Automation on the generation of genome scale metabolic models

Background: Nowadays, the reconstruction of genome scale metabolic models is a non-automatized and interactive process based on decision taking. This lengthy process usually requires a full year of one person's work in order to satisfactory collect, analyze and validate the list of all metabolic reactions present in a specific organism. In order to write this list, one manually has to go through a huge amount of genomic, metabolomic and physiological information. Currently, there is no optimal algorithm that allows one to automatically go through all this information and generate the models taking into account probabilistic criteria of unicity and completeness that a biologist would consider. Results: This work presents the automation of a methodology for the reconstruction of genome scale metabolic models for any organism. The methodology that follows is the automatized version of the steps implemented manually for the reconstruction of the genome scale metabolic model of a photosynthetic organism, {\it Synechocystis sp. PCC6803}. The steps for the reconstruction are implemented in a computational platform (COPABI) that generates the models from the probabilistic algorithms that have been developed. Conclusions: For validation of the developed algorithm robustness, the metabolic models of several organisms generated by the platform have been studied together with published models that have been manually curated. Network properties of the models like connectivity and average shortest mean path of the different models have been compared and analyzed.Comment: 24 pages, 2 figures, 2 table

Nuevas citas y ampliación de la distribución conocida de Ropalóceros en la Comunidad Valenciana y provincia de Teruel

The authors summarize data for 18 species of Rhopalocera to complete knowledge of their distribution and biology in Comunidad Valenciana and Teruel province. These species have been selected for two reasons: 1) Danaus plexippus (Linnaeus, 1758), Erebia meolans (de Prunner, 1798), Polyommatus (Meleageria) daphnis (Denis & Schiffermüller, 1775), Laeosopis roboris (Esper, 1789), Nordmannia acaciae (Fabricius, 1787) and Plebeius hespericus (Rambur, 1839) are new records for Comunidad Valenciana and 2) Euchloe belemia (Esper, 1800), Pieris mannii (Mayer, 1851), Zegris eupheme (Esper, 1804), Colotis evagore (Klug, 1829), Aporia crataegi (Linnaeus 1758), Erebia epistygne (Hübner, 1819), Melitaea cinxia (Linnaeus, 1758), Libythea celtis (Laicharting, 1782), Glaucopsyche (Iolana) iolas (Ochsenheimer, 1816), Scolitantides orion (Pallas, 1771), Neozephyrus quercus (Linnaeus, 1758) and Plebeius (Aricia) morronensis Ribbe, 1910, for these species, known distribution is considerably extended and interesting data about their biology are provided.Se aporta información sobre 18 especies de ropalóceros presentes en la Comunidad Valenciana y provincia de Teruel. Algunas de estas especies se dan a conocer por vez primera de esta región, como es el caso de Danaus plexippus (Linnaeus, 1758), Erebia meolans (de Prunner, 1798), Polyommatus (Meleageria) daphnis (Denis & Schiffermüller, 1775), Laeosopis roboris (Esper, 1789), Nordmannia acaciae (Fabricius, 1787) y Plebeius hespericus (Rambur, 1839). Para el resto se amplía considerablemente su distribución conocida y/o se acompaña de algunos comentarios de interés sobre su biología: Euchloe belemia (Esper, 1800), Pieris mannii (Mayer, 1851), Zegris eupheme (Esper, 1804), Colotis evagore (Klug, 1829), Aporia crataegi (Linnaeus 1758), Erebia epistygne (Hübner, 1819), Melitaea cinxia (Linnaeus, 1758), Libythea celtis (Laicharting, 1782), Glaucopsyche (Iolana) iolas (Ochsenheimer, 1816), Scolitantides orion (Pallas, 1771), Neozephyrus quercus (Linnaeus, 1758) y Plebeius (Aricia) morronensis Ribbe, 1910

Diffractive Corneal Inlays: A New Concept for Correction of Presbyopia

A new class of corneal inlays for treatment of presbyopia is described, which uses diffraction as the working principle. The inlay consists of an opaque disk with a small central aperture surrounded by an array of micro-holes that are distributed following the order of a given Fresnel zone plate having N zones. In this way, the central hole of the disk produces an extension of the depth of focus of the eye for distance vision and contributes to the zero order of diffraction, and the light diffracted by the micro-holes in the periphery produces a real focus for near vision. In our general design, the number of zones and the diameter of the central hole are free parameters that can be used to design customized devices with different addition power and near-focus intensity. Two different designs are analyzed to show this property. In the analysis, we employed a ray tracing software to study the performance of the new inlays in the two different model eyes. The results are compared with those obtained with a model of the small-aperture inlay that is currently in the market. The different merit functions used in the comparison and the image simulations performed with the inlays in the model eyes show the excellent performance of our proposal

