Molecular Dynamics Simulations for Genetic Interpretation in Protein Coding Regions: Where we Are, Where to Go and When

The increasing ease with which massive genetic information can be obtained from patients or healthy individuals has stimulated the development of interpretive bioinformatics tools as aids in clinical practice. Most such tools analyze evolutionary information and simple physical–chemical properties to predict whether replacement of one amino acid residue with another will be tolerated or cause disease. Those approaches achieve up to 80–85% accuracy as binary classifiers (neutral/pathogenic). As such accuracy is insufficient for medical decision to be based on, and it does not appear to be increasing, more precise methods, such as full-atom molecular dynamics (MD) simulations in explicit solvent, are also discussed. Then, to describe the goal of interpreting human genetic variations at large scale through MD simulations, we restrictively refer to all possible protein variants carrying single-amino-acid substitutions arising from single-nucleotide variations as the human variome. We calculate its size and develop a simple model that allows calculating the simulation time needed to have a 0.99 probability of observing unfolding events of any unstable variant. The knowledge of that time enables performing a binary classification of the variants (stable-potentially neutral/unstable-pathogenic). Our model indicates that the human variome cannot be simulated with present computing capabilities. However, if they continue to increase as per Moore’s law, it could be simulated (at 65°C) spending only 3 years in the task if we started in 2031. The simulation of individual protein variomes is achievable in short times starting at present. International coordination seems appropriate to embark upon massive MD simulations of protein variants

Nuclear data requirements for the ADS conceptual design EFIT: Uncertainty and sensitivity study

In this paper, we assess the impact of activation cross-section uncertainties on relevant fuel cycle parameters for a conceptual design of a modular European Facility for Industrial Transmutation (EFIT) with a “double strata” fuel cycle. Next, the nuclear data requirements are evaluated so that the parameters can meet the assigned design target accuracies. Different discharge burn-up levels are considered: a low burn-up, corresponding to the equilibrium cycle, and a high burn-up level, simulating the effects on the fuel of the multi-recycling scenario. In order to perform this study, we propose a methodology in two steps. Firstly, we compute the uncertainties on the system parameters by using a Monte Carlo simulation, as it is considered the most reliable approach to address this problem. Secondly, the analysis of the results is performed by a sensitivity technique, in order to identify the relevant reaction channels and prioritize the data improvement needs. Cross-section uncertainties are taken from the EAF-2007/UN library since it includes data for all the actinides potentially present in the irradiated fuel. Relevant uncertainties in some of the fuel cycle parameters have been obtained, and we conclude with recommendations for future nuclear data measurement programs, beyond the specific results obtained with the present nuclear data files and the limited available covariance information. A comparison with the uncertainty and accuracy analysis recently published by the WPEC-Subgroup26 of the OECD using BOLNA covariance matrices is performed. Despite the differences in the transmuter reactor used for the analysis, some conclusions obtained by Subgroup26 are qualitatively corroborated, and improvements for additional cross sections are suggested

Two-temperature model of the coronal irradiated pellets

A two electron-temperature, quasi-steady model of the corona of a laser-ablated pellet is considered. Ablation pressure, critical radius and mass flow rate are determined. Results are close to those obtained with heat flux saturation well below the free-streaming limit

Selective synthesis of phenanthrenes and dihydrophenanthrenes via gold-catalyzed cycloisomerization of biphenyl embedded trienynes

Readily available o′-alkenyl-o-alkynylbiaryls, a particular type of 1,7-enynes, undergo a selective cycloisomerization reaction in the presence of a gold(I) catalyst to give interesting phenanthrene and dihydrophenanthrene derivatives in high yields. The solvent used provokes a switch in the evolution of the gold intermediate and plays a key role in the reaction outcome.Ministerio de Economıá y Competitividad (MINECO), AEI and FEDER (projects CTQ2017- 85263-R and CTQ2016-75023-C2-1-P), Instituto de Salud Carlos III (FEDER funds, ISCIII RETIC REDINREN RD16/ 0009/0015), Junta de Castilla y León and FEDER (BU291P18), and University of Alcalá (projects CCGP2017- EXP/016 and CCG2018/EXP-00

