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.     

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.     

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.     

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.     

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.     

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.     

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.     

Bayesian Spatial Point Process Modeling of Line Transect Data

This paper develops a Bayesian approach for spatial inference on animal density from line transect survey data. We model the spatial distribution of animals within a geographical area of interest by an inhomogeneous Poisson process whose intensity function incorporates both covariate effects and spatial smoothing of residual variation. Independently thinning the animal locations according to their estimated detection probabilities results into another spatial Poisson process for the sightings (the observations). Prior distributions are elicited for all unknown model parameters. Due to the sparsity of data in the application we consider, eliciting sensible prior distributions is important in order to get meaningful estimation results. A reversible jump Markov Chain Monte Carlo (MCMC) algorithm for simulation of the posterior distribution is developed. We present results for simulated data and a real data set of minke whale pods from Antarctic waters. The main advantages of our method compared to design-based analyses are that it can use data arising from sources other than specifically designed surveys and its ability to link covariate effects to variation of animal density. The Bayesian paradigm provides a coherent framework for quantifying uncertainty in estimation results.     

Preservation of seed viability during 25 years of storage under standard genebank conditions

Maintaining sufficient viability is critical to the sustainability of ex situ conserved seed collections. For this reason, accessions are regenerated when viability falls below a predefined threshold. Viability is monitored by determining the germination ability of accessions at predefined time intervals. Optimizing the frequency of these germination tests, in order to avoid waste of resources, is hampered by the scarce availability of data about seed longevity, particularly for material maintained under genebank conditions. Here we report on the analysis of nearly 40,000 germination test results collected for a wide range of crop species over a 25-years period by the centre for genetic resources, the Netherlands (CGN), where seeds of genebank accessions are dried to 3–7 % moisture content and stored for the long term under near-vacuum in aluminium foil bags at ?20 °C. The results indicate that seed viability is well maintained for the large majority of seed lots during the first 25 years after regeneration as only 3.3 % of the monitoring tests revealed below-threshold germination values. It is argued that the majority of these sub-standard seed lots are due to other causes than seed ageing, including dormancy problems and estimation error in germination testing. For material, maintained under the seed management procedures and storage conditions practiced by CGN, it is therefore recommended to delay the first germination monitoring tests to 25 years after regeneration.     

Residues of a Triazole Fungicide in Soil After 4 Years of Application to Sugar Beet

An experimental study to investigate the potential soil accumulation of the triazole fungicide difenoconazole in soil was carried out in northwestern Italy. The fungicide was applied to sugar beet for 4 years with three applications per year at a rate of 75 g ha^?1 each, according to formulated product recommended use. Soil cores were collected each year before the first application, after each application and at harvest of the crop. The soil samples were then split into 0–10 and 10–40 cm depth layers, extracted and quantitatively analysed by gas chromatography for difenoconazole residues. The study evidenced that difenoconazole residues could be detected in the upper soil layer only, in quantities detectable after several applications (0.14 to 0.32 mg kg^?1 after the third application) which then become undetectable the following year. It can be concluded, therefore, that difenoconazole does not accumulate in soil.     

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.     

Fate of 15 N-labeled fertilizer in soils under dryland agriculture after 19 years of different fertilizations

This study addressed if long-term combined application of organic manure and inorganic fertilizers could improve the synchrony between nitrogen (N) supply and crop demand. ¹⁵?N-labeled urea was applied to micro-plots within three different fertilized treatments (no fertilizer, No-F soil; inorganic NPK fertilizers, NPK soil; and manure plus inorganic NPK fertilizers, MNPK soil) of a long-term field trial (1990–2009) in a dryland wheat field in the south Loess Plateau, China. After one season of wheat harvest, ¹⁵?N use efficiency was 20, 58, and 65 % in the No-F, NPK, and MNPK soil, respectively. During the early wheat growth stage, microbial immobilization of applied ¹⁵?N was significantly (P?<?0.05) highest in the MNPK soil (15.3 %), higher in the NPK soil (12.6 %), and lowest in the No-F soil (7.4 %). Of the ¹⁵?N immobilized by the soil microbial biomass, 69 % (NPK soil) to 83 % (MNPK soil) was released between the stem elongation and flowering of wheat. Compared with the NPK soil, the MNPK soil had significantly (P?<?0.05) higher grain yield. Our findings highlight that long-term application of organic manure with inorganic fertilizers cannot only improve the synchrony of N supply for crop demand but also increase N use efficiency and grain yield.     

