Mitochondrial genomic divergence in coelacanths (Latimeria): slow rate of evolution or recent speciation?

Dating the divergence between the two known living species of coelacanths has remained a difficult issue because of the very ancient origin of this lineage of fish, which is more closely related to tetrapods than to other fishes. We sequenced the complete mitochondrial genome of a recently captured individual of the Indonesian coelacanth in order to solve this issue. Using an approach based on loglinear models, we studied the molecular divergence between the two species of coelacanths and three other pairs of species, one that has diverged recently (Pan) and two that have diverged more distantly in the past. The loglinear models showed that the divergence between the two species of coelacanths is not significantly different from the two species of Pan. A detailed gene by gene analysis of the patterns of nucleotide and amino acid substitutions between these two pairs of species further supports the similarity of these divergences. On the other hand, a molecular dating analysis suggested a much older origin of the two coelacanth species (between 20 and 30 million years ago). We discuss the potential reasons for this discrepancy. The analysis of new individuals of the Indonesian coelacanth will certainly help to solve this issue.     

Empirical likelihood confidence intervals for adaptive cluster sampling

Adaptive cluster sampling (ACS) is an efficient sampling design for estimating parameters of rare and clustered populations. It is widely used in ecological research. The modified Hansen-Hurwitz (HH) and Horvitz-Thompson (HT) estimators based on small samples under ACS have often highly skewed distributions. In such situations, confidence intervals based on traditional normal approximation can lead to unsatisfactory results, with poor coverage properties. Christman and Pontius (Biometrics 56:503–510, 2000) showed that bootstrap percentile methods are appropriate for constructing confidence intervals from the HH estimator. But Perez and Pontius (J Stat Comput Simul 76:755–764, 2006) showed that bootstrap confidence intervals from the HT estimator are even worse than the normal approximation confidence intervals. In this article, we consider two pseudo empirical likelihood functions under the ACS design. One leads to the HH estimator and the other leads to a HT type estimator known as the Hájek estimator. Based on these two empirical likelihood functions, we derive confidence intervals for the population mean. Using a simulation study, we show that the confidence intervals obtained from the first EL function perform as good as the bootstrap confidence intervals from the HH estimator but the confidence intervals obtained from the second EL function perform much better than the bootstrap confidence intervals from the HT estimator, in terms of coverage rate.     

Continuity,social change and Katrina

For some time, disaster researchers have looked for social change and mostly found continuity. This paper argues that shifting the focus from investigating social change to documenting continuity may enhance the understanding and planning of post‐disaster situations especially in industrialised societies like the United States. Drawing from qualitative data from post‐Katrina New Orleans, it proposes using the concept of continuity as an analytical device both to identify the axes of continuity and evaluate the likelihood and possible dimensions of social change. The analysis of long‐term recovery plans, along with field observations and interviews with evacuees, suggest that despite the well‐documented emergence of conflict in post‐Katrina New Orleans, the likelihood of social change appears limited.     

Proposing an information criterion for individual-based models developed in a pattern-oriented modelling framework

Individual-based models (IBMs) have been improved in quality and reliability in recent years with an approach called pattern-oriented modelling (POM). POM proposes guidelines to develop models reproducing multiple patterns observed on the field and to test systematically how well the IBMs reproduce them. POM studies used generally traditional methods of goodness of fit such as the sum of squares evaluation or ad hoc comparisons of fitting errors and variations. Model selection, however, can be a rigorous statistical approach based on information theory and information criteria such as the Akaike's information criterion (AIC) or the deviance information criterion (DIC). So far, it has not been tried to link POM to these rigorous techniques. The main problems to achieve that are: (a) the difficulty to have likelihood functions for IBMs’ parameters and (b) the possibility to obtain posterior distributions of IBMs’ parameters given the patterns to reproduce. In a first part, this paper answers problem (a) by proposing and explaining how to calculate a deviance measure (POMDEV) for models developed in a context of POM. And while answering the second problem, a second part of the paper proposes an information criterion for model selection in a POM context (the pattern-oriented modelling information criterion: POMIC). This criterion does not yet have the same theoretical foundation as, e.g., AIC, but uses formal analogies to the DIC. In a third part POMIC is tested with a modelling exercise. This exercise shows the potential of POMIC to use multiple patterns for selecting among multiple potential submodels and eventually select the most parsimonious and well fitting model version. We conclude that POMIC, although being a heuristically derived approach, can greatly improve the POM framework.     

