also be used to improve Holm's sequentially rejective Bonferroni test procedure (cf. HOLM, 1979). The percentage points for all pair comparisons are obtained by large simulations. Especially for 3×3-tables the limit distribution of the test statistic under H₀ is derived also for samples of unequal size. Also these bounds can improve the corresponding Bonferroni-Holm procedure. Finally from SKIDÁK's probability inequality for normal random vectors (cf. SKIDÁK, 1967) a similar inequality is derived for dependent X²-variables applicable to simultaneous X²-tests.     

A New Nonparametric Approach to the Comparison of K Independent Samples of Response Curves

Two simultaneous distribution free test procedures to test the homogeneity of K samples of response curves measured at T points of time each are proposed which react upon the shape of the response curve. One procedure is based on the comparison of K T-tupels of FRIEDMAN-rank sums, the other on the comparison of K T × T-incidence tables, which first were introduced by KANNEMANN (1976). The application of the two procedures is illustrated by a numerical example. In the discussion the tests are compared with each other and with concurring tests.     

Using Discrete Distributions to Compute Powers for Goodness-of-Fit Test Statistics in a One-Way Multinomial Setting

Both the Bionomial and Poisson distributions are employed in this study to compute approximate powers for goodness-of-fit test statistics. The procedure adopted involves simulating 1000 samples from each of these distributions. These samples are then employed to compute both the randomized nominal critical values and estimated powers. The type I error rates returned from the use of the randomized critical levels Cα fall within the acceptable regions. We illustrate the use of the procedure with the Pearson's X² test statistic and show that this can readily be extended to any of the other well known goodness-of-fit test statistics.     

Exploiting the full power of temporal gene expression profiling through a new statistical test: Application to the analysis of muscular dystrophy data

Background  

The identification of biologically interesting genes in a temporal expression profiling dataset is challenging and complicated by high levels of experimental noise. Most statistical methods used in the literature do not fully exploit the temporal ordering in the dataset and are not suited to the case where temporal profiles are measured for a number of different biological conditions. We present a statistical test that makes explicit use of the temporal order in the data by fitting polynomial functions to the temporal profile of each gene and for each biological condition. A Hotelling T ²-statistic is derived to detect the genes for which the parameters of these polynomials are significantly different from each other.     

<Emphasis Type="Italic">Streptomyces urticae</Emphasis> sp. nov., isolated from rhizosphere soil of <Emphasis Type="Italic">Urtica urens</Emphasis> L.

Two novel Gram-stain positive, spore-forming, aerobic actinomycetes, designated NEAU-PCY-1^T and NEAU-PCY-2, were isolated from rhizosphere soil of Urtica urens L. collected from Anshan, Liaoning Province, northeast China. The 16S rRNA gene sequence analysis showed that strains NEAU-PCY-1^T and NEAU-PCY-2 exhibited 99.8% similarity with each other and are closely related to Streptomyces abietis DSM 42080^T (98.2, 98.3%) and Streptomyces fildesensis DSM 41987^T (98.0, 98.1%). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the two strains formed a cluster with these two closely related species. Moreover, DNA–DNA hybridization results and some phenotypic, physiological and biochemical properties differentiated the two strains from their close relatives in the genus Streptomyces. Based on a polyphasic taxonomy study, strains NEAU-PCY-1^T and NEAU-PCY-2 are considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces urticae sp. nov. is proposed, with NEAU-PCY-1^T (=?DSM 105115^T?=?CCTCC AA 2017015^T) as the type strain.     

