Testing the Intraclass Version of Kappa Coeffcient of Agreement with Binary Scale and Sample Size Determination

The intraclass version of kappa coefficient has been commonly applied as a measure of agreement for two ratings per subject with binary outcome in reliability studies. We present an efficient statistic for testing the strength of kappa agreement using likelihood scores, and derive asymptotic power and sample size formula. Exact evaluation shows that the score test is generally conservative and more powerful than a method based on a chi‐square goodness‐of‐fit statistic (Donner and Eliasziw , 1992, Statistics in Medicine 11 , 1511–1519). In particular, when the research question is one directional, the one‐sided score test is substantially more powerful and the reduction in sample size is appreciable.     

Mapping of brain activity in mesencephalic and diencephalic structures of toads during presentation of visual key stimuli: a computer assisted analysis of (14C)2DG autoradiographs

Summary The (¹⁴C)2DG autoradiographic technique has been employed to quantitatively map glucose utilization in the mesencephalon, the diencephalon and the cerebellum, of toads in response to configurational moving visual stimuli: (i) a 0.4 cm × 2.8 cm worm-like stripe (W) which elicited prey catching responses, (ii) a 8.4 cm × 8.4 cm square (S) that released predator avoidance responses, and (iii) a 2.8 cm × 0.4 cm antiworm-like stripe (A) which elicited no motor activity.For various brain nuclei different relationships were obtained: The optic tectum showed statistical significant higher 2DG uptake during worm-stimulation (¯X _W) than during antiworm stimulation (¯X _A), i.e.¯X _W>¯X _A. The latter visual pattern led to a 2DG utilization that was statistically significant stronger than during stimulation with a square (¯X _S), i.e.¯X _A>¯X _S. Thus, in comparison between right and left hemisphere as well as between brains the following ratios were obtained:Optic tectum:¯X _W>¯X _A>¯X _S; nucleus isthmi:¯X _W>¯X _A-¯X _s; posterodorsal lateral thalamic nucleus:¯X _S>¯X _A>¯X _W; posteroventral lateral thalamic nucleus:¯X _S>¯X _A¯X _W; posterior thalamic nucleus:¯X _W>¯X _A¯X _S; anteripr division of the lateral thalamic nucleus:¯X _W>¯X _A¯X _S; anterior thalamic nucleus:¯X _A>¯X _S>¯X _W; nucleus of Bellonci and dorsal division of the ventrolateral thalamic nucleus:¯X _W¯X _A¯X _S; cerebellum:¯X _S¯X _W>¯X _A.Abbreviations A anterior thalamic nucleus - Cb cerebellum - Hyp hypothalamus - Ist nucleus isthmi - cl. Ist contralateral Ist - La lateral thalamic nucleus, anterior division - Lpd lateral thalamic nucleus, posterodorsal division - Lpv lateral thalamic nucleus, posteroventral division - MP medial pallium - NB/VLd nucleus of Bellonci and ventrolateral thalamic nucleus, dorsal division - P posterior thalamic nucleus - PO preoptic area - Sna snapping evoking area=ventrolateral tectum - Str striatum - Tec tectum opticum     

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.     

UMP(U)‐Tests for a Binomial Parameter: A Paradox

We consider uniformly most powerful (UMP) as well as uniformly most powerful unbiased (UMPU) tests and their non‐randomized versions for certain hypotheses concerning a binomial parameter. It will be shown that the power function of a UMP(U)‐test based on sample size n can coincide on the entire parameter space with the power function of the corresponding test based on sample size n + 1. A complete characterization of this paradox will be derived. Apart some exceptional cases for two‐sided tests and equivalence tests the paradox appears if and only if a test based on sample size n is non‐randomized.     

