The extension reached by the minimization of the polarity distances during the evolution of the genetic code

Summary The level reached by the optimization of the polarity distances during the evolution of the genetic code was investigated. The results, although not conclusive, indicate that this optimization level is higher than the data reported in the literature. The results seem compatible with the reaching of an evolutionary minimum, with respect to the optimization of the polarity distances, by the genetic code during its formation.     

Spatial autocorrelation invalidates the Dow-Cheverud test

Dow and Cheverud (Am. J. Phys. Anthropol. 68:367–373, 1985) have published a statistical test for comparing any three similarity matrices. Using both simulations and analytical arguments, I establish that the presence of spatial autocorrelation, a common feature of geographically based anthropological and biological data, causes this test to reject too often. Increasing the spatial autocorrelation increases the spurious rejection rate. About 20% of the papers that reference Dow and Cheverud's paper have used their test with spatially autocorrelated data. Mantel's (Cancer Res. 27:209–220, 1967) method, when used as a test of spatial autocorrelation, is unaffected by these considerations, since its null hypothesis is that the data are uncorrelated. © 1992 Wiley-Liss, Inc.     

Selective burning of forest vegetation in Canton Ticino (southern Switzerland)

Abstract

Detailed knowledge of factors controlling fire regime is a prerequisite for efficient fire management. We analyzed the fire selectivity of given forest vegetation classes both in terms of fire frequency and fire size for the present fire regime (1982–2005) in Canton Ticino (southern Switzerland). To this end, we investigated the dataset in four categories (all fires, anthropogenic winter fires, anthropogenic summer fires, and natural summer fires) and performed 1000 random Monte Carlo simulations on frequency and size. Anthropogenic winter and summer fires have a similar selectivity, occurring mostly at low elevations in chestnut stands, broadleaved forests, and in the first 50 m from the forest edge. In winter half of the fires in chestnut stands are significantly larger than 1.0 ha and the average burnt area in some coniferous forests tends to be high. Lightning fires seem to occur more frequently in spruce stands and less often in the summer‐humid chestnut and beech stands and the 50–100 m buffer area. In beech forests, in mixed forests, and in the spruce stands affected by natural fire in summer, the fires tend to be small in size. The selectivity observed, especially the selectivity of anthropogenic fires in terms of fire frequency, seems to be also related to geographical parameters such as altitude and aspect, and to anthropogenic characteristics such as closeness to roads or buildings.     

Robust inference for the stepped wedge design

Stepped wedge designed trials are a type of cluster-randomized study in which the intervention is introduced to each cluster in a random order over time. This design is often used to assess the effect of a new intervention as it is rolled out across a series of clinics or communities. Based on a permutation argument, we derive a closed-form expression for an estimate of the intervention effect, along with its standard error, for a stepped wedge design trial. We show that these estimates are robust to misspecification of both the mean and covariance structure of the underlying data-generating mechanism, thereby providing a robust approach to inference for the intervention effect in stepped wedge designs. We use simulations to evaluate the type 1 error and power of the proposed estimate and to compare the performance of the proposed estimate to the optimal estimate when the correct model specification is known. The limitations, possible extensions, and open problems regarding the method are discussed.     

Randomization inference with general interference and censoring

Interference occurs between individuals when the treatment (or exposure) of one individual affects the outcome of another individual. Previous work on causal inference methods in the presence of interference has focused on the setting where it is a priori assumed that there is “partial interference,” in the sense that individuals can be partitioned into groups wherein there is no interference between individuals in different groups. Bowers et al. (2012, Political Anal, 21, 97–124) and Bowers et al. (2016, Political Anal, 24, 395–403) consider randomization-based inferential methods that allow for more general interference structures in the context of randomized experiments. In this paper, extensions of Bowers et al. that allow for failure time outcomes subject to right censoring are proposed. Permitting right-censored outcomes is challenging because standard randomization-based tests of the null hypothesis of no treatment effect assume that whether an individual is censored does not depend on treatment. The proposed extension of Bowers et al. to allow for censoring entails adapting the method of Wang et al. (2010, Biostatistics, 11, 676–692) for two-sample survival comparisons in the presence of unequal censoring. The methods are examined via simulation studies and utilized to assess the effects of cholera vaccination in an individually randomized trial of 73 000 children and women in Matlab, Bangladesh.     

EDISON-WMW: Exact Dynamic Programing Solution of the Wilcoxon–Mann–Whitney Test

In many research disciplines, hypothesis tests are applied to evaluate whether findings are statistically significant or could be explained by chance. The Wilcoxon–Mann–Whitney(WMW) test is among the most popular hypothesis tests in medicine and life science to analyze if two groups of samples are equally distributed. This nonparametric statistical homogeneity test is commonly applied in molecular diagnosis. Generally, the solution of the WMW test takes a high combinatorial effort for large sample cohorts containing a significant number of ties. Hence, P value is frequently approximated by a normal distribution. We developed EDISON-WMW, a new approach to calculate the exact permutation of the two-tailed unpaired WMW test without any corrections required and allowing for ties. The method relies on dynamic programing to solve the combinatorial problem of the WMW test efficiently. Beyond a straightforward implementation of the algorithm, we presented different optimization strategies and developed a parallel solution. Using our program,the exact P value for large cohorts containing more than 1000 samples with ties can be calculated within minutes. We demonstrate the performance of this novel approach on randomly-generated data, benchmark it against 13 other commonly-applied approaches and moreover evaluate molecular biomarkers for lung carcinoma and chronic obstructive pulmonary disease(COPD). We foundthat approximated P values were generally higher than the exact solution provided by EDISONWMW. Importantly, the algorithm can also be applied to high-throughput omics datasets, where hundreds or thousands of features are included. To provide easy access to the multi-threaded version of EDISON-WMW, a web-based solution of our algorithm is freely available at http://www.ccb.uni-saarland.de/software/wtest/.     