MR Proton Relaxivities of Some Ions, Albumin, and Cholesterol Added to Odontogenic Jaw Cysts

The relaxation rates (1 / T ₁ and 1 / T ₂) in cysts have already been analyzed in terms of materials such as albumin, cholesterol, manganese, iron, and copper. However, the relaxivities of these materials have not been determined yet. In this work, five sets containing the ions, albumin, and cholesterol were prepared by addition of increasing concentration of one material to each set. The relaxation times in these sets were measured by MRI, and the relaxation rates were fitted versus concentrations. The slopes of the fits were used as relaxivities. The (r ₁, r ₂) values of manganese, iron, and copper in mM⁻¹ s⁻¹, and those of albumin and cholesterol in (g/dl)⁻¹ s⁻¹ were found to be (32.64, 89.77), (0.31, 1.19), (0.5, 1.479), (0.01, 0.066) and (0.03, 0.458), respectively. The r ₂/r ₁ ratio ranged from 2.75 to 15.27. Manganese is an efficient relaxer, but iron and copper are poor ones. Albumin and cholesterol are efficient relaxers for only T ₂. The contribution of water associated with native manganese of the cystic fluid to T ₁ was 0.268 s⁻¹, whereas those of water associated with native manganese, albumin, cholesterol, and iron to T ₂ were 0.736, 0.185, 0.092, and 0.076 s⁻¹, respectively. The other contributions were much smaller than 0.076 s⁻¹. Manganese is most likely the compound altering T ₁-weighted images between different jaw cysts, whereas manganese and albumin are most likely the compounds altering the T ₂-weighted images. Present data suggest that such alterations may be used to separate jaw cysts from other jaw masses. The high r ₂/r ₁ suggests that T ₂ is a more convenient parameter than T ₁ for diagnostic use. This work is a part of the PhD thesis of U. Nezih Yilmaz supervised by R. Guner.     

A New Nonparametric Approach to the Comparison of K Independent Samples of Response Curves II: A K Sample Generalization of the FRIEDMAN Test

A K sample generalization of the FRIEDMAN test (1937) is introduced which can be used as a nonparametric procedure for testing the homogeneity of the profiles of K independent samples of response curves measured at T identical points of time. While a similar procedure in LEHMACHER & WALL (1978), section 3, is based on T combined tests, each of them at level a/T, here a finite and asymptotic test is presented which is based on a single test statistic. The application of the new multivariate test is illustrated by the same numerical example as in LEHMACHER & WALL (1978). The properties of this test are discussed and compared with the combined test mentioned above.     

Biased distribution of adenine and thymine in gene nucleotide sequences

We analyzed occurrences of bases in 20,352 introns, exons of 25,574 protein-coding genes, and among the three codon positions in the protein-coding sequences. The nucleotide sequences originated from the whole spectrum of organisms from bacteria to primates. The analysis revealed the following: (1) In most exons, adenine dominates over thymine. In other words, adenine and thymine are distributed in an asymmetric way between the exon and the complementary strand, and the coding sequence is mostly located in the adenine-rich strand. (2) Thymine dominates over adenine not only in the strand complementary to the exon but also in introns. (3) A general bias is further revealed in the distribution of adenine and thymine among the three codon positions in the exons, where adenine dominates over thymine in the second and mainly the first codon position while the reverse holds in the third codon position. The product (A₁/T₁) × (A₂/T₂) × (T₃/A₃) is smaller than one in only a few analyzed genes. Correspondence to: J. Kypr     

Viability of Cururbita pepo pollen: biophysical and structural data

During ageing of the short-lived pollen grains of Cucurbita pepo L., water loss was examined in relation to viability using biophysical (¹H-nuclear magnetic resonance, NMR) and cytological methods (fluorochromatic reaction test, freezefracture and scanning electron microscopy). A semi-logarithmic representation of the pollen weight loss demonstrated the complexity of the dehydration process. A the study of proton loss using ¹H-NMR indicated that two major releases water of had taken place, each with different flux rates. Pulse ¹H-NMR experiments showed the occurrene of non-exponential signal decay as a function of time, indicating the existence of different fractions of water in a pollen grain sample. These fractions leave the pollen grain at different times during pollen dehydration, and one of them (that of the so-called vital water) can be related to pollen viability. The quantity of protons giving a signal during pulse ¹H-NMR experiments was very low when the pollen grains were judged to be dead according to the fluorochromatic test. Freeze-fracture replicas of these dead pollen grains (less than 25% water content) showed that the plasma membrane had become detached from the intine surface; this ultrastructural feature might therefore be involved in the loss of pollen viability.Abbreviations A initial amplitude of the NMR signal - A₂ quantity of water charcterized by T_2-2 - A₅ quantity of water characterized by T_2–5 - FCR fluorochromatic reaction - NMR nuclear magnetic resonance - T₂ transverse relaxation time - T_2-2 T₂ measured with 2 ms between each pulse of radiofrequency - T_2–5 T₂ measured with 5 ms between each pulse of radiofrequency     