Contributions of the σW, σM and σX regulons to the lantibiotic resistome of Bacillus subtilis

In Bacillus subtilis, the extracytoplasmic function (ECF) σ factors σ^M, σ^W and σ^X all contribute to resistance against lantibiotics. Nisin, a model lantibiotic, has a dual mode of action: it inhibits cell wall synthesis by binding lipid II, and this complex also forms pores in the cytoplasmic membrane. These activities can be separated in a nisin hinge‐region variant (N20P M21P) that binds lipid II, but no longer permeabilizes membranes. The major contribution of σ^M to nisin resistance is expression of ltaSa, encoding a stress‐activated lipoteichoic acid synthase, and σ^X functions primarily by activation of the dlt operon controlling d ‐alanylation of teichoic acids. Together, σ^M and σ^X regulate cell envelope structure to decrease access of nisin to its lipid II target. In contrast, σ^W is principally involved in protection against membrane permeabilization as it provides little protection against the nisin hinge region variant. σ^W contributes to nisin resistance by regulation of a signal peptide peptidase (SppA), phage shock proteins (PspA and YvlC, a PspC homologue) and tellurite resistance related proteins (YceGHI). These defensive mechanisms are also effective against other lantibiotics such as mersacidin, gallidermin and subtilin and comprise an important subset of the intrinsic antibiotic resistome of B. subtilis.     

Parasitism of cotton leafworm Alabama argillacea eggs by Trichogramma pretiosum in commercial cotton fields

Release of natural enemies in commercial fields is challenging and has been inconsistent in the results achieved. This work discusses the augmentative releases of Trichogramma pretiosum to control the cotton leafworm (CLW) Alabama argillacea and also examines the parasitoid–host interaction under grower field conditions. The treatments consisted of fields with and without releases of T. pretiosum set up in Primavera do Leste and Campo Verde Counties, MT, Brazil, during three different seasons (2003 and 2004 dry and 2004 regular summer seasons). Trichogramma wasps were weekly released in the treated fields throughout the entire sampling period (14–15 week period) at a rate of 100 000 wasps per hectare. One‐way repeated measures analysis of variance was performed for the number of parasitized eggs, followed by a meta‐analysis procedure to determine the contribution of T. pretiosum release on overall parasitism. In addition, regression analysis was conducted with each season’s data sets to study the relationship of the host density and parasitism response by T. pretiosum. The overall results of Trichogramma augmentative releases did not result in significant increase of CLW egg parasitism beyond the natural parasitism in the areas studied. However, based on Cohen’s d effect sizes from the meta‐analysis, the parasitism rate was greater in fields under T. pretiosum releases during four out of 15 weeks surveyed. The parasitism of CLW eggs by T. pretiosum exhibited host density‐dependence only in one out of three seasons surveyed. These findings are encouraging as they are evidence that T. pretiosum is able to maintain a considerable level of parasitism under commercial field conditions, highlighting their potential value in large‐scale commercial areas of cotton as previously found at the small and diverse farming scale. Future studies should address the potential of early‐season, low density releases of the parasitoid.     

MULTIPLE ORIGINS OF SEX CHROMOSOME FUSIONS CORRELATED WITH CHIASMA LOCALIZATION IN HABRONATTUS JUMPING SPIDERS (ARANEAE: SALTICIDAE)

Entelegyne spiders rarely show fusions yielding neo‐Y chromosomes, which M. J. D. White attributed to a constraint in spiders, namely their proximal chiasma localization acting to upset meiotic segregation in males with fusions. Of the 75 taxa of Habronattus and outgroups studied, 47 have X₁X₂0 sex chromosomes in males, 10 have X₁X₂Y, 15 have X₁X₂X₃Y, 2 have X0, and one has both X₁X₂0 and X₁X₂X₃Y. Chromosome numbers and behavior suggest neo‐Ys formed by an autosome‐X fusion to make X₁X₂Y, with a second fusion to an autosome to make X₁X₂X₃Y. Phylogeny shows at least 8–15 gains (or possibly some losses) of neo‐Y (i.e., X‐autosome fusions), a remarkable number for such a small clade. In contrast to the many X‐autosome fusions, at most one autosome–autosome fusion is indicated. Origins of neo‐Y are correlated significantly with distal localization of chiasmata, supporting White's hypothesis that evolution of neo‐Y systems is facilitated by looser pairing (distal chiasmata) at meiosis. However, an alternative (or contributing) explanation for the correlation is that X‐autosome fusions were selected to permit isolation of male‐favored alleles to the neo‐Y chromosome, aided by distal chiasmata limiting recombination. This intralocus sexual conflict hypothesis could explain both the many X‐autosome fusions, and the stunning complexity of male Habronattus courtship displays.     

