IMT Mines Alès

Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Secondly, each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and alignment.We present an algorithm that has the same space and time complexity as the classical Needleman-Wunsch algorithm while accommodating sequencing errors and other biological deviations from the coding frame. The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons). MACSE is the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.MACSE is distributed as an open-source java file executable with freely available source code and can be used via a web interface at: http://mbb.univ-montp2.fr/macse.

Chitosan is a well-known biopolymer, whose high nitrogen content confers remarkable ability for the sorption of metal ions from dilute effluents. However, its sorption performance in both equilibrium and kinetic terms is controlled by diffusion processes. Gel bead formation allows an expansion of the polymer network, which improves access to the internal sorption sites and enhances diffusion mechanisms. Molybdate and vanadate recovery using glutaraldehyde cross-linked chitosan beads reaches uptake capacities as high as 7−8 mmol g-1, depending on the pH. The optimum pH (3−3.5) corresponded to the predominance range of hydrolyzed polynuclear metal forms and optimum electrostatic attraction. While for beads, particle size does not influence equilibrium, for flakes, increasing sorbent radius significantly decreases uptake capacities to 1.5 mmol g-1. Sorption kinetics are mainly controlled by intraparticle diffusion for beads, while for flakes the controlling mechanisms are both external and intraparticle diffusions. The gel conditioning increases the intraparticle diffusivity by 3 orders of magnitude: intraparticle diffusivities range between 10-13 and 10-10 m2 min-1, depending on the sorbent size and the conditioning.

Significance Many applications in engineering require stretchable materials that dissipate little energy during normal operation of cyclic loads (low hysteresis), but dissipate much energy to resist rupture (high toughness), and survive prolonged cyclic loads (fatigue resistant). However, existing stretchable materials cannot meet these requirements simultaneously. Here we present a principle to achieve this goal, and demonstrate the principle by a composite of two stretchable materials of low hysteresis, with large modulus contrast and strong adhesion. The composite retains the low hysteresis, but is much tougher and more fatigue resistant than the constituents. The same principle applies to elastomers, gels, and elastomer–gel hybrids. This class of materials provides opportunities to create high-cycle and low-dissipation soft robots and soft human–machine interfaces.

Abstract The Cévennes–Vivarais Mediterranean Hydrometeorological Observatory (OHM-CV) is a research initiative aimed at improving the understanding and modeling of the Mediterranean intense rain events that frequently result in devastating flash floods in southern France. A primary objective is to bring together the skills of meteorologists and hydrologists, modelers and instrumentalists, researchers and practitioners, to cope with these rather unpredictable events. In line with previously published flash-flood monographs, the present paper aims at documenting the 8–9 September 2002 catastrophic event, which resulted in 24 casualties and an economic damage evaluated at 1.2 billion euros (i.e., about 1 billion U.S. dollars) in the Gard region, France. A description of the synoptic meteorological situation is first given and shows that no particular precursor indicated the imminence of such an extreme event. Then, radar and rain gauge analyses are used to assess the magnitude of the rain event, which was particularly remarkable for its spatial extent with rain amounts greater than 200 mm in 24 h over 5500 km2. The maximum values of 600–700 mm observed locally are among the highest daily records in the region. The preliminary results of the postevent hydrological investigation show that the hydrologic response of the upstream watersheds of the Gard and Vidourle Rivers is consistent with the marked space–time structure of the rain event. It is noteworthy that peak specific discharges were very high over most of the affected areas (5–10 m3 s−1 km−2) and reached locally extraordinary values of more than 20 m3 s−1 km−2. A preliminary analysis indicates contrasting hydrological behaviors that seem to be related to geomorphological factors, notably the influence of karst in part of the region. An overview of the ongoing meteorological and hydrological research projects devoted to this case study within the OHM-CV is finally presented.

HyMeX-SOP1 collected unprecedented observations of atmosphere, ocean, land, and rivers

Abstract Cyphos IL 101 (tetradecyl(trihexyl)phosphonium chloride) was immobilized on Amberlite XAD-7. The extractant impregnated resin (EIR) was very efficient at removing Zn(II) from HCl solutions (optimum found between 2 and 4 M HCl). Metal ions were removed as anionic chlorocomplexes (ZnCl4 2−) by ion exchange mechanism. The sorption strongly depended on the Cyphos IL 101 concentration in the EIR. The maximum sorption capacity was close to 20 mg Zn(II) g−1 EIR (i.e. 0.40 mol Zn(II) mol−1 Cyphos IL 101). The uptake kinetics were controlled by intraparticle diffusion (De: 1.2 10−11 − 6 10−11 m2 min−1). Zn(II) can be easily desorbed using a number of eluents (including water and 0.1 M solution of HNO3, H2SO4, and Na2SO4), which maintained performance levels over 5 cycles.

