1,879 research outputs found

    MMonCa: A flexible and powerful new Kinetic Monte Carlo simulator

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    Kinetic Monte Carlo (KMC) is a widely used technique to simulate the evolution of radiation damage inside solids. Despite de fact that this technique was developed several decades ago, there is not an established and easy to access simulating tool for researchers interested in this field, unlike in the case of molecular dynamics or density functional theory calculations. In fact, scientists must develop their own tools or use unmaintained ones in order to perform these types of simulations. To fulfil this need, we have developed MMonCa, the Modular Monte Carlo simulator. MMonCa has been developed using professional C++ programming techniques and has been built on top of an interpreted language to allow having a powerful yet flexible, robust but customizable and easy to access modern simulator. Both non lattice and Lattice KMC modules have been developed. We will present in this conference, for the first time, the MMonCa simulator. Along with other (more detailed) contributions in this meeting, the versatility of MMonCa to study a number of problems in different materials (particularly, Fe and W) subject to a wide range of conditions will be shown. Regarding KMC simulations, we have studied neutron-generated cascade evolution in Fe (as a model material). Starting with a Frenkel pair distribution we have followed the defect evolution up to 450 K. Comparison with previous simulations and experiments shows excellent agreement. Furthermore, we have studied a more complex system (He-irradiated W:C) using a previous parametrization [1]. He-irradiation at 4 K followed by isochronal annealing steps up to 500 K has been simulated with MMonCa. The He energy was 400 eV or 3 keV. In the first case, no damage is associated to the He implantation, whereas in the second one, a significant Frenkel pair concentration (evolving into complex clusters) is associated to the He ions. We have been able to explain He desorption both in the absence and in the presence of Frenkel pairs and we have also applied MMonCa to high He doses and fluxes at elevated temperatures. He migration and trapping dominate the kinetics of He desorption. These processes will be discussed and compared to experimental results. [1] C.S. Becquart et al. J. Nucl. Mater. 403 (2010) 7

    Inspecting the potential physiological and biomedical value of 44 conserved uncharacterised proteins of Streptococcus pneumoniae

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    BACKGROUND: The major Gram-positive coccoid pathogens cause similar invasive diseases and show high rates of antimicrobial resistance. Uncharacterised proteins shared by these organisms may be involved in virulence or be targets for antimicrobial therapy. RESULTS: Forty four uncharacterised proteins from Streptococcus pneumoniae with homologues in Enterococcus faecalis and/or Staphylococcus aureus were selected for analysis. These proteins showed differences in terms of sequence conservation and number of interacting partners. Twenty eight of these proteins were monodomain proteins and 16 were modular, involving domain combinations and, in many cases, predicted unstructured regions. The genes coding for four of these 44 proteins were essential. Genomic and structural studies showed one of the four essential genes to code for a promising antibacterial target. The strongest impact of gene removal was on monodomain proteins showing high sequence conservation and/or interactions with many other proteins. Eleven out of 40 knockouts (one for each gene) showed growth delay and 10 knockouts presented a chaining phenotype. Five of these chaining mutants showed a lack of putative DNA-binding proteins. This suggest this phenotype results from a loss of overall transcription regulation. Five knockouts showed defective autolysis in response to penicillin and vancomycin, and attenuated virulence in an animal model of sepsis. CONCLUSIONS: Uncharacterised proteins make up a reservoir of polypeptides of different physiological importance and biomedical potential. A promising antibacterial target was identified. Five of the 44 examined proteins seemed to be virulence factors.This work was supported by a Miguel Servet Research contract funded by the Fondo de Investigación Sanitaria (Ministerio de Economía y Competitividad de España) to Antonio J. Martin-Galiano, a Plan Nacional de I + D + I of Ministerio de Ciencia e Innovación grant (BIO2011-25343) to Adela G. de la Campa, and funds from the CIBER Enfermedades Respiratorias group (an initiative of the Instituto de Salud Carlos III).S

    Angiotensin Type 1 Receptor Antagonists Protect Against Alpha-Synuclein-Induced Neuroinflammation and Dopaminergic Neuron Death

