Evaluation of the Accuracy of Diagnostic Tests From Repeated Measurements Without a Gold Standard

A model is presented to evaluate the accuracy of diagnostic tests from data from individuals that are repeatedly tested in time. Repeated measurements from three diagnostic tests for foot-and-mouth disease, applied to vaccinated and experimentally infected cattle, were analyzed. At any time the true disease status of the individuals was unknown, i.e., no gold standard was available. The model allows for correlation between repeated test results, in consequence of the underlying structure for the unknown true disease status, but also by the distribution of the test results conditional upon true disease status. The model also allows for dependence between the different diagnostic tests conditional upon true disease status. Prior information about the structure of the prevalence and the specificity of the tests was incorporated in a Bayesian analysis. Posterior inference was carried out with Markov chain Monte Carlo. Simulated data were analyzed to gain insight into the performance of the posterior Bayesian inference. The simulated data are typical for the expensive and, therefore, modestly sized infection experiments that are conducted under controlled conditions.     

Hypothesis Tests on Mixture Model Components with Applications in Ecology and Agriculture

Multiple comparisons are widely used to compare gross features of distributions across populations. However, often a scientific hypothesis is more easily couched in terms of more focused null and alternative statistical hypotheses. For example, among distributions exhibiting clusters of continuous measurements across strata, are there clusters of measurements similar in terms of location, spread, or weight? We propose testing such hypotheses using a sequence of nested finite mixture models. Reasonable, data-driven priors are suggested based on estimates of the sample spreads and midpoints. Formal hypothesis testing is carried out through the computation of Bayes factors. The method is illustrated on Holling’s (Ecological Monographs 62:447–502, 1992) forest and prairie bird body mass data, and data on the time-to-abortion in dairy cows. Supplemental simulations are available online.     

A Measurement Error Model for Heterogeneous Capture Probabilities in Mark-Recapture Experiments: An Estimating Equation Approach

Logistic models for capture probabilities that depend on covariates are effective if the covariates can be measured exactly. If there is measurement error so that a surrogate for the covariate is observed rather than the covariate itself, simple adjustments may be made if the parameters of joint distribution of the covariate and the surrogate are known. Here we consider the case when a surrogate is observed whenever an individual is captured and the parameters must also be estimated from the data. An estimating equation regression calibration approach is developed and it is illustrated on a real dataset where the surrogate is an individual bird’s wing-length, which varies from occasion to occasion.     

Capture-Recapture Smooth Estimation of Age-Specific Survival Probabilities in Animal Populations

Yielding sound estimates of survival according to age in wild populations where senescence or other age-related variations may occur is very important to management decision makers, and remains challenging. This paper proposes to use penalized maximum likelihood to obtain smooth estimates of annual survival probabilities across age in populations of wild animals followed by capture–recapture. We propose to use two different types of smoothing penalties, and we use ν-fold cross-validation to select the best value of the tuning parameter for the intensity of smoothing. We then assess the accuracy of the method by a simulation study with two different shapes of the relationship between age and survival, and we conclude that a careful use of this method provides reliable noise-free estimates of age-specific annual survival. We apply this procedure to the motivating data from a population of roe deer known to exhibit a marked decrease of survival with age, and we compare our results with those previously published on this population.     

Independent Component Analysis for Three-Way Data With an Application From Atmospheric Science

In this paper, a new approach to independent component analysis (ICA) for three-way data is considered. The rotational freedom of the three-mode component analysis (Tucker3) model is exploited to implement ICA in one mode of the data. The performance of the proposed approach is evaluated by means of numerical experiments. An illustration with real data from atmospheric science is presented, where the first mode is spatial location, the second is time and the third is a set of different meteorological variables representing geopotential heights at various vertical pressure levels. The results show that the three-mode decomposition finds spatial patterns of climate anomalies which can be interpreted in a meteorological sense and as such gives an insightful low-dimensional representation of the data.     