Characterization of multifocal lenses through a virtual laboratory based on Fourier optics

[ES] En este trabajo presentamos un nuevo laboratorio virtual, desarrollado en Python, que permite la caracterización óptica de una serie de lentes multifocales bajo diferentes parámetros de configuración (esfera, cilindro, eje, diámetro de pupila, aberración esférica, ...) mediante diferentes métricas basadas en la óptica de Fourier, tales como la Función de Transferencia de Modulación (MTF), la Función de Dispersión del Punto (PSF) y la simulación de formación de imágenes de diferentes optotipos.[EN] In this paper we present a new Python developed virtual laboratory that allows the optical characterization of a series of multifocal lenses under different setup parameters (sphere, cylinder, axis, pupil diameter, spherical aberration, ...) by using different metrics based on the Fourier optics, such as the Modulation Transfer Function (MTF), the Point Spread Function (PSF) and the image forming simulation of different optotypes.Este trabajo ha sido financiado por el Ministerio de Ciencia e Innovación de España [PID2019-107391RB-I00] y por la Generalitat Valenciana (España) [PROMETEO/2019/048]. D.  M.-M. también agradece la financiación otorgada por la beca Margarita Salas del Ministerio de Universidades de España financiado por the European Union-Next Generation EU. Este trabajo ha sido desarrollado por el Equipo de Innovación y Calidad Educativa MSEL de la Universitat Politècnica de València.Ferrando Martín, V.; Montagud-Martínez, D.; Monsoriu, JA.; Remón, L.; Furlan, WD. (2023). Caracterización de lentes multifocales mediante un laboratorio virtual basado en la óptica de Fourier. Modelling in Science Education and Learning. 16(2):5-11. https://doi.org/10.4995/msel.2023.1906151116

Anisotropy of Magnetic Field and Velocity Fluctuations in the Solar Wind

We present a large statistical study of the fluctuation anisotropy in minimum variance (MV) frames of the magnetic field and solar wind velocity. We use 2, 10, 20, and 40 minute intervals of simultaneous magnetic field (the Wind spacecraft) and velocity (the Spektr-R spacecraft) observations. Our study confirms that magnetic turbulence is a composite of fluctuations varying along the mean magnetic field and those changing in the direction perpendicular to the mean field. Regardless of the length scale within the studied range of spacecraft-frame frequencies, ≈90% of the observed magnetic field fluctuations exhibit an MV direction aligned with the mean magnetic field, ≈10% of events have the MV direction perpendicular to the background field, and a negligible portion of fluctuations has no preferential direction. On the other hand, the MV direction of velocity fluctuations tends to be distributed more uniformly. An analysis of magnetic compressibility and density fluctuations suggests that the fluctuations resemble properties of Alfvénic fluctuations if the MV direction is aligned with background magnetic field whereas slow-mode-like fluctuations have the MV direction perpendicular to the background field. The proportion between Alfvénic and slow-mode-like fluctuations depends on plasma β and length scale: the dependence on the solar wind speed is weak. We present 3D numerical MHD simulations and show that the numerical results are compatible with our experimental results

Hot sanitary water production with CO2 heat pumps: Effect of control strategy on system performance and stratification inside the storage tank

