This paper is concerned with studying the dependence structure between two random variables Y₁ and Y₂ conditionally upon a covariate X. The dependence structure is modelled via a copula function, ...which depends on the given value of the covariate in a general way. Gijbels et al. (Comput. Statist. Data Anal., 55, 2011, 1919) suggested two non-parametric estimators of the 'conditional' copula and investigated their numerical performances. In this paper we establish the asymptotic properties of the proposed estimators as well as conditional association measures derived from them. Practical recommendations for their use are then discussed.
Purpose
Common scab of potatoes (CS) is influenced by plant-microbe-soil interactions, which are locally specific. The study aims to identify any common trends in such interactions across a landscape ...differentiated by soil pH and CS severity.
Methods
The 33 sites and 17 cultivars were characterized using soil and periderm nutrient contents and microbial communities. Quantitative PCR and Illumina amplicon sequencing were used to assess abundance of bacteria, actinobacteria and pathogens, and community composition.
Results
Comparisons between bulk and tuberosphere soil compartments as well as potato cultivars divided to three categories of CS susceptibility revealed that nitrogen was elevated in tuberosphere soil and N, Mg and Fe were lowered in periderm of resistant cultivars. The susceptible cultivar Agria grown at 7 sites had higher Ca content in tuberosphere soil, while the resistant cultivar Adela grown at 10 sites had higher S, P and Mg contents in its tuberosphere soil and P and Fe in periderm. That suggests further interactions between plants and bacterial community involving nutrient uptake. Diversity of bacteria was positively correlated with CS severity suggesting interactions between the
Streptomyces
pathogen populations and the local soil community.
Conclusions
Overall, pathogen abundance assessed by quantifying the thaxtomin biosynthetic
txtB
genes were randomly dispersed among the sites without connections to CS severity or soil pH. Thus, the significant differences between bacterial communities of bulk and tuberosphere soils together with cultivar CS susceptibility showed that the susceptible cultivars select bacterial community relatively similar to the bulk soil, while the resistant cultivars promote more distinct communities.
Multivariate tail coefficients are an important tool when investigating dependencies between extreme events for different components of a random vector. Although bivariate tail coefficients are ...well-studied, this is, to a lesser extent, the case for multivariate tail coefficients. This paper contributes to this research area by (i) providing a thorough study of properties of existing multivariate tail coefficients in the light of a set of desirable properties; (ii) proposing some new multivariate tail measurements; (iii) dealing with estimation of the discussed coefficients and establishing asymptotic consistency; and, (iv) studying the behavior of tail measurements with increasing dimension of the random vector. A set of illustrative examples is given, and practical use of the tail measurements is demonstrated in a data analysis with a focus on dependencies between stocks that are part of the EURO STOXX 50 market index.
Common scab of potatoes is a disease, which is difficult to manage due to complex interactions of the pathogenic bacteria (Streptomyces spp.) with soil, microbial community and potato plants. In ...Bohemian-Moravian Highlands in the Czech Republic two sites (Vyklantice and Zdirec) were selected for a study of common scab disease suppressivity. At both sites, a field with low disease severity occurs next to one with high severity and the situation was regularly observed over four decades although all four fields undergo a crop rotation. In the four fields, quantities of bacteria, actinobacteria and the gene txtB from the biosynthetic gene cluster of thaxtomin, the main pathogenicity factor of common scab, were analyzed by real-time PCR. Microbial community structure was compared by terminal fragment length polymorphism analysis. Soil and potato periderm were characterized by contents of carbon, nitrogen, phosphorus, sulphur, calcium, magnesium, and iron. Quality of organic matter was assessed by high performance liquid chromatography of soil extracts. The study demonstrated that the suppressive character of the fields is locally specific. At Zdirec, the suppressivity was associated with low txtB gene copies in bulk soil, while at Vyklantice site it was associated with low txtB gene copies in the tuberosphere. The differences were discussed with respect to the effect of abiotic conditions at Zdirec and interaction between potato plant and soil microbial community at Vyklantice. Soil pH, Ca soil content or cation concentrations, although different were not in the range to predict the disease severity. Low severity of common scab was associated with low content of soil C, N, C/N, Ca and Fe suggesting that oligotrophic conditions may be favorable to common scab suppression.
Testing homogeneity of dispersions may be of its own scientific interest as well as an important auxiliary step verifying assumptions of a main analysis. The problem is that many biological and ...ecological data are highly skewed and zero-inflated. Also the number of variables often exceeds the sample size. Thus data analysts often do not rely on parametric assumptions, but use a particular dissimilarity measure to calculate a matrix of pairwise differences. This matrix is then the basis for further statistical inference. Anderson (2006) proposed a distance-based test of homogeneity of multivariate dispersions for a one-way ANOVA design, for which a matrix of pairwise dissimilarities can be taken as an input. The key idea, like in Levene's test, is to replace each observation with its distance to an estimated group center. In this paper we suggest an alternative approach that is based on the means of within-group distances and does not require group centre calculations to obtain the test statistic. We show that this approach can have theoretical as well as practical advantages. A permutation procedure that gives type I error close to the prescribed value even in small samples is described.