Responsive surfaces composed of cylindrical or square micrometer-sized thermoresponsive pillars made of thiol-ene nematic main-chain liquid crystalline elastomers (LCEs) are produced by replica molding. The individual pillars behave as microactuators, showing ultralarge and reversible contractions of around 300-400% at the nematic to isotropic phase transition. The nematic main-chain LCE microactuators described here present contractions as large as the best macroscopic systems reported in the literature. Moreover, the contraction observed for this new system outperforms the best values already reported for other LCE microsystems.

Interacting particle systems are known for their ability to generate large-scale selforganized structures from simple local interaction rules between each agent and its neighbors.In addition to studying their emergent behavior, a main focus of the mathematical community has been concentrated on deriving their large-population limit.In particular, the mean-field limit consists of describing the limit system by its population density in the product space of positions and labels.The strategy to derive such limits is often based on a careful combination of methods ranging from analysis of PDEs and stochastic analysis, to kinetic equations and graph theory.In this article, we focus on a generalization of multi-agent systems that includes higher-order interactions, which has largely captured the attention of the applied community in the last years.In such models, interactions between individuals are no longer assumed to be binary (i.e. between a pair of particles).Instead, individuals are allowed to interact by groups so that a full group jointly generates a non-linear force on any given individual.The underlying graph of connections is then replaced by a hypergraph, which we assume to be dense, but possibly non-uniform and of unbounded rank.For the first time in the literature, we show that when the interaction kernels are regular enough, then the mean-field limit is determined by a limiting Vlasov-type equation, where the hypergraph limit is encoded by a socalled UR-hypergraphon (unbounded-rank hypergraphon), and where the resulting mean-field force admits infinitely-many orders of interactions.

The durability of a control method for plant protection is defined as the persistence of its efficacy in space and time. It depends on (i) the selection pressure exerted by it on populations of plant pathogens and (ii) on the capacity of these pathogens to adapt to the control method. Erosion of effectiveness of conventional plant protection methods has been widely studied in the past. For example, apparition of resistance to chemical pesticides in plant pathogens or pests has been extensively documented. The durability of biological control has often been assumed to be higher than that of chemical control. Results concerning pest management in agricultural systems have shown that this assumption may not always be justified. Resistance of various pests to one or several toxins of Bacillus thuringiensis and apparition of resistance of the codling moth Cydia pomonella to the C. pomonella granulovirus have, for example, been described. In contrast with the situation for pests, the durability of biological control of plant diseases has hardly been studied and no scientific reports proving the loss of efficiency of biological control agents against plant pathogens in practice has been published so far. Knowledge concerning the possible erosion of effectiveness of biological control is essential to ensure a durable efficacy of biological control agents on target plant pathogens. This knowledge will result in identifying risk factors that can foster the selection of strains of plant pathogens resistant to biological control agents. It will also result in identifying types of biological control agents with lower risk of efficacy loss, i.e., modes of action of biological control agents that does not favor the selection of resistant isolates in natural populations of plant pathogens. An analysis of the scientific literature was then conducted to assess the potential for plant pathogens to become resistant to biological control agents.

Infrared laser irradiation has been established as an appropriate stimulus for primary sensory neurons under conditions where sensory receptor cells are impaired or lost. Yet, development of clinical applications has been impeded by lack of information about the molecular mechanisms underlying the laser-induced neural response. Here, we directly address this question through pharmacological characterization of the biological response evoked by midinfrared irradiation of isolated retinal and vestibular ganglion cells from rodents. Whole cell patch-clamp recordings reveal that both voltage-gated calcium and sodium channels contribute to the laser-evoked neuronal voltage variations (LEVV). In addition, selective blockade of the LEVV by micromolar concentrations of ruthenium red and RN 1734 identifies thermosensitive transient receptor potential vanilloid channels as the primary effectors of the chain reaction triggered by midinfrared laser irradiation. These results have the potential to facilitate greatly the design of future prosthetic devices aimed at restoring neurosensory capacities in disabled patients.