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    Altres ajuts: This study received funding from the Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas' intramural program (2014/01 and 2017/02), Galician Government (Xunta de Galicia, Consellería de Educación; GRC2014/002), Navarra Government (Departamento de Salud; 046-2017), and Fondo Europeo de Desarrollo Regional (Regional European Development Fund).The loss of dopaminergic neurons and α-synuclein accumulation are major hallmarks of Parkinson's disease (PD), and it has been suggested that a major mechanism of α-synuclein toxicity is microglial activation. The lack of animal models that properly reproduce PD, and particularly the underlying synucleinopathy, has hampered the clarification of PD mechanisms and the development of effective therapies. Here, we used neurospecific adeno-associated viral vectors serotype 9 coding for either the wild-type or mutated forms of human alpha-synuclein (WT and SynA53T, respectively) under the control of a synapsin promoter to further induce a marked dopaminergic neuron loss together with an important microglial neuroinflammatory response. Overexpression of neuronal alpha-synuclein led to increased expression of angiotensin type 1 receptors and NADPH oxidase activity, together with a marked increase in the number of OX-6-positive microglial cells and expression of markers of phagocytic activity (CD68) and classical pro-inflammatory/M1 microglial phenotype markers such as inducible nitric oxide synthase, tumor necrosis factor alpha, interleukin-1β, and IL-6. Moreover, a significant decrease in the expression of markers of immunoregulatory/M2 microglial phenotype such as the enzyme arginase-1 was constantly observed. Interestingly, alpha-synuclein-induced changes in microglial phenotype markers and dopaminergic neuron death were inhibited by simultaneous treatment with the angiotensin type 1 blockers candesartan or telmisartan. Our results suggest the repurposing of candesartan and telmisartan as a neuroprotective strategy for PD

    A Complementary Scale of Biased Agonism for Agonists with Differing Maximal Responses

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    Compelling data in the literature from the recent years leave no doubt about the pluridimensional nature of G protein-coupled receptor function and the fact that some ligands can couple with different efficacies to the multiple pathways that a receptor can signal through, a phenomenon most commonly known as functional selectivity or biased agonism. Nowadays, transduction coefficients (log(τ/K)), based on the Black and Leff operational model of agonism, are widely used to calculate bias. Nevertheless, combining both affinity and efficacy in a single parameter can result in compounds showing a defined calculated bias of one pathway over other though displaying varying experimental bias preferences. In this paper, we present a novel scale (log(τ)), that attempts to give extra substance to different compound profiles in order to better classify compounds and quantify their bias. The efficacy-driven log(τ) scale is not proposed as an alternative to the affinity&efficacy-driven log(τ/K) scale but as a complement in those situations where partial agonism is present. Both theoretical and practical approaches using μ-opioid receptor agonists are presented

    Remote Substituent Effects on the Stereoselectivity and Organocatalytic Activity of Densely Substituted Unnatural Proline Esters in Aldol Reactions

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    The organocatalytic activities of highly substituted proline esters obtained through asymmetric [3+2] cycloadditions of azomethine ylides derived from glycine iminoesters have been analyzed by 19F NMR and through kinetic isotope effects. Kinetic rate constants have been determined for unnatural proline esters incorporating different substituents. It has been found that exo-L and endo-L unnatural proline methyl esters yield opposite enantiomers in aldol reactions between cyclic ketones and aromatic aldehydes. The combined results reported in this study show subtle and remote effects that determine the organocatalytic behavior of these synthetic but readily available amino acid derivatives. These data can be used as design criteria for the development of new pyrrolidine-based organocatalysts.Financial support was provided by the Spanish Ministerio de Economía y Competitividad (MINECO) and the Fondo Europeo de Desarrollo Regional (FEDER) (projects CTQ2010-16959/BQU, CTQ2012-35535, CTQ2013-40855-R, CTQ2007-62771/BQU, CTQ2010-20387, CTQ2010-17436, and Consolider-Ingenio CSD2007-00006), the University of the Basque Country (UPV/EHU, UFI11/22 QOSYC), the Basque Government (GV/EJ, grant IT-324-07), the Generalitat Valenciana-FEDER (PROMETEO/2009/039), the Gobierno de Aragón-FSE (research group E40), and the University of Alicante. M. d. G. R. thanks the Donostia International Physics Center (DIPC) for a postdoctoral contract. M. S. and L. C. gratefully thank MINECO for a contract funding their PhD projects

