Efficient complementary sequences-based architectures and their application to ranging measurements

Premio Extraordinario de Doctorado de la UAH en 2015En las últimas décadas, los sistemas de medición de distancias se han beneficiado de los avances en el área de las comunicaciones inalámbricas. En los sistemas basados en CDMA (Code-Division Multiple-Access), las propiedades de correlación de las secuencias empleadas juegan un papel fundamental en el desarrollo de dispositivos de medición de altas prestaciones. Debido a las sumas ideales de correlaciones aperiódicas, los conjuntos de secuencias complementarias, CSS (Complementary Sets of Sequences), son ampliamente utilizados en sistemas CDMA. En ellos, es deseable el uso de arquitecturas eficientes que permitan generar y correlar CSS del mayor número de secuencias y longitudes posibles. Por el término eficiente se hace referencia a aquellas arquitecturas que requieren menos operaciones por muestra de entrada que con una arquitectura directa. Esta tesis contribuye al desarrollo de arquitecturas eficientes de generación/correlación de CSS y derivadas, como son las secuencias LS (Loosely Synchronized) y GPC (Generalized Pairwise Complementary), que permitan aumentar el número de longitudes y/o de secuencias disponibles. Las contribuciones de la tesis pueden dividirse en dos bloques: En primer lugar, las arquitecturas eficientes de generación/correlación para CSS binarios, derivadas en trabajos previos, son generalizadas al alfabeto multinivel (secuencias con valores reales) mediante el uso de matrices de Hadamard multinivel. Este planteamiento tiene dos ventajas: por un lado el aumento del número de longitudes que pueden generarse/correlarse y la eliminación de las limitaciones de las arquitecturas previas en el número de secuencias en el conjunto. Por otro lado, bajo ciertas condiciones, los parámetros de las arquitecturas generalizadas pueden ajustarse para generar/correlar eficientemente CSS binarios de mayor número de longitudes que con las arquitecturas eficientes previas. En segundo lugar, las arquitecturas propuestas son usadas para el desarrollo de nuevos algoritmos de generación/correlación de secuencias derivadas de CSS que reducen el número de operaciones por muestra de entrada. Finalmente, se presenta la aplicación de las secuencias estudiadas en un nuevo sistema de posicionamiento local basado en Ultra-Wideband y en un sistema de posicionamiento local basado en ultrasonidos

The Gene Ontology Handbook

bioinformatics; biotechnolog

Handbook of Mathematical Geosciences

This Open Access handbook published at the IAMG's 50th anniversary, presents a compilation of invited path-breaking research contributions by award-winning geoscientists who have been instrumental in shaping the IAMG. It contains 45 chapters that are categorized broadly into five parts (i) theory, (ii) general applications, (iii) exploration and resource estimation, (iv) reviews, and (v) reminiscences covering related topics like mathematical geosciences, mathematical morphology, geostatistics, fractals and multifractals, spatial statistics, multipoint geostatistics, compositional data analysis, informatics, geocomputation, numerical methods, and chaos theory in the geosciences

Development of an integrated omics in silico workflow and its application for studying bacteria-phage interactions in a model microbial community

Microbial communities are ubiquitous and dynamic systems that inhabit a multitude of environments. They underpin natural as well as biotechnological processes, and are also implicated in human health. The elucidation and understanding of these structurally and functionally complex microbial systems using a broad spectrum of toolkits ranging from in situ sampling, high-throughput data generation ("omics"), bioinformatic analyses, computational modelling and laboratory experiments is the aim of the emerging discipline of Eco-Systems Biology. Integrated workflows which allow the systematic investigation of microbial consortia are being developed. However, in silico methods for analysing multi-omic data sets are so far typically lab-specific, applied ad hoc, limited in terms of their reproducibility by different research groups and suboptimal in the amount of data actually being exploited. To address these limitations, the present work initially focused on the development of the Integrated Meta-omic Pipeline (IMP), a large-scale reference-independent bioinformatic analyses pipeline for the integrated analysis of coupled metagenomic and metatranscriptomic data. IMP is an elaborate pipeline that incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning as well as genomic signature-based visualizations. The IMP-based data integration strategy greatly enhances overall data usage, output volume and quality as demonstrated using relevant use-cases. Finally, IMP is encapsulated within a user-friendly implementation using Python while relying on Docker for reproducibility. The IMP pipeline was then applied to a longitudinal multi-omic dataset derived from a model microbial community from an activated sludge biological wastewater treatment plant with the explicit aim of following bacteria-phage interaction dynamics using information from the CRISPR-Cas system. This work provides a multi-omic perspective of community-level CRISPR dynamics, namely changes in CRISPR repeat and spacer complements over time, demonstrating that these are heterogeneous, dynamic and transcribed genomic regions. Population-level analysis of two lipid accumulating bacterial species associated with 158 putative bacteriophage sequences enabled the observation of phage-host population dynamics. Several putatively identified bacteriophages were found to occur at much higher abundances compared to other phages and these specific peaks usually do not overlap with other putative phages. In addition, there were several RNA-based CRISPR targets that were found to occur in high abundances. In summary, the present work describes the development of a new bioinformatic pipeline for the analysis of coupled metagenomic and metatranscriptomic datasets derived from microbial communities and its application to a study focused on the dynamics of bacteria-virus interactions. Finally, this work demonstrates the power of integrated multi-omic investigation of microbial consortia towards the conversion of high-throughput next-generation sequencing data into new insights

Glucocorticoids

As one class of the most important steroid hormones, glucocorticoids have long been recognised and their therapeutic benefits have been widely used in clinical treatment, especially in anti-inflammation cases. Glucocorticoids regulate various processes in the body including the mobilization of energy stores, immune functions, gene expression, and maintenance of the homeostasis as well as the stress response, this is not surprising that the concept of "glucocorticoids" is mentioned in almost all medical text books that focus on specific organs or systems such as the cardiovascular system, the immune system, and the neuroendocrine system. The book of Glucocorticoids - New Recognition of Our Familiar Friend aims to introduce the latest findings relating to glucocorticoids, either freshly from the laboratory or from clinical case studies, and to open up a new angle of looking at the issue of balancing the therapeutic benefits and side effects brought up by glucocorticoids

Idaho National Laboratory LDRD Annual Report FY 2012

This report provides a glimpse into our diverse research and development portfolio, wwhich encompasses both advanced nuclear science and technology and underlying technologies. IN keeping with the mission, INL's LDRD program fosters technical capabilities necessary to support current and future DOE-Office of Nuclear Energy research and development needs

Ecosystem Services, Green Infrastructure and Spatial Planning

National governments hardly identify their ecological networks or make an effort to integrate them into their spatial policies and plans. Under this perspective, an important scientific and technical issue is to focus on preserving corridors for enabling species mobility and on achieving connectivity between natural protected areas. This Special Issue takes a step forward insofar as it aims at proposing a theoretical and methodological discussion on the definition and implementation of ecological networks that provide a wide range of ecosystem services