EFFECTS OF MIXING RATIO AND PROCESSING METHODS ON RESISTANT STARCH CONTENT OF PRODUCTS OF RICE＇ JIANGTANGDAO 1＇

以高抗性淀粉含量功能性粳稻品系“降糖稻1号”稻米为主要材料,研究其与不同比例稻米混配后经蒸煮、膨化、制作米粉及发酵加工后,对稻米产品直链淀粉含量和抗性淀粉（RS）含量的影响。结果表明,稻米中RS含量随加工温度和加工压力的提高而大大降低,表明“降糖稻1号”不宜高温高压蒸煮、膨化、加工米粉和发酵食品。“降糖稻l号”与“金丰”稻米按不同比例混合蒸煮后,其直链淀粉含量、RS含量及蒸煮品质有明显改善,“降糖稻1号”与“金丰”稻米以2：1混配,不仅明显改善米饭的食味,而且RS含量能保持较高的水平。     

EFFECT OF PREHARVEST SPRAYS OF CALCIUM CHLORIDE AND SUCROSE ON CRACKING AND QUALITY OF ‘BURLAT’ SWEET CHERRY FRUIT

The aim of the study was to examine impact of preharvest sprays of calcium (Ca) and sucrose on splitting and quality of ‘Burlat’ sweet cherry fruit. The study was carried out during 2009–2010 in Poland and Turkey, on mature trees planted at a moderate density on coarse- and medium-textured soils. Sweet cherries were sprayed with calcium chloride (CaCl₂) and/or sucrose at a rate of 5 kg of each material per ha, using ca. 1000 L of water. In Poland, sprays of CaCl₂ and/or sucrose were applied 8–14 h before each rain, starting 21 d before harvest, whereas in Turkey the spray treatments were made schematically: 7, 14 and 21 d before harvest. Sprays of water were treated as the control. The results showed that preharvest sprays of CaCl₂ and/or sucrose did not affect yield, mean fruit weight, and fruit acidity. Sprays of CaCl₂ increased fruit Ca status, and simultaneously reduced fruit cracking in an orchard or laboratory test. In the trial performed in Turkey, part of fruit sprayed with CaCl₂ (<5%) had spray deposit on the peel. Sucrose sprays did not affect fruit cracking. In one year of the study in Turkey, sucrose sprays increased soluble solids concentration of fruit; however, part of fruit treated with sucrose (<2%) had spray deposit on the skin.     

Nonparametric Threshold Model of Zero-Inflated Spatio-Temporal Data with Application to Shifts in Jellyfish Distribution

There is increasing scientific interest in studying the spatial distribution of species abundance in relation to environmental variability. Jellyfish in particular have received considerable attention in the literature and media due to regional population increases and abrupt changes in distribution. Jellyfish distribution and abundance data, like many biological datasets, are characterized by an excess of zero counts or nonstationary processes, which hampers their analyses by standard statistical methods. Here we further develop a recently proposed statistical framework, the constrained zero-inflated generalized additive model (COZIGAM), and apply it to a spatio-temporal dataset of jellyfish biomass in the Bering Sea. Our analyses indicate systematic spatial variation in the process that causes the zero inflation. Moreover, we show strong evidence of a range expansion of jellyfish from the southeastern to the northwestern portion of the survey area beginning in 1991. The proposed methodologies could be readily applied to ecological data in which zero inflation and spatio-temporal nonstationarity are suspected, such as data describing species distribution in relation to changes of climate-driven environmental variables. Some supplemental materials including an animation of jellyfish annual biomass and web appendices are available online.     

区域农田有机物质投入量的估算方法 —— 以陕西长武县为例

以黄土高原典型沟壑区长武县为研究区域,进行区域农田有机物质投入量估算方法的研究。将农田有机物质投入分为秸秆还田、秸秆根茬残留、作物地下生物量和有机肥4个部分分别进行估算。基于LANDSAT 5卫星遥感资料,利用CASA模型估算植物第一净生产力,获得作物整株重,结合作物根冠比估算作物地上生物量和地下生物量,以地上生物量和实地秸秆调查来估算秸秆根茬量和秸秆还田量。估算结果显示,长武县农田年总有机物质投入量为42 700 t。     

Estimating Population Growth Rate From Capture–Recapture Data in Presence of Capture Heterogeneity

The direct estimation and modeling of population growth rate from capture–recapture data has now seen a number of applications. However, the original model cannot accommodate heterogeneous capture probabilities. While studying a population of small mammals Peromyscus maniculatus, we became concerned that the peak of population size may be estimated too late in the year because of heterogeneous catchability. Hence, we developed a variation of the original model with a finite number of catchability classes. The results obtained with the new model are more in agreement with the known biology of this population. A bibliographic appendix and computer code are available online.     

