Reply to the EFSA (2016) on the relevance of recent publications (Hofmann et al. 2014, 2016) on environmental risk assessment and management of Bt-maize events (MON810, Bt11 and 1507)

In this commentary, we respond to a report of the EFSA GMO Panel (EFSA EFSA Supp Publ, 1) that criticises the outcomes of two studies published in this journal (Hofmann et al. Environ Sci Eur 26: 24, 2; Environ Sci Eur 28: 14, 3). Both publications relate to the environmental risk assessment and management of Bt-maize, including maize events MON810, Bt11 and maize 1507. The results of Hofmann et al. (Environ Sci Eur 26: 24, 2), using standardised pollen mass filter deposition measurements, indicated that the EFSA Panel model had underestimated pollen deposition and, hence, exposure of non-target organisms to Bt-maize pollen. The results implied a need for safety buffer distances in the kilometre range for protected nature reserve areas instead of the 20–30 m range recommended by the EFSA Panel. As a result, the EFSA Panel revised their model (EFSA EFSA J 13: 4127, 4), adopting the slope of the empirical data from Hofmann et al. The intercept, however, was substantially reduced to less than 1% at one point by introducing further assumptions based on the estimates of mainly panel members, citing possible ‘uncertainty’. Hofmann et al. (Environ Sci Eur 28: 14, 3) published extensive empirical data regarding pollen deposition on leaves. These results were part of a larger 3-year study involving detailed measurements of pollen release, dispersal and deposition over the maize flowering period. The data collected in situ confirmed the previous predictions of Hofmann et al. (Environ Sci Eur 26: 24, 2). Mean levels and observed variability of pollen deposition on maize and four lepidopteran host plants exceeded the assumptions and disagreed with the conclusions of the EFSA Panel. The EFSA Panel reacted in a report (EFSA EFSA Supp Publ, 1) criticising the methods and outcomes of the two published studies of Hofmann et al. while reaffirming their original recommendations. We respond here point-by-point, showing that the critique is not justified. Based on our results on Urtica leaf pollen density, we confirm the need for specific environmental impact assessments for Bt-maize cultivation with respect to protected habitats within isolation buffer distances in the kilometre range.     

Modeling and experiments of polydisperse particle clouds

A model for polydisperse particle clouds has been developed in this study. We extended the monodisperse particle cloud model of Lai et al. (Environ Fluid Mech 13(5):435–463, 2013) to the case of polydisperse particles. The particle cloud is first considered to be a thermal or buoyant vortex ring, with the thermal induced velocity field modeled by an expanding spherical Hill’s vortex. The buoyancy of the composite thermal is assumed to be the sum of buoyancy contributed by the all particles inside the thermal. Individual particles (of different particle properties) in the cloud are then tracked by the particle tracking equation using the computed induced velocity field. The turbulent dispersion effect is also accounted for by using a random walk model. Experiments of polydisperse particle clouds were carried out to validate the model. The agreement between model predictions and experiments was reasonable. We further validate our model by comparing it with the LES study of Wang et al. (J Hydraul Eng ASCE 141(7):06015006, 2014). The limitations of our model are then discussed with reference to the comparison. Overall, although some flow details are not captured by our model, the simplicity and generality of the model makes it useful in engineering applications.     

A copula-based inference to piecewise exponential models under dependent censoring,with application to time to metamorphosis of salamander larvae

In ecology and evolutionary biology, controlled animal experiments are often conducted to measure time to metamorphosis which is possibly censored by the competing risk of death and the follow-up end. This paper considers the problem of estimating the survival function of time-to-event when it is subject to dependent censoring. When the censorship is due to competing risks, the traditional assumption of independent censorship may not be satisfied, and hence, the usual application of the Kaplan–Meier estimator yields a biased estimation for the survival function of the event time. This paper follows an assumed copula approach (Zheng and Klein in Biometrika 82(1):127–138, 1995) to adjust for dependence between the event time of interest and the competing event time. While the literature on an assumed copula approach has mostly focused on semiparametric settings, we alternatively consider a parametric approach with piecewise exponential models for fitting the survival function. We develop maximum likelihood estimation under the piecewise exponential models with an assumed copula. A goodness-of-fit procedure is also developed, which touches upon the identifiability issue of the copula. We conduct simulations to examine the performance of the proposed method and compare it with an existing semiparametric method. The method is applied to real data analysis on time to metamorphosis for salamander larvae living in Hokkaido, Japan (Michimae et al. in Evol Ecol Res 16:617–629, 2014).     

