Valuing lagoons using a meta-analytical approach: Methodological and practical issues

Among coastal areas, lagoons are probably one of the most active and sensitive areas. They provide numerous goods and services that are of value to people. As public goods, there are freely accessible but in counterpart there are more endangered than other areas. Conflict uses between activities inside and outside the lagoons or between occasional and regular users imply to implement the lagoons economic values in order to provide a useful management tool. Many studies have been driven in order to estimate the impacts of the different activities on water quality and the willingness to pay for a better environment. We collect 32 lagoon studies providing 67 value observations in order to present a comprehensive meta-analysis of the valuation literature. This method allows estimating a function that takes into account the sites characteristics, methodological variables and lagoons services. The estimation of a meta-analytic function proves that all theses kinds of variables are important for the calculus of values. Moreover, we precisely determine the influence of the different variables on the value. Performing the transfer, we find an average transfer error amount equal to 87% but a median transfer error equal to 24%. This result due to a very small number of aberrant values is interesting with one-fourth of the transfers showing errors lower to 10% and nearly three-fourth of the transfers present errors lower to 50%.

Environmental Good Production in the Optimum Activities Portfolio of a Risk Averse Farmer

An analytical framework is proposed for analysis of environmental good production by farmers in the case of price uncertainty. Environmental good production contracted by means of agri-environmental agreements is treated as a risk less option in the farmer's production activities portfolio. Efficient frontiers were generated using mathematical programming farm level models of suckler cow farms in Monts du Cantal, in France. It was demonstrated that for a DARA risk averse farmer: 1) the agreement payment level is not without impact on the farming intensity on parcels not subscribed under the corresponding argi-environmental programme, 2) a lump sum payment matters under uncertainty, 3) the overall impact of the lump sum payment on environmental good production depends on the type of jointness in production of agricultural and environmental goods, and on the level of uncertainty.uncertainty, portfolio optimisation, biodiversity, agricultural policy, mathematical programming, Agricultural and Food Policy, Resource /Energy Economics and Policy, Q12, Q18, Q28,

Environmental good production in the optimum activities portfolio of a risk averse-farmer

An analytical framework is proposed for analysis of environmental good production by farmers in the case of price uncertainty. Environmental good production contracted by means of agri-environmental agreements is treated as a riskless option in the farmer’s production activities portfolio. It is shown that agri-environmental agreements aiming at biodiversity competing with beef production are likely to increase management intensity on the non-enrolled land, and that the effect of the payments for these agreements on the number of hectares enrolled is ambiguous. It is also demonstrated that an increase in the output price variability and/or a decrease in the level of decoupled subsidies will induce an increase (decrease) in the area enrolled in agreements aiming at biodiversity competing with (complementary to) beef production. The obtained results are illustrated by means of efficient frontiers generated using mathematical programming farm level models of suckler cow farms in Monts du Cantal, in France.uncertainty, portfolio optimisation, biodiversity, agricultural policy, mathematical programming

Host cell traversal is important for progression of the malaria parasite through the dermis to the liver

The malaria sporozoite, the parasite stage transmitted by the mosquito, is delivered into the dermis and differentiates in the liver. Motile sporozoites can invade host cells by disrupting their plasma membrane and migrating through them (termed cell traversal), or by forming a parasite-cell junction and settling inside an intracellular vacuole (termed cell infection). Traversal of liver cells, observed for sporozoites in vivo, is thought to activate the sporozoite for infection of a final hepatocyte. Here, using Plasmodium berghei, we show that cell traversal is important in the host dermis for preventing sporozoite destruction by phagocytes and arrest by nonphagocytic cells. We also show that cell infection is a pathway that is masked, rather than activated, by cell traversal. We propose that the cell traversal activity of the sporozoite must be turned on for progression to the liver parenchyma, where it must be switched off for infection of a final hepatocyte.Inst Pasteur, Unite Biol & Genet Paludisme, F-75724 Paris 15, FranceUniversidade Federal de São Paulo, Dept Bioquim, BR-04044020 São Paulo, BrazilUniv Montpellier 2, CNRS, UMR 5539, F-34095 Montpellier 05, FranceMie Univ, Sch Med, Tsu, Mie 5140001, JapanUniversidade Federal de São Paulo, Dept Bioquim, BR-04044020 São Paulo, BrazilWeb of Scienc

