Emulation Engines: Choice and Quantification of Uncertainty for Complex Hydrological Models

Complex, mechanistic hydrological models can be computationally expensive, have large numbers of input parameters, and generate multivariate output. Model emulators can be constructed to approximate these complex models with substantial computational savings, making activities such as sensitivity analysis, calibration and uncertainty analysis feasible. Success in the use of an emulator relies on it making accurate and precise predictions of the model output. However, it is often unclear what type of emulation approach will be suitable. We present a comparison of reduced-rank, multivariate emulators built upon different ‘emulation engines’ and apply them to the Australian Water Resource Assessment System model. We examine first-order and second-order approaches which focus on specifying the mean and covariance, respectively. We also introduce a nonparametric approach for quantifying the uncertainty associated with the emulated prediction where this has bounded support. Our results demonstrate that emulation engines based on second-order approaches, such as Gaussian processes, can be computationally burdensome and may be comparable in performance to computationally efficient, first-order methods such as random forests.Supplementary materials accompanying this paper appear online.     

A Bayesian Generalized Linear Model for Crimean–Congo Hemorrhagic Fever Incidents

Global spread of the Crimean–Congo hemorrhagic fever (CCHF) is a fatal viral infection disease found in parts of Africa, Asia, Eastern Europe and Middle East, with a fatality rate of up to 30%. A timely prediction of the prevalence of CCHF incidents is highly desirable, while CCHF incidents often exhibit nonlinearity in both temporal and spatial features. However, the modeling of discrete incidents is not trivial. Moreover, the CCHF incidents are monthly observed in a long period and take a nonlinear pattern over a region at each time point. Hence, the estimation and the data assimilation for incidents require extensive computations. In this paper, using the data augmentation with latent variables, we propose to utilize a dynamically weighted particle filter to take advantage of its population controlling feature in data assimilation. We apply our approach in an analysis of monthly CCHF incidents data collected in Turkey between 2004 and 2012. The results indicate that CCHF incidents are higher at Northern Central Turkey during summer and that some beforehand interventions to stop the propagation are recommendable. Supplementary materials accompanying this paper appear on-line.     

A New Probability Model for Hydrologic Events: Properties and Applications

Upon the motivation of unstable climatic conditions of the world like excess of rains, drought and huge floods, we introduce a versatile hydrologic probability model with two scale parameters. The proposed model contains Lindley and exponentiated exponential (Lindley in J R Stat Soc Ser B 20:102–107, 1958; Gupta and Kundu in Biom J 43(1):117–130, 2001) distributions as special cases. Various properties of the distribution are obtained, such as shapes of the density and hazard functions, moments, mean deviation, information-generating function, conditional moments, Shannon entropy, L-moments, order statistics, information matrix and characterization via hazard function. Parameters are estimated via maximum likelihood estimation method. A simulation scheme is provided for generating the random data from the proposed distribution. Four data sets are used for comparing the proposed model with a set of well-known hydrologic models, such as generalized Pareto, log normal (3), log Pearson type III, Kappa(3), Gumbel, generalized logistic and generalized Lindley distributions, using some goodness-of-fit tests. These comparisons render the proposed model suitable and representative for hydrologic data sets with least loss of information attitude and a realistic return period, which render it as an appropriate alternate of the existing hydrologic models. Supplementary materials for this paper are available online.     

Contribution of technic materials to the mobile fraction of metals in urban soils in Marrakech (Morocco)

