PhyleasProg: a user-oriented web server for wide evolutionary analyses

Evolutionary analyses of biological data are becoming a prerequisite in many fields of biology. At a time of high-throughput data analysis, phylogenetics is often a necessary complementary tool for biologists to understand, compare and identify the functions of sequences. But available bioinformatics tools are frequently not easy for non-specialists to use. We developed PhyleasProg (http://phyleasprog.inra.fr), a user-friendly web server as a turnkey tool dedicated to evolutionary analyses. PhyleasProg can help biologists with little experience in evolutionary methodologies by analysing their data in a simple and robust way, using methods corresponding to robust standards. Via a very intuitive web interface, users only need to enter a list of Ensembl protein IDs and a list of species as inputs. After dynamic computations, users have access to phylogenetic trees, positive/purifying selection data (on site and branch-site models), with a display of these results on the protein sequence and on a 3D structure model, and the synteny environment of related genes. This connection between different domains of phylogenetics opens the way to new biological analyses for the discovery of the function and structure of proteins

Permanent Pancreatic Duct Occlusion With Neoprene-based Glue Injection After Pancreatoduodenectomy at High Risk of Pancreatic Fistula : A Prospective Clinical Study

OBJECTIVE: The aim of this study was to assess safety and efficacy of pancreatic duct occlusion (PDO) with neoprene-based glue in selected patients undergoing pancreatoduodenectomy (PD) at high risk of postoperative pancreatic fistula (POPF). BACKGROUND DATA: PD is the reference standard approach for tumors of the pancreaticoduodenal region. POPF is the most relevant complication after PD. PDO has been proposed as an alternative to anastomosis to manage the pancreatic stump. METHODS: A single-center, prospective, nonrandomized trial enrolled 100 consecutive PD for cancer. Patients at high risk for POPF according to Fistula Risk Score (FRS) >15% ( 656 points) were treated with PDO using neoprene glue (study cohort); patients with FRS 6415% ( 645 points) received pancreaticojejunal anastomosis (PJA: control cohort). Primary endpoint was complication rate grade 653 according to Dindo-Clavien Classification (DCC). Other postoperative outcomes were monitored (ClinicalTrials.gov NCT03738787). RESULTS: Fifty-one patients underwent PDO and 49 PJA. DCC 653, postoperative mortality, and POPF grade B-C were 25.5% versus 24.5% (P = 0.91), 5.9% versus 2% (P = 0.62), and 11.8% versus 16.3% (P = 0.51) in the study versus control cohort, respectively. At 1 and 3 years, new-onset diabetes was diagnosed in 13.7% and 36.7% of the study cohort versu 4.2% and 12.2% in controls (P = 0.007). CONCLUSIONS: PDO with neoprene-based glue is a safe technique that equalizes early outcome of selected patients at high risk of POPF to those at low risk undergoing PJA. Neoprene-based PDO, however, triples the risk of diabetes at 1 and 3 years

A new equation for the mid-plane potential of power law discs. II. Exact solutions and approximate formulae

The first-order ordinary differential equation (ODE) that describes the mid-plane gravitational potential in flat finite size discs in which the surface density is a power-law function of the radius R with exponent s (Hur\'e & Hersant 2007) is solved exactly in terms of infinite series. The formal solution of the ODE is derived and then converted into a series representation by expanding the elliptic integral of the first kind over its modulus before analytical integration. Inside the disc, the gravitational potential consists of three terms: a power law of radius R with index 1+s, and two infinite series of the variables R and 1/R. The convergence of the series can be accelerated, enabling the construction of reliable approximations. At the lowest-order, the potential inside large astrophysical discs (s ~ -1.5 +/- 1) is described by a very simple formula whose accuracy (a few percent typically) is easily increased by considering successive orders through a recurrence. A basic algorithm is given. Applications concern all theoretical models and numerical simulations where the influence of disc gravity must be checked and/or reliably taken into account.Comment: Accepted for publication in A&A, 13 pages, 8 figure

Life cycle assessment of Polychlorinated Biphenyl contaminated soil remediation processes

Goal and scope. A life-cycle assessment (LCA) was performed to evaluate the environmental impacts of the remediation of industrial soils contaminated by polychlorobiphenyl (PCB). Two new bioremediation treatment options were compared with the usual incineration process. In this attributional LCA, only secondary impacts were considered. The contaminated soil used for the experiments contained 200 mg of PCB per kg. Methods. Three off-site treatments scenarios were studied: 1) bioremediation with mechanical aeration, 2) bioremediation with electric aeration and 3) incineration with natural gas. Bioremediation processes were designed from lab-scale, scale-up and pilot experiments. The incineration technique was inspired by a French plant. A semi-quantitative uncertainty analysis was performed on the data. Environmental impacts were evaluated with the CML 2001 method using the Simapro software program. Results and discussion. In most compared categories, the bioremediation processes are favorable. Of the bioremediation options, the lowest environmental footprint was observed for electric aeration. The uncertainty analysis supported the results that compared incineration and bioremediation but decreased the difference between the options of aeration. The distance of transportation was one of the most sensitive parameters, especially for bioremediation. At equal distances between the polluted sites and the treatment plant, bioremediation had fewer impacts than incineration in eight out of thirteen categories. Conclusions. The use of natural gas for the incineration process generated the most impacts. Irrespective of the aeration option, bioremediation was better than incineration. Recommendations. The time of treatment should be taken into account. More precise and detailed data are required for the incineration scenario. More parameters of biological treatments should be measured. LCA results should be completed using ecological and health risk assessment and an acceptability evaluation