Tests for profile analysis of paired curves based on friedman ranking methods

Two nonparametric tests are proposed for the comparison of a paired sample of response curves with T congruent time points. The first procedure rank transforms each curve and tests the homogeneity of the resulting pair of averaged rank vectors. The second procedure rank transforms each pair of curves and tests the homogeneity of the related pair of averaged rank vectors. The first test detects only pure interactions; the second test checks if any difference exists between the rank curves. Both tests are presented in finite and asymptotic as well as in combined (by T singular tests) and multivariate form.     

A Confidence‐Limit‐Based Approach to the Assessment of Hardy–Weinberg Equilibrium

The classical χ²‐procedure for the assessment of Hardy–Weinberg equilibrium (HWE) is tailored for detecting violations of HWE. However, many applications in genetic epidemiology require approximate compatibility with HWE. In a previous contribution to the field (Wellek, S. (2004). Biometrics, 60 , 694–703), the methodology of statistical equivalence testing was exploited for the construction of tests for problems in which the assumption of approximate compatibility of a given genotype distribution with HWE plays the role of the alternative hypothesis one aims to establish. In this article, we propose a procedure serving the same purpose but relying on confidence limits rather than critical bounds of a significance test. Interval estimation relates to essentially the same parametric function that was previously chosen as the target parameter for constructing an exact conditional UMPU test for equivalence with a HWE conforming genotype distribution. This population parameter is shown to have a direct genetic interpretation as a measure of relative excess heterozygosity. Confidence limits are constructed using both asymptotic and exact methods. The new approach is illustrated by reanalyzing genotype distributions obtained from published genetic association studies, and detailed guidance for choosing the equivalence margin is provided. The methods have been implemented in freely available SAS macros.     

Peptoniphilus coxii sp. nov. and Peptoniphilus tyrrelliae sp. nov. isolated from human clinical infections

Two groups of previously undescribed anaerobic, gram-positive cocci recovered from human clinical infections were characterized using phenotypic and molecular genotypic methods. Comparative genotypic analysis showed that the strains within each of these two groups were homogeneous within the group and that each group was unique within the genus Peptoniphilus. The first group is most closely related to Peptoniphilus ivorii and the second group to Peptoniphilus harei. Based on these findings we propose two novel species, Peptoniphilus coxii sp. nov. and Peptoniphilus tyrrelliae sp. nov. The type strains are P. coxii sp. nov., RMA 16757^T (= JCM 16892^T = CCUG 59622^T = ATCC BAA-2106^T) and P. tyrrelliae sp. nov., RMA 19911^T (= JCM 16893^T = CCUG 59621^T = ATCC BAA-2105^T).     