Effect of environmental factors on tenuazonic acid production by Alternaria alternata on soybean-based media

Aims: To determine the effects of water activity (a_W; 0·995–0·90), temperature (5, 18, 25 and 30°C), time of incubation (7–35 days) and their interactions on tenuazonic acid (TA) production on 2% soybean‐based agar by two Alternaria alternata strains isolated from soybean in Argentina. Methods and Results: TA production by two isolates of A. alternata was examined under interacting conditions of a_W, temperature and time of incubation on 2% soybean‐based agar. Maximum TA production was obtained for both strains at 0·98 a_W, but at 30 and 25°C for the strains for RC 21and RC 39, respectively. The toxin concentration varied considerably depending on a_W, temperature, incubation time and strain interactions. TA was produced over the temperature range from 5 to 30°C and a_W range from 0·92 to 0·995, however at 5 and 18°C little TA was produced at a_W below 0·94. Contour maps were developed from these data to identify areas where conditions indicate a significant risk for TA accumulation. Conclusions: The optimum and marginal conditions for TA production by A. alternata on soybean‐based agar were identified. The results indicated that TA production by A. alternata is favoured by different temperatures in different strains. Significance and Impact of the Study: Data obtained provide very useful information for predicting the possible risk factors for TA contamination of soybean as the a_W and temperature range used in this study simulate those occurring during grain ripening. The knowledge of TA production under marginal or sub‐optimal temperature and a_W conditions for growth are relevant as improper storage conditions accompanied by elevated temperature and moisture content in the grain can favour further mycotoxin production and lead to reduction in grain quality.     

A metal‐chelate affinity reverse micellar system for protein extraction

A new nonionic reverse micellar system is developed by blending two nonionic surfactants, Triton X‐45 and Span 80. At total surfactant concentrations lower than 60 mmol/L and molar fractions of Triton X‐45 less than 0.6, thermodynamically stable reverse micelles of water content (W₀) up to 30 are formed. Di(2‐ethylhexyl) phosphoric acid (HDEHP; 1–2 mmol/L) is introduced into the system for chelating transition metal ions that have binding affinity for histidine‐rich proteins. HDEHP exists in a dimeric form in organic solvents and a dimer associated with one transition metal ion, including copper, zinc, and nickel. The copper‐chelate reverse micelles (Cu‐RM) are characterized for their W₀, hydrodynamic radius (R_h), and aggregation number (N_ag). Similar with reverse micelles of bis‐2‐ethylhexyl sodium sulfosuccinate (AOT), R_h of the Cu‐RM is also linearly related to W₀. However, N_ag is determined to be 30–90 at W₀ of 5–30, only quarter to half of the AOT reverse micelles. Then, selective metal‐chelate extraction of histidine‐rich protein (myoglobin) by the Cu‐RM is successfully performed with pure and mixed protein systems (myoglobin and lysozyme). The solubilized protein can be recovered by stripping with imidazole or ethylinediaminetetraacetic acid (EDTA) solution. Because various transition metal ions can be chelated to the reverse micelles, it is convinced that the system would be useful for application in protein purification as well as simultaneous isolation and refolding of recombinant histidine‐tagged proteins expressed as inclusion bodies. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Cumulative Damage Survival Models for the Randomized Complete Block Design

A continuous time discrete state cumulative damage process {X(t), t ≥ 0} is considered, based on a non‐homogeneous Poisson hit‐count process and discrete distribution of damage per hit, which can be negative binomial, Neyman type A, Polya‐Aeppli or Lagrangian Poisson. Intensity functions considered for the Poisson process comprise a flexible three‐parameter family. The survival function is S(t) = P(X(t) ≤ L) where L is fixed. Individual variation is accounted for within the construction for the initial damage distribution {P(X(0) = x) | x = 0, 1, …,}. This distribution has an essential cut‐off before x = L and the distribution of L – X(0) may be considered a tolerance distribution. A multivariate extension appropriate for the randomized complete block design is developed by constructing dependence in the initial damage distributions. Our multivariate model is applied (via maximum likelihood) to litter‐matched tumorigenesis data for rats. The litter effect accounts for 5.9 percent of the variance of the individual effect. Cumulative damage hazard functions are compared to nonparametric hazard functions and to hazard functions obtained from the PVF‐Weibull frailty model. The cumulative damage model has greater dimensionality for interpretation compared to other models, owing principally to the intensity function part of the model.     