Background, Aim and Scope  In urban areas, soils are often dramatically altered by anthropogenic activity and these modifications distinguish these soils (Anthrosols, Technosols) from those in natural systems. In urban environments, they receive considerable pollution from industry, traffic and refuse. Since contaminated soil particles can be easily inhaled or ingested, there is a potential transfer of toxic pollutants to humans. Risk assessment is essentially based on the determination of the total or mobile contents of pollutants in soils using chemical extractions. This approach could be improved by taking into consideration the bioavailable fractions of these toxic elements as measured by biotests. The coarse soil fraction usually neglected in analyses can nevertheless have an effect on the concentration of metals in the soil solution. This coarse fraction is made up of the natural materials and of technic materials constituting anthropogenic soils (plastic, paper, fabric, wood, bones, metallic elements and building materials). These materials have variable capacities to release or adsorb trace elements. Samples representative of different technic fraction components of Marrakech urban soils permit one to quantify their contribution to the enrichment of the soluble metal concentrations. Works are carried out to achieve partial extractions of metals from the three fractions (less than 2 mm, coarse natural and coarse technic) of selected urban soils in order to determine their contribution to the metal contamination of soils. Materials and Methods  Selected soils were collected from 9 sites according to a gradient of increasing anthropogenic influence from suburban to urban zones. Soils were air-dried, homogenized, and sieved (2 mm). The coarse fraction was sorted to separate the different technic materials and natural materials. Water extractions were run, on the natural, coarse fraction, on the complete technic fraction of the 9 soils and on average samples made of technic materials sorted out of 58 topsoils sampled from different sites in the city of Marrakech. Results  Results show that the percentage of the technic fraction increases while approaching the historic city center. It represented about 14% in the most anthropogenically disturbed soils. Along this gradient, soils changed progressively from Anthrosols to Technosols according to the WRB classification of urban and industrial soils. Analyses of metal contents showed that the fine fraction (<2 mm) mainly contributed to the metallic contamination of the water soluble fraction. The natural coarse fraction had the highest contribution to the copper release and was responsible for the release of all water-extractable copper in some soils. Concerning the technic fraction, it has a significant contribution essentially in the most anthropogenically disturbed soils as characterized by an elevated percentage of anthropogenic elements. The water extractable metal contents of average samples of these anthropogenic elements shows that elevated metal concentrations were released by bones, wood, plastic and fabric/paper. Discussion  This study concerns soils in urban areas, which are strongly impacted by human activities. Part of the soils can be classified as Anthrosols, profoundly impacted through the addition of organic materials from household wastes, irrigation, or cultivation. Other soils strongly impacted by human activities are Technosols dominated or strongly influenced by man-made materials. Technosols appear mostly in urban and industrial areas and are more likely to be contaminated than Anthrosols. The composition and heterogeneity of urban soils lead to modifications of the mobility and availability of pollutants depending on successive land-uses and on the composition of technic materials. The fine fraction offers a high transferring surface capacity, leading to a high mobilization of metals. The technic fraction contributes significantly to the metal release in the Technosols. This property can be explained by a reversible adsorption of metals on the organic matter. Conclusions  Results confirm that anthropogenic activity causes a wide spatial diversity of soil quality in the urban and suburban area. It introduces large amounts of technic materials in soils that could have an impact on the metal availability. It therefore acts on the metal bioavailability in the urban Technosols. Recommendations and Perspectives  These results show that it is necessary, in addition to the characterization of the fine particles, to take into account the contribution of the coarse fraction of the Technosols in the evaluation of risks of transfer of metals to the food chain.     

A semi-fertile interspecific hybrid of <Emphasis Type="Italic">Brassica rapa</Emphasis> and <Emphasis Type="Italic">B. nigra</Emphasis> and the cytogenetic analysis of its progeny

Black rot is a bacterial disease of Brassica rapa caused by Xanthomonas campestris pv. campestris (Xcc.). Sources of resistance to this disease within B. rapa are insufficient and control measures are limited, making the development of resistant breeding lines extremely important. Certain lines of B. nigra exhibit very high resistance to Xcc. For this study, an interspecific cross between Brassica rapa and B. nigra was performed, and a total of 6 F₁ hybrids were obtained through ovary culture. Five plants (H_1–5) were relatively slow-growing, entirely sterile, and had 18 chromosomes in the majority of pollen mother cells (PMCs). GISH analysis showed that most of the PMCs had 8 B. nigra chromosomes, which indicated the expected AB genomic constitution. The last plant (H₆) was partially fertile and the majority of PMCs contained 10 chromosomes of B. rapa and 16 chromosomes of B. nigra, indicating an ABB genomic constitution. Ovary culture techniques were not necessary for the development of the first- or second-backcross generation. Sequence-related amplified polymorphism analysis of F₁, BC₁, and BC₂ plants indicated that some fragments from B. nigra were lost, particularly in the genome of BC₁/BC₂ in successive generation(s). The BC₂ plants expressing good resistance to Xcc. were observed.     

Assessment of genetic variation in common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.) from Nebrodi mountains (Sicily,Italy)

This study was carried out to estimate the level of diversity existing within some common bean landraces still cultivated in Nebrodi mountains, North-western area of Sicily. The multidisciplinary approach adopted to reach this goal involved the characterisation of collected material through morphological, biochemical and molecular marker analyses. The nutritional quality of seeds was also investigated in view of the proposition of the best landraces as niche products. Results showed that those bean landraces retain a considerable level of heterogeneity. The use of both biochemical and molecular markers showed that all landraces clustered into two main groups, corresponding to the Andean and Mesoamerican gene pools. Our results suggest that the best strategy for preserving the diversity of common bean from a restricted area such as Nebrodi mountains, necessitates of a deep knowledge of germplasm to avoid the loss of precious genetic resources or, on the contrary, the safeguard of populations genetically redundant.     

