An empirical bayes estimator of seismic events using wavelet packet bases

An empirical Bayes (EB) estimator is constructed to denoise a time series containing quarry blasts in New England. This estimator is portable and can be used more generally to denoise seismic events. The EB estimator uses adaptive wavelet packet analysis (WPA) for transformation selection via an EB approximation to the standard entropy functional. We compare this basis selection method to the discrete wavelet transform (DWT) and best basis selection via Stein’s unbiased risk estimator (SURE). The relation of sparsity of representation to quality of estimation over a range of signal-to-noiserations (SNR) for synthetic quarry blast events is demonstrated. For functions with sparse representations, we have found that, at moderate SNR, WPA significantly out performs DWT. The EB best basis performs similarly to SURE best basis, thereby lending credence to the EB method. Finally, we compare DWT and WPA. methods for denoising quarry blast events recorded in New England.     

A new variance estimator for parameters of semiparametric generalized additive models

Generalized additive models (GAMs) have become popular in the air pollution epidemiology literature. Two problems, recently surfaced, concern implementation of these semiparametric models. The first problem, easily corrected, was laxity of the default convergence criteria. The other, noted independently by Klein, Flanders, and Tolbert, and Ramsay, Burnett, and Krewski concerned variance estimates produced by commercially available software. In simulations, they were as much as 50% too small. We derive an expression for a variance estimator for the parametric component of generalized additive models that can include up to three smoothing splines, and show how the standard error (SE) estimated by this method differs from the corresponding SE estimated with error in a study of air pollution and emergency room admissions for cardiorespiratory disease. The derivation is based on asymptotic linearity. Using Monte Carlo experiments, we evaluated performance of the estimator in finite samples. The estimator performed well in Monte Carlo experiments, in the situations considered. However, more work is needed to address performance in additional situations. Using data from our study of air pollution and cardiovascular disease, the standard error estimated using the new method was about 10% to 20% larger than the biased, commercially available standard error estimate.     

A blended estimator for a measure of agreement with a gold standard

St. Laurent developed a measure of agreement for method comparison studies in which an approximate method of measurement was compared to a gold standard method of measurement. The measure of agreement proposed was shown to be related to a population intraclass correlation coefficient. In this paper, the authors develop a family of estimators for the measure of agreement based on pivotal quantities. A blend of two particular members of the family is suggested as an estimator itself. In general, the blended estimator outperforms the maximum likelihood estimator in terms of bias and mean-squared error.     

植物抗旱生理研究概述

本文介绍了近年来植物抗旱生理研究进展。其内容渗透调节作用、在干旱条件下生物膜结构的变化和膜脂过氧化、干旱诱导蛋白的研究和作物生理生态及抗旱节水增产。     

Estimating the proportions of closely related species: Performance of the two-phase ratio estimator

In many ecological field contexts, accurately classifying closely related species based on phenotypic characteristics may be difficult. In such cases, definitive classification of species may require expensive genetic analysis of tissues or extensive quantitative measurements. If inexpensive phenotype-based species classifications are highly correlated with expensive but definitive classifications, however, then estimating the proportion of a target species in a mixed species complex using a two-phase ratio estimator may prove cost-efficient. In two-phase ratio estimation, a first-phase sample is randomly selected, and phenotype is used to classify all individuals in the sample. A smaller, second-phase sample is then randomly selected from the first-phase sample, and a definitive method is used to classify the individuals in this subsample. Net relative efficiency (i.e., cost-effectiveness) of the optimally allocated two-phase ratio estimator of a proportion depends on the relative costs of classification at the first and second phases, on the phenotypic classification accuracy for the target species (sensitivity) and nontarget species (specificity), and on the magnitude of the target species proportion. Results are presented that allow assessment of the circumstances in which this two-phase estimation approach can be recommended over an equal-cost single-phase approach based only on expensive but definitive classification. An illustrative application of these methods is provided using an example of two closely related, sympatric, anadromous salmonid species: steelhead (Oncorhynchus mykiss) and coastal cutthroat trout (O. clarki clarki).     