IMPLICACIONES DEL METABOLISMO FOSFOCÁLCIO Y NIVELES DE VITAMINA D EN NIÑAS CON PUBERTAD PRECOZ

Existe un gran interés en la función que realiza la vitamina D, no sólo a nivel del metabolismo mineral óseo, sino también por su papel a nivel extraesquelético, a pesar de lo cual, su déficit ha aumentado a nivel mundial. Asimismo, se ha observado un adelanto progresivo de la menarquia con un aumento en la incidencia de pubertad precoz, especialmente en niñas. Este hecho responde no sólo al componente genético sino también a factores ambientales y su modificación puede contribuir a la disminución de enfermedades relacionadas con una pubertad precoz. El presente estudio pretende evaluar la relación entre ambos hechos, por lo que se llevó a cabo un estudio observacional descriptivo transversal en niñas diagnosticadas de pubertad precoz (PP) a las que se les realizó un despistaje de déficit de vitamina D en un sector sanitario de Zaragoza, analizando un total de 20 pacientes. Se observó una prevalencia media de déficit de vitamina D en pacientes afectas de PP de 21 ±7,12 ng/mL, significativamente mayor a la obtenida de la población general pediátrica del mismo sector. Además, se estudió diferentes parámetros antropométricos y bioquímicos implicados en la pubertad precoz, que pudieran estar relacionados con niveles bajos de vitamina D, hallándose únicamente una correlación con valores mayores de hormona luteinizante en el test diagnóstico de estimulación con análogos de LHRH. Como conclusión, nuestro estudio sugiere una implicación del déficit de vitamina D en el desarrollo de pubertad precoz, aunque se necesitaría continuar la línea de investigación con un mayor tamaño muestral.<br /

Design and evaluation of a natural interface for remote operation of underwater roter

Nowadays, an increasing need of intervention robotic systems can be observed in all kind of hazardous environments. In all these intervention systems, the human expert continues playing a central role from the decision making point of view. For instance, in underwater domains, when manipulation capabilities are required, only Remote Operated Vehicles, commercially available, can be used, normally using master-slave architectures and relaying all the responsibility in the pilot. Thus, the role played by human- machine interfaces represents a crucial point in current intervention systems. This paper presents a User Interface Abstraction Layer and introduces a new procedure to control an underwater robot vehicle by using a new intuitive and immersive interface, which will show to the user only the most relevant information about the current mission. Finally, some experiments have been carried out to compare a traditional setup and the new procedure, demonstrating reliability and feasibility of our approach.This research was partly supported by Spanish Ministry of Research and Innovation DPI2011-27977-C03 (TRITON Project)

A natural interface for remote operation of underwater robots

Nowadays, an increasing need of intervention robotic systems can be observed in all kind of hazardous environments. In all these intervention systems, the human expert continues playing a central role from the decision-making point of view. For instance, in underwater domains, when manipulation capabilities are required, only Remote Operated Vehicles, commercially available, can be used, normally using master-slave architectures and relaying all the responsibility in the pilot. Thus, the role played by human- machine interfaces represents a crucial point in current intervention systems. This paper presents a User Interface Abstraction Layer and introduces a new procedure to control an underwater robot vehicle by using a new intuitive and immersive interface, which will show to the user only the most relevant information about the current mission. We conducted an experiment and found that the highest user preference and performance was in the immersive condition with joystick navigation.This research was partly supported by Spanish Ministry of Research and Innovation DPI2011-27977-C03 (TRITON Project)

Prey choice, provisioning behaviour, and effects of early nutrition on nestling phenotype of titmice

