Fitting animal survival models with temporal random effects

Estimating temporal variance in animal demographic parameters is of particular importance in population biology. We implement the Schall’s algorithm for incorporating temporal random effects in survival models using recovery data. Our frequentist approach is based on a formulation of band-recovery models with random effects as generalized linear mixed models and a linearization of the link function conditional on the random effects. A simulation study shows that our procedure provides unbiased and precise estimates. The method is then implemented on two case studies using recovery data on fish and birds.     

Description and preliminary validation of the PMSS fast response parallel atmospheric flow and dispersion solver in complex built-up areas

Noxious atmospheric releases may originate from both accidents and malicious activities. They are a major concern for public authorities or first responders who may wish to have the most accurate situational awareness. Nonetheless, it is difficult to reliably and accurately model the flow, transport, and dispersion processes in large complex built-up environments in a limited amount of time and resources compatible with operational needs. The parallel version of Micro-SWIFT-SPRAY (PMSS) is an attempt to propose a physically sound and fast response modelling system applicable to complicated industrial or urban sites in case of a hazardous release. This paper presents and justifies the choice of the diagnostic flow and Lagrangian dispersion models in PMSS. Then, it documents in detail the development of the parallel algorithms used to reduce the computational time of the models. Finally, the paper emphasizes the preliminary model validation and parallel performances of PMSS based on data from both wind tunnel (Evaluation of Model Uncertainty) and in-field reduced-scale (Mock Urban Setting Test) and real-scale (Oklahoma City) experimental campaigns.     

Public regulatory relief and the adoption of environmental management systems: a European survey

An increasing number of organizations across the world have adopted Environmental Management Systems (EMSs) based on certifiable standards, notably the European Eco-Management and Audit Scheme (EMAS) and the ISO 14001 standards. Although the specialized literature has studied the motivations, obstacles and benefits of the adoption of these standards for EMSs extensively, the impact of the public incentives on the adoption of such environmental management tools has been overlooked. In order to fill this gap in the literature, this article aims to shed light on the level of companies' knowledge and application of the main regulatory relief initiatives provided by public administrations around the EU for organizations with a certified EMS. For that purpose, this article summarizes the main findings of a survey carried out with the participation of 244 European EMAS-registered organizations. The findings of the survey highlight the fact that most of the surveyed companies have adopted or benefitted from some form of regulatory relief, mainly by making use of the measures granting an extended duration of some permits (44%), reductions in financial guarantees in the waste-treatment sector (31%) and tax reductions (26%). Moreover, it emerges that, among countries, the role of regulatory relief to support companies in the path to the adoption of EMSs is not univocal.     

Methylmercury speciation in the dissolved phase of a stratified lake using the diffusive gradient in thin film technique

The diffusive gradient in thin film (DGT) technique was successfully used to monitor methylmercury (MeHg) speciation in the dissolved phase of a stratified boreal lake, Lake 658 of the Experimental Lakes Area (ELA) in Ontario, Canada. Water samples were conventionally analysed for MeHg, sulfides, and dissolved organic matter (DOM). MeHg accumulated by DGT devices was compared to MeHg concentration measured conventionally in water samples to establish MeHg speciation. In the epilimnion, MeHg was almost entirely bound to DOM. In the top of the hypolimnion an additional labile fraction was identified, and at the bottom of the lake a significant fraction of MeHg was potentially associated to colloidal material. As part of the METAALICUS project, isotope enriched inorganic mercury was applied to Lake 658 and its watershed for several years to establish the relationship between atmospheric Hg deposition and Hg in fish. Little or no difference in MeHg speciation in the dissolved phase was detected between ambient and spike MeHg.     

Detection of fungal development in closed spaces through the determination of specific chemical targets

In addition to the biodegradation problems encountered in buildings, exposure of their occupants to moulds is responsible for numerous diseases: infections (invasive nosocomial aspergillosis), immediate or delayed allergies, food-borne infections and different types of irritation. In this context, the aim of our work has been to determine specific chemical tracers for fungal development on construction materials. More generally, by detecting a specific chemical fingerprint of fungal development, our objective was to propose a microbiological alert system which could control systems and/or procedures for the microbiological treatment of indoor areas.

We therefore characterized the chemical emissions from six types of construction material contaminated artificially by moulds. Chemical fingerprints were established for 19 compounds arising specifically from fungal metabolism: 2-ethylhexanoic acid methyl ester, 1-octen-3-ol, 3-heptanol, 3-methyl-1-butanol, 2-methyl-1-butanol, 1,3-octadiene, 2-(5H)-furanone, 2-heptene, -pinene, 2-methylisoborneol, 4-heptanone, 2-methylfuran, 3-methylfuran, dimethyldisulfide, methoxybenzene, a terpenoid and three sesquiterpenes.

Determining the origin of these compounds and their specific links with a growth substrate or fungal species made it possible to judge the pertinence of choosing these compounds as tracers.

Thus the detecting specific volatile organic compounds emitted as from the second day of fungal growth demonstrated that this approach had the advantage of detecting fungal development both reliably and rapidly before any visible signs of contamination could be detected.     