Abstract Chitosan has unique properties among biopolymers, especially due to the presence of primary amino groups. Chitosan has been used for the chelation of metal ions in near‐neutral solution, the complexation of anions in acidic solution (cationic properties due to amine protonation), the coagulation of negatively charged contaminants under acidic conditions, and for precipitative flocculation at pH above the pKa of chitosan. The coagulation and flocculation properties can be used to treat particulate suspensions (organic or inorganic) and also to treat dissolved organic materials (including dyes and humic acid). This paper will give an overview of the principal results obtained in the treatment of various suspensions and solutions: (a) bentonite suspensions; (b) organic suspensions; (c) anionic dye solutions; and (d) humic acid solutions. Stoichiometry and charge restabilization were determined for the coagulation of humic acid, kaolin, and organic dyes with chitosan, indicating charge neutralization as the dominant mechanism for removal. Charge patch destabilization and bridging mechanisms were inferred in other cases, based on the effects of the apparent molecular weight of the chitosan preparations and effectiveness of sub‐stoichiometric doses of chitosan. For dye solutions, results showed that color can be removed either by sorption onto solid‐state chitosan or by coagulation‐flocculation using dissolved‐state chitosan; the reactivity of amine groups was significantly increased when dissolved chitosan was used. For humic materials, chitosan can be used as a primary coagulant or as a flocculant after coagulation with alum or other inexpensive coagulants. The influence of the degree of deacetylation and the molecular weight of chitosan on its performance as coagulant/flocculant is illustrated by several examples.

International audience

Source characterization alone is not sufficient to account for the effective impact of odours on citizens, which would require to quantify odours directly at receptors. However, despite a certain simplicity of odour measurement at the emission source, odour measurement in the field is a quite more complicated task. This is one of the main reasons for the spreading of odour impact assessment approaches based on odour dispersion modelling. Currently, just a very limited number of reports discussing the use of tracer gas dispersion experiments both in the field and in wind tunnels for model validation purposes can be found in literature. However, when dealing with odour emissions, it is not always possible to identify a limited number of tracer compounds, nor to relate analytical concentrations to odour properties, thus giving that considering single odorous compounds might be insufficient to account for effective odour perception. For these reasons, the possibility of measuring of odours in the field, both as a way for directly assessing odour annoyance or for verifying that modelled odour concentrations correspond to the effective odour perception by humans, is still an important objective. The present work has the aim to review the techniques that can be adopted for measuring odours in the field, particularly discussing how such techniques can be used in alternative or in combination with odour dispersion models for odour impact assessment purposes, and how the results of field odour measurements and model outputs can be related and compared to each other.

Abstract The properties of chitosan depend on several parameters including its origin (shrimp, squid, fungi etc), characteristics (mol fraction of N ‐acetylation; molecular weight) and treatments used to condition it (dissolving, precipitation, drying). These parameters can influence the material's sorption properties for metal ions. It has been suggested that the changes in sorption properties are related to the crystallinity of the material. The present work focuses on the study of the crystallographic properties of samples prepared from shrimp, squid and fungi sources, with different characteristics and conditioned by several physical treatments (dissolving, reprecipitation and drying, including oven‐drying, freeze‐drying), prior to subsequent studies of their sorption properties for platinum (discussed in Part II of this manuscript). © 2003 Society of Chemical Industry

Abstract Chitosan (an amino‐polysaccharide obtained from deacetylation of chitin, the major constituent of crustaceous shells and insect cuticles) presents a cationic character in acidic media allowing its dissolution, its shaping and possible ion‐exchange interactions with anionic compounds (a property applied in adsorption and coagulation–flocculation processes). In neutral media, non‐protonated amino groups allow complexation of metal cations or organic chemicals. These different properties explain the interest taken by the scientific community in using this biopolymer. In solution it contributes to complex metals and their recovery by complexation‐assisted ultrafiltration. It can also be used to coagulate–flocculate organic compounds (as anionic dyes). In the solid state, it can be used for metal ion adsorption, as well as adsorption of organic compounds (dyes, pesticides, drugs, endocrine disruptors, etc.). The adsorption and coagulation–flocculation processes will be compared and examples considered. Moreover, it is noteworthy that the thermal degradation of this type of material is also more environmentally friendly than that of conventional synthetic resins (production of hazardous by‐products, etc.), a supplementary advantage of these biopolymer‐based sorbents. Combined with its ability to be chemically or physically modified improving the potential and phase separation of chitosan‐based materials, all these properties mean it is an excellent candidate for wastewater treatment. © 2017 Society of Chemical Industry

Several unmet needs have been identified in allergic rhinitis: identification of the time of onset of the pollen season, optimal control of rhinitis and comorbidities, patient stratification, multidisciplinary team for integrated care pathways, innovation in clinical trials and, above all, patient empowerment. MASK-rhinitis (MACVIA-ARIA Sentinel NetworK for allergic rhinitis) is a simple system centred around the patient which was devised to fill many of these gaps using Information and Communications Technology (ICT) tools and a clinical decision support system (CDSS) based on the most widely used guideline in allergic rhinitis and its asthma comorbidity (ARIA 2015 revision). It is one of the implementation systems of Action Plan B3 of the European Innovation Partnership on Active and Healthy Ageing (EIP on AHA). Three tools are used for the electronic monitoring of allergic diseases: a cell phone-based daily visual analogue scale (VAS) assessment of disease control, CARAT (Control of Allergic Rhinitis and Asthma Test) and e-Allergy screening (premedical system of early diagnosis of allergy and asthma based on online tools). These tools are combined with a clinical decision support system (CDSS) and are available in many languages. An e-CRF and an e-learning tool complete MASK. MASK is flexible and other tools can be added. It appears to be an advanced, global and integrated ICT answer for many unmet needs in allergic diseases which will improve policies and standards.