Exclusion effects on vegetation characteristics and their correlation to soil factors in the semi-arid rangeland of Mu Us Sandland, China

Exclusion has been applied as a main measure for re-vegetation all over the world. This paper, by comparing the results of year-round exclusion, seasonal exclusion, and non-exclusion, quantified the vegetation variations under three different exclusion measures and their correlation to soil factors. The analysis results for community species component and plant diversity using multi-response permutation procedures (MRPPs) showed that exclusion did change the species component and increase plant diversity remarkably, while the period of exclusion had no significant influence on these two community features. The indicator species analysis and calculation of similarity indices indicated that community for year-round exclusion were becoming xerophytization and unpalatability, and showed highly spatial heterogeneity of plant species distribution, whereas community for seasonal exclusion was under stable non-equilibrium condition. Detrended correspondence analysis (DCA) and detrend canonical correspondence analysis (DCCA) results of relationship between plant species and soil variables demonstrated that soil moisture was a controlling factor for plant species component, microbiotic soil crust cover, soil organic matter, and soil bulk density had significant effects on soil moisture, among which microbiotic soil crust was a leading factor owing to its limitation to rainfall infiltration on the one hand, and its constraints to entrance of herbaceous seeds into soil or to germination of soil seeds on the other hand. As a result of long-term removal of animal grazing, crust kept intact in year-round exclusion community, which was a main reason of community xerophytization. It was also obvious from ordination results that some important environmental factors, such as tempo-spatial change of rainfall and corresponding tempo-spatial change of soil moisture, were neglected during direct gradient analysis. In addition, biodiversity was close related to soil nutrients as well as to soil moisture condition (soil water content and crust cover), and it had positive relation to available N, and negative relation to available P. Higher soil N had advantage to non-leguminous plants growth on nutrition-poor sand land definitely. The impact of P to community component was unclear and should be studied from plant physiology. Further researches on non-equilibrium theory in semi-arid rangeland will provide a scientific and flexible animal development paradigm for being implementing livestock fen-raising and grazing-forbidden policies in China. __________ Translated from Acta Ecologica Sinica, 2005, 25(12): 3212–3219 [译自: 生态学报]     

Exclusion effects on vegetation characteristics and their correlation to soil factors in the semi-arid rangeland of Mu Us Sandland,China

Exclusion has been applied as a main measure for re-vegetation all over the world.This paper,by comparing the results of year-round exclusion,seasonal exclusion,and non-exclusion,quantified the vegetation variations under three different exclusion measures and their correlation to soil factors.The analysis results for community species component and plant diversity using multi-response permutation procedures (MRPPs)showed that exclusion did change the species component and increase plant diversity remarkably,while the period of exclusion had no significant influence on these two community features.The indicator species analysis and calculation of similarity indices indicated that community for year-round exclusion were becoming xerophytization and unpalatability,and showed highly spatial heterogeneity of plant species distribution,whereas community for seasonal exclusion was under stable non-equilibrium condition.Detrended correspondence analysis (DCA)and detrend canonical correspondence analysis (DCCA)results of relationship between plant species and soil variables demonstrated that soil moisture was a controlling factor for plant species component,microbiotic soil crust cover,soil organic matter,and soil bulk density had significant effects on soil moisture,among which microbiotic soil crust was a leading factor owing to its limitation to rainfall infiltration on the one hand,and its constraints to entrance of herbaceous seeds into soil or to germination of soil seeds on the other hand.As a result of long-term removal of animal grazing,crust kept intact in year-round exclusion community,which was a main reason of community xerophytization.It was also obvious from ordination results that some important environmental factors,such as tempo-spatial change of rainfall and corresponding tempo-spatial change of soil moisture,were neglected during direct gradient analysis.In addition,biodiversity was close related to soil nutrients as well as to soil moisture condition (soil water content and crust cover),and it had positive relation to available N,and negative relation to available P.Higher soil N had advantage to non-leguminous plants growth on nutrition-poor sand land definitely.The impact of P to community component was unclear and should be studied from plant physiology.Further researches on nonequilibrium theory in semi-arid rangeland will provide a scientific and flexible animal development paradigm for being implementing livestock fen-raising and grazing-forbidden policies in China.     

Alteration of the disulfide-coupled folding pathway of BPTI by circular permutation

The kinetics of disulfide-coupled folding and unfolding of four circularly permuted forms of bovine pancreatic trypsin inhibitor (BPTI) were studied and compared with previously published results for both wild-type BPTI and a cyclized form. Each of the permuted proteins was found to be less stable than either the wild-type or circular proteins, by 3-8 kcal/mole. These stability differences were used to estimate effective concentrations of the chain termini in the native proteins, which were 1 mM for the wild-type protein and 2.5 to 4000 M for the permuted forms. The circular permutations increased the rates of unfolding and caused a variety of effects on the kinetics of refolding. For two of the proteins, the rates of a direct disulfide-formation pathway were dramatically increased, making this process as fast or faster than the competing disulfide rearrangement mechanism that predominates in the folding of the wild-type protein. These two permutations break the covalent connectivity among the beta-strands of the native protein, and removal of these constraints appears to facilitate direct formation and reduction of nearby disulfides that are buried in the folded structure. The effects on folding kinetics and mechanism do not appear to be correlated with relative contact order, a measure of overall topological complexity. These observations are consistent with the results of other recent experimental and computational studies suggesting that circular permutation may generally influence folding mechanisms by favoring or disfavoring specific interactions that promote alternative pathways, rather than through effects on the overall topology of the native protein.