Can the sample variance estimator be improved by using a covariate?

Variance componentsare quantities of central interest in many applications, e.g., in cultivar yield stability analysis and in the analysis of measurement errors. In some applications, the feasible sample size is rather limited, leading to estimates of variance components that are subject to considerable sampling variation. For example, new crop cultivars are tested in only a few environments before release to the market, so the sample size for the variance across environments is small. Similarly, testing a new measurement instrument for some chemical compound may be costly, allowing only a limited number of replications. This article investigates the potential for improving the usual sample variance estimator by exploiting covariate information. In a cultivartrial, yield data may be available for only a few environments while meteorological data or data on a standard cultivar has been recorded for a very large number of environments. Likewise, in the analysis of measurement errors, there may be long-term data on a standard measurement procedure that can be used as a covariate to improve the variance estimate for a new instrument. It is shown in this article that the gain in accuracy achieved by using a covariate can be considerable, provided there is sufficient correlation between the covariate and the variable of interest.     

Randomization tests for time effects and heterogeneity in capture probabilities for closed populations

We propose the use of randomization tests to detect time effects and heterogeneity in capture probabilities of individuals in a closed-population mark-recapture study. The results of a simulation study show the randomization procedures can be implemented so that tests are robust to extraneous sources of variation, with good power to detect the desired effects. We apply the tests to two examples of real data, finding very strong evidence of heterogeneous capture probabilities in both data sets and highly significant time effects for one of the sets.     

Evaluating the physical capture method of terminal restriction fragment length polymorphism for comparison of soil microbial communities

Terminal restriction fragment length polymorphism (T-RFLP) is a popular method of comparative microbial community analysis which is normally accomplished by tagging terminal restriction fragments (T-RFs) with a fluorescent primer. Here, we evaluate an alternative method of T-RFLP where T-RFs are physically captured using a biotinylated primer and streptavidin-coated beads. This eliminates one of the primary criticisms of T-RFLP, namely that T-RFs cannot be identified by sequence analysis, and also represents an alternative method for collecting T-RFLP profiles. Microbial communities from forest, agricultural, and turf soils were investigated using several sets of primers specific for different microbial groups. The physical capture method of T-RFLP resulted in similar profiles to those generated by fluorescent T-RFLP. The relationships among ecosystem types captured by both methods and revealed by ordination were virtually identical. The total variance in the profiles that was attributed to ecosystem type was approximately equal, or greater, when generated by the physical capture method, depending on the primers used. However, physical capture T-RFLP resolved fewer T-RFs than fluorescent T-RFLP, and this may reduce the sensitivity to changes in non-dominant populations within the community. Direct cloning and sequencing of physical capture T-RFs revealed that most bands were not comprised of sequences related to those in the database that would generate T-RFs of similar size. T-RFs should therefore be identified by sequencing, rather than by comparing the sizes of T-RFs to computer digests of database sequences. Physical capture T-RFLP should be a useful tool to identify T-RFs by sequencing, and for laboratories without economical access to equipment required to perform fluorescent T-RFLP.     

An appreciation of the contribution of Frank Stevenson to the advancement of studies of soil organic matter and humic substances

Purpose

The aims of this paper are to outline the state of knowledge with regard to the chemistry of soil organic matter (SOM) prior to 1950; then, to review and evaluate the contributions made by Frank Stevenson during Stevenson’s research period (1950–1994); and subsequently to outline advances that are being made in the modern era.

