Systems biology in animal sciences

Systems biology is a rapidly expanding field of research and is applied in a number of biological disciplines. In animal sciences, omics approaches are increasingly used, yielding vast amounts of data, but systems biology approaches to extract understanding from these data of biological processes and animal traits are not yet frequently used. This paper aims to explain what systems biology is and which areas of animal sciences could benefit from systems biology approaches. Systems biology aims to understand whole biological systems working as a unit, rather than investigating their individual components. Therefore, systems biology can be considered a holistic approach, as opposed to reductionism. The recently developed ‘omics’ technologies enable biological sciences to characterize the molecular components of life with ever increasing speed, yielding vast amounts of data. However, biological functions do not follow from the simple addition of the properties of system components, but rather arise from the dynamic interactions of these components. Systems biology combines statistics, bioinformatics and mathematical modeling to integrate and analyze large amounts of data in order to extract a better understanding of the biology from these huge data sets and to predict the behavior of biological systems. A ‘system’ approach and mathematical modeling in biological sciences are not new in itself, as they were used in biochemistry, physiology and genetics long before the name systems biology was coined. However, the present combination of mass biological data and of computational and modeling tools is unprecedented and truly represents a major paradigm shift in biology. Significant advances have been made using systems biology approaches, especially in the field of bacterial and eukaryotic cells and in human medicine. Similarly, progress is being made with ‘system approaches’ in animal sciences, providing exciting opportunities to predict and modulate animal traits

Transport Layer solution for bulk data transfers over Heterogeneous Long Fat Networks in Next Generation Networks

