A jackknife variance estimator for unequal probability sampling

The jackknife method is often used for variance estimation in sample surveys but has only been developed for a limited class of sampling designs.We propose a jackknife variance estimator which is defined for any without-replacement unequal probability sampling design. We demonstrate design consistency of this estimator for a broad class of point estimators. A Monte Carlo study shows how the proposed estimator may improve on existing estimators.

Variance estimation with highly stratified sampling designs with unequal probabilities

It is common practice to design a survey with a large number of strata. However, in this case the usual techniques for variance estimation can be inaccurate. This paper proposes a variance estimator for estimators of totals. The method proposed can be implemented with standard statistical packages without any specific programming, as it involves simple techniques of estimation, such as regression fitting.

Variance estimation for systematic sampling from deliberately ordered populations

The systematic sampling (SYS) design (Madow and Madow, 1944) is widely used by statistical offices due to its simplicity and efficiency (e.g., Iachan, 1982). But it suffers from a serious defect, namely, that it is impossible to unbiasedly estimate the sampling variance (Iachan, 1982) and usual variance estimators (Yates and Grundy, 1953) are inadequate and can overestimate the variance significantly (Särndal et al., 1992). We propose a novel variance estimator which is less biased and that can be implemented with any given population order. We will justify this estimator theoretically and with a Monte Carlo simulation study.

Variance estimation with Chao's sampling scheme

We show that the Hájek (Ann. Math Statist. (1964) 1491) variance estimator can be used to estimate the variance of the Horvitz–Thompson estimator when the Chao sampling scheme (Chao, Biometrika 69 (1982) 653) is implemented. This estimator is simple and can be implemented with any statistical packages. We consider a numerical and an analytic method to show that this estimator can be used. A series of simulations supports our findings.

A predictive model for early-warning of Septoria leaf blotch on winter wheat

Disease-weather relationships influencing Septoria leaf blotch (SLB) preceding growth stage (GS) 31 were identified using data from 12 sites in the UK covering 8 years. Based on these relationships, an early-warning predictive model for SLB on winter wheat was formulated to predict the occurrence of a damaging epidemic (defined as disease severity of 5% or > 5% on the top three leaf layers). The final model was based on accumulated rain > 3 mm in the 80-day period preceding GS 31 (roughly from early-February to the end of April) and accumulated minimum temperature with a 0A degrees C base in the 50-day period starting from 120 days preceding GS 31 (approximately January and February). The model was validated on an independent data set on which the prediction accuracy was influenced by cultivar resistance. Over all observations, the model had a true positive proportion of 0.61, a true negative proportion of 0.73, a sensitivity of 0.83, and a specificity of 0.18. True negative proportion increased to 0.85 for resistant cultivars and decreased to 0.50 for susceptible cultivars. Potential fungicide savings are most likely to be made with resistant cultivars, but such benefits would need to be identified with an in-depth evaluation.

The utility of leaf flavonoids as taxonomic markers for some Malaysian species of the tribe Shoreae (Dipterocarpaceae)

A flavonoid survey was carried out on 45 taxa from the genera Shorea, Hopea, Parashorea, Neobalanocarpus, and Dryobalanops of the tribe Shoreae in the Dipterocarpaceae. The study showed significant chemotaxonomic differences in leaf flavonoid aglycone patterns and the presence of tannins in these taxa. The flavonoid patterns are useful in the delimitation of some taxa. For example, the genus Parashorea is distinguished by the universal presence of kaempferol 3-methyl ether, and the monotypic genus Neobalanocarpus is unique in not producing ellagic and gallo tannins. The presence of chalcones and flavone C-glycosides supports the separation of the genus Hopea into two sections, section Dryobalanoides and section Hopea in Ashton's classification, which is based on the type of venation. The flavonoid distributions in this study show that they can be very useful for differentiating between the Balau group in the genus Shorea, and some scaly barked Hopea species, particularly H. helferi (lintah bukit), H. nutans (giam), and H. ferrea (malut). (C) 2008 The Linnean Society of London.