Progress in the Stevenson period

Frank Stevenson’s research career began in the middle of the twentieth century when a number of techniques of colloid chemistry were available to him, but relatively few of the recently developed instrumental techniques and other procedures of analytical organic chemistry that have enabled significant advances to be made in the chemistry and properties of SOM components.The contributions that Frank Stevenson has made to the chemistry of SOM and of humic substances (HSs) are an integral part of his book (first and second editions) Humus Chemistry: Genesis, Composition, Reactions. The validity of the terms humus and HSs are being questioned as legitimate terms that describe definable components, and SOM is being viewed as a ‘continuum of progressively decomposing organic compounds’. The legitimacy of isolating the organic matter components from their native soil environment is questioned. Those who pose such questions would do well to consider how progress could have been made in the vital life sciences areas of, for example, proteomics and genomics, without the isolation of the relevant cellular components. We recognise the importance of clear and rigorous definitions of HS components and stress the need to isolate these components from the SOM matrix as a prerequisite to the study of the composition, structure and reactivity of these components. We disagree with proposals or suggestions that do not recognise HSs as a scientific entity, and we feel sure that Frank Stevenson would have supported this stance. Various studies of SOM and of HSs have taken place over the centuries, but progress was slow because the tools required to study such complex systems were not available. Frank Stevenson’s research involved many areas of humic chemistry, and his major advances were in aspects of functionality and in the interactions of humic functional groups with metals and to a lesser extent with anthropogenic organic chemicals. His studies of nitrogen and of ammonia in relation to organic matter also had a very great impact.

Progress in the modern era

Frank Stevenson can be said to have provided the stimulation that enabled beginners and established scientists to obtain a good grasp of the fundamentals of SOM and the humic sciences. His scientific contributions have catalysed many of the significant advances that have been made in the field since he retired. In the final section, some of the advances that have been made using modern analytical techniques are addressed and some of the controversial topics that have recently arisen are discussed.

     

Identification of mtDNA lineages of Sus scrofa by multiplex single base extension for the authentication of processed food products

A genetic method to identify the breed of origin could serve as a useful tool for inspecting the authenticity of the increasing number of monobreed foodstuffs, such as those derived from small local European pig breeds. Mitochondrial DNA (mtDNA) is practically the only reliable genomic target for PCR in processed products, and its haploid nature and strict maternal inheritance greatly facilitate genetic analysis. As a result of strategies that sought to improve the production traits of European pigs, most industrial breeds presently show a high frequency of Asian alleles, while the absence or low frequency of such Asian alleles has been observed in small rustic breeds from which highly prized dry-cured and other traditional products are derived. Therefore, the detection of Asian ancestry would indicate nonconformity in Protected Denomination of Origin products. This study presents a single base extension assay based on 15 diagnostic mtDNA single nucleotide polymorphisms to discriminate between Asian and European Sus scrofa lineages. The test was robust, sensitive and accurate in a wide range of processed foodstuffs and allowed accurate detection of pig genetic material and identification of maternal ancestry. A market survey suggested that nonconformity of products derived from Portuguese breeds is an unusual event at present, but regular surveys both in the local populations and in commercial products would be advisible. Taking into consideration the limitations presented by other methodologies, this mtDNA-based test probably attains the highest resolution for the direct genetic test for population of origin in Sus scrofa food products.     

Collaborative study of an extension of the Mills et al. method for the determination of pesticide residues in foods.

Fifteen laboratories collaboratively determined parathion, o,p'-DDT, p,p'-DDT, and p,p'-DDE in kale, and lindane, dieldrin, heptachlor epoxide, and p,p'-DDE in eggs, using electron capture gas-liquid chromatography (potassium chloride thermionic detector for parathion). Pesticide levels ranged from 0.033 ppm heptachlor epoxide to 3.32 ppm p,p'-DDT. Mean recoveries (+/- standard deviations) were: parathion 91+/-15%, o,p'-DDT 99+/-8%, P,P'-DDT 97+/-8%, lindane 94+/-4%, dieldrin 106+/-8%, heptachloro epoxide 106+/-5%, p,p'-DDE 94+/-8% in eggs and 101+/-9% in kale. The methods have been adopted as official first action.     