Two long-term contaminated soils differing in contents of Pb, Zn, As, Cd were compared in a microcosm experiment for changes in microbial community structure and respiration after various treatments. ...We observed that the extent of long-term contamination (over 200 years) by toxic elements did not change the total numbers and diversity of bacteria but influenced their community composition. Namely, numbers of
determined by phylum specific qPCR increased and also the proportion of
and
increased in Illumina sequence libraries in the more contaminated soil. In the experiment, secondary disturbance by supplemented cadmium (doses from double to 100-fold the concentration in the original soil) and organic substrates (cellobiose or straw) increased bacterial diversity in the less contaminated soil and decreased it in the more contaminated soil. Respiration in the experiment was higher in the more contaminated soil in all treatments and correlated with bacterial numbers. Considering the most significant changes in bacterial community, it seemed that particularly
withstand contamination by toxic elements. The results proved higher resistance to secondary disturbance in terms of both, respiration and bacterial community structure in the less contaminated soil.
Accurate methods of HIV incidence determination are critically needed to monitor the epidemic and determine the population level impact of prevention trials. One such trial, Project Accept, a Phase ...III, community-randomized trial, evaluated the impact of enhanced, community-based voluntary counseling and testing on population-level HIV incidence. The primary endpoint of the trial was based on a single, cross-sectional, post-intervention HIV incidence assessment.
Test performance of HIV incidence determination was evaluated for 403 multi-assay algorithms MAAs that included the BED capture immunoassay BED-CEIA alone, an avidity assay alone, and combinations of these assays at different cutoff values with and without CD4 and viral load testing on samples from seven African cohorts (5,325 samples from 3,436 individuals with known duration of HIV infection 1 month to >10 years). The mean window period (average time individuals appear positive for a given algorithm) and performance in estimating an incidence estimate (in terms of bias and variance) of these MAAs were evaluated in three simulated epidemic scenarios (stable, emerging and waning). The power of different test methods to detect a 35% reduction in incidence in the matched communities of Project Accept was also assessed. A MAA was identified that included BED-CEIA, the avidity assay, CD4 cell count, and viral load that had a window period of 259 days, accurately estimated HIV incidence in all three epidemic settings and provided sufficient power to detect an intervention effect in Project Accept.
In a Southern African setting, HIV incidence estimates and intervention effects can be accurately estimated from cross-sectional surveys using a MAA. The improved accuracy in cross-sectional incidence testing that a MAA provides is a powerful tool for HIV surveillance and program evaluation.
Disease-suppressive soils encompass specific plant-pathogen-microbial interactions and represent a rare example of an agroecosystem where soil conditions and microbiome together prevent the pathogen ...from causing disease. Such soils have the potential to serve as a model for characterizing soil pathogen-related aspects of soil health, but the mechanisms driving the establishment of suppressive soils vary and are often poorly characterized. Yet, they can serve as a resource for identifying markers for beneficial activities of soil microorganisms concerning pathogen prevention. Many recent studies have focused on the nature of disease-suppressive soils, but it has remained difficult to predict where and when they will occur. This review outlines current knowledge on the distribution of these soils, soil manipulations leading to pathogen suppression, and markers including bacterial and fungal diversity, enzymes, and secondary metabolites. The importance to consider soil legacy in research on the principles that define suppressive soils is also highlighted. The goal is to extend the context in which we understand, study, and use disease-suppressive soils by evaluating the relationships in which they occur and function. Finally, we suggest that disease-suppressive soils are critical not only for the development of indicators of soil health, but also for the exploration of general ecological principles about the surrounding landscape, effects of deeper layers of the soil profile, little studied soil organisms, and their interactions for future use in modern agriculture.
The rank statistic... (equation omitted), with Ri(t) being the rank of... and... being the random sample from a distribution with a cdf F, is considered as a random process with t in the role of ...parameter. Under some assumptions on ci, xi and on the underlying distribution, it is proved that the process... converges weakly to the Gaussian process. This generalizes the existing results where the one-dimensional case... was considered. It is believed that the method of the proof can be easily modified for the signed-rank statistics of Wilcoxon type. Finally, the results are used to find the second order asymptotic distribution of the R-estimator based on the Wilcoxon scores and also to investigate the length of the confidence interval for a single parameter Beta l.
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