Apical leaf necrosis as a defence mechanism against pathogen attack: effects of high nutrient availability on onset and rate of necrosis

An outdoor experiment was conducted to increase understanding of apical leaf necrosis in the presence of pathogen infection. Holcus lanatus seeds and Puccinia coronata spores were collected from two adjacent and otherwise similar habitats with differing long-term N fertilization levels. After inoculation, disease and necrosis dynamics were observed during the plant growing seasons of 2003 and 2006. In both years high nutrient availability resulted in earlier disease onset, a higher pathogen population growth rate, earlier physiological apical leaf necrosis onset and a reduced time between disease onset and apical leaf necrosis onset. Necrosis rate was shown to be independent of nutrient availability. The results showed that in these nutrient-rich habitats H. lanatus plants adopted necrosis mechanisms which wasted more nutrients. There was some indication that these necrosis mechanisms were subject to local selection pressures, but these results were not conclusive. The findings of this study are consistent with apical leaf necrosis being an evolved defence mechanism.

Application of real-time and multiplex PCR assays to study leaf blotch epidemics in barley

Leaf blotch, caused by Rhynchosporium secalis, was studied in a range of winter barley cultivars using a combination of traditional plant pathological techniques and newly developed multiplex and real-time polymerase chain reaction (PCR) assays. Using PCR, symptomless leaf blotch colonization was shown to occur throughout the growing season in the resistant winter barley cv. Leonie. The dynamics of colonization throughout the growing season were similar in both Leonie and Vertige, a susceptible cultivar. However, pathogen DNA levels were approximately 10-fold higher in the susceptible cultivar, which expressed symptoms throughout the growing season. Visual assessments and PCR also were used to determine levels of R. secalis colonization and infection in samples from a field experiment used to test a range of winter barley cultivars with different levels of leaf blotch resistance. The correlation between the PCR and visual assessment data was better at higher infection levels (R(2) = 0.81 for leaf samples with >0.3% disease). Although resistance ratings did not correlate well with levels of disease for all cultivars tested, low levels of infection were observed in the cultivar with the highest resistance rating and high levels of infection in the cultivar with the lowest resistance rating.

Changes in the flavonoid and phenolic acid contents and antioxidant activity of red leaf lettuce (Lollo Rosso) due to cultivation under plastic films varying in ultraviolet transparency

Red leaf lettuce (Lollo Rosso) was grown under three types of plastic films that varied in transparency to UV radiation (designated as UV block, UV low, and UV window). Flavonoid composition was determined by high-performance liquid chromatography (HPLC), total phenolics by the Folin-Ciocalteu assay, and antioxiclant capacity by the oxygen radical absorbance capacity (ORAC) assay. Exposure to increased levels of UV radiation during cultivation caused the leaves to redden and increased concentrations of total phenols and the main flavonoids, quercetin and cyanidin glycosides, as well as luteolin conjugates and phenolic acids. The total phenol content increased from 1.6 mg of gallic acid equivalents (GAE)/g of fresh weight (FW) for lettuce grown under UV block film to 2.9 and 3.5 mg of GAE/g of FW for lettuce grown under the UV low and UV window films. The antioxiclant activity was also higher in lettuce exposed to higher levels of UV radiation with ORAC values of 25.4 and 55.1 mu mol of Trolox equivalents/g of FW for lettuce grown under the UV block and UV window films, respectively. The content of phenolic acids, quantified as caffeic acid, was also different, ranging from 6.2 to 11.1 mu mol/g of FW for lettuce cultivated under the lowest and highest UV exposure plastic films, respectively. Higher concentrations of the flavonoid glycosides were observed with increased exposure to UV radiation, as demonstrated by the concentrations of aglycones after hydrolysis, which were cyanidin (ranging from 165 to 793 mu g/g), quercetin (ranging from 196 to 880,mu g/g), and luteolin (ranging from 19 to 152 mu g/g). The results demonstrate the potential of the use of UV-transparent plastic as a means of increasing beneficial flavonoid content of red leaf lettuce when the crop is grown in polytunnels.