Aquesta tesi per compendi centra les seves contribucions en l'aprenentatge i innovació de les Xarxes de Nova Generació. És per això que es proposen diferents contribucions en diferents àmbits (Smart Cities, Smart Grids, Smart Campus, Smart Learning, Mitjana, eHealth, Indústria 4.0 entre d'altres) mitjançant l'aplicació i combinació de diferents disciplines (Internet of Things, Building Information Modeling, Cloud Storage, Ciberseguretat, Big Data, Internet de el Futur, Transformació Digital). Concretament, es detalla el monitoratge sostenible del confort a l'Smart Campus, la que potser es la meva aportació més representativa dins de la conceptualització de Xarxes de Nova Generació. Dins d'aquest innovador concepte de monitorització s'integren diferents disciplines, per poder oferir informació sobre el nivell de confort de les persones. Aquesta investigació demostra el llarg recorregut que hi ha en la transformació digital dels sectors tradicionals i les NGNs. Durant aquest llarg aprenentatge sobre les NGN a través de les diferents investigacions, es va poder observar una problemàtica que afectava de manera transversal als diferents camps d'aplicació de les NGNs i que aquesta podia tenir una afectació en aquests sectors. Aquesta problemàtica consisteix en el baix rendiment durant l'intercanvi de grans volums de dades sobre xarxes amb gran capacitat d'ample de banda i remotament separades geogràficament, conegudes com a xarxes elefant. Concretament, això afecta al cas d'ús d'intercanvi massiu de dades entre regions Cloud (Cloud Data Sharing use case). És per això que es va estudiar aquest cas d'ús i les diferents alternatives a nivell de protocols de transport,. S'estudien les diferents problemàtiques que pateixen els protocols i s'observa per què aquests no són capaços d'arribar a rendiments òptims. Deguda a aquesta situació, s'hipotetiza que la introducció de mecanismes que analitzen les mètriques de la xarxa i que exploten eficientment la capacitat de la mateixa milloren el rendiment dels protocols de transport sobre xarxes elefant heterogènies durant l'enviament massiu de dades. Primerament, es dissenya l’Adaptative and Aggressive Transport Protocol (AATP), un protocol de transport adaptatiu i eficient amb l'objectiu de millorar el rendiment sobre aquest tipus de xarxes elefant. El protocol AATP s'implementa i es prova en un simulador de xarxes i un testbed sota diferents situacions i condicions per la seva validació. Implementat i provat amb èxit el protocol AATP, es decideix millorar el propi protocol, Enhanced-AATP, sobre xarxes elefant heterogènies. Per això, es dissenya un mecanisme basat en el Jitter Ràtio que permet fer aquesta diferenciació. A més, per tal de millorar el comportament del protocol, s’adapta el seu sistema de fairness per al repartiment just dels recursos amb altres fluxos Enhanced-AATP. Aquesta evolució s'implementa en el simulador de xarxes i es realitzen una sèrie de proves. A l'acabar aquesta tesi, es conclou que les Xarxes de Nova Generació tenen molt recorregut i moltes coses a millorar causa de la transformació digital de la societat i de l'aparició de nova tecnologia disruptiva. A més, es confirma que la introducció de mecanismes específics en la concepció i operació dels protocols de transport millora el rendiment d'aquests sobre xarxes elefant heterogènies.Esta tesis por compendio centra sus contribuciones en el aprendizaje e innovación de las Redes de Nueva Generación. Es por ello que se proponen distintas contribuciones en diferentes ámbitos (Smart Cities, Smart Grids, Smart Campus, Smart Learning, Media, eHealth, Industria 4.0 entre otros) mediante la aplicación y combinación de diferentes disciplinas (Internet of Things, Building Information Modeling, Cloud Storage, Ciberseguridad, Big Data, Internet del Futuro, Transformación Digital). Concretamente, se detalla la monitorización sostenible del confort en el Smart Campus, la que se podría considerar mi aportación más representativa dentro de la conceptualización de Redes de Nueva Generación. Dentro de este innovador concepto de monitorización se integran diferentes disciplinas, para poder ofrecer información sobre el nivel de confort de las personas. Esta investigación demuestra el recorrido que existe en la transformación digital de los sectores tradicionales y las NGNs. Durante este largo aprendizaje sobre las NGN a través de las diferentes investigaciones, se pudo observar una problemática que afectaba de manera transversal a los diferentes campos de aplicación de las NGNs y que ésta podía tener una afectación en estos sectores. Esta problemática consiste en el bajo rendimiento durante el intercambio de grandes volúmenes de datos sobre redes con gran capacidad de ancho de banda y remotamente separadas geográficamente, conocidas como redes elefante, o Long Fat Networks (LFNs). Concretamente, esto afecta al caso de uso de intercambio de datos entre regiones Cloud (Cloud Data Data use case). Es por ello que se estudió este caso de uso y las diferentes alternativas a nivel de protocolos de transporte. Se estudian las diferentes problemáticas que sufren los protocolos y se observa por qué no son capaces de alcanzar rendimientos óptimos. Debida a esta situación, se hipotetiza que la introducción de mecanismos que analizan las métricas de la red y que explotan eficientemente la capacidad de la misma mejoran el rendimiento de los protocolos de transporte sobre redes elefante heterogéneas durante el envío masivo de datos. Primeramente, se diseña el Adaptative and Aggressive Transport Protocol (AATP), un protocolo de transporte adaptativo y eficiente con el objetivo maximizar el rendimiento sobre este tipo de redes elefante. El protocolo AATP se implementa y se prueba en un simulador de redes y un testbed bajo diferentes situaciones y condiciones para su validación. Implementado y probado con éxito el protocolo AATP, se decide mejorar el propio protocolo, Enhanced-AATP, sobre redes elefante heterogéneas. Además, con tal de mejorar el comportamiento del protocolo, se mejora su sistema de fairness para el reparto justo de los recursos con otros flujos Enhanced-AATP. Esta evolución se implementa en el simulador de redes y se realizan una serie de pruebas. Al finalizar esta tesis, se concluye que las Redes de Nueva Generación tienen mucho recorrido y muchas cosas a mejorar debido a la transformación digital de la sociedad y a la aparición de nueva tecnología disruptiva. Se confirma que la introducción de mecanismos específicos en la concepción y operación de los protocolos de transporte mejora el rendimiento de estos sobre redes elefante heterogéneas.This compendium thesis focuses its contributions on the learning and innovation of the New Generation Networks. That is why different contributions are proposed in different areas (Smart Cities, Smart Grids, Smart Campus, Smart Learning, Media, eHealth, Industry 4.0, among others) through the application and combination of different disciplines (Internet of Things, Building Information Modeling, Cloud Storage, Cybersecurity, Big Data, Future Internet, Digital Transformation). Specifically, the sustainable comfort monitoring in the Smart Campus is detailed, which can be considered my most representative contribution within the conceptualization of New Generation Networks. Within this innovative monitoring concept, different disciplines are integrated in order to offer information on people's comfort levels. . This research demonstrates the long journey that exists in the digital transformation of traditional sectors and New Generation Networks. During this long learning about the NGNs through the different investigations, it was possible to observe a problematic that affected the different application fields of the NGNs in a transversal way and that, depending on the service and its requirements, it could have a critical impact on any of these sectors. This issue consists of a low performance operation during the exchange of large volumes of data on networks with high bandwidth capacity and remotely geographically separated, also known as Elephant networks, or Long Fat Networks (LFNs). Specifically, this critically affects the Cloud Data Sharing use case. That is why this use case and the different alternatives at the transport protocol level were studied. For this reason, the performance and operation problems suffered by layer 4 protocols are studied and it is observed why these traditional protocols are not capable of achieving optimal performance. Due to this situation, it is hypothesized that the introduction of mechanisms that analyze network metrics and efficiently exploit network’s capacity meliorates the performance of Transport Layer protocols over Heterogeneous Long Fat Networks during bulk data transfers. First, the Adaptive and Aggressive Transport Protocol (AATP) is designed. An adaptive and efficient transport protocol with the aim of maximizing its performance over this type of elephant network.. The AATP protocol is implemented and tested in a network simulator and a testbed under different situations and conditions for its validation. Once the AATP protocol was designed, implemented and tested successfully, it was decided to improve the protocol itself, Enhanced-AATP, to improve its performance over heterogeneous elephant networks. In addition, in order to upgrade the behavior of the protocol, its fairness system is improved for the fair distribution of resources among other Enhanced-AATP flows. Finally, this evolution is implemented in the network simulator and a set of tests are carried out. At the end of this thesis, it is concluded that the New Generation Networks have a long way to go and many things to improve due to the digital transformation of society and the appearance of brand-new disruptive technology. Furthermore, it is confirmed that the introduction of specific mechanisms in the conception and operation of transport protocols improves their performance on Heterogeneous Long Fat Networks