Detecting interaction(s) and assessing the impact of component subsets in a chemical mixture using fixed-ratio mixture ray designs

An important environmental and regulatory issue is the protection of human health from potential adverse effects of cumulative exposure to multiple chemicals. Earlier literature suggested restricting inference to specific fixed-ratio rays of interest. Based on appropriate definitions of additivity, single chemical data are used to predict the relationship among the chemicals under the zero-interaction case. Parametric comparisons between the additivity model and the model fit along the fixed-ratio ray(s) are used to detect departure from additivity. Collection of data along reduced fixed-ratio rays, where subsets of chemicals of interest are removed from the mixture and the remaining compounds are at the same relative ratios as considered in the full ray, allow researchers to make inference about the effect of the removed chemicals. Methods for fitting simultaneous confidence bands about the difference between the best fitting model and the model predicted under additivity are developed to identify regions along the rays where significant interactions occur. This general approach is termed the “single chemicals required” (SCR) method of analysis. A second approach, termed “single chemicals not required” (SCNR) method of analysis, is based on underlying assumptions about the parameterization of the response surface. Under general assumptions, polynomial terms for models fit along fixed-ratio rays are associated with interaction terms. Consideration is given to the case where only data along the mixture rays are available. Tests of hypotheses, which consider interactions due to subsets of chemicals, are also developed.     

Organic geochemical parameters for estimation of petrogenic inputs in the coastal area of Kavala City,Greece

Background, aims, and scope  Sediments and soils in coastal areas are frequently polluted by anthropogenic contaminants as the result of both riverine or terrestrial discharge and autochthonic marine emissions. In order to determine petrogenic contamination in the coastal industrial area of Kavala City in northern Greece, a combination of polycyclic aromatic hydrocarbon (PAH) and organic geochemical petroleum biomarker analyses has been performed on marine and freshwater sediments as well as soils. Materials and methods  Soils, freshwater, and marine sediments have been treated by standard extraction methods. The dried and desulphurized sample extracts have been fractionated by column chromatography, followed by addition of surrogate standards. Qualitative and quantitative data were obtained by gas chromatograph connected with a flame ionization and electron capture detector (GC-FID/ECD) and by GC linked to a mass spectrometer (GC/MS), whereas identification of compounds was based on EI⁺-mass spectra and gas chromatographic retention times. Quantitative data were obtained by integration of specific ion chromatograms. Results  The total PAH concentrations measured in the area varied highly, showing different levels from 18 up to 318,000 ng g⁻¹ dry weight (dw). Several PAH ratios, as well as the ratio of pristane (Pr) to phytane (Phyt), have been considered. Out of 39 samples, 22 revealed a specific distribution of hopane fingerprints indicating petrogenic input. Finally, in numerous samples, the ratio of 17α(H)-22,29,30-trisnorhopane (Tm) and 18α(H)-22,29,30-trisnorhopane (Ts) was calculated, as well as the ratio of 22S-17α(H),21β(H)-30 homohopane (αβC₃₁-hopane 22S) and 22R-17α(H),21β(H)-30 homohopane (αβC₃₁-hopane 22R). Discussion  Based on the specific PAH ratios, a group of samples was clearly characterized to be contaminated dominantly by combustion-derived emissions, whereas a second group of samples exhibited mixed influence from petrogenic and pyrogenic PAHs. On the other hand, the exhibition of specific hopane fingerprints in many samples indicates a direct petrogenic input. Finally, the values of the ratio of Tm/(Ts + Tm) and of αβC₃₁-hopanes 22S/(22S+22R)-isomer demonstrated an input of highly mature organic matter that has to be clearly attributed to petroleum-derived contamination, while the ratio of Pr/Phyt showed that most samples exhibited an input of organic matter. Conclusions  The coastal area of Kavala is strongly affected by anthropogenic contaminants. Petrogenic emissions were pointed out firstly by PAH analyses that separated dominantly pyrogenic contaminated sites from areas affected by both pyrogenic and petrogenic emissions. However, analyses of organic geochemical biomarkers revealed a much higher sensitivity in identifying petroleum-derived contaminations and were successfully used to differentiate several petrogenic contaminations in the marine and terrestrial samples. Recommendations and perspectives  Based on this study, it was recommended to use a complementary approach of source-specific substances to successfully characterize petrogenic emissions. Generally, a PAH-based source identification of petrogenic versus pyrogenic contaminations should be combined with petroleum biomarker analysis. PAH and biomarker ratios as well as individual biomarker fingerprints revealed a more comprehensive view on the quality and quantity of petrogenic emissions in sediments and soils.