[EN] In this work three different control strategies for the production of sanitary hot water by means of an electric heat pump working with CO2 are investigated. The heat pump is a prototype, here modelled in the vapour-compression software package IMST-ART. By simulating this model, the performance of the heat pump is correlated to the boundary conditions and is scaled to different sizes, namely 1, 1.5, and 2 times larger than the reference system. After having chosen an application for which the load profile of sanitary hot water during the year is known, these heat pumps are simulated in a TRNSYS16 model where the production of sanitary hot water and the consumption are buffered by the presence of a tank. Key parameter in guaranteeing comfort and good performance of the system is the stratification inside the storage tank. The size of the tank necessary to keep a certain level of comfort at the user is then determined through a parametric analysis for each size of the heat pump. The energetic performance is also evaluated for each system in terms of seasonal performance factor. Then, the results obtained are compared with a different system where the heat pump is equipped with an inverter and the circulation pump follows a different control logic. The size of the tank and the seasonal performance factor are therefore determined in this case too. Moreover, a night&day control logic is compared to these first two options to have a baseline of comparison in terms of volume of storage needed to guarantee a same level of comfort and performance. To provide information also on the running costs, a parametric analysis was run varying the type of control, the heat pump and the tank sizes for different load profiles. The results show that the size of the heat pump has a significant effect on the comfort of the user, which usually leads to oversizing of the storage tank when the load profile is unknown. With regard to this, the results obtained for the alternative control system show a 20% reduction of the volume of the tank, given a certain level of comfort, and is therefore useful to reduce the size of the storage tank.The study related to thiswork has been partially supported by the FP7 European project ‘Next Generation of Heat Pumpsworkingwith Natural fluids’ (NxtHPG) Grant agreement no: 307169. The work of M. Tammaro on electric heat pumps is financially supported by Universita degli Studi di Napoli Federico II throughthe FP7 European project 'Next Generation of Heat Pumps working with Natural fluids' (NxtHPG).Tammaro, M.; Mauro, AW.; Montagud Montalvá, CI.; Corberán Salvador, JM.; Mastrullo, R. (2016). Hot sanitary water production with CO2 heat pumps: Effect of control strategy on system performance and stratification inside the storage tank. Applied Thermal Engineering. 101:730-740. https://doi.org/10.1016/j.applthermaleng.2016.01.094S73074010

Optical performance of a new design of trifocal intraocular lens based on the Devil's diffractive lens

In this work, we propose a new diffractive trifocal intraocular lens design with focus extension, conceived to provide a high visual performance at intermediate distances. This design is based on a fractal structure known as the "Devil's staircase". To assess its optical performance, numerical simulations have been performed with a ray tracing program using the Liou-Brennan model eye under polychromatic illumination. The simulated through the focus visual acuity was the merit function employed to test its pupil-dependence and its behavior against decentering. A qualitative assessment of the multifocal intraocular lens (MIOL) was also performed experimentally with an adaptive optics visual simulator. The experimental results confirm our numerical predictions. We found that our MIOL design has a trifocal profile, which is very robust to decentration and has low degree of pupil dependence. It performs better at intermediate distances than at near distances and, for a pupil diameter of 3 mm, it works like an EDoF lens over almost the entire defocus range

A 3D TLM code for the study of the ELF electromagnetic wave propagation in the Earth's atmosphere

The interest in the study of electromagnetic propagation through planetary atmospheres is briefly discussed. Special attention is devoted to extremely-low-frequency fields in the Earth's atmosphere for its global nature and possible applications to climate monitoring studies among others. In the Earth's case, the system can be considered as a spherical electromagnetic shell resonator in which two concentric and large conducting spheres with a radius around 6300 km are separated by a very small distance of around 100 km, the atmosphere height. A numerical solution using the Transmission Line Method is proposed. The classical spherical-coordinate description is easy to use, however, the important difference in the dimensions along the three coordinate directions causes high numerical dispersion in the results. A Cartesian scheme with equal node size for all directions is used to reduce this undesired dispersion. A pre-processing stage is the key point introduced to lessen the resulting high demand of memory and time calculation and make the solution feasible. A parallelized Fortran code together with pre- and post-processing Python programs to ease the user interface are provided with this work. Details on the Fortran code and the Python modules are included both in the paper and the source codes to allow the use and modifications by other researchers interested in electromagnetic propagation through planetary atmospheres. The program allows calculation of the time evolution of the electromagnetic field at any point in the atmosphere. It includes the possibility of considering multiple time-dependent sources and different homogeneous and inhomogeneous conductivity profiles to model different situations. Profiles to study day-night asymmetries or locally perturbed profiles which have been attributed to earthquakes in the literature are implemented, for instance.MCIN/AEI 10.13039/501100011033 (grant PID 2020-112805 GA-I00)Grant PID 2020-112805 GA-I00 funded by MCIN/AEI/10.13039/ 50110001103