Greenhouse gas fluxes during rewetting of peatlands by use of effluents – a lysimeter study

Abstract

The present study aims at assessing the effect of using the effluent of a wastewater treatment plant as an alternative measure for rewetting nutrient-rich fen soils over the growing season on the emission of greenhouse gas (GHG) and at discussing possible changes in the greenhouse potential as a result of this practice. In order to allow a discussion on GHG based on integrated CH₄, N₂O, and CO₂ flux rates, fluxes were measured in our lysimeter study using the chamber methodology from May to December in 2003 and 2004. The study compares the gaseous fluxes of fen soils in lysimeters treated with the effluent and/or freshwater for rewetting. Only freshwater was applied to the control lysimeter. The source of water hardly had any statistically significant effect on trace gas fluxes. However, there was a trend towards higher CH₄ emissions at the effluent lysimeters compared to the control lysimeter. Effluent usage did not decrease the greenhouse effect at the same rate, which could be observed at the control. Nevertheless, regarding gaseous emissions the use of effluents could prove to be a solution to the current problem of today's major peat oxidation and fen soil loss by drainage.     

EFFECTS OF POTASSIUM NITRATE SPRAYING ON FRUIT CHARACTERISTICS OF ‘MALAS YAZDI’ POMEGRANATE

The present research was carried out to investigate the effects of potassium nitrate on pomegranate fruit quality. Treatments were: 1) control, distilled water was used; 2) potassium nitrate 250 mg L-¹ plus Tween-20 and 3) potassium nitrate 500 mg L-¹ plus Tween-20. All treatments were sprayed on fruits with a diameter of 30 mm. Juice, peel, seed characters, and fruit quality components were evaluated when fruits were harvested. Results indicated that 250 mg L-¹ potassium treatment increased juice volume and weight compared with the control and the 500 mg L-¹ K treatments. As the potassium nitrate level increased, aril length and diameter decreased. Although there was not a significant difference among treatments on titrable acidity and pH contents of fruits, the highest total soluble solids and vitamin C were obtained in the 250 mg L-¹ potassium nitrate treatment when compared with the others. These findings show that applied potassium nitrate significantly influences fruit quality of pomegranate when fruit are in the beginning stages of growth and development.     

RESPONSE OF ‘GRANNY SMITH’ APPLE TREES TO FOLIAR TITANIUM SPRAYS UNDER CONDITIONS OF LOW SOIL AVAILABILITY OF IRON,MANGANESE, AND ZINC

The aim of the study was to examine impact of foliar titanium (Ti) sprays on vegetative and reproductive response of apple (Malus domestica Borkh.) trees under conditions of low soil availability of iron (Fe), manganese (Mn), and zinc (Zn). The experiment was conducted during 2005–2006 at a Experimental Station in Isparta region, Turkey, on mature ‘Granny Smith’ apple trees/M.9, planted at a spacing of 3.5 × 1.5 m, on fine-textured soil with neutral reaction, medium status of organic matter, high amounts of available phosphorus (P), potassium (K), and magnesium (Mg), and low availability of Fe, Mn, and Zn. The trees were sprayed with Ti-ascorbate at the green and pink bud stage, petal fall, and 3, 6, and 9 weeks after full bloom, at a rate of 3 g Ti ha^?1 per spray. The efficiency of Ti sprays was compared to combined sprays of Fe, Mn, and Zn [chelated with ethylenediaminetetraacetic acid (EDTA)], applied at the same terms as Ti sprays, at rate of 36 g, 36 g and 24 g per spray, respectively. Trees unsprayed with Ti, Fe, Mn, and Zn served as the control. It was shown that summer leaf Ti concentrations of the trees untreated with Ti were high, varying from 34 to 36 mg kg^?1 dry matter. Foliar Ti sprays increased leaf status of this nutrient but they had no effect on nutrition of essential macro- and microelements, tree vigor, and fruit yield. Mean apple weight, coloring, firmness, soluble solids concentration, and titratable acidity of fruit were not also influenced by Ti sprays. Foliar sprays of Fe, Mn, and Zn improved leaf status of nitrogen (N), Mg, Fe, Mn, and Zn; leaves of the trees sprayed with those micronutrients were also greener, and contained more Fe²⁺ than those of the control plants. Combined sprays of Fe, Mn, and Zn improved tree vigor and fruit yield.     

