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Search Results: 1 - 10 of 298079 matches for " J. Roche "
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Incidence des puits sur la protection cathodique des plates-formes fixes Influence of Welles on the Cathodic Protection of Fixed Platform
Roche M.,Samaran J. -P.
Oil & Gas Science and Technology , 2006, DOI: 10.2516/ogst:1976034
Abstract: Les puits d'exploitation des gisements pétroliers onshore ne sont pas systématiquement protégés cathodiquement. Par contre les puits offshore supportés par les plates-formes fixes de forage sont nécessairement soumis aux systemes de protection cathodique destinés à celles-ci. La conception de ces systèmes doit prendre en compte la demande en courant des puits, considérée généralement comme parasite. Différentes méthodes de calcul existent, plus ou moins étayées par des considérations scientifiques. Aucune ne peut véritablement prévoir ce que sera la réalité et l'emploi de méthodes de mesure est nécessaire si l'on veut vérifier ce qui se passe exactement. Les différentes méthodes de calcul et de mesure sont passées en revue et critiquées, ce qui conduit à évoquer les points qui nous paraissent devoir être mieux étudiés dans le futur. Production wells on onshore cil fields are not systematically cathodically protected. On the contrary, offshore weils attained from fixed drilling plotforms are necessorily subjected to cathodic protection systems designed for such structures. The design of such systems must Cake into consideration the amount of current demanded by the well, generally considered as parositic current. Different colculoting methods exist, more or less based on scientific considerations. None con truly foresee what the reality will be, and measuring methods have ta be used if we want to check to see exactly what is happening. The different calculating and measuring methods are reviewed and criticized, thus bringing out points that we feel should be further investigated in the future.
A Toxicological Assessment of Endocrine Disrupting Chemicals Found in the BMW (Border, Midland and Western) Region of Ireland  [PDF]
Kathryn M. Quinn-Hosey, James J. Roche, Andrew M. Fogarty, Concepta A. Brougham
Journal of Environmental Protection (JEP) , 2012, DOI: 10.4236/jep.2012.34039
Abstract: A battery of tests was established to determine the oestrogenic, mutagenic and genotoxic potential of two categories of endocrine disrupting chemicals (EDCs), phthalates and alkylphenols. Diisononylphthalate (DINP), diethylhexylphthalate (DEHP), dibutylphthalate (DBP), diisododecylphthalate (DIDP) and 4-nonylphenol (4-NP) were oestrogenic in the yeast estrogen screen (YES) assay and potently oestrogenic in the MVLN and E-SCREEN assays at environmentally relevant concentrations. DINP and 4-NP were mutagenic in the Ames assay and also induced significant levels of unscheduled DNA synthesis and DNA strand breakage. Significant induction in the percentage of cells containing micronuclei was observed after treatment with DINP, DEHP and 4-NP. In addition, sewage effluents from sewage treatment plants (STPs) in the Border, Midlands and Western (BMW) region of Ireland were significantly oestrogenic in the YES assay. Moreover, analysis of levels of phthalates and alkylphenol identified in Irish rivers receiving treated effluent showed potent oestrogenicity in the YES assay. The proliferative and genotoxic ability of the phthalates and alkylphenol, and the oestrogenicity of the treated effluents reported here, is significant as these EDCs and EDCs within the effluent may play a role in the etiology of human abnormalities.
Screening for Genotoxicity and Oestrogenicity of Endocrine Disrupting Chemicals in Vitro  [PDF]
Karthryn M. Quinn-Hosey, James J. Roche, Andrew M. Fogarty, Concepta A. Brougham
Journal of Environmental Protection (JEP) , 2012, DOI: 10.4236/jep.2012.328105
Abstract: A diverse range of endocrine disrupting chemicals (EDCs) was examined, using an in vitro test system, for critical events required for the onset of carcinogenesis in vivo. The initiation stage of carcinogenesis is a genotoxic process. 4-Octylphenol (alkylphenol), bisphenol A (plasticiser), coumestrol and genistein (phytoestrogens), 2,4-dichlorophe- noxyacetic acid and toxaphene (pesticides) and ethinylestradiol (synthetic hormone) were investigated for potential mutagencicity, DNA strand breakage, clastogenicity and DNA repair. Significant induction in the percentage of cells containing micronuclei was observed for all the EDCs. Toxaphene and coumestrol were mutagenic in the Ames assay. They also induced significant levels of unscheduled DNA synthesis and DNA strand breakage. Bisphenol A induced low level DNA strand breakage in HepG2 cells in the comet assay. The EDCs, with the exception of toxaphene, induced transcriptional activation in the yeast estrogen screen (YES) assay. They were potently oestrogenic in the mammalian based MVLN (transactivation) and E-SCREEN (proliferation) assays. This report on the transactivational, proliferative and genotoxic ability of the EDCs suggests that these chemicals may play a role in the etiology of male and female reproductive cancers.
FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins
Daniel B Roche, Stuart J Tetchner, Liam J McGuffin
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-160
Abstract: The FunFOLD method shows a significant improvement over the best available servers and is shown to be competitive with the top manual prediction groups that were tested at CASP8. The FunFOLD method is also competitive with both the top server and manual methods tested at CASP9. When tested using common subsets of targets, the predictions from FunFOLD are shown to achieve a significantly higher mean Matthews Correlation Coefficient (MCC) scores and Binding-site Distance Test (BDT) scores than all server methods that were tested at CASP8. Testing on the CASP9 set showed no statistically significant separation in performance between FunFOLD and the other top server groups tested.The FunFOLD software is freely available as both a standalone package and a prediction server, providing competitive ligand binding site residue predictions for expert and non-expert users alike. The software provides a new fully automated approach for structure based function prediction using 3D models of proteins.Because of a protein's essential cellular role, it is important to fully understand its structure and interactions. Predicting the location of the binding site and the ligand binding residues, is a necessary step towards elucidating how a protein functions [1]. The determination of the ligand binding site residues in a protein is also important, because substrate specificity of an enzyme is determined by the fine details of the binding site residues, such as side chain orientation and physiochemical properties [2].Several different protein ligand binding site prediction methods have been developed, which mostly fall into two major categories: sequence-based methods and structure-based methods [3]. The sequence-based methods rely on identifying conserved residues that may be structurally or functionally important and include methods such as firestar (CASP9 group FN315) [4], WSsas [5], FRcons [6], ConFunc (CASP8 - FN437) [7], ConSurf [8], FPSDP (CASP8 - FN242) [9] and INTERPID [10]. Th
Laboratory-scale method for enzymatic saccharification of lignocellulosic biomass at high-solids loadings
Christine M Roche, Clare J Dibble, Jonathan J Stickel
Biotechnology for Biofuels , 2009, DOI: 10.1186/1754-6834-2-28
Abstract: We identified roller bottle reactors (RBRs) as laboratory-scale reaction vessels that can provide adequate mixing for enzymatic saccharifications at high-solids biomass loadings without any additional hand mixing. Using the RBRs, we developed a method for screening both pretreated biomass and enzyme systems at process-relevant conditions. RBRs were shown to be scalable between 125 mL and 2 L. Results from enzymatic saccharifications of five biomass pretreatments of different severities and two enzyme preparations suggest that this system will work well for a variety of biomass substrates and enzyme systems. A study of intermittent mixing regimes suggests that mass transfer limitations of enzymatic saccharifications at high-solids loadings are significant but can be mitigated with a relatively low amount of mixing input.Effective initial mixing to promote good enzyme distribution and continued, but not necessarily continuous, mixing is necessary in order to facilitate high biomass conversion rates. The simplicity and robustness of the bench-scale RBR system, combined with its ability to accommodate numerous reaction vessels, will be useful in screening new biomass pretreatments and advanced enzyme systems at high-solids loadings.As the demand for non-petroleum based fuels continues to grow, more emphasis will be placed on producing a cost-competitive liquid transportation biofuel such as ethanol. One clean and renewable domestic energy source that can feasibly displace a significant fraction of petroleum usage in the USA is ethanol produced from lignocellulosic biomass [1-3]. Although large-scale ethanol production is not a new concept, converting lignocellulosic biomass to ethanol is not a trivial matter. Significant challenges lie with hydrolysis of biomass into fermentable sugars. Advanced conversion technologies must be developed to allow for the efficient conversion of lignocellulosic biomass to ethanol [4,5].Research indicates that a chemical pretreatment follo
The Be/X-ray Transient V0332+53: Evidence for a tilt between the orbit and the equatorial plane?