Changes in the flavonoid and phenolic acid contents and antioxidant activity of red leaf lettuce (Lollo Rosso) due to cultivation under plastic films varying in ultraviolet transparency

Red leaf lettuce (Lollo Rosso) was grown under three types of plastic films that varied in transparency to UV radiation (designated as UV block, UV low, and UV window). Flavonoid composition was determined by high-performance liquid chromatography (HPLC), total phenolics by the Folin-Ciocalteu assay, and antioxiclant capacity by the oxygen radical absorbance capacity (ORAC) assay. Exposure to increased levels of UV radiation during cultivation caused the leaves to redden and increased concentrations of total phenols and the main flavonoids, quercetin and cyanidin glycosides, as well as luteolin conjugates and phenolic acids. The total phenol content increased from 1.6 mg of gallic acid equivalents (GAE)/g of fresh weight (FW) for lettuce grown under UV block film to 2.9 and 3.5 mg of GAE/g of FW for lettuce grown under the UV low and UV window films. The antioxiclant activity was also higher in lettuce exposed to higher levels of UV radiation with ORAC values of 25.4 and 55.1 mu mol of Trolox equivalents/g of FW for lettuce grown under the UV block and UV window films, respectively. The content of phenolic acids, quantified as caffeic acid, was also different, ranging from 6.2 to 11.1 mu mol/g of FW for lettuce cultivated under the lowest and highest UV exposure plastic films, respectively. Higher concentrations of the flavonoid glycosides were observed with increased exposure to UV radiation, as demonstrated by the concentrations of aglycones after hydrolysis, which were cyanidin (ranging from 165 to 793 mu g/g), quercetin (ranging from 196 to 880,mu g/g), and luteolin (ranging from 19 to 152 mu g/g). The results demonstrate the potential of the use of UV-transparent plastic as a means of increasing beneficial flavonoid content of red leaf lettuce when the crop is grown in polytunnels.

Apical leaf necrosis and leaf nitrogen dynamics in diseased leaves: a model study

Apical leaf necrosis is a physiological process related to nitrogen (N) dynamics in the leaf. Pathogens use leaf nutrients and can thus accelerate this physiological apical necrosis. This process differs from necrosis occurring around pathogen lesions (lesion-induced necrosis), which is a direct result of the interaction between pathogen hyphae and leaf cells. This paper primarily concentrates on apical necrosis, only incorporating lesion-induced necrosis by necessity. The relationship between pathogen dynamics and physiological apical leaf necrosis is modelled through leaf nitrogen dynamics. The specific case of Puccinia triticina infections on Triticum aestivum flag leaves is studied. In the model, conversion of indirectly available N in the form of, for example, leaf cell proteins (N-2(t)) into directly available N (N-1(t), i.e. the form of N that can directly be used by either pathogen or plant sinks) results in apical necrosis. The model reproduces observed trends of disease severity, apical necrosis and green leaf area (GLA) and leaf N dynamics of uninfected and infected leaves. Decreasing the initial amount of directly available N results in earlier necrosis onset and longer necrosis duration. Decreasing the initial amount of indirectly available N, has no effect on necrosis onset and shortens necrosis duration. The model could be used to develop hypotheses on how the disease-GLA relation affects yield loss, which can be tested experimentally. Upon incorporation into crop simulation models, the model might provide a tool to more accurately estimate crop yield and effects of disease management strategies in crops sensitive to fungal pathogens.

Adjusted jackknife for imputation under unequal probability sampling without replacement

Imputation is commonly used to compensate for item non-response in sample surveys. If we treat the imputed values as if they are true values, and then compute the variance estimates by using standard methods, such as the jackknife, we can seriously underestimate the true variances. We propose a modified jackknife variance estimator which is defined for any without-replacement unequal probability sampling design in the presence of imputation and non-negligible sampling fraction. Mean, ratio and random-imputation methods will be considered. The practical advantage of the method proposed is its breadth of applicability.