Silver and thallium historical trends in the Seine River basin

Records on pollution by metals of minor economic importance (e.g. silver and thallium) but which prove to be toxic are rarely documented in river sediment. This study used two sediment cores collected downstream of the Seine River to describe the temporal evolution of Ag and Tl concentrations in an urban catchment. Radionuclide analysis (i.e. Cs-137 and Pb-210) allowed dating sediment deposition within the cores (1933-2003). Ag concentration reached maximum values of 14.3-24.6 mg kg(-1) in the 1960s and 1970s, before gradually decreasing up to values which approximated 4 mg kg(-1) in 2003. In contrast, Tl concentrations remained roughly constant throughout the core (median value of 0.86 mg kg(-1)). Suspended solids was collected at upstream locations in the catchment to derive the background concentrations in Ag and Tl. Very high Ag concentrations were measured in the upstream Seine River sites (0.33-0.59 mg kg(-1)), compared to the values reported in the literature (0.055 mg kg(-1)). This suggests the presence of a widespread and ancient Ag pollution in the Seine River basin, as demonstrated by the very high Ag enrichment ratios recorded in the cores. Annual flux of particulate Ag in the Seine River was estimated at 1.7 t yr(-1) in 2003. In contrast, Tl concentrations remained in the same order of magnitude as the natural background signal (0.3-0.5 mg kg(-1)). This study suggests that the Seine River basin is free of Tl contamination. Future concerns should hence mostly rely on Ag contamination, in a context of increasing Ag uses and possible releases to the environment.     

Hare or Tortoise? Trade-offs in Recovering Sustainable Bioeconomic Systems

In this paper, we develop a framework for (a) the study of sustainability of dynamic bioeconomic systems and (b) the definition of recovery paths from unsustainable situations. We assume that the system follows a sustainable trajectory if it evolves over time within a set of multidimensional constraints. We use the mathematical concept of viability to characterize sustainability. Recovery paths are studied with regards to their duration and their acceptability. This general framework is applied to the issue of recovering sustainable fisheries. We define sustainability in a fishery as the requirement that a set of economic, ecological, and social constraints is satisfied at all times. Recovery paths are characterized by the time required to obtain sustainable exploitation conditions in the fishery and by the acceptable recovery costs for fishermen. In particular, we identify the recovery path which minimizes the time of crisis under a minimum transition profit constraint. We then describe the trade-off between speed and accepted costs of recovery paths, by comparing “Hare”-like high-speed–high-cost strategies to “Tortoise”-like low-speed–low-cost strategies. We illustrate our results by means of a numerical analysis of the Bay of Biscay Nephrops fishery.     

Mercury speciation in plankton from the Cabo Frio Bay,SE - Brazil

Mercury (Hg) is considered a global pollutant, and the scientific community has shown great concern about its toxicity as it may affect the biota of entire systems, through bioaccumulation and bioamplification processes of its organic form, methylmercury (MeHg), along food web. However, few research studies deal with bioaccumulation of Hg from marine primary producers and the first-order consumers. So, this study aims to determine Hg distribution and concentration levels in phytoplankton and zooplankton in the Cabo Frio Bay, Brazil, a site influenced by coastal upwelling. The results from Hg speciation analyses show that inorganic mercury Hg(II) was the predominant specie in plankton from this bay. The annual Hg species distribution in plankton shown mean concentration of 2.00?±?1.28 ng Hg(II)?g^?1 and 0.15?±?0.08 ng MeHg g^?1 wet weight (phytoplankton) and 2.5?±?2.03 ng Hg(II)?g^?1 and 0.25?±?0.09 ng MeHg g^?1 wet weight (zooplankton). Therefore, upwelling zones should be considered in the Hg biogeochemical cycle models as a process that enhances Hg(II) bioaccumulation in plankton, raising its bioavailability and shelf deposition.     

Correction to: Documenting lemming population change in the Arctic: Can we detect trends?

Ambio - In the original published article, some of the symbols in figure 1A were modified incorrectly during the typesetting and publication process. The correct version of the figure is provided...     

Characterization of chlordecone-tolerant fungal populations isolated from long-term polluted tropical volcanic soil in the French West Indies

The insecticide chlordecone is a contaminant found in most of the banana plantations in the French West Indies. This study aims to search for fungal populations able to grow on it. An Andosol heavily contaminated with chlordecone, perfused for 1 year in a soil–charcoal system, was used to conduct enrichment cultures. A total of 103 fungal strains able to grow on chlordecone-mineral salt medium were isolated, purified, and deposited in the MIAE collection (Microorganismes d'Intérêt Agro-Environnemental, UMR Agroécologie, Institut National de la Recherche Agronomique, Dijon, France). Internal transcribed spacer sequencing revealed that all isolated strains belonged to the Ascomycota phylum and gathered in 11 genera: Metacordyceps, Cordyceps, Pochonia, Acremonium, Fusarium, Paecilomyces, Ophiocordyceps, Purpureocillium, Bionectria, Penicillium, and Aspergillus. Among predominant species, only one isolate, Fusarium oxysporum MIAE01197, was able to grow in a liquid culture medium that contained chlordecone as sole carbon source. Chlordecone increased F. oxysporum MIAE01197 growth rate, attesting for its tolerance to this organochlorine. Moreover, F. oxysporum MIAE01197 exhibited a higher EC₅₀ value than the reference strain F. oxysporum MIAE00047. This further suggests its adaptation to chlordecone tolerance up to 29.2 mg l^?1. Gas chromatography–mass spectrometry (GC-MS) analysis revealed that 40 % of chlordecone was dissipated in F. oxysporum MIAE01197 suspension culture. No chlordecone metabolite was detected by GC-MS. However, weak amount of ¹⁴CO₂ evolved from ¹⁴C₁₀-chlordecone and ¹⁴C₁₀-metabolites were observed. Sorption of ¹⁴C₁₀-chlordecone onto fungal biomass followed a linear relationship (r ²?=?0.99) suggesting that it may also account for chlordecone dissipation in F. oxysporum MIAE01197 culture.