After more than 70 years of chemical pesticide use, modern agriculture is increasingly using biological control products. Resistances to conventional insecticides are wide spread, while those to bio-insecticides have raised less attention, and resistance management is frequently neglected. However, a good knowledge of the limitations of a new technique often provides greater sustainability. In this review, we compile cases of resistance to widely used bio-insecticides and describe the associated resistance mechanisms. This overview shows that all widely used bio-insecticides ultimately select resistant individuals. For example, at least 27 species of insects have been described as resistant to Bacillus thuringiensis toxins. The resistance mechanisms are at least as diverse as those that are involved in resistance to chemical insecticides, some of them being common to bio-insecticides and chemical insecticides. This analysis highlights the specific properties of bio-insecticides that the scientific community should use to provide a better sustainability of these products.

Chlorotoxin is a small 36 amino-acid peptide identified from the venom of the scorpion Leiurus quinquestriatus. Initially, chlorotoxin was used as a pharmacological tool to characterize chloride channels. While studying glioma-specific chloride currents, it was soon discovered that chlorotoxin possesses targeting properties towards cancer cells including glioma, melanoma, small cell lung carcinoma, neuroblastoma and medulloblastoma. The investigation of the mechanism of action of chlorotoxin has been challenging because its cell surface receptor target remains under questioning since two other receptors have been claimed besides chloride channels. Efforts on chlorotoxin-based applications focused on producing analogues helpful for glioma diagnosis, imaging and treatment. These efforts are welcome since gliomas are very aggressive brain cancers, close to impossible to cure with the current therapeutic arsenal. Among all the chlorotoxin-based strategies, the most promising one to enhance patient mean survival time appears to be the use of chlorotoxin as a targeting agent for the delivery of anti-tumor agents. Finally, the discovery of chlorotoxin has led to the screening of other scorpion venoms to identify chlorotoxin-like peptides. So far several new candidates have been identified. Only detailed research and clinical investigations will tell us if they share the same anti-tumor potential as chlorotoxin.

The selection of pharmacotherapy for patients with allergic rhinitis (AR) depends on several factors, including age, prominent symptoms, symptom severity, control of AR, patient preferences, and cost. Allergen exposure and the resulting symptoms vary, and treatment adjustment is required. Clinical decision support systems (CDSSs) might be beneficial for the assessment of disease control. CDSSs should be based on the best evidence and algorithms to aid patients and health care professionals to jointly determine treatment and its step-up or step-down strategy depending on AR control. Contre les MAladies Chroniques pour un VIeillissement Actif en Languedoc-Roussillon (MACVIA-LR [fighting chronic diseases for active and healthy ageing]), one of the reference sites of the European Innovation Partnership on Active and Healthy Ageing, has initiated an allergy sentinel network (the MACVIA-ARIA Sentinel Network). A CDSS is currently being developed to optimize AR control. An algorithm developed by consensus is presented in this article. This algorithm should be confirmed by appropriate trials.

The Allergic Rhinitis and its Impact on Asthma (ARIA) initiative commenced during a World Health Organization workshop in 1999. The initial goals were (1) to propose a new allergic rhinitis classification, (2) to promote the concept of multi-morbidity in asthma and rhinitis and (3) to develop guidelines with all stakeholders that could be used globally for all countries and populations. ARIA-disseminated and implemented in over 70 countries globally-is now focusing on the implementation of emerging technologies for individualized and predictive medicine. MASK [MACVIA (Contre les Maladies Chroniques pour un Vieillissement Actif)-ARIA Sentinel NetworK] uses mobile technology to develop care pathways for the management of rhinitis and asthma by a multi-disciplinary group and by patients themselves. An app (Android and iOS) is available in 20 countries and 15 languages. It uses a visual analogue scale to assess symptom control and work productivity as well as a clinical decision support system. It is associated with an inter-operable tablet for physicians and other health care professionals. The scaling up strategy uses the recommendations of the European Innovation Partnership on Active and Healthy Ageing. The aim of the novel ARIA approach is to provide an active and healthy life to rhinitis sufferers, whatever their age, sex or socio-economic status, in order to reduce health and social inequalities incurred by the disease.