Aerospace medicine and biology: A continuing bibliography with indexes (supplement 349)

This bibliography lists 149 reports, articles and other documents introduced into the NASA Scientific and Technical Information System during April, 1991. Subject coverage includes: aerospace medicine and psychology, life support systems and controlled environments, safety equipment, exobiology and extraterrestrial life, and flight crew behavior and performance

Simulation of site-specific irrigation control strategies with sparse input data

Crop and irrigation water use efficiencies may be improved by managing irrigation application timing and volumes using physical and agronomic principles. However, the crop water requirement may be spatially variable due to different soil properties and genetic variations in the crop across the field. Adaptive control strategies can be used to locally control water applications in response to in-field temporal and spatial variability with the aim of maximising both crop development and water use efficiency. A simulation framework ‘VARIwise’ has been created to aid the development, evaluation and management of spatially and temporally varied adaptive irrigation control strategies (McCarthy et al., 2010). VARIwise enables alternative control strategies to be simulated with different crop and environmental conditions and at a range of spatial resolutions. An iterative learning controller and model predictive controller have been implemented in VARIwise to improve the irrigation of cotton. The iterative learning control strategy involves using the soil moisture response to the previous irrigation volume to adjust the applied irrigation volume applied at the next irrigation event. For field implementation this controller has low data requirements as only soil moisture data is required after each irrigation event. In contrast, a model predictive controller has high data requirements as measured soil and plant data are required at a high spatial resolution in a field implementation. Model predictive control involves using a calibrated model to determine the irrigation application and/or timing which results in the highest predicted yield or water use efficiency. The implementation of these strategies is described and a case study is presented to demonstrate the operation of the strategies with various levels of data availability. It is concluded that in situations of sparse data, the iterative learning controller performs significantly better than a model predictive controller

CERN openlab Whitepaper on Future IT Challenges in Scientific Research

This whitepaper describes the major IT challenges in scientific research at CERN and several other European and international research laboratories and projects. Each challenge is exemplified through a set of concrete use cases drawn from the requirements of large-scale scientific programs. The paper is based on contributions from many researchers and IT experts of the participating laboratories and also input from the existing CERN openlab industrial sponsors. The views expressed in this document are those of the individual contributors and do not necessarily reflect the view of their organisations and/or affiliates

Air pollution and livestock production

The air in a livestock farming environment contains high concentrations of dust particles and gaseous pollutants. The total inhalable dust can enter the nose and mouth during normal breathing and the thoracic dust can reach into the lungs. However, it is the respirable dust particles that can penetrate further into the gas-exchange region, making it the most hazardous dust component. Prolonged exposure to high concentrations of dust particles can lead to respiratory health issues for both livestock and farming staff. Ammonia, an example of a gaseous pollutant, is derived from the decomposition of nitrous compounds. Increased exposure to ammonia may also have an effect on the health of humans and livestock. There are a number of technologies available to ensure exposure to these pollutants is minimised. Through proactive means, (the optimal design and management of livestock buildings) air quality can be improved to reduce the likelihood of risks associated with sub-optimal air quality. Once air problems have taken hold, other reduction methods need to be applied utilising a more reactive approach. A key requirement for the control of concentration and exposure of airborne pollutants to an acceptable level is to be able to conduct real-time measurements of these pollutants. This paper provides a review of airborne pollution including methods to both measure and control the concentration of pollutants in livestock buildings