Metalloid Reducing Bacteria Isolated from Deep Ocean Hydrothermal Vents of the Juan de Fuca Ridge, Pseudoalteromonas telluritireducens sp. nov. and Pseudoalteromonas spiralis sp. nov

Five strains of Gram-negative, rod, curved rod and spiral-shaped bacteria were isolated from the vicinity of deep ocean hydrothermal vents along the Main Endeavour Segment of the Juan de Fuca Ridge in the Pacific Ocean. All strains showed remarkable resistance to high levels of toxic metalloid oxyanions, and were capable of reducing the oxyanions tellurite and selenite to their less toxic elemental forms. Phylogenetic analysis of four strains identified these isolates as close relatives of the genus Pseudoalteromonas within the class Gammaproteobacteria. Pseudoalteromonas agarivorans was the closest relative of strains Te-1-1 and Se-1-2-red^T, with, respectively, 99.5 and 99.8% 16S rDNA sequence similarity. Strain Te-2-2^T was most closely related to Pseudoalteromonas paragorgicola, with 99.8% 16S rDNA sequence similarity. The DNA G+C base composition was 39.6 to 41.8 mol%, in agreement with other members of the genus Pseudoalteromonas. However, the isolates showed important morphological and physiological differences from previously described species of this genus, with one group forming rod-shaped bacteria typical of Pseudoalteromonas and the other forming vibrioid- to spiral-shaped cells. Based on these differences, and on phylogenetic data, we propose the creation of the new species Pseudoalteromonas telluritireducens sp. nov., with strain Se-1-2-red^T (DSMZ=16098^T=VKM B-2382^T) as the type strain, and Pseudoalteromonas spiralis sp. nov., with strain Te-2-2^T (DSMZ=16099^T=VKM B-2383^T) as the type strain. The EMBL accession numbers for the 16S rDNA sequences are: Te-1-1, AJ314843; Te-2-2^T, AJ314842; Se-1-2-or, AJ314844; Se-1-2-red^T, AJ314845.     

Computational experience with a parallel algorithm for tetrangle inequality bound smoothing

Determining molecular structure from interatomic distances is an important and challenging problem. Given a molecule with n atoms, lower and upper bounds on interatomic distances can usually be obtained only for a small subset of the atom pairs, using NMR. Given the bounds so obtained on the distances between some of the atom pairs, it is often useful to compute tighter bounds on all the pairwise distances. This process is referred to as bound smoothing. The initial lower and upper bounds for the pairwise distances not measured are usually assumed to be 0 and ∞. One method for bound smoothing is to use the limits imposed by the triangle inequality. The distance bounds so obtained can often be tightened further by applying the tetrangle inequality—the limits imposed on the six pairwise distances among a set of four atoms (instead of three for the triangle inequalities). The tetrangle inequality is expressed by the Cayley—Menger determinants. For every quadruple of atoms, each pass of the tetrangle inequality bound smoothing procedure finds upper and lower limits on each of the six distances in the quadruple. Applying the tetrangle inequalities to each of the ( ₄ ⁿ ) quadruples requires O(n ⁴) time. Here, we propose a parallel algorithm for bound smoothing employing the tetrangle inequality. Each pass of our algorithm requires O(n ³ log n) time on a CREW PRAM (Concurrent Read Exclusive Write Parallel Random Access Machine) with processors. An implementation of this parallel algorithm on the Intel Paragon XP/S and its performance are also discussed.     

Denaturation of DNA in the presence of chromous (Cr2+) ions

The effect of Cr²⁺ ions on the T_m (melting temperature) of DNA has been investigated under appropriate conditions for the stabilization of DNA by Mg²⁺ ions. A significant lowering of T_m, analogous to that observed for Cu²⁺ under normal conditions, was found, for Cr²⁺ at pH = 4.2 and [Mg²⁺] = 5.3 mol per mole of DNA base pair. Cu²⁺ also lowers T_m under similar conditions. The similarity of the effects of Cr²⁺ and Cu²⁺ under comparable conditions may be related to similarities in their coordination properties. It is proposed that Cr²⁺ and Cu²⁺ ions facilitate denaturation by holding together groups on the DNA chains in such a manner that base pairing and base stacking are inhibited. Comparative results for Cr³⁺ and Co²⁺ are also given for these low pH/Mg²⁺ ion conditions.     

