Application of the Bubble model on a virtual bronchial tree to analyse tuberculosis lesion spread and growth on macaques

The Bubble model is a mathematical model that aims to recreate the dynamics of a tuberculosis infection in the lungs. It has proved successful in recreating experimental data in minipigs. Our objective in this work is to implement this model in a macaque virtual lung, as well as to perform a first parameter exploration to pave the way into recreating recent experimental data regarding tuberculosis lesions spread in Rhesus macaques. In particular, we deal with the experimental data processing, the implementation of the virtual framework to run the simulations and the analysis of the results using different parameter configurations, defining an objective error function to evaluate the quality of the simulations2022/202

Microbial ecology of the Iberian pyrite belt deep subsurface

Tesis Doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 06-05-2016Esta tesis tiene embargado el acceso al texto completo hasta el 06-11-201

SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline

The improvement of sequencing technologies has facilitated generalization of metagenomic sequencing, which has become a standard procedure for analyzing the structure and functionality of microbiomes. Bioinformatic analysis of sequencing results poses a challenge because it involves many different complex steps. SqueezeMeta is a fully automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support that enables co-assembly of related metagenomes and retrieval of individual genomes via binning procedures. SqueezeMeta features several unique characteristics: co-assembly procedure or co-assembly of unlimited number of metagenomes via merging of individual assembled metagenomes, both with read mapping for estimation of the abundances of genes in each metagenome. It also includes binning and bin checking for retrieving individual genomes. Internal checks for the assembly and binning steps provide information about the consistency of contigs and bins. Moreover, results are stored in a MySQL database, where they can be easily exported and shared, and can be inspected anywhere using a flexible web interface that allows simple creation of complex queries. We illustrate the potential of SqueezeMeta by analyzing 32 gut metagenomes in a fully automatic way, enabling retrieval of several million genes and several hundreds of genomic bins. One of the motivations in the development of SqueezeMeta was producing a software capable of running in small desktop computers and thus amenable to all users and settings. We were also able to co-assemble two of these metagenomes and complete the full analysis in less than one day using a simple laptop computer. This reveals the capacity of SqueezeMeta to run without high-performance computing infrastructure and in absence of any network connectivity. It is therefore adequate for in situ, real time analysis of metagenomes produced by nanopore sequencing. SqueezeMeta can be downloaded from https://github.com/jtamames/SqueezeMeta

The emergence of interstellar molecular complexity explained by interacting networks

Recent years have witnessed the detection of an increasing number of complex organicmolecules in interstellar space, some of them being of prebiotic interest. Disentanglingthe origin of interstellar prebiotic chemistry and its connection to biochemistry andultimately, to biology is an enormously challenging scientific goal where the applicationof complexity theory and network science has not been fully exploited. Encouragedby this idea, we present a theoretical and computational framework to model theevolution of simple networked structures toward complexity. In our environment,complex networks represent simplified chemical compounds and interact optimizing thedynamical importance of their nodes. We describe the emergence of a transition fromsimple networks toward complexity when the parameter representing the environmentreaches a critical value. Notably, although our system does not attempt to model the rulesof real chemistry nor is dependent on external input data, the results describe the emer-gence of complexity in the evolution of chemical diversity in the interstellar medium.Furthermore, they reveal an as yet unknown relationship between the abundances ofmolecules in dark clouds and the potential number of chemical reactions that yieldthem as products, supporting the ability of the conceptual framework presented here toshed light on real scenarios. Our work reinforces the notion that some of the propertiesthat condition the extremely complex journey from the chemistry in space to prebioticchemistry and finally, to life could show relatively simple and universal patterns

Docencia de Dibujo Técnico a través de herramientas de animación asistida por ordenador

Es sabido por todos los que se mueven en el ámbito de la Expresión Gráfica y el Diseño la necesidad de poseer un amplio desarrollo de la concepción espacial para solucionar proyectos concretos. Este aspecto lo desarrolla el alumno de ingeniería mediante las asignaturas de Dibujo Técnico. La insuficiente formación del alumnado al iniciar estudios universitarios y la disminución de tiempos en los nuevos planes de estudio ofrece un problema para su desarrollo. En esta comunicación se ofrece la animación asistida por ordenador como una metodología docente complementaria para disminuir los tiempos de su impartición sin afectar sus contenidos

Ampliación de la formación en CAD dentro de las asignaturas de Dibujo Técnico: Modelado tridimensional

En el curso 96/97 se incorporaron las prácticas de CAD a la docencia de Dibujo Técnico para los alumnos de Ingeniería Técnica Industrial en la Escuela Universitaria Politécnica de Sevilla. Dichas prácticas recogen el carácter bidimensional del CAD durante el primer curso, mientras que en la asignatura de segundo curso se analizan las posibilidades que ofrece el uso de esta herramienta en tres dimensiones. Con esta comunicación, pretendemos exponer las ventajas que introduce el modelado tridimensional de objetos mediante CAD así como los resultados de nuestra experiencia con estas prácticas