Seasonal variation in carbon isotopic composition of bog plant litter during 3 years of field decomposition

In this study, we describe the seasonal variation in ¹³C abundance in the litter of two Sphagnum species and four vascular plant species during 3 years of field decomposition in an Italian alpine bog. Litter bags were periodically retrieved at the end of summer and winter periods, and the δ¹³C in residual litter was related to mass loss, litter chemistry, and climatic conditions. In Sphagnum litter, higher rates of decomposition during summer months were associated with an increase of δ¹³C probably due to the incorporation of microbial organic compounds rich in ¹³C in the residual litter. In the litter of Eriophorum vaginatum, Carex rostrata and Calluna vulgaris, we observed a decrease of δ¹³C with an increase in the concentration of lignin-like compounds. The residual litter of Potentilla erecta showed a decrease of ¹³C abundance during the first 2 years, but on proceeding the decomposition, the δ¹³C increased again probably reflecting the incorporation of microbial organic compounds.     

Seasonal variation in nitrogen isotopic composition of bog plant litter during 3 years of field decomposition

In this study, we describe the seasonal variation in ¹⁵N abundance in the litter of two Sphagnum species and four vascular plant species during 3 years of field decomposition in an Italian Alpine bog. Litter bags were periodically retrieved at the end of summer and winter periods, and the δ¹⁵N in residual litter was related to mass loss, litter chemistry, and climatic conditions. In Sphagnum litter, higher rates of decomposition during summer months were associated with an increase of δ¹⁵N probably due to the incorporation of microbial organic compounds rich in ¹⁵N. The litter of Eriophorum vaginatum and Carex rostrata was characterized by a decrease of δ¹⁵N, so that the final signature was significantly lower than in initial litter. On the other hand, the residual litter of Potentilla erecta and Calluna vulgaris was characterized by a final δ¹⁵N higher than in initial litter. Our data reported a seasonality of ¹⁵N abundance in the residual litter of Sphagnum species, but not in that of vascular plant species, thus highlighting the role of differences in litter chemistry.     

Paleolimnological Fingerprinting of the Impact of Acid Mine Drainage After 50 Years of Chronic Pollution in a Southern Finnish Lake

Acid mine drainage (AMD) is acknowledged to have long-lasting impacts on aquatic environments. Hence, mines have also been detected to pose problems years after closure due to the leaching of toxic drainage initiated by sulfide oxidation. To assess the effects of chronic but relatively low volume acid mine drainage derived from the Haveri copper–gold mine operating between 1938 and 1960 on a freshwater bay in southern Finland, we compared cladoceran assemblages from the pre-mining period with contemporary populations using paleolimnological approaches and multiple sediment cores. The cladoceran community of the pre-mining era differed significantly from the contemporary community of the lake (ANOSIM R = 0.91; p = 0.0001), but closely resembled the contemporary community of a nearby non-polluted reference site. Our results suggest that the differences in species compositions between pre-mining and contemporary samples are most likely caused by eutrophication and not by the AMD impact. Because AMD at our study site is most intense during the spring snowmelt period, cladocerans may avoid seasonal pollution peaks through winter dormancy. Possible pollution peaks resulting from heavy rains during the summer may have negative impacts on the cladoceran community, but such short-term impacts are probably rapidly counteracted by immigration from cleaner areas of the lake.     

Time of Day Effect on Foliar Nutrient Concentrations in Corn and Soybean

Foliar nutrient concentrations vary during the day. Field research was conducted to quantify and better understand this variation in corn (Zea mays L.) and soybean (Glycine max L. Merr.) with foliar sampling during the vegetative and reproductive stages. Time of day effects occurred inconsistently across nutrients. Nitrogen (N), manganese (Mn), iron (Fe), and zinc (Zn) foliar concentrations were generally high early in the day. Phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), and sulfur (S) foliar concentrations varied inconsistently with time of day, while concentrations of boron (B) in both crops and copper (Cu) in corn were not affected. Limiting foliar sampling to after 10:00 AM reduced the variation for soybean but not for corn. Interpretation by Diagnosis and Recommendation Integrated System (DRIS) did not reduce the time of day effect. The variation caused by time of day, along with other causes, affects confidence in interpretation of foliar results suggesting use of the information with either additional foliar sampling or soil testing in making nutrient management decisions.     