Spatial Inference of Nitrate Concentrations in Groundwater

We develop a method for multiscale estimation of pollutant concentrations, based on a nonparametric spatial statistical model. We apply this method to estimate nitrate concentrations in groundwater over the mid-Atlantic states, using measurements gathered during a period of 10 years. A map of the fine-scale estimated nitrate concentration is obtained, as well as maps of the estimated county-level average nitrate concentration and similar maps at the level of watersheds and other geographic regions. The fine-scale and coarse-scale estimates arise naturally from a single model, without refitting or ad hoc aggregation. As a result, the uncertainty associated with each estimate is available, without approximations relying on high spatial density of measurements or parametric distributional assumptions.     

NITROGEN–PHOSPHORUS–POTASSIUM EFFECTS ON FORMS OF SULFUR IN LEAVES AND FRUITS OF CUCUMBER

ABSTRACT

The impact that nitrogen (N), phosphorus (P), and potassium (K) application rates on the sulfur (S) fractions in leaves and fruits of greenhouse-grown cucumbers plants (Cucumis sativus L. cv. Brunex) are presented. The treatments were as follows: N (N1=5 g NO₃NH₄/m², N2=10 g NO₃NH₄/m², N3=20 g NO₃NH₄/m², N4=40 g NO₃NH₄/m²), two levels of P (P1=8 g H₃PO₄/m² and P2=16 g H₃PO₄/m²), and two levels of K (K1=20 g K₂SO₄/m² and K2=40 g K₂SO₄/m²). The foliar and fruit contents were determined for total S, organic S and sulfate. The influence of the N treatments on the total S (St: organic S +sulfate) concentration, proved significant, showing a progressive increase in the leaf and fruit concentrations. In the leaves, the P slightly diminished the St concentration but values in the fruits did not appreciably differ from control. The K dosage did not cause the St concentration to differ from that of P, although in the fruit a slightly lower St concentration appeared in the K2 treatment. The response of the organic-S concentration in the leaves resembled that of St, and thus organic S should not be used as a diagnostic method for S status. In the relationship SO₄ ^2-/St, the SO₄ ^2- concentration proved more influential than did the St form, providing a more accurate representation of the potential status of this nutrient in the plant.     

Microbial processes and community composition in the rhizosphere of European beech - The influence of plant C exudates

Plant roots strongly influence C and N availability in the rhizosphere via rhizodeposition and uptake of nutrients. This study aimed at investigating the effect of resource availability on microbial processes and community structure in the rhizosphere. We analyzed C and N availability, as well as microbial processes and microbial community composition in rhizosphere soil of European beech and compared it to the bulk soil. Additionally, we performed a girdling experiment in order to disrupt root exudation into the soil. By this novel approach we were able to demonstrate that enhanced resource availability positively affected N mineralization and hydrolytic enzyme activities in the rhizosphere, but negatively affected nitrification rates and oxidative enzyme activities, which are involved in the degradation of soil organic matter. Both rhizosphere effects on N mineralization and oxidative enzyme activities disappeared in the girdling treatment. Microbial community structure in the rhizosphere, assessed by phospholipid fatty acid analysis, differed only slightly from bulk soil but was markedly altered by the girdling treatment, indicating additional effects of the girdling treatment beyond the reduction of root exudation. Differences in oxidative enzyme activities and nitrification rates between rhizosphere soil and bulk soil, however, suggest considerable differences in the (functional) microbial community composition.     

Comparative Study of Different Soil Amendments and Microbes for Integrated Nutrient Management and Growth Promotion of Jatropha Curcas

Increased alkalinity caused reduction in growth of Jatropha curcas plant. This experiment was designed to test the efficacy of beneficial microbes and vermicompost individually and in combinations to alleviate the stressful effect of alkaline stress on growth of Jatropha. Plants inoculated with bacterial consortia had significantly increase in vegetative growth parameters. Soil analysis showed increase in total organic carbon (TOC) by 68% compared to soil before plantation treated with Bacterial consortia + vermicompost. Nitrogen (N) and phosphorus (P) content in the soil was increased by 25% and 84% before plantation treated with Bacterial consortia. Maximum uptake of potassium (K) and sodium (Na) content was observed in consortia. Plant analysis showed that consortia could increase uptake of micronutrients compared to control and other treatments. It can be concluded that multispecies bacterial consortia alone or in combination with mycorrhiza and vermicompost can reduce alkaline stress and enhances the seed germination potential, vegetative growth, and nutrient status of soil.     

