Scalable Inference of Gene Regulatory Networks with the Spark Distributed Computing Platform Cristo

Inference of Gene Regulatory Networks (GRNs) remains an important open challenge in computational biology. The goal of bio-model inference is to, based on time-series of gene expression data, obtain the sparse topological structure and the parameters that quantitatively understand and reproduce the dynamics of biological system. Nevertheless, the inference of a GRN is a complex optimization problem that involve processing S-System models, which include large amount of gene expression data from hundreds (even thousands) of genes in multiple time-series (essays). This complexity, along with the amount of data managed, make the inference of GRNs to be a computationally expensive task. Therefore, the genera- tion of parallel algorithmic proposals that operate efficiently on distributed processing platforms is a must in current reconstruction of GRNs. In this paper, a parallel multi-objective approach is proposed for the optimal inference of GRNs, since min- imizing the Mean Squared Error using S-System model and Topology Regularization value. A flexible and robust multi-objective cellular evolutionary algorithm is adapted to deploy parallel tasks, in form of Spark jobs. The proposed approach has been developed using the framework jMetal, so in order to perform parallel computation, we use Spark on a cluster of distributed nodes to evaluate candidate solutions modeling the interactions of genes in biological networks.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Thickness characterization of thin Silicon Strip Detectors and its impact in Nuclear Physics Experiments

Tese de Mestrado Integrado, Engenharia Física , 2022, Universidade de Lisboa, Faculdade de CiênciasThe identification and precise characterization of nuclear reaction products is crucial for the study and understanding of the interactions that govern physics at the subatomic level. One of the options developed to discriminate different particles with similar energy is the composition of several stage detectors, usually called Telescope Detection Systems. In this work four Single Sided Silicon Stripped detectors with thicknesses of ≈20 µm have been characterized to improve their response as ∆E in Telescope detection systems. The characterization resulted in the precise determination of the detector thickness throughout its surface. Two different methods were applied to achieve this goal. Maximum deviations of up to 35 % were observed. This charactererization will allow for a better resolution of the system and a clearer discrimination of the reaction products. Several steps were undertaken during the analysis. The angular calibration of the setup was performed using the scattering reaction 10Be + 197Au at energies below the Coulomb barrier. The energy calibration of the E stage was performed using radioactive sources and corrected for high energies by applying a gain match procedure that allowed a tighter constrain in the event selection. The energy calibration of the thin detectors, done with low energy nuclear reactions and radioactive sources, had to consider the struggling of particles in the dead layers of the material to correctly determine the energy deposited by incident particles in the active detector layer. The results of this work will allow a more precise analysis of the reaction data on the exotic nucleus 10Be on the magic nucleus 120Sn, measured for the first time at energies around the Coulomb Barrier, at the LNS laboratory in Catania (Italy)

Las prácticas integradas de relaciones laborales y el espacio europeo de educación superior

La actual configuración de la Prácticas Integradas en la Diplomatura de Relaciones Laborales de la Universidad de Huelva, aparece en su diseño y organización docentes, estrechamente conectada con los principios que presiden la construcción del Espacio europeo de Educación Superior. De manera singular, la asignatura Prácticas Integradas pretende promover la formación integral del estudiante e incidir en el desarrollo de las competencias profesionales en función de los perfiles propios de la titulación. Al mismo tiempo, se persigue aumentar la empleabilidad del estudiante y mejorar el proceso de inserción de éstos en el mercado laboral. Todo ello bajo los parámetros de coordinación docente, orientación, tutorización y seguimiento personalizados, dentro de una evaluación continuada del proceso de aprendizaje._____________________________The current configuration of the Integrated Practice Diploma in Industrial Relations at the University of Huelva, appears in the design and educational organization, which is closely connected with the principles that inform the construction of the European Higher Education Area. In a unique way, the course aims to promote the Intégrated Practice integral formation of the student, and influence the development of skills depending on the profiles of the deeds themselves. At the same time, it seeks to increase the employability of students and improve the process of integrating them into the labor market. All this under the coordination parameters teaching, counseling, tutoring and monitoring customized within a continuous assessment of the learning process

Effects of drought-induced forest die-off on litter decomposition

Aims: drought-induced forest die-off and subsequent species replacement may modify environmental conditions and eventually affect litter decomposition. We aimed to disentangle the effects of tree species and die-off state on litter decomposition in a mixed forest where Pinus sylvestris populations experiencing severe drought-induced die-off are being replaced by Quercus ilex. - Methods: litter bags with leaves and fine roots from both species were placed under canopies representing three habitats of the die-off and replacement process (healthy and dead P. sylvestris and healthy Q. ilex). Mass was assessed over 3 years. - Results: species-specific chemistry of litter (C:N ratio) had a direct effect on mass loss, but also indirect effects, attributed to the decomposer microbial community associated with a given habitat-species. In their respective original habitats, oak leaves decomposed 44 % faster than pine needles, whereas oak roots decomposed 46 % slower than pine roots. - Conclusions: forest die-off and species replacement affected litter decomposition. This effect can have great implications in forest functioning, particularly if drought-induced die-off worsens in the next decades, according with the trend observed in the studied system

Uniqueness for SQG patch solutions

This paper is about the evolution of a temperature front governed by the surface quasi-geostrophic equation. The existence part of that program within the scale of Sobolev spaces was obtained by the third author (2008). Here we revisit that proof introducing some new tools and points of view which allow us to conclude the also needed uniqueness result.Ministerio de Economía y CompetitividadJunta de AndalucíaEuropean Research Counci

The Rayleigh-Taylor condition for the evolution of irrotational fluid interfaces

For the free boundary dynamics of the two-phase Hele-Shaw and Muskat problems, and also for the irrotational incompressible Euler equation, we prove existence locally in time when the Rayleigh-Taylor condition is initially satisfied for a 2D interface. The result for water waves was first obtained by Wu in a slightly different scenario (vanishing at infinity), but our approach is different because it emphasizes the active scalar character of the system and does not require the presence of gravity.Ministerio de Educación y CienciaEuropean Research Counci

Interface evolution: water waves in 2-D

We study the free boundary evolution between two irrotational, incompressible and inviscid fluids in 2-D without surface tension. We prove local-existence in Sobolev spaces when, initially, the difference of the gradients of the pressure in the normal direction has the proper sign, an assumption which is also known as the Rayleigh-Taylor condition. The well-posedness of the full water wave problem was first obtained by S. Wu. Well-posedness in Sobolev spaces of the full water wave problem in 2-D. Invent. math. 130, 39-72, 1997. The methods introduced in this paper allows us to consider multiple cases: with or without gravity, but also a closed boundary or a periodic boundary with the fluids placed above and below it. It is assumed that the initial interface does not touch itself, being a part of the evolution problem to check that such property prevails for a short time, as well as it does the Rayleigh-Taylor condition, depending conveniently upon the initial data. The addition of the pressure equality to the contour dynamic equations is obtained as a mathematical consequence, and not as a physical assumption, from the mere fact that we are dealing with weak solutions of Euler’s equation in the whole space.Ministerio de Educación y CienciaMinisterio de Ciencia e InnovaciónEuropean Research Counci