Managed aquifer recharge in weathered crystalline basement aquifers in India: Monitoring of the effect of tank infiltration on water quality over several monsoon events

International audienceManaged aquifer recharge (MAR) structures like percolation tanks are considered by the Indian national and regional governments as major option for tackling declining groundwater levels due to overexploitation for irrigation purposes (Boisson et al., 2014). Their main purpose is to restore groundwater availability under strong climatic and anthropogenic pressure. Furthermore, MAR-induced dilution with fresh surface water is generally expected to improve groundwater quality with respect to both anthropogenic and geogenic contaminants (total mineralisation, nitrates, chlorides, sulphates and fluoride contents). The impact of a percolation tank on groundwater quality was investigated in a context that is typical for hydro-climatic and geological settings in southern and eastern India: fractured crystalline basement aquifers overlain by a weathering zone under semi-arid climate. Water level data and geochemical indicators (stable isotopes and major ions) were monitored for both groundwater and surface water, over several successive monsoon events. In case of high to very high water levels, the groundwater quality is globally improved. However, in a few cases, the quality of the groundwater can be negatively impacted due to leaching of salts under the tank, particularly during the first rain events of the monsoon. Geogenic fluoride contents in groundwater, induced by water-rock interaction and enhanced by recycling of agricultural return flow under paddy fields, is found to be relatively stable over the year. This finding points out that the underlying processes, mainly dissolution of F-bearing phases like fluorapatites combined with Ca/Na cation exchange and calcite precipitation , both limiting the possibility of F-removal via fluorite precipitation (Pettenati et al., 2013, 2014), are not impacted by the hydrological conditions. This work highlights the complexity of the recharge processes in crystalline aquifers, enhanced by the variability of hydrological conditions. It also provides insights into the possible risk for groundwater quality deterioration in cases of light and short monsoons periods

Life-threatening influenza pneumonitis in a child with inherited IRF9 deficiency

Life-threatening pulmonary influenza can be caused by inborn errors of type I and III IFN immunity. We report a 5-yr-old child with severe pulmonary influenza at 2 yr. She is homozygous for a loss-of-function IRF9 allele. Her cells activate gamma-activated factor (GAF) STAT1 homodimers but not IFN-stimulated gene factor 3 (ISGF3) trimers (STAT1/STAT2/IRF9) in response to IFN-α2b. The transcriptome induced by IFN-α2b in the patient's cells is much narrower than that of control cells; however, induction of a subset of IFN-stimulated gene transcripts remains detectable. In vitro, the patient's cells do not control three respiratory viruses, influenza A virus (IAV), parainfluenza virus (PIV), and respiratory syncytial virus (RSV). These phenotypes are rescued by wild-type IRF9, whereas silencing IRF9 expression in control cells increases viral replication. However, the child has controlled various common viruses in vivo, including respiratory viruses other than IAV. Our findings show that human IRF9- and ISGF3-dependent type I and III IFN responsive pathways are essential for controlling IAV

Dominant-negative mutations in human IL6ST underlie hyper-IgE syndrome

Autosomal dominant hyper-IgE syndrome (AD-HIES) is typically caused by dominant-negative (DN) STAT3 mutations. Patients suffer from cold staphylococcal lesions and mucocutaneous candidiasis, severe allergy, and skeletal abnormalities. We report 12 patients from 8 unrelated kindreds with AD-HIES due to DN IL6ST mutations. We identified seven different truncating mutations, one of which was recurrent. The mutant alleles encode GP130 receptors bearing the transmembrane domain but lacking both the recycling motif and all four STAT3-recruiting tyrosine residues. Upon overexpression, the mutant proteins accumulate at the cell surface and are loss of function and DN for cellular responses to IL-6, IL-11, LIF, and OSM. Moreover, the patients’ heterozygous leukocytes and fibroblasts respond poorly to IL-6 and IL-11. Consistently, patients with STAT3 and IL6ST mutations display infectious and allergic manifestations of IL-6R deficiency, and some of the skeletal abnormalities of IL-11R deficiency. DN STAT3 and IL6ST mutations thus appear to underlie clinical phenocopies through impairment of the IL-6 and IL-11 response pathways

Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis

Computational analyses of human patient exomes aim to filter out as many nonpathogenic genetic variants (NPVs) as possible, without removing the true disease-causing mutations. This involves comparing the patient's exome with public databases to remove reported variants inconsistent with disease prevalence, mode of inheritance, or clinical penetrance. However, variants frequent in a given exome cohort, but absent or rare in public databases, have also been reported and treated as NPVs, without rigorous exploration. We report the generation of a blacklist of variants frequent within an in-house cohort of 3,104 exomes. This blacklist did not remove known pathogenic mutations from the exomes of 129 patients and decreased the number of NPVs remaining in the 3,104 individual exomes by a median of 62%. We validated this approach by testing three other independent cohorts of 400, 902, and 3,869 exomes. The blacklist generated from any given cohort removed a substantial proportion of NPVs (11-65%). We analyzed the blacklisted variants computationally and experimentally. Most of the blacklisted variants corresponded to false signals generated by incomplete reference genome assembly, location in low-complexity regions, bioinformatic misprocessing, or limitations inherent to cohort-specific private alleles (e.g., due to sequencing kits, and genetic ancestries). Finally, we provide our precalculated blacklists, together with ReFiNE, a program for generating customized blacklists from any medium-sized or large in-house cohort of exome (or other next-generation sequencing) data via a user-friendly public web server. This work demonstrates the power of extracting variant blacklists from private databases as a specific in-house but broadly applicable tool for optimizing exome analysis

Sanitation and water supply coverage thresholds associated with active trachoma: Modeling cross-sectional data from 13 countries.

BACKGROUND: Facial cleanliness and sanitation are postulated to reduce trachoma transmission, but there are no previous data on community-level herd protection thresholds. We characterize associations between active trachoma, access to improved sanitation facilities, and access to improved water sources for the purpose of face washing, with the aim of estimating community-level or herd protection thresholds. METHODS AND FINDINGS: We used cluster-sampled Global Trachoma Mapping Project data on 884,850 children aged 1-9 years from 354,990 households in 13 countries. We employed multivariable mixed-effects modified Poisson regression models to assess the relationships between water and sanitation coverage and trachomatous inflammation-follicular (TF). We observed lower TF prevalence among those with household-level access to improved sanitation (prevalence ratio, PR = 0.87; 95%CI: 0.83-0.91), and household-level access to an improved washing water source in the residence/yard (PR = 0.81; 95%CI: 0.75-0.88). Controlling for household-level water and latrine access, we found evidence of community-level protection against TF for children living in communities with high sanitation coverage (PR80-90% = 0.87; 95%CI: 0.73-1.02; PR90-100% = 0.76; 95%CI: 0.67-0.85). Community sanitation coverage levels greater than 80% were associated with herd protection against TF (PR = 0.77; 95%CI: 0.62-0.97)-that is, lower TF in individuals whose households lacked individual sanitation but who lived in communities with high sanitation coverage. For community-level water coverage, there was no apparent threshold, although we observed lower TF among several of the higher deciles of community-level water coverage. CONCLUSIONS: Our study provides insights into the community water and sanitation coverage levels that might be required to best control trachoma. Our results suggest access to adequate water and sanitation can be important components in working towards the 2020 target of eliminating trachoma as a public health problem

Human MCTS1-dependent translation of JAK2 is essential for IFN-γ immunity to mycobacteria.

Human inherited disorders of interferon-gamma (IFN-γ) immunity underlie severe mycobacterial diseases. We report X-linked recessive MCTS1 deficiency in men with mycobacterial disease from kindreds of different ancestries (from China, Finland, Iran, and Saudi Arabia). Complete deficiency of this translation re-initiation factor impairs the translation of a subset of proteins, including the kinase JAK2 in all cell types tested, including T lymphocytes and phagocytes. JAK2 expression is sufficiently low to impair cellular responses to interleukin-23 (IL-23) and partially IL-12, but not other JAK2-dependent cytokines. Defective responses to IL-23 preferentially impair the production of IFN-γ by innate-like adaptive mucosal-associated invariant T cells (MAIT) and γδ T lymphocytes upon mycobacterial challenge. Surprisingly, the lack of MCTS1-dependent translation re-initiation and ribosome recycling seems to be otherwise physiologically redundant in these patients. These findings suggest that X-linked recessive human MCTS1 deficiency underlies isolated mycobacterial disease by impairing JAK2 translation in innate-like adaptive T lymphocytes, thereby impairing the IL-23-dependent induction of IFN-γ