I. Negueruela,P. Roche,J. Fabregat,M. J. Coe
Physics , 1999, DOI: 10.1046/j.1365-8711.1999.02682.x
Abstract: We present optical and infrared observations of BQ Cam, the optical counterpart to the Be/X-ray transient system V0332+53. BQ Cam is shown to be an O8-9Ve star, which places V0332+53 at a distance of ~7 kpc. H-alpha spectroscopy and infrared photometry are used to discuss the evolution of the circumstellar envelope. Due to the low inclination of the system, parameters are strongly constrained. We find strong evidence for a tilt of the orbital plane with respect to the circumstellar disc (pressumably on the equatorial plane). Even though the periastron distance is only ~ 10 R_*, during the present quiescent state the circumstellar disc does not extend to the distance of periastron passage. Under these conditions, X-ray emission is effectively prevented by centrifugal inhibition of accretion. The circumstellar disc is shown to be optically dense at optical and infrared wavelengths, which together with its small size, is taken as an indication of tidal truncation.
Distinct Effects of Contraction-Induced Injury In Vivo on Four Different Murine Models of Dysferlinopathy
Joseph A. Roche,Lisa W. Ru,Robert J. Bloch
Journal of Biomedicine and Biotechnology , 2012, DOI: 10.1155/2012/134031
Abstract: Mutations in the DYSF gene, encoding dysferlin, cause muscular dystrophies in man. We compared 4 dysferlinopathic mouse strains: SJL/J and B10.SJL-Dysfim/AwaJ (B10.SJL), and A/J and B6.A-Dysfprmd/GeneJ (B6.A/J). The former but not the latter two are overtly myopathic and weaker at 3 months of age. Following repetitive large-strain injury (LSI) caused by lengthening contractions, all except B6.A/J showed ~40% loss in contractile torque. Three days later, torque in SJL/J, B10.SJL and controls, but not A/J, recovered nearly completely. B6.A/J showed ~30% torque loss post-LSI and more variable recovery. Pre-injury, all dysferlinopathic strains had more centrally nucleated fibers (CNFs) and all but A/J showed more inflammation than controls. At D3, all dysferlinopathic strains showed increased necrosis and inflammation, but not more CNFs; controls were unchanged. Dystrophin-null DMDmdx mice showed more necrosis and inflammation than all dysferlin-nulls. Torque loss and inflammation on D3 across all strains were linearly related to necrosis. Our results suggest that (1) dysferlin is not required for functional recovery 3 days after LSI; (2) B6.A/J mice recover from LSI erratically; (3) SJL/J and B10.SJL muscles recover rapidly, perhaps due to ongoing myopathy; (4) although they recover function to different levels, all 4 dysferlinopathic strains show increased inflammation and necrosis 3 days after LSI.
FunFOLDQA: A Quality Assessment Tool for Protein-Ligand Binding Site Residue Predictions
Daniel B. Roche, Maria T. Buenavista, Liam J. McGuffin
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0038219
Abstract: The estimation of prediction quality is important because without quality measures, it is difficult to determine the usefulness of a prediction. Currently, methods for ligand binding site residue predictions are assessed in the function prediction category of the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment, utilizing the Matthews Correlation Coefficient (MCC) and Binding-site Distance Test (BDT) metrics. However, the assessment of ligand binding site predictions using such metrics requires the availability of solved structures with bound ligands. Thus, we have developed a ligand binding site quality assessment tool, FunFOLDQA, which utilizes protein feature analysis to predict ligand binding site quality prior to the experimental solution of the protein structures and their ligand interactions. The FunFOLDQA feature scores were combined using: simple linear combinations, multiple linear regression and a neural network. The neural network produced significantly better results for correlations to both the MCC and BDT scores, according to Kendall’s τ, Spearman’s ρ and Pearson’s r correlation coefficients, when tested on both the CASP8 and CASP9 datasets. The neural network also produced the largest Area Under the Curve score (AUC) when Receiver Operator Characteristic (ROC) analysis was undertaken for the CASP8 dataset. Furthermore, the FunFOLDQA algorithm incorporating the neural network, is shown to add value to FunFOLD, when both methods are employed in combination. This results in a statistically significant improvement over all of the best server methods, the FunFOLD method (6.43%), and one of the top manual groups (FN293) tested on the CASP8 dataset. The FunFOLDQA method was also found to be competitive with the top server methods when tested on the CASP9 dataset. To the best of our knowledge, FunFOLDQA is the first attempt to develop a method that can be used to assess ligand binding site prediction quality, in the absence of experimental data.