Part I : <Emphasis Type="Italic">a priori</Emphasis> study of erosion and deposition with large eddy simulation of turbulent flow over multiple 2D sandy Gaussian hills

The micro-scale prediction of sand trapping or take-off over hilly terrains is a crucial issue in semi-arid regions for soil depletion. In this context, large eddy simulations around one or several hills are performed in order to provide statistical parameters to characterize the flow at micro-scales and provide data for mesoscale modelling. We focus on the determination of recirculation zones since they play an important role in solid particle erosion or entrapment. A new wall modeling adapted from Huang et al. (J Turbul 17:1–24, 2016) for rough boundary layers is found to improve the prediction of the recirculation zone length downstream of an isolated hill and is used for all the numerical cases presented here. A geometrical parameterization of the recirculation zones is proposed. When the recirculation region is assumed to have an ellipsoidal shape, the total surface of the recirculation can be obtained from this new parameterization and easily extrapolated to more general dune configurations. Numerical results are compared with experiments performed in our laboratory (Simoëns et al. in Procedia IUTAM 17:110–118, 2015) and good agreement is achieved. We explore general aerodynamic cases deduced from the urban canopy scheme of Oke (Energy Build 11:103–113, 1988). In this scheme the momentum and mass exchange between the upper layer and the space between hills is sorted according to the streamwise hill spacing within three basic cases of skimming, wake or isolated flow. The study of the recirculation zones, the mean velocity and Reynolds stress profiles around an isolated or two consecutive hills with different distances shows that the double hill configuration with 3H separation behaves as much as a whole to the upcoming flow. The vortex formed between the crests does not strongly affect the overall evolution of the outer flow. By an a priori prediction of the preferential zones of erosion and accumulation of fictive particles, it is shown that isolated dunes present more deposition and less erosion than two-hill configurations. The results presented in this study will be discussed in the presence of Lagrangian transport of sand particles above 2D Gaussian hills in future work.     

Fitting the truncated negative binomial distribution to count data

Modeling empirical distributions of repeated counts with parametric probability distributions is a frequent problem when studying species abundance. One must choose a family of distributions which is flexible enough to take into account very diverse patterns and possess parameters with clear biological/ecological interpretations. The negative binomial distribution fulfills these criteria and was selected for modeling counts of marine fish and invertebrates. This distribution depends on a vector \(\left( K,\mathfrak {P}\right) \) of parameters, and ranges from the Poisson distribution (when \(K\rightarrow +\infty \)) to Fisher’s log-series, when \(K\rightarrow 0\). Moreover, these parameters have biological/ecological interpretations which are detailed in the literature and in this study. We compared three estimators of K, \(\mathfrak {P}\) and the parameter \(\alpha \) of Fisher’s log-series, following the work of Rao CR (Statistical ecology. Pennsylvania State University Press, University Park, 1971) on a three-parameter unstandardized variant of the negative binomial distribution. We further investigated the coherence underlying parameter values resulting from the different estimators, using both real count data collected in the Mauritanian Exclusive Economic Zone (MEEZ) during the period 1987–2010 and realistic simulations of these data. In the case of the MEEZ, we first built homogeneous lists of counts (replicates), by gathering observations of each species with respect to “typical environments” obtained by clustering the sampled stations. The best estimation of \(\left( K,\mathfrak {P}\right) \) was generally obtained by penalized minimum Hellinger distance estimation. Interestingly, the parameters of most of the correctly sampled species seem compatible with the classical birth-and-dead model of population growth with immigration by Kendall (Biometrika 35:6–15, 1948).     

