Balancing Accuracy and Cost of Confinement Simulations by Interpolation and Extrapolation of Confinement Energies

Improvements to the confinement method for the calculation of conformational free energy differences are presented. By taking advantage of phase space overlap between simulations at different frequencies, significant gains in accuracy and speed are reached. The optimal frequency spacing for the simulations is obtained from extrapolations of the confinement energy, and relaxation time analysis is used to determine time steps, simulation lengths, and friction coefficients. At postprocessing, interpolation of confinement energies is used to significantly reduce discretization errors in the calculation of conformational free energies. The efficiency of this protocol is illustrated by applications to alanine n-peptides and lactoferricin. For the alanine-n-peptide, errors were reduced between 2- and 10-fold and sampling times between 8- and 67-fold, while for lactoferricin the long sampling times at low frequencies were reduced 10-100-fold

De Plenderleith a Al Gore: o ideário vigente na conservação de bens culturais móveis no século XXI

O texto discute idéias predominantes, hoje, nas práticas de conservação de bens culturais móveis no Ocidente. São apontadas, também, algumas tendências de pensamento em diferentes contextos de trabalho, identificando-se eventuais mudanças e semelhanças entre as idéias anteriormente vigentes e aquelas que muito provavelmente sejam, já, um legado para este novo século.This article discusses the prevailing concepts referring to the conservation of cultural heritage collections. Some trends such as some lines of thought are also indicated, identifying occasional changes and similarities among the ideas previously in force and those that, probably, are already a legacy for this new century

State of nature 2023

This is the fourth State of Nature Report. It provides a comprehensive overview of species trends across the UK, including specific assessments for England, Northern Ireland, Scotland and Wales, and for the UK’s Overseas Territories

Current trends in cannulation and neuroprotection during surgery of the aortic arch in Europe†‡

OBJECTIVES To conduct a survey across European cardiac centres to evaluate the methods used for cerebral protection during aortic surgery involving the aortic arch. METHODS All European centres were contacted and surgeons were requested to fill out a short, comprehensive questionnaire on an internet-based platform. One-third of more than 400 contacted centres completed the survey correctly. RESULTS The most preferred site for arterial cannulation is the subclavian-axillary, both in acute and chronic presentation. The femoral artery is still frequently used in the acute condition, while the ascending aorta is a frequent second choice in the case of chronic presentation. Bilateral antegrade brain perfusion is chosen by the majority of centres (2/3 of cases), while retrograde perfusion or circulatory arrest is very seldom used and almost exclusively in acute clinical presentation. The same pumping system of the cardio pulmonary bypass is most of the time used for selective cerebral perfusion, and the perfusate temperature is usually maintained between 22 and 26°C. One-third of the centres use lower temperatures. Perfusate flow and pressure are fairly consistent among centres in the range of 10-15 ml/kg and 60 mmHg, respectively. In 60% of cases, barbiturates are added for cerebral protection, while visceral perfusion still receives little attention. Regarding cerebral monitoring, there is a general tendency to use near-infrared spectroscopy associated with bilateral radial pressure measurement. CONCLUSIONS These data represent a snapshot of the strategies used for cerebral protection during major aortic surgery in current practice, and may serve as a reference for standardization and refinement of different approache

Adsorption in heterogeneous porous media: Hierarchical and composite solids

SSCI-VIDE+ING+DFAInternational audienceExperiment and molecular simulation are used to investigate adsorption in heterogeneous porous media consisting of hierarchical solids (combining different porosity scales) or composite solids (such as silver nanoparticles adsorbed at the external surface of zeolite). It is shown that adsorption in such heterogeneous materials can be written as a linear combination of the adsorption isotherms in its different domains (i.e. porosity scales for the hierarchical sample and constituents for the composite sample). In the case of the composite material, we also show that the linear combination can be used with weighing parameters obtained for a different adsorbate. Such a superimposition principle, which is validated using well-characterized experimental samples, is of interest for characterization purpose as well as industrial applications as they can be used to determine accurately the amount of phases in a given sample (volume corresponding to a given porosity scale or constituent). In contrast, significant departure between the experimental adsorption isotherm and the linear combination can be used to detect coupling effects between the different domains or restrained access to a given domain type. Such a characterization strategy of complex heterogeneous media is complementary to other experiments, such as those probing capillary hysteresis shapes, scanning curves and subloops, which allow determining the distribution of domains within the framework of the independent domain theory. (C) 2016 Elsevier Inc. All rights reserved

Assessment of Mutational Effects on Peptide Stability through Confinement Simulations

The evaluation of free energy differences between specific states of a system is of fundamental interest in the study of (bio)chemical systems. Herein, we examine the use of the recently introduced confinement method (CM) to evaluate relative free energy changes upon protein/peptide mutations. CM is a path-independent technique that involves the transformation of a configurational state of the system into an ideal crystal permitting the direct computation of free energy differences. We illustrate the method by evaluating the differential stabilities between native and mutant sequences of a model peptide that has been extensively characterized by experimental approaches, the GB1 hairpin. We show a good correlation between calculated and experimental relative stabilities and discuss other possible applications of this method in the context of complex molecular conversions

Urgent endovascular treatment of a non-atherosclerotic penetrating aortic ulcer complicated by an aortic dissection

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Nuclear magnetic resonance spectroscopy of excised human hearts

Background—Phosphorus nuclear magnetic resonance spectroscopy has been proposed as a method of studying the metabolism of the myocardium in patients. Little is known about (31)P nuclear magnetic resonance spectroscopy of diseased human hearts. Methods—Two donor hearts meeting the requirements for heart transplantation and 11 diseased hearts were removed during a transplantation procedure and were studied in a horizontal 2·35 T superconducting magnet. Spectra were obtained at 0°C about 30 minutes after the excision. The areas of the inorganic phosphate peak (Pi) and of the phosphocreatine peak (PCr) were summed and expressed as a ratio with respect to the area of the β ATP peak. Results—The ratio (Pi + Pcr)/β ATP was found to be significantly lower in five hearts with a myocardial infarct (0·77 (0·18)) than in hearts with dilated cardiomyopathy (1·25 (0·29)) and in normal hearts (1·69 (0·11)). The area of the phosphodiester peak was expressed as a ratio with respect to the area of the β ATP peak: no differences were found between the three groups. Conclusions—These results suggest that the phosphocreatine concentration is lower in ischaemic heart disease than in dilated cardiomyopathy and that the phosphodiester peak is probably not useful in distinguishing between these two types of heart disease