Autonomous on-board data processing and instrument calibration software for the SO/PHI

The extension of on-board data processing capabilities is an attractive option to reduce telemetry for scientific instruments on deep space missions. The challenges that this presents, however, require a comprehensive software system, which operates on the limited resources a data processing unit in space allows. We implemented such a system for the Polarimetric and Helioseismic Imager (PHI) on-board the Solar Orbiter (SO) spacecraft. It ensures autonomous operation to handle long command-response times, easy changing of the processes after new lessons have been learned and meticulous book-keeping of all operations to ensure scientific accuracy. This contribution presents the requirements and main aspects of the software implementation, followed by an example of a task implemented in the software frame, and results from running it on SO/PHI. The presented example shows that the different parts of the software framework work well together, and that the system processes data as we expect. The flexibility of the framework makes it possible to use it as a baseline for future applications with similar needs and limitations as SO/PHI.Comment: Conference: SPIE Astronomical Telescopes + Instrumentatio, Software and Cyberinfrastructure for Astronomy

Performance Analysis of the SO/PHI Software Framework for On-board Data Reduction

The Polarimetric and Helioseismic Imager (PHI) is the first deep-space solar spectropolarimeter, on-board the Solar Orbiter (SO) space mission. It faces: stringent requirements on science data accuracy, a dynamic environment, and severe