Empirical evaluation of two-sample statistical tests for differences of stepping phase during insect walking

In order to determine which statistical tests can validly be applied to data that describe a temporal relationship between two or more repetitive movements by an animal, we evaluated empirically seven two-sample tests that seemed potentially useful: Student's t test, the Watson Williams test for means, the variance-ratio F test, the Watson Williams test for the concentration parameter k, the Wallraff test, the Mann Whitney test and the Watson U² test. Evaluations were carried out on the timing (phases) of bursts of muscular activity in one leg relative to those in another during free walking in cockroaches. Each statistical test was evaluated by dividing randomly a single parent set of data into two subsets, each subset containing about half the original data set. This division was repeated 400 times, thus generating 400 different pairs of subsets. Each statistical test was used separately on the pairs of subsets to test the null hypothesis that the two samples of each pair came from the same population;; this procedure generated 400 statistics for each test, one for each pair of subsets. An estimate of the reliability of each statistical test was obtained by comparing the number of times the test actually indicated a significant difference between subsets to the number of times it might be expected to do so out (20 out of 400 when tested at the 5% level of significance). This procedure was repeated on ten different sets of data. The outcome of the evaluation suggested that, from an empirical point of view, Student's t, the Mann Whitney, the Wallraff and the Watson U² tests may be useful in assessing differences among the data we analyzed. The variance-ratio F test and the Watson Williams test for the concentration parameter k were clearly not usable. The Watson Williams test for means might be useful in some circumstances. Performing an arcsine transformation of the data did not significantly alter these results. Possible causes of the inapplicability of some of these tests to phase data are discussed.     

Energetics and possible mechanisms of ion-beam protein tritiation based on ab initio potential surfaces

Ab initio self-consistent field potential energy surfaces for the approach of T. T₂. T⁺. T⁺₃ and HeT⁺ to glycine in the gas phase have been determined and this data used to obtain insight into mechanisms of experimental ion-beam protein tritiation processes. Results of these calculations show that the ionic species T⁺, T⁺₃ and HeT⁺ can form stable adducts with glycine (Gly) and that each functions as a tritiation agent forming the complex GlyT⁺. Neutral T and T₂ experience a purely repulsive interaction with Gly and do not form an intermediate complex. These neutral species are expected to be less effective tritiation agents than the respective ions, in agreement with experimental observations. The fate of the stable GlyT⁺ complex is discussed and it is proposed that this species is neutralized by electron capture to give GlyT which spontaneously dissociates to either Gly+T or tritiated glycine (Gly^*)+H, with the latter reaction product channel favored statistically. The most likely site of exchange is predicted to be at the amine nitrogen although significance exchange is expected to occur at the α-carbon site by a somewhat more complex reaction mechanism.     

<Emphasis Type="Italic">Saturnispora serradocipensis</Emphasis> sp. nov. and <Emphasis Type="Italic">Saturnispora gosingensis</Emphasis> sp. nov., two ascomycetous yeasts from ephemeral habitats

Two novel ascomycetous yeast species, Saturnispora serradocipensis and Saturnispora gosingensis, were isolated from leaf detritus in a tropical stream of Southeastern Brazil and a mushroom collected in Taiwan, respectively. Analysis of the D1/D2 domains of the large-subunit of the rRNA gene of these strains showed that these species are related to Saturnispora hagleri, their closest relative. Saturnispora serradocipensis and S. gosingensis differed from S. hagleri, respectively, by seven nucleotide substitutions and two indels and three nucleotide substitutions and three indels in D1/D2 rRNA sequences. The two new species differ from each another by four nucleotide substitutions and one indel in D1/D2 rRNA sequences. However, the ITS sequences of S. serradocipensis, S. gosingensis and S. hagleri were quite divergent, showing that they are genetically separate species. The type strain of S. serradocipensis is UFMG-DC-198^T (=CBS 11756^T = NRRL Y-48717^T), and of S. gosingensis GA4M05^T is (CBS 11755^T = NRRL Y-48718^T).