Reactivity of neonicotinoid insecticides with carbonate radicals

“NOTICE: this is the author’s version of a work that was accepted for publication in Water Research. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in WATER RESEARCH, [VOL46, ISSUE11, jul 2012] DOI10.1016/j.watres.2012.03.051¨ ©IWA Publishing 2012. The definitive peer-reviewed and edited version of this article is published in Water Research 46 11 3476-3489 2012 10.1016/j.watres.2012.03.051 and is available at www.iwapublishing.comThe reaction of three chloronicotinoid insecticides, namely Imidacloprid (IMD), Thiacloprid (THIA) and Acetamiprid (ACT), with carbonate radicals (CO3 center dot-) was investigated. The second order rate constants (4 +/- 1) x 10(6), (2.8 +/- 0.5) x 10(5), and (1.5 +/- 1) x 10(5) M-1 s(-1) were determined for IMD, THIA and ACT, respectively. The absorption spectra of the organic intermediates formed after CO3 center dot- is approximately equal to attack to IMD is in line with those reported for alpha-aminoalkyl radicals. A reaction mechanism involving an initial charge transfer from the amidine nitrogen of the insecticides to CO3 center dot- is proposed and further supported by the identified reaction products. The pyridine moiety of the insecticides remains unaffected until nicotinic acid is formed. CO3 center dot- radical reactivity towards IMD, ACT, and THIA is low compared to that of HO center dot radicals, excited triplet states, and O-1(2), and is therefore little effective in depleting neonicotinoid insecticides. (C) 2012 Elsevier Ltd. All rights reserved.This research was financially supported by Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Agencia Nacional de Promocion Cientifica y Tecnologica (Argentina, project PICT 2007 number 00308), and Agencia Espanola de Cooperacion Internacional (project A/8199/07). M.L.D. thanks CONICET for a graduate studentship. M.C.G. is a research member of CONICET. D.O.M. is a research member of Comision de Investigaciones Cientificas de la Provincia de Buenos Aires (CIC), Argentina. L.S.J. acknowledges Ministerio de Ciencia e Innovacion for his Juan de la Cierva scholarship.Dell'arciprete, ML.; Soler Escoda, JM.; Santos-Juanes Jordá, L.; Arques Sanz, A.; Martire, DO.; Furlong, JP.; González, MC. (2012). Reactivity of neonicotinoid insecticides with carbonate radicals. Water Research. 46(11):3476-3489. https://doi.org/10.1016/j.watres.2012.03.051S34763489461

Privaros: A Framework for Privacy-Compliant Delivery Drones

We present Privaros, a framework to enforce privacy policies on drones. Privaros is designed for commercial delivery drones, such as the ones that will likely be used by Amazon Prime Air. Such drones visit a number of host airspaces, each of which may have different privacy requirements. Privaros provides an information flow control framework to enforce the policies of these hosts on the guest delivery drones. The mechanisms in Privaros are built on top of ROS, a middleware popular in many drone platforms. This paper presents the design and implementation of these mechanisms, describes how policies are specified, and shows that Privaros's policy specification can be integrated with India's Digital Sky portal. Our evaluation shows that a drone running Privaros can robustly enforce various privacy policies specified by hosts, and that its core mechanisms only marginally increase communication latency and power consumption

Photochemical generation of carbonate radicals and their reactivity with phenol

International audienceThe reaction of carbonate radical with phenol in aqueous solution has been investigated in systems in which carbonate radicals were generated by UV irradiation of an aqueous solution of [Co(NH3)5CO3]+ (pH 8.0 phosphate buffer). Both steady state and time resolved photolysis experiments were performed. Upon continuous irradiation of complex phenol mixtures, phenol was converted into benzoquinone and dihydroxybenzenes. Benzoquinone was the major by-product in the early stages of the reaction. Laser flash excitation (266 and 355 nm) of the cobalt complex clearly showed the formation of the carbonate radical. When phenol was added to the solution of the complex, a second species was observed which was assigned to the phenoxyl radical. The second-order rate constant of reaction between phenol and carbonate radical was found to be equal to 1.6 × 107 M-1 s-1, in agreement with literature data of 2.2 × 107 M-1 s-1