Multivariate Homogeneity Testing Using an Extended Concept of Nearest Neighbors

Given independent multivariate random samples {X_ij: j = 1, …, n_i} from F_i, for i = 1,2, a test is desired for H₀: F₁ = F₂ against general alternatives. Consider the k · (n₁ + n₂) possible ways of choosing one observation from the combined samples and then one of its k nearest neighbors, and let S_k be the proportion of these choices in which the point and neighbor are in the same sample. Schilling (1986) proposed S_k as a test statistic, but did not indicate how to determine k. We suggest as test statistic W = N Σ kS_k, which we show is equivalent to a sum of N Wilcoxon rank sums, and also to a sum of two two-sample U-statistics of degrees (1, 2) and (2, 1). Simulation with multivariate normal data suggests that our test is generally more powerful than Schilling's test using k = 1, 2, or 3. We illustrate its use with Fisher's iris data.     

Comparisons of Some Chi-squared Tests for the Test of Independence in Sparse Two-Way Contingency Tables

We consider in this paper, the behaviour of a class of the CRESSIE READ (1984) power divergence test statistics indexed by parameter λ - I (λ), with the modified X₂ test statistics (LU) proposed by LAWAL and UPTON (1984), for sparse contingency tables ranging from the 3×3 to the 10×10. We present a sample of our results here. The results indicate that the LU test out-performs either the Cressie-Read suggested test I(2/3) or the Pearson's test - I(1). Our results further show that the modification to the likelihood ratio test [Y₂ = I'(0)] proposed by WILLIAMS (1976) performs like the parent Y₂ test, very poorly compared with either the I(2/3), X₂ or the LU test statistics. Power results also indicate that the powers of the LU test are in all cases considered in this study slightly higher than those of X₂ and I(2/3) tests. The LU test is therefore strongly recommended for use with sparse two-way contingency tables because in all of the cases considered, none of the other test statistics consistently out-performs the LU test with respect to attained α level or power.     

Lysine Requirements of Rats of Various Body Weights

The lysine requirements of rats of various body weights were estimated using the feeding and isotope tests.

The regression equation obtained by the feeding test was Y= 1.03 – 0.58 log X. Where Y is lysine percentage of the diet and X is the mean of initial and final body weights (g) of rats achieving optimal growth gains during the feeding period.

The regression equation obtained by the isotope test was 7=0.90 – 0.49 log X, where Y and X are lysine percentage in the diet and body weights (g) of rats achieving optimal growth gains at the injection time respectively.     

Comparison of stool antigen immunoassay and serology for screening for Helicobacter pylori infection in intellectually disabled children

Diagnosis of active Helicobacter pylori infection in intellectually disabled (ID) children is problematic because they are unable to cooperate with performance of invasive tests. In this study, the non‐invasive methods of measuring serum IgG antibody concentrations and performing stool antigen tests were used to screen for H. pylori infection in ID children. Eighty‐seven children with intellectual disabilities were studied. The amount of serum IgG antibody against H. pylori was measured by the ELISA method. Stool samples were examined using an amplified IDEIA HpStAR kit. To assess categorical variables, X², Fisher's exact and Kappa tests were used. The stool antigen tests showed that 93.1% of the children had H. pylori antigen and the serology test that 85.1% of children were positive for H. pylori IgG antibodies. Agreement between results of H. pylori stool antigen (HpSA) testing and IgG antibody serology was 82.8%; however, according to the kappa measure of agreement this agreement is not statistically significant (value, 0.128; P = 0.19). Discordant results were observed for 15 children (17.2%): 11 (12.6%) who were positive on HpSA test but negative by serology and 4 (4.6%) who were IgG seropositive but had negative HpSA tests. This study showed a notably higher rate of H. pylori infection in ID children than has been reported by others for non‐ID children from the same geographical area. The HpSA test is a valid method for primary screening for H. pylori infection in ID children; it detects the specific antigens shed during active infections and has less cross‐reactivity than serological tests that detect antibodies. HpSA is a sensitive non‐invasive method for detecting infection in ID children and may serve as an accurate alternative to serology.     