How did Marine Isotope Stage 3 and Last Glacial Maximum climates differ? – Perspectives from equilibrium simulations
C. J. Van Meerbeeck, H. Renssen,D. M. Roche
Climate of the Past (CP) & Discussions (CPD) , 2009,
Abstract: Dansgaard-Oeschger events occurred frequently during Marine Isotope Stage 3 (MIS3), as opposed to the following MIS2 period, which included the Last Glacial Maximum (LGM). Transient climate model simulations suggest that these abrupt warming events in Greenland and the North Atlantic region are associated with a resumption of the Thermohaline Circulation (THC) from a weak state during stadials to a relatively strong state during interstadials. However, those models were run with LGM, rather than MIS3 boundary conditions. To quantify the influence of different boundary conditions on the climates of MIS3 and LGM, we perform two equilibrium climate simulations with the three-dimensional earth system model LOVECLIM, one for stadial, the other for interstadial conditions. We compare them to the LGM state simulated with the same model. Both climate states are globally 2°C warmer than LGM. A striking feature of our MIS3 simulations is the enhanced Northern Hemisphere seasonality, July surface air temperatures being 4°C warmer than in LGM. Also, despite some modification in the location of North Atlantic deep water formation, deep water export to the South Atlantic remains unaffected. To study specifically the effect of orbital forcing, we perform two additional sensitivity experiments spun up from our stadial simulation. The insolation difference between MIS3 and LGM causes half of the 30–60° N July temperature anomaly (+6°C). In a third simulation additional freshwater forcing halts the Atlantic THC, yielding a much colder North Atlantic region ( 7°C). Comparing our simulation with proxy data, we find that the MIS3 climate with collapsed THC mimics stadials over the North Atlantic better than both control experiments, which might crudely estimate interstadial climate. These results suggest that freshwater forcing is necessary to return climate from warm interstadials to cold stadials during MIS3. This changes our perspective, making the stadial climate a perturbed climate state rather than a typical, near-equilibrium MIS3 climate.
Efecto in vitro del extracto acuoso de Dichrostachys cinerea (L.) Wight & Arn. en el desarrollo de las fases exógenas de estrongílidos gastrointestinales de ovinos In vitro effect of the aqueous extract of Dichrostachys cinerea (L.) Wight &Arn. on the development of exogenous stages of gastrointestinal strongyles in sheep
J Arece,Yaíma Roche,Y López,M Molina
Pastos y Forrajes , 2012,
Abstract: Se evaluó el efecto in vitro de extractos acuosos de hojas de marabú (Dichrostachys cinerea) en la eclosión de huevecillos, el desarrollo larvario y la migración de las larvas del tercer estadio de estrongílidos gastrointestinales. Los tratamientos fueron tres concentraciones de extractos acuosos de hojas de marabú (500, 250 y 125 mg/mL), soluciones de albendazol y levamisol, así como el Phosphate Buffer Saline (PBS) y el dimetilsulfóxido (DMSO) como controles; el dise o fue completamente aleatorizado. Los porcentajes de eclosión presentaron diferencias significativas entre postratamientos. El PBS ocasionó la mayor tasa de eclosión (96,68%); el 30,51% eclosionó con el albendazol y los extractos de hojas de marabú mostraron tasas de eclosión moderadas (entre 49,75 y 66,54%), al parecer dependientes de la dosis. El desarrollo de las larvas L1/L2 a las L3 tratadas con extracto acuoso de marabú también presentó efectos dosis-dependientes y diferencias significativas con respecto a los grupos controles positivos y negativos. La dosis de 500 mg/mL inhibió el desarrollo larvario en porcentajes similares a los del albendazol (8,89 y 1,28%, respectivamente). El medio PBS no interfirió en la capacidad de migración de las larvas, mientras que con el levamisol los valores se redujeron de 86,45 a 93,92%; los extractos acuosos también redujeron significativamente dicha migración, con valores entre 77,67 y 48,97%. Los extractos acuosos de D. cinerea presentaron actividad antihelmíntica in vitro en los tres estadios de desarrollo del ciclo exógeno de los estrongílidos gastrointestinales de ovinos; esta actividad resultó más evidente en el desarrollo y la migración de las larvas de estos nemátodos. The in vitro effect of aqueous extract of leaves from Dichrostachys cinerea on egg hatching, larval development and migration of third-stage larvae of gastrointestinal strongyles, was evaluated. The treatments were three concentrations of aqueous extracts of D. cinerea leaves (500, 250 and 125 mg/mL), albendazole and levamisole solutions, as well as Phosphate Buffer Saline (PBS) and dimethyl sulfoxide (DMSO) as controls; the design was completely randomized. The hatching percentages showed significant differences among post-treatments. PBS caused the highest hatching rate (96,68%); 30,51% hatched with albendazole and the D. cinerea leaf extracts showed moderate hatching rates (between 49,75 and 66,54%), seemingly dose-dependent. The development of L1/L2 larvae to L3 treated with aqueous D. cinerea extract also showed dose-dependent effects and significant differences with reg
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