    Nivolumab after selective internal radiation therapy for the treatment of hepatocellular carcinoma: a phase 2, single-arm study

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    Purpose: To evaluate the safety and efficacy of selective internal radiation therapy (SIRT) in combination with a PD-1 inhibitor in patients with unresectable hepatocellular carcinoma (uHCC) and liver-only disease ineligible for chemoembolization. Patients and methods: NASIR-HCC is a single-arm, multicenter, open-label, phase 2 trial that recruited from 2017 to 2019 patients who were naïve to immunotherapy and had tumors in the BCLC B2 substage (single or multiple tumors beyond the up-to-7 rule), or unilobar tumors with segmental or lobar portal vein invasion (PVI); no extrahepatic spread; and preserved liver function. Patients received SIRT followed 3 weeks later by nivolumab (240 mg every 2 weeks) for up to 24 doses or until disease progression or unacceptable toxicity. Safety was the primary endpoint. Secondary objectives included objective response rate (ORR), time to progression (TTP), and overall survival (OS). Results: 42 patients received SIRT (31 BCLC-B2, 11 with PVI) and were followed for a median of 22.2 months. 27 patients discontinued and 1 never received Nivolumab. 41 patients had any-grade adverse events (AE) and 21 had serious AEs (SAE). Treatment-related AEs and SAEs grade 3-4 occurred in 8 and 5 patients, respectively. Using RECIST 1.1 criteria, ORR reported by investigators was 41.5% (95% CI 26.3% to 57.9%). Four patients were downstaged to partial hepatectomy. Median TTP was 8.8 months (95% CI 7.0 to 10.5) and median OS was 20.9 months (95% CI 17.7 to 24.1). Conclusions: The combination of SIRT and nivolumab has shown an acceptable safety profile and signs of antitumor activity in the treatment of patients with uHCC that were fit for SIRT

    COPD is a clear risk factor for increased use of resources and adverse outcomes in patients undergoing intervention for colorectal cancer : a nationwide study in Spain

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    We hypothesized that patients undergoing surgery for colorectal cancer (CRC) with COPD as a comorbidity would consume more resources and have worse in-hospital outcomes than similar patients without COPD. Therefore, we compared different aspects of the care process and short-term outcomes in patients undergoing surgery for CRC, with and without COPD. This was a prospective study and it included patients from 22 hospitals located in Spain - 472 patients with COPD and 2,276 patients without COPD undergoing surgery for CRC. Clinical variables, postintervention intensive care unit (ICU) admission, use of invasive mechanical ventilation, and postintervention antibiotic treatment or blood transfusion were compared between the two groups. The reintervention rate, presence and type of complications, length of stay, and in-hospital mortality were also estimated. Hazard ratio (HR) for hospital mortality was estimated by Cox regression models. COPD was associated with higher rates of in-hospital complications, ICU admission, antibiotic treatment, reinterventions, and mortality. Moreover, after adjusting for other factors, COPD remained clearly associated with higher and earlier in-hospital mortality. To reduce in-hospital morbidity and mortality in patients undergoing surgery for CRC and with COPD as a comorbidity, several aspects of perioperative management should be optimized and attention should be given to the usual comorbidities in these patients

    Effect of carbon nanostructures and fatty acid treatment on the mechanical and thermal performances of flax/polypropylene composites

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    Four different strategies for mitigating the highly hydrophilic nature of flax fibers were investigated with a view to increase their compatibility with apolar polypropylene. The effects of two carbon nanostructures (graphene nanoplatelets (GNPs) and carbon nanotubes (CNTs)), of a chemical modification with a fatty acid (stearic acid), and of maleated polypropylene on interfacial adhesion, mechanical properties (tensile and flexural), and thermal stability (TGA) were compared. The best performance was achieved by a synergistic combination of GNPs and maleated polypropylene, which resulted in an increase in tensile strength and modulus of 42.46% and 54.96%, respectively, compared to baseline composites. Stearation proved to be an effective strategy for increasing the compatibility with apolar matrices when performed in an ethanol solution with a 0.4 M concentration. The results demonstrate that an adequate selection of surface modification strategies leads to considerable enhancements in targeted properties
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