TESTING FOR PHYLOGENETIC SIGNAL IN BIOLOGICAL TRAITS: THE UBIQUITY OF CROSS‐PRODUCT STATISTICS

To evaluate rates of evolution, to establish tests of correlation between two traits, or to investigate to what degree the phylogeny of a species assemblage is predictive of a trait value so‐called tests for phylogenetic signal are used. Being based on different approaches, these tests are generally thought to possess quite different statistical performances. In this article, we show that the Blomberg et al. K and K*, the Abouheif index, the Moran's I, and the Mantel correlation are all based on a cross‐product statistic, and are thus all related to each other when they are associated to a permutation test of phylogenetic signal. What changes is only the way phylogenetic and trait similarities (or dissimilarities) among the tips of a phylogeny are computed. The definitions of the phylogenetic and trait‐based (dis)similarities among tips thus determines the performance of the tests. We shortly discuss the biological and statistical consequences (in terms of power and type I error of the tests) of the observed relatedness among the statistics that allow tests for phylogenetic signal. Blomberg et al. K* statistic appears as one on the most efficient approaches to test for phylogenetic signal. When branch lengths are not available or not accurate, Abouheif's C_mean statistic is a powerful alternative to K*.     

Limits to xylem refilling under negative pressure in Laurus nobilis and Acer negundo

The ability of juvenile Laurus nobilis and Acer negundo plants to refill embolized xylem vessels was tested under conditions of soil drought when xylem sap pressure was substantially negative, thus violating the expected condition that pressure must rise to near atmospheric for refilling. Intact potted plants were dried to a stem water potential (Σ_W) corresponding with approximately 80% loss of hydraulic conductivity (PLC) in shoots. Then plants were re‐watered and kept at a less negative target Ψ_W for 1–48 h. The Ψ_W was measured continuously with stem psychrometers. Rewatered L. nobilis held at the target Ψ_W for 1 h showed no evidence for refilling unless Ψ_W was within a few tenths of a MPa of zero. In contrast, re‐watered L. nobilis held for 24 and 48 h at water potentials well below zero showed a significant reduction in PLC. The recovery was highly variable, being complete in some stem segments, and scarcely evident in others. Embolism repair was accompanied by a significant but moderate decrease in the osmotic potential (Ψ) of the bulk xylem sap (Ψ = ?67 kPa in recovering plants versus ?31 kPa in controls). In contrast, embolized and re‐watered A. negundo plants held for 24 h at target Ψ_W of ?0·9 and ?0·3 MPa showed no embolism reversal. The mechanism allowing L. nobilis plants to refill under negative pressure is unknown, but does not appear to operate in A. negundo, and is slower to act for drought‐induced embolism than when embolism was artificially induced by air injection as previously shown for L. nobilis.     

Multivariate Probability in Terms of Marginal Probability and Correlation Coefficient

This paper is motivated by a practical problem relating to student performance in a number of subjects of equal standing. Its mathematical formulation is to find an approximation to a multivariate probability of the form Pr {X₁⩾a, X₂⩾a, …, X_N⩾a} for arbitrary a and N, in terms of p = Pr {X₁⩾a} and q = Corr (X_i, X_j), i≠j, where X_i, i = 1, …, N are exchangeable random variables with mean 0 and variance unity.     

Predation of cotton leafworm first instar larvae,Alabama argillacea [Lep.: Noctuidae]

Natural predation first instar larvae of the cotton leafworm (CLW)A. argillacea was studied in cotton fields in Jaboticabal, Sao Paulo State, Brazil, during 1986. The presence of naturally occurring arthropod predators showed a first instar larvae predation rate of 78.6 and 88.9% after 24 h and 48 h of exposure, respectively. A predator prey ratio of 1∶1 (1 CLW key predator per 1 prey/plant) maintained a level of no more than 1 CLW small larvae per plant. The most evident arthropod predators in the studied fields were: beetles (Coleoptera: Coccinellidae), antsPheidole sp. andConomyrma sp.;Dermaptera Doru lineare (Eschs);Hemiptera Geocoris sp., andOrius insidiosus Say; and the spidersTheridion volubile, Chrysso pulcherrima, Misumenops sp.,Chiracanthium sp., andOxyopes salticus Hentz.