Tolerance of West Indian manatees to capture and handling

Ninety-two West Indian manatees (Trichechus manatus) have been captured in the southeastern United States from October 1975 through November 1983 with no evidence of an unusual susceptibility to capture myopathy. Of these, 53 were radio-tracked or observed in the field following capture with no evidence of delayed capture stress. Blood samples obtained at capture for 20 wild individuals displayed no elevation in biochemical variables typically seen in mammalian capture myopathy cases. Thirty-one manatees captured for rescue and rehabilitation generally did not exhibit symptoms of capture myopathy, although in one case marked elevations in creatinine phosphokinase were observed, probably related to lengthy transport. Necropsy findings for 20 terminal cases that died of various causes unrelated to their rescue or handling did not indicate the involvement of any gross or histological lesions of capture myopathy. Historical records for the capture and handling of about 150 West Indian manatees during the 1900s also suggest a tolerance to these activities. Recent observations on the probable susceptibility of dugongs (Dugong dugon) to capture stress apparently cannot be extended to West Indian manatees.     

Modified method for electron capture gas-liquid chromatographic determination of diethylstilbestrol residues in urine of fattened bulls

A gas-liquid chromatographic (GLC) method with electron capture (EC) detection was developed for determining diethylstilbestrol residues in the urine of fattened bulls. Diethylstilbestrol (DES) is extracted into benzene, and then into 1N sodium hydroxide. The pH of the phenolic fraction (alkaline phase) is adjusted to 10.2 and DES is extracted again into benzene. Sample extracts are cleaned up on silica gel. Trifluoroacetic anhydride (TFAA) is used as acylation reagent, and the derivatized sample is chromatographed on a 3% OV-17 column and measured with a 63Ni EC detector. The method is suitable for determining residues at levels as low as 2 ppb.     

Incidental capture of marine turtles by the Italian trawl fishery in the north Adriatic Sea

In the north Adriatic Sea on-board observations on midwater and bottom trawlers were carried out during years 1999 and 2000. Results indicate that the north Adriatic Sea, and especially the north-east part, is a very important foraging and overwintering habitat for loggerhead turtles (Caretta caretta). Since the distribution of fishing effort in the area is not known, the total turtle catch by the Italian bottom trawl fleet was conservatively estimated from the lower catch rate observed in the south-west sub-area: 4273 turtle captures/year (95% C.I.=2186-8546). The actual total catch in the whole north Adriatic is likely to be much higher, due both to an unknown Italian trawling effort in the south-west part with multi-gear vessels and to the Italian and Croatian trawling efforts in the north-east part, where catch rate was 15 times greater than in the south-west part. In the south-west sub-area 9.4% of captured turtles were dead and potential mortality (assuming that all comatose turtles would die too) was 43.8%. Hence, trawling in the north Adriatic is likely to represent a serious threat to the populations, and possible conservation measures are discussed.     

浅析农技推广信息综合服务系统建设中的风险管理

本文以农技推广信息综合服务系统项目的建设为例,通过一定的专家评分方法,得出项目建设过程中存在的六个主要风险,并提出相应的风险控制对策,以降低对项日的影响。     

Ecological studies in the ratanica catchment (Carpathian foothills,S Poland) — An overview

This paper includes an overview of ecological studies conducted since 1986 in the Ratanica pine-beech forested catchment located in the polluted, high populated southern part of Poland. General characteristics of the catchment (including soil and vegetation, air pollution, input/output of nutrients and pollutants, element budget data and forest health assessment) are presented. Based on biogeochemical and bioindication results, the Ratanica catchment has been classified as a moderately to heavily deteriorated area. Predictions for this forested catchment for various deposition of anthropogenic pollutants, are also disscused.     

四种客观权重确定方法在粮虫可拓分类中的应用比较

储粮害虫的数字特征多,特征之间混合度比较大,可用可拓决策分析来解决其分类问题。在粮虫的可拓分类中,需要自动确定特征的客观权重,以避免传统的专家经验法在确定权重方面所带来的人为因素的影响。该文提出了模糊决策矩阵和均值决策矩阵2种构建决策矩阵的方法。将最大离差法、类间标准差法、CRITIC法和熵值法4种确定客观权重的方法分别应用到粮虫的分类中,并通过基于经典域和节域不同构建方法的2种可拓分类器进行了分析和比较。对粮仓中危害严重的9类粮虫进行了自动分类,结果表明基于模糊决策矩阵的最大离差法权重是粮虫可拓分类的最佳方案,识别率达到93%。