RESPONSE OF ‘BURLAT’ SWEET CHERRY TREES TO POSTHARVEST SPRAYS OF NITROGEN,BORON AND ZINC

The aim of the study was to examine effects of postharvest sprays of nitrogen (N), boron (B), and zinc (Zn) on reproductive response of sweet cherry (Prunus avium L.) trees, fruit quality and plant nutrition. The experiment was conducted during 2007–2009 in central Poland on mature ‘Burlat’ sweet cherry trees/F12, grown on a coarse-textured soil with low level of organic matter, and optimal soil reaction. Soil status of phosphorus (P), potassium (K), magnesium (Mg), calcium (Ca), iron (Fe), manganese (Mn), Zn and copper (Cu) was optimal, whereas B – low. Sweet cherry trees were sprayed with boric acid-B, ethylenediaminetetraacetic acid (EDTA)-Zn, and urea-N at 30–40 d prior to initiation of leaf fall according to following schema: i) spray of N at a rate of 23 kg ha^?1; ii) spray of B and Zn at a dose of 1.1 kg ha^?1 and 0.5 kg ha^?1, respectively; and iii) spray of N, B and Zn at the same rates as in the above spray combinations. The trees sprayed with water served as the control. The results showed that fall spray treatments had no influence on cold damage of flower buds, plant N status and soluble solids concentration in fruit. Postharvest spray of N and combined spray of N, B and Zn injured leaves in the fall but did not cause defoliation. Sprays of B and Zn with or without N increased status of Zn and B in fall leaves, and B in flowers and midsummer leaves. Those sprays also improved fruit set and yield. In one out of two years of the study, fall sprays of N with or without B and Zn decreased mean fruit weight. The above results indicate that only leaf-applied B in the fall improved reproductive response of sweet cherry trees. It is concluded that under conditions of B shortage in a soil and/or plant tissues, postharvest B sprays can be recommended in sweet cherry orchards to improve reproductive growth of the trees.     

INFLUENCE OF PREHARVEST SPRAYS OF A MIXTURE OF CALCIUM FORMATE,CALCIUM ACETATE,CALCIUM CHLORIDE AND CALCIUM NITRATE ON QUALITY AND ‘JONAGOLD’ APPLE STORABILITY

The aim of the study was to examine effect of preharvest sprays of a mixture of calcium (Ca) formate, Ca-acetate, Ca-chloride (CaCl₂) and Ca-nitrate [Ca(NO₃)₂] on quality and apple storability. The experiment was conducted during 2008–2009 at the Experimental Station of the Research Institute of Horticulture in Skierniewice, Poland, on mature ‘Jonagold’ apple trees/M.26, planted at a moderate density on a coarse-textured soil with low status of organic matter and abundant in exchangeable Ca. Apple trees were sprayed with Ca, 7 times per season, at 2-week intervals, starting 3 weeks after blooming. In the spray treatments a mixture of Ca-formate, Ca-acetate, CaCl₂ and Ca(NO₃)₂ (as Insol Wap fertilizer), CaCl₂ or Ca(NO₃)₂ were used at rates of 7.3 kg Ca, 11.8 kg Ca, and 9.9 kg Ca ha^?1 per season, respectively. The trees sprayed with water were treated as the control. The results showed that Ca sprays caused no leaf and fruit injury. Calcium spray measures did not affect yield, mean fruit weight, and soluble solids concentration (SSC), titratable acidity and starch index of fruit at harvest. However, at harvest apples sprayed with Ca contained more this nutrient and were firmer than those of the control plots. After storage apples sprayed with Ca had more acids, and were firmer and less liable to bitter pit than the control fruit. Calcium sprays did not affect SSC of fruit after storage but reduced postharvest decay of fruit caused by Peziculla spp. and Penicillium expansum fungi. Apples sprayed with Insol Wap material were the least affected by the above pathogens. It is concluded that in apple orchards preharvest sprays of a mixture of Ca-formate, Ca-acetate, CaCl₂ and Ca(NO₃)₂, containing 10% Ca (w/w) with ca. 50% in an organic form, can be the alternative to sprays of CaCl₂ or Ca(NO₃)₂.