[EN] It is generally assumed that blue and great tits (Cyanistes caeruleus, Parus major) compete for the same type of food (Lepidoptera larvae) during the breeding season and that the former have some advantage because they are usually earlier and can exploit small caterpillars that are often more abundant and are not consumed by great tits. However, it is not clear whether, when confronted with similar circumstances (e.g., nestling demand), blue and great tits show similar preferences for a particular caterpillar type. In this 2-y study, we compare the diet of both tit species in detail by controlling for hatching date and brood size. We also examine how the contribution of caterpillars and spiders to the diet is related to nestling development. A positive relationship was found between the percentage of spiders in the diet and nestling tarsus length in both species, reinforcing the idea that neonatal nutrition could have a strong influence on nestling phenotype (e.g., offspring size). Such a correlation may arise because spiders contain a high level of taurine, an essential nutrient in the early development of young, and/or this prey type contains more calcium than other food items, which may affect the rate of nestling bone mineralization. Blue tits fed their young double the number of tortricid larvae in comparison with great tits, whereas the latter showed a clear preference for noctuids and exploited, with a low frequency, a type of larvae not consumed by blue tits, hairy caterpillars (Lasiocampidae). Our results point to resource partitioning by these species in this forest ecosystem and contribute to a better understanding of feeding ecology of titmice, which is particularly timely in a global warming context [FR] Il est généralement admis que les mésanges bleues (Cyanistes caeruleus) et les mésanges charbonnières (Parus major) se font compétition pour le même type de nourriture (larves de lépidoptères) durant la période de reproduction. Il est également admis que les mésanges bleues possèdent un certain avantage, car elles se reproduisent plus tôt et mangent de petites chenilles souvent plus abondantes qui ne sont pas consommées par les mésanges charbonnières. Cependant, il n'est pas clair si dans les mêmes conditions (ex. de demande en nourriture des oisillons), les mésanges bleues et charbonnières préfèrent les mêmes types de chenilles. Dans cette étude de 2 ans, nous avons comparé en détail les régimes alimentaires des 2 espèces de mésanges en contrôlant pour la date de ponte et la taille de la couvée. Nous avons aussi examiné si les contributions des chenilles et des araignées au régime alimentaire étaient reliées au développement des oisillons. Chez les 2 espèces, une relation positive a été trouvée entre le pourcentage d'araignées dans le régime alimentaire et la longueur du tarse des oisillons renforçant ainsi l'idée que la nutrition néonatale peut avoir une grande influence sur le phénotype des oisillons (ex. la taille des jeunes). Une telle corrélation peut résulter du fait que les araignées ont un taux élevé de taurine, un nutriment essentiel au développement précoce des jeunes, et/ou que ce type de proie contient plus de calcium que d'autres aliments ce qui peut influencer le taux de minéralisation des os chez les oisillons. Les mésanges bleues ont nourri leurs jeunes avec deux fois plus de larves de tortricidés que les mésanges charbonnières qui elles ont montré une nette préférence pour les noctuidés. Ces dernières ont aussi consommé, quoique peu fréquemment, des livrées (Lasiocampidae), un type de larves boudé par les mésanges bleues. Nos résultats pointent vers une division des ressources entre ces espèces dans cet écosystème forestier et contribuent à une meilleure compréhension de l'écologie alimentaire des mésanges ce qui est particulièrement utile dans un contexte de réchauffement climatiqueV. García-Navas was supported by a FPI predoctoral fellowship (Spanish Ministry of Science and Innovation (MICINN)-European Social Fund). This study was financed by the MICINN (grant reference: GCL2007-61395)Peer Reviewe

Integración de una cámara pan-tilt subacuática para detección de objetos y guiado de un ROV submarino

Resumen] En este documento se expone un sistema adaptativo y semiautónomo, el cual genera una interfaz de alto nivel para facilitar el trabajo de supervisión humana, capaz de detectar un objeto de interés, con la finalidad de trackear su posición y guiar a un Remote Operated Vehicle (ROV) haciendo uso de una cámara pan-tilt submarina, mediante la utilización de herramientas conocidas de visión por computador, y a través del middleware Robot Operating System (ROS). El trabajo se ha llevado a cabo en el contexto del proyecto coordinado MERBOTS (www.irs.uji.es/merbots), para mejorar la realimentación visual en intervenciones reales submarinas.Ministerio de Economía y Competitividad; DPI2014-57746-C3Ministerio de Economía y Competitividad; DPI2017-86372-C3-1-RUniversitat Jaume I; P1-1B2015-68Generalitat Valenciana; PROMETEO/2016/06