Photooxidation of the phenylazonaphthol AO20 on TIO2: kinetic and mechanistic investigations.

The results of the photocatalytic and photosensitized degradations of the monoazo dye AO20 in aqueous solution using suspended titanium dioxide are presented. Kinetic and mechanistic details have been elucidated using UV/Vis, FTIR and TCO techniques. It was proven that adsorption of dye molecules onto the support material is essential for the processes to be effective. Moreover, even if their mechanisms differ during the early stages, photocatalysis and photosensitization lead to very similar ultimate breakdown products. Indeed, the original dye anchored to the oxide surface systematically undergoes fast decomposition until it is transformed into CO2 or aliphatic acids (formic, acetic, oxalic acids), which react rather slowly with hydroxyl radicals or trapped holes.     

Evaluation of leaching and extraction procedures for soil and waste

Laboratory leaching tests may be used for source term determination as a basis for risk assessment for soil-groundwater pathways on contaminated sites. In order to evaluate different leaching procedures, batch extraction tests and percolation tests were performed using three reference materials produced from contaminated soil, demolition waste and municipal solid waste incinerator bottom ash. Emphasis was placed on the investigation of the leachability of the heavy metals copper and chromium, polycyclic aromatic hydrocarbons (PAHs) and the anions chloride and sulfate. Significant discrepancies between column experiments and batch/extraction tests were found for the release of PAHs and to a lesser extent for the heavy metals Cu and Cr. Additionally interlaboratory comparisons were conducted based on different leaching tests with the reference materials and evaluated using the criteria of comparability and reproducibility. The best reproducibility was achieved for all investigated substances in column tests. The reproducibility of batch tests was acceptable except for PAHs. The results from the experimental work will help establish standardized and feasible laboratory procedures as fundamental for substance specific risk assessment of contaminated sites.     

Leaching behaviour of hazardous demolition waste

Demolition wastes are generally disposed of in unlined landfills for inert waste. However, demolition wastes are not just inert wastes. Indeed, a small fraction of demolition waste contains components that are hazardous to human health and the environment, e.g., lead-based paint, mercury-contained in fluorescent lamps, treated wood, and asbestos. The objective of this study is to evaluate the release potential of pollutants contained in these hazardous components when they are mixed with inert wastes in unlined landfills. After identification of the different building products which can contain hazardous elements and which can be potentially pollutant in landfill scenario, we performed leaching tests using three different lysimeters: one lysimeter containing only inert wastes and two lysimeters containing inert wastes mixed with hazardous demolition wastes. The leachates from these lysimeters were analysed (heavy metals, chlorides, sulphates fluoride, DOC (Dissolved Organic Carbon), phenol index, and PAH). Finally, we compared concentrations and cumulative releases of elements in leachates with the limits values of European regulation for the acceptance of inert wastes at landfill. Results indicate that limit values are exceeded for some elements. We also performed a percolation column test with only demolition hazardous wastes to evaluate the specific contribution of these wastes in the observed releases.     

Photochimie et environnement X- evaluation de la toxicite des produits de phototransformation de l'hydroquinone et des chlorophenols en milieu aqueux

A test of acute toxicity on DAPHNIA MAGNA is suggested to evaluate the efficiency of the phototransformation as a route of abiotic degradation. This test is recommended for compounds phototransformed into a complex mixture of products. Hydroquinone, 2-chloro-, 4-chloro-, 2,4-dichloro-, 2,4,6-trichloro- and pentachlorophenol were studied as examples. In any case the phototransformation is an useful depollution technique on condition the irradiation to be completed as far as the ultimate step of phototransformation.     

Cleft palate: Confirmation of prenatal diagnosis by colour Doppler ultrasound

We present a case of a twin with trisomy 47,XX+i(9p) in whom the diagnosis of cleft palate was confirmed by colour Doppler imaging demonstrating abnormal fluid flow across the fetal pharyngeal bone defect. Application of this technique in cases predisposed for this congenital lesion may prove beneficial in the diagnosis of the more subtle types of isolated cleft palate.