LiLO: Lightweight and low-bias LiDAR Odometry method based on spherical range image filtering

In unstructured outdoor environments, robotics requires accurate and efficient odometry with low computational time. Existing low-bias LiDAR odometry methods are often computationally expensive. To address this problem, we present a lightweight LiDAR odometry method that converts unorganized point cloud data into a spherical range image (SRI) and filters out surface, edge, and ground features in the image plane. This substantially reduces computation time and the required features for odometry estimation in LOAM-based algorithms. Our odometry estimation method does not rely on global maps or loop closure algorithms, which further reduces computational costs. Experimental results generate a translation and rotation error of 0.86\% and 0.0036{\deg}/m on the KITTI dataset with an average runtime of 78ms. In addition, we tested the method with our data, obtaining an average closed-loop error of 0.8m and a runtime of 27ms over eight loops covering 3.5Km.Comment: This paper is under review at the journal "Autonomous Robots" (Springer

Aplicación de Herramientas Multimedia al Dibujo Electrónico y su Normalización, en los Nuevos Planes de Estudio de Ingeniero Técnico Industrial

El objeto de la ponencia presentada es el de compartir la experiencia llevada a cabo en la nueva titulación de Ingeniero Técnico Industrial en Electrónica (plan 2001), mediante la introducción de nuevas herramientas TIC aplicadas a las asignaturas del Área de Expresión Gráfica. Las herramientas en concreto constituyen un entorno profesional en electrónica y serán utilizadas en una práctica o trabajo final de dibujo electrónico

Estudio y caracterización del efecto kink en transistores HEMT de GaN

Using as test vehicles virgin and aged GaN HEMT devices, a study of the kink effect evolution with the applied electric field and ambient temperature has been performed. The obtained results lead to a physics explanation of the kink effect origin as well as its dependence on ambient temperature. Experimental results, showing the different effects taking place in the transistor, will be reported for several GaN devices operating at different electric field and temperature conditions

Biomarker Profiling of Microbial Mats in the Geothermal Band of Cerro Caliente, Deception Island (Antarctica): Life at the Edge of Heat and Cold

© María Ángeles Lezcano et al. 2019.Substrate–atmosphere interfaces in Antarctic geothermal environments are hot–cold regions that constitute thin habitable niches for microorganisms with possible counterparts in ancient Mars. Cerro Caliente hill in Deception Island (active volcano in the South Shetland Islands) is affected by ascending hydrothermal fluids that form a band of warm substrates buffered by low air temperatures. We investigated the influence of temperature on the community structure and metabolism of three microbial mats collected along the geothermal band of Cerro Caliente registering 88°C, 8°C, and 2°C at the time of collection. High-throughput sequencing of small subunit ribosomal ribonucleic acid (SSU rRNA) genes and Life Detector Chip (LDChip) microarray immunoassays revealed different bacterial, archaeal, and eukaryotic composition in the three mats. The mat at 88°C showed the less diverse microbial community and a higher proportion of thermophiles (e.g., Thermales). In contrast, microbial communities in the mats at 2°C and 8°C showed relatively higher diversity and higher proportion of psychrophiles (e.g., Flavobacteriales). Despite this overall association, similar microbial structures at the phylum level (particularly the presence of Cyanobacteria) and certain hot- and cold-tolerant microorganisms were identified in the three mats. Daily thermal oscillations recorded in the substrate over the year (4.5–76°C) may explain the coexistence of microbial fingerprints with different thermal tolerances. Stable isotope composition also revealed metabolic differences among the microbial mats. Carbon isotopic ratios suggested the Calvin–Benson–Bassham cycle as the major pathway for carbon dioxide fixation in the mats at 2°C and 8°C, and the reductive tricarboxylic acid cycle and/or the 3-hydroxypropionate bicycle for the mat at 88°C, indicating different metabolisms as a function of the prevailing temperature of each mat. The comprehensive biomarker profile on the three microbial mats from Cerro Caliente contributes to unravel the diversity, composition, and metabolism in geothermal polar sites and highlights the relevance of geothermal-cold environments to create habitable niches with interest in other planetary environments.This study has been funded by the Spanish Research Agency (AEI) from the Ministry of Science Innovation and Universities and the European FEDER Grants Nos. ESP2015-69540-R, RYC2014-19446, and CGL2015-74254-JIN; the AEI Project No. MDM-2017-0737 Unidad de Excelencia ‘‘Marı´a de Maeztu,’’ and the European Research Council Starting Grant (ERC StG) No. 307496. M.A´ . Lezcano and M.A´ . Fernández Martínez were supported by a postdoctoral fellowship by the Youth Employment Initiative from the European Union and implanted in Comunidad de Madrid