Improvement of the Electrochemical Behavior of (Sb, Sn, Cu)O Ceramic Electrodes as Electrochemical Advanced Oxidation Anodes

This is the peer reviewed version of the following article: Giner-Sanz, J. J., Sanchez-Rivera, M. J., Garcia-Gabaldon, M., Ortega, E. M., Mestre, S., & Perez-Herranz, V. (2019). Improvement of the Electrochemical Behavior of (Sb, Sn, Cu)O Ceramic Electrodes as Electrochemical Advanced Oxidation Anodes. ChemElectroChem, 6(9), 2430-2437. https://doi.org/10.1002/celc.201801766, which has been published in final form at https://doi.org/10.1002/celc.201801766. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.[EN] This work explores the possibility of increasing the active surface of a Sb-doped SnO2 ceramic electrode using CuO as sintering aid, by incorporating petroleum coke as a pore generator. In order to fulfil this goal, three series of (Sb, Sn, Cu)O electrodes with different coke contents were synthetized. The properties of the electrodes, and their microstructure, change significantly as a function of the coke content before sintering. The electrochemical characterization of the synthesized electrodes showed that the coke addition before sintering causes two antagonist effects on the performance of the (Sn, Sb, Cu)O as anodes in electrochemical advanced oxidation processes (EAOP). On one hand, it significantly improves the electrochemical roughness factor of the electrode, solving the densification problem in this way. On the other hand, it worsens the electrochemical behavior of the electrode: narrowing its electrochemical window; and ¿activating¿ it slightly. The addition of coke before sintering changes the kinetic parameters, leading to a kinetic situation in which the accumulation of hydroxyl radicals is slightly lower. A balance must be sought: an intermediate coke content will improve significantly the electrochemical roughness factor of the electrode, but will only worsen slightly its electrochemical behavior, leading to an optimum (Sn, Sb, Cu)O EAOP anode.The authors are very grateful to the Ministerio de Economia y Competitividad (Projects: CTQ2015-65202-C2-1-R and CTQ2015- 65202-C2-2-R) and to the European Regional Development Fund (FEDER), for their economic support.Giner-Sanz, JJ.; Sánchez-Rivera, MJ.; García Gabaldón, M.; Ortega Navarro, EM.; Mestre, S.; Pérez-Herranz, V. (2019). Improvement of the Electrochemical Behavior of (Sb, Sn, Cu)O Ceramic Electrodes as Electrochemical Advanced Oxidation Anodes. ChemElectroChem. 6(9):2430-2437. https://doi.org/10.1002/celc.201801766S2430243769Schwarzenbach, R. P., Egli, T., Hofstetter, T. B., von Gunten, U., & Wehrli, B. (2010). Global Water Pollution and Human Health. 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Electrochimica Acta, 264, 350-357. doi:10.1016/j.electacta.2018.01.141Giner-Sanz, J. J., Ortega, E. M., & Pérez-Herranz, V. (2017). Experimental Quantification of the Effect of Nonlinearities on the EIS Spectra of the Cathodic Electrode of an Alkaline Electrolyzer. Fuel Cells, 17(3), 391-401. doi:10.1002/fuce.201600137Giner-Sanz, J. J., Ortega, E. M., & Pérez-Herranz, V. (2018). Mechanistic equivalent circuit modelling of a commercial polymer electrolyte membrane fuel cell. Journal of Power Sources, 379, 328-337. doi:10.1016/j.jpowsour.2018.01.066Orazem, M. E., & Tribollet, B. (2008). Electrochemical Impedance Spectroscopy. doi:10.1002/9780470381588Agarwal, P., Orazem, M. E., & Garcia‐Rubio, L. H. (1995). Application of Measurement Models to Impedance Spectroscopy: III . Evaluation of Consistency with the Kramers‐Kronig Relations. Journal of The Electrochemical Society, 142(12), 4159-4168. doi:10.1149/1.2048479Giner-Sanz, J. J., Ortega, E. M., & Pérez-Herranz, V. (2015). 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