Ploidy levels of Dioscorea alata L. germplasm determined by flow cytometry

Dioscorea alata L. is a highly important crop, widely distributed in the humid and semi-humid tropics. Flow cytometry was used to determine the ploidy levels of 74 D. alata genotypes collected mainly from West African countries. Sixty three of the genotypes were found to be tetraploid, one was hexaploid and ten were octoploid. The high percentage of tetraploids together with the small percentage of hexaploid individuals and the absence of diploid individuals gives us some more clues on the possible origin of these species. No association between ploidy level and place of cultivation was found for the tested material. The obtained results represent important knowledge for enhancing the breeding methodologies and optimize germplasm management of this species. It also offers further insights to the phylogeny and evolution of Dioscorea species.     

Assessment of soil erosion rate trends in two agricultural regions of European Russia for the last 60 years

Purpose

Forest–steppe and the southern forest ecotones of European Russia (ER) are the most productive agricultural areas in Russia. Both climate and land use changes have occurred within the ER during last 30 years. These changes can lead to changes in the timing, magnitude, and spatial distribution of soil erosion rates on cultivated lands. The objective of this research was to assess the trends in soil erosion rates since the 1960s for two agricultural regions of ER.

Materials and methods

Rates of soil erosion were estimated for two time windows (1963–1986 and 1986–2015) within the two agricultural regions. Both regions are characterized by a high proportion of cropland (>?60%), and within each region, one river basin and one 1st–3rd-order agricultural catchment were selected for a detailed assessment of soil erosion rates. Erosion models and visual interpretation of satellite images were used for the evaluation of the erosion rates for the river basins. Sediment budget assessments, ¹³⁷Cs dating, geomorphologic mapping, and erosion models were used for the evaluation of the sediment redistribution for the two time windows in agricultural catchments.

Results and discussion

At the river basin scale, the mean annual erosion rate did not change in the western part of forest–steppe ecotone; however, there was a weak negative trend in the mean annual erosion rate for the eastern part of the southern forest ecotone. A large negative trend in the erosion rate was found for both small agricultural catchments. In all cases, the reduction in the erosion rates was mainly associated with a decrease of surface runoff during snowmelt, as a result of an increase in both the air and soil temperatures during winter season. The soil loss reduction during snowmelt was counteracted by an equal increase in rainfall erosion due to increase of rainfall intensity in western part of forest–steppe ecotone.

Conclusions

Reduction of surface runoff during spring snowmelt was the main reason the erosion rates declined on cultivated lands within the forest–steppe and southern forest ecotones of ER. Evaluation of ephemeral gully erosion rate was not incorporated into State Hydrological Institute erosion model used for the evaluation of the soil losses during snowmelt. This has led to an underestimation of the total soil losses for the 1963–1986 time window for all study sites.

     

Impact of Supplemental Calcium Chloride on Yield,Quality, Nutrient Status,and Postharvest Attributes of Tomato

Little is known regarding the impact of calcium chloride applications during growth and development on tomato postharvest quality. This trial investigated supplemental calcium chloride applications on yield, nutrient content, texture, and postharvest quality of tomato fruit. Calcium (Ca) nutrient solution concentrations were: 60, 180, and 360 mg·L^?1 calcium, while foliar applications were (0, 1, and 2% calcium chloride w/v). Plants grown with 60 mg·L^?1 Ca had a high incidence of blossom end rot, which was not affected by calcium chloride sprays. Fruit nutrient concentrations were affected by calcium delivered through the nutrient solution. As fruit cluster position increased, fruit nutrient concentrations significantly decreased. Foliar calcium chloride sprays affected fruit soluble solids content and dry weight, but did not affect texture. Pericarp elasticity increased concomitantly with calcium in the nutrient solution. Postharvest disease incidence was not affected by calcium treatment, though weight loss during storage was negatively affected by calcium chloride sprays.