Buffer sensitivity of photosynthetic carbon utilisation in eight tropical seagrasses

Some of the mechanisms involved in inorganic carbon (Ci) acquisition by tropical seagrasses from the western Indian Ocean were described by Björk et al. (Mar Biol 129:363–366, 1997). However, since then, it has been found that an additional, buffer-sensitive, system of Ci utilisation may operate in some temperate seagrasses (Hellblom et al. in Aquat Bot 69:55–62, 2001, Hellblom and Axelsson in Photos Res 77:173–191, 2003); this buffer sensitivity indicates a mechanism in which electrogenic H⁺ extrusion may form acidic diffusion boundary layers, in which either HCO ₃ ^? –H⁺ is co-transported into the cells, or where HCO ₃ ^? is converted to CO₂ (as catalysed by carbonic anhydrase) prior to uptake of the latter Ci form. Because a buffer was used in the 1997 study, we found it important to reinvestigate those same eight species, taking into account the direct effect of buffers on this potential mode of Ci acquisition in these plants. In doing so, it was found that all seagrass species investigated except Cymodocea serrulata were sensitive to 50 mM TRIS buffer of the same pH as the natural seawater in which they grew (pH 8.0). Especially sensitive were Halophila ovalis, Halodule wrightii and Cymodocea rotundata, which grow high up in the intertidal zone (only ca. 50–65% of the net photosynthetic activity remained after the buffer additions), followed by the submerged Enhalus acoroides and Syringodium isoetifolium (ca. 75% activity remaining), while Thalassia hemprichii and Thalassodendron ciliatum, which grow in-between the two zones, were less sensitive to buffer additions (ca. 80–85% activity remaining). In addition to buffer sensitivity, all species were also sensitive to acetazolamide (AZ, an inhibitor of extracellular carbonic anhydrase activity) such that ca. 45–80% (but 90% for H. ovalis) of the net photosynthetic activity remained after adding this inhibitor. Raising the pH to 8.8 (in the presence of AZ) drastically reduced net photosynthetic rates (0–14% remaining in all species); it is assumed that this reduction in rates was due to the decreased CO₂ concentration at the higher pH. These results indicate that part of the 1997 results for the same species were due to a buffer effect on net photosynthesis. Based on the present results, it is concluded that (1) photosynthetic Ci acquisition in six of the eight investigated species is based on carbonic anhydrase catalysed HCO ₃ ^? to CO₂ conversions within an acidified diffusion boundary layer, (2) C. serrulata appears to support its photosynthesis by extracellular carbonic anhydrase catalysed CO₂ formation from HCO ₃ ^? without the need for acidic zones, (3) H. ovalis features a system in which H⁺ extrusion may be followed by HCO ₃ ^? –H⁺ co-transport into the cells, and (4) direct, non-H⁺-mediated, uptake of HCO ₃ ^? is improbable for any of the species.     

Bayesian estimation of species relative abundances and habitat preferences using opportunistic data

We develop a new statistical procedure to monitor relative species abundances and their respective preferences for different habitat types, using opportunistic data. Following Giraud et al. (Biometrics 72(2):649–658, 2015), we combine the opportunistic data with some standardized data in order to correct the bias inherent to the opportunistic data collection. Species observations are modeled by Poisson distributions whose parameters quantify species abundances and habitat preferences, and are estimated using Bayesian computations. Our main contributions are (i) to tackle the bias induced by habitat selection behaviors, (ii) to handle data where the habitat type associated to each observation is unknown, (iii) to estimate probabilities of selection of habitat for the species. As an illustration, we estimate common bird species habitat preferences and abundances in the region of Aquitaine (France).     

Geochemical distribution of trace element concentrations in the vicinity of Boroo gold mine,Selenge Province,Mongolia

The environmental impacts of Boroo gold mine project in Mongolia was evaluated by chemical characterization of trace element concentrations in water, soils and tailing dam sediment samples. The results showed that concentrations of B, Cd, Ni and Se in the water samples were within the accepted levels of the Mongolia water quality standard (MNS4586: 1998). However, the concentrations of Al, As, Cu, Mn, Fe, Pb, U and Zn were higher than the maximum allowable concentration especially in the monitoring and heap leach wells. The average concentrations of As, Cd, Cu, Ni, Pb and Zn in the tailing dam sediment were 4419, 58.5, 56.0, 4.8, 20.6 and 25.7 mg/kg, respectively. Generally, arsenic and heavy metals in the soil samples were within the acceptable concentrations of the soil standard of Mongolia (MNS 5850: 2008). The chemical characterization of As solid phase in tailing dam sediment showed that the majority of As were found in the residual fraction comprising about 74% of total As. Assessing the potential risk to humans, simple bioavailability extraction test was used to estimate bioavailability of arsenic and heavy metals, and the concentrations extracted from tailing dam sediment were; 288.2 mg/kg As, 7.2 mg/kg Cd, 41.1 mg/kg Cu, 13.5 mg/kg Pb, 4.7 mg/kg Ni and 23.5 mg/kg Zn, respectively. From these results, the Boroo gold mine project has presently not significantly impacted the environment, but there is a high probability that it may act as a source of future contamination.     

Writing it down: suggestions for a new approach towards understanding pro-environmental behaviour

A fashionable field of enquiry – the relationship between expressed attitudes and actual behaviour in the context of sustainable development – is complex (Staats et al. 2004 Staats, H, Harland, P and Wilke, H. 2004. Effecting durable change: a team approach to improve environmental behaviour in the household. Environ Behav., 36(3): 341–367. [Crossref], [Web of Science ®] , [Google Scholar]) and difficult to apply in a policy-relevant manner (Aall and Norland 2005 Aall, C and Norland, I. 2005. The use of the ecological footprint in local politics and administration: results and implications from Norway. Local Environ., 10(2): 159–172. [Taylor & Francis Online] , [Google Scholar]). However, recent research indicates that the use of a household diary can be beneficial in helping to quantify household environmental impact, in educating householders about their impact, and in identifying major ‘behavioural turning points’, where householders may focus efforts to reduce their environmental impact (Hunter et al. 2006 Hunter, C, Carmichael, K and Pangbourne, K. 2006. Household ecological footprinting using a new diary-based data-gathering approach. Local Environ, 11(3): 307–327. [Taylor & Francis Online] , [Google Scholar]). In other words, the use of a diary by householders is a potentially powerful tool in encouraging and facilitating desired behavioural change. This paper reports on the initial findings of an innovative study that assessed the use of a household diary approach as a means of framing and collecting household environmental data and, critically, as an educational vehicle for bringing about behavioural change. Based on the initial findings, it is clear that there is some potential to develop practical policy measures that empower householders by allowing them to better grasp their environmental impact and, consequently, recoup positive implications in terms of financial savings (e.g. reducing the amount of food thrown out) and health benefits (e.g. more walking/cycling).     

On conditional skewness with applications to environmental data

The statistical literature contains many univariate and multivariate skewness measures that allow two datasets to be compared, some of which are defined in terms of quantile values. In most situations, the comparison between two random vectors focuses on univariate comparisons of conditional random variables truncated in quantiles; this kind of comparison is of particular interest in the environmental sciences. In this work, we describe a new approach to comparing skewness in terms of the univariate convex transform ordering proposed by van Zwet (Convex transformations of random variables. Mathematical Centre Tracts, Amsterdam, 1964), associated with skewness as well as concentration. The key to these comparisons is the underlying dependence structure of the random vectors. Below we describe graphical tools and use several examples to illustrate these comparisons.     

Four genes,morphology and ecology: distinguishing a new species of <Emphasis Type="Italic">Acesta</Emphasis> (Mollusca; Bivalvia) from the Gulf of Mexico

There is currently an active scientific debate about the most correct and efficient way to identify species. To date, few studies in the marine realm have combined the available taxonomic methods. In this study we have used morphology, ecology and molecular analyses to identify a new species within the bivalve genus Acesta. All four genes studied (12S, 16S, Cytb, COI) suggested that a common cold-seep species in the Gulf of Mexico, A. bullisi, should be divided into two distinct species. This conclusion was supported by morphological traits and by observations of ecological distribution. A. oophaga Järnegren, Schander and Young n. sp. is described here, and A. bullisi Vokes (Tulane Stud Geol 2:75–92, 1963) is re-described. This study shows that DNA barcoding in combination with traditional morphological and ecological analyses may be an important tools to identify hidden biodiversity among deep-water organisms such as bivalves.     

Ecotoxicological risks of the abandoned F–Ba–Pb–Zn mining area of Osor (Spain)

Due to its potential toxic properties, metal mobilization is of major concern in areas surrounding Pb–Zn mines. In the present study, metal contents and toxicity of soils, aqueous extracts from soils and mine drainage waters from an abandoned F–Ba–Pb–Zn mining area in Osor (Girona, NE Spain) were evaluated through chemical extractions and ecotoxicity bioassays. Toxicity assessment in the terrestrial compartment included lethal and sublethal endpoints on earthworms Eisenia fetida, arthropods Folsomia candida and several plant species, whereas aquatic tests involved bacteria Vibrio fischeri, microalgae Raphidocelis subcapitata and crustaceans Daphnia magna. Total concentrations of Ba (250–5110 mg kg^?1), Pb (940 to >5000 mg kg^?1) and Zn (2370–11,300 mg kg^?1) in soils exceeded intervention values to protect human health. Risks for the aquatic compartment were identified in the release of drainage waters and in the potential leaching and runoff of metals from contaminated soils, with Cd (1.98–9.15 µg L^?1), Pb (2.11–326 µg L^?1) and Zn (280–2900 µg L^?1) concentrations in filtered water samples surpassing US EPA Water Quality Criteria (2016a, b). Terrestrial ecotoxicity tests were in accordance with metal quantifications and identified the most polluted soil as the most toxic. Avoidance and reproduction tests with earthworms showed the highest sensitivity to metal contamination. Aquatic bioassays performed in aqueous extracts from soils confirmed the results from terrestrial tests and also detected toxic effects caused by the mine drainage waters. Algal growth inhibition was the most sensitive aquatic endpoint. In view of the results, the application of a containment or remediative procedure in the area is encouraged.     

Evaluation of existing equations for temporal scour depth around circular bridge piers

Scour is defined as the processes of removal of sediment particles from water stream bed by the erosive action of activated water, and also carries sediment away from the hydraulic structures. Scour is the main cause of pier failure. Numerous equations are available for estimating temporal and equilibrium scour depth. The present study describes the phenomenon of temporal scour depth variation at bridge piers and deals with the methods for its estimation. The accuracy of six temporal scour depth equations are also checked in this study. After graphical and statistical analysis, it was found that the relationship proposed by Oliveto and Hager (J Hydraul Eng (ASCE) 128(9):811–520, 2002) predicts temporal scour depth better than other equations. Three equations of equilibrium time of scour are also used for computing equilibrium time. Equilibrium time equation proposed by Choi and Choi (Water Environ J 30(1–2):14–21, 2016) gives better agreements with observed values.     

Population density and conservation status of the teiid lizard <Emphasis Type="Italic">Cnemidophorus littoralis</Emphasis>, an endangered species endemic to the sandy coastal plains (restinga habitats) of Rio de Janeiro state,Brazil

The threatened lizard Cnemidophorus littoralis occurs in only four restinga habitats of Brazilian coast and its current conservation status is “endangered”. Due to its restricted distribution, the effects of habitat degradation are especially harmful to them. To prevent a local or even total extinction, we analyzed changes in population density and in amount of disturbances of three restinga areas during a seven-year gap. This study took place in three restingas of Rio de Janeiro State, Brazil: Maricá, Jurubatiba and Grussaí. We compared C. littoralis current density with the one registered in 2005 by Menezes and Rocha (2013) with 2 ha transections in each restinga. We also made another group of transects to estimate population density along the entire extension of the restingas. Conservation index of each site was based on satellite images and field samplings. Data showed a decreasing trend of Cnemidophorus littoralis population density over the years. Grussaí had the lowest population density and the highest degradation index among the three sites, whereas Jurubatiba had the lowest degree of disturbance, the largest area and the highest lizard population density. Data showed an increase in the amount of disturbance in restingas over the years, which seemed to have a negative effect in C. littoralis population density. Improvement of surveillance and implementation of education programs in the protected areas and its surroundings, and periodic monitoring of C. littoralis populations to follow their density changes, are essential for the maintenance of the species.     

Optimal model averaging by data perturbation for spatial noisy data

Geostatistical models play an important role in spatial data analysis, in which model selection is inevitable. Model selection methods, such as AIC and BIC, are popular for selecting appropriate models. In recent years, some model averaging methods, such as smoothed AIC and smoothed BIC, are also applied to spatial data models. However, the corresponding averaging estimators are outperformed by optimal model averaging estimators (Hansen in Econometrica 75:1175–1189, 2007) for the ordinary linear models. Therefore, this paper focuses on the optimal model averaging method for geostatistical models. We propose a weight choice criterion for the model averaging estimator on the basis of the generalized degrees of freedom and data perturbation technique. We further theoretically prove the resultant estimator is asymptotically optimal in terms of the mean squared error, and numerically demonstrate its satisfactory performance. Finally, the proposed method is applied to a mercury data set.     

On the front conditions for gravity currents in channels of general cross-section

We consider the propagation of a high-Reynolds-number gravity current in a horizontal channel with general cross-section whose width is \(f(z), 0 \le z\le H\), and the gravity acceleration g acts in \(-z\) direction. (The classical rectangular cross-section is covered by the particular case \(f(z) =\) const.) We assume a two-layer system of homogeneous fluids of constant densities \(\rho _{c}\) (current, of height \(h < H \)) and smaller \(\rho _{a}\) (ambient, filling the remaining part of the channel). We focus attention on the calculation and assessment of the nose Froude-number condition \(Fr = U/(g' h)^{1/2}\); here U is the speed of propagation of the current and \(g' = (\rho _{c}/\rho _{a}-1) g\) is the reduced gravity. We first revisit the steady-state current, and derive compact insightful expressions of Fr and energy dissipation as a function of \(\varphi \) (\(=\) area fraction occupied by the current in the cross-section). We show that the head loss \(\delta _0\) on the stagnation line is formally a degree of freedom in the determination of \(Fr(\varphi )\), and we clarify the strong connections with the head loss \(\delta \) in the ambient fluid, and with the overall rate of dissipation \(\dot{{\mathcal{D}}}\). We demonstrate that the closure \(\delta _0 = 0\) [suggested by Benjamin (J Fluid Mech 31, 209–248, 1968) for the rectangular cross-section] produces in general the smallest Fr for a given \(\varphi \); the results are valid for a significant range \([0, \varphi _{\max }]\), in which the current is dissipative, except for the point \(\varphi _{\max }\) where \(\delta = \dot{{\mathcal{D}}} = 0\). We show that imposing the closure \(\delta = \dot{{\mathcal{D}}} = 0\), which corresponds to an energy-conserving or non-dissipative current, produces in general unacceptable restrictions of the range of validity, and large values of Fr; in particular, deep currents (\(\varphi < 0.3\) say) must be excluded because they are inherently dissipative. On the other hand, the compromise closure \(\delta (\varphi ) =\delta _0(\varphi )\) produces the simple \(Fr(\varphi ) = \sqrt{2}(1 - \varphi )\) formula whose values and dissipation properties are very close, and the range of validity is identical, to these obtained with Benjamin’s closure (moreover, we show that this corresponds to circulation-conservation solutions). The results are illustrated for practical cross-section geometries (rectangle, \(\Delta \) and \(\nabla \) triangle, circle, and the general power-law \(f(z) = b z ^\alpha \) (\(b>0, \alpha \ge 0, 0< z \le H\)). Next, we investigate the connection of the steady-state results with the time-dependent current, and show that in a lock-released current the rate of dissipation of the system is equal to, or larger than, that obtained for Fr corresponding to the conditions at the nose of the current. The results and insights of this study cover a wide range of cross-section geometry and apply to both Boussinesq and non-Boussinesq systems; they reveal a remarkable robustness of Fr as a function of \(\varphi \).     

The role of black carbon as a catalyst for environmental redox transformation

Black carbon (BC) is an important class of geosorbents that control the fate and transport of organic pollutants in soil and sediment. We previously demonstrated a new role of BC as an electron transfer mediator in the abiotic reduction of nitroaromatic and nitramine compounds by Oh and Chiu (Environ Sci Technol 43:6983–6988, 2009). We proposed that BC can catalyze the reduction of nitro compounds because it contains microscopic graphitic (graphene) domains, which facilitate both sorption and electron transfer. In this study, we assessed the ability of different types of BC—graphite, activated carbon, and diesel soot—to mediate the reduction of 2,4-dinitrotoluene (DNT) and 2,4-dibromophenol (DBP) by H₂S. All three types of BC enhanced DNT and DBP reduction. H₂S supported BC-mediated reduction, as was observed previously with a thiol reductant. The results suggest that BC may influence the fate of organic pollutants in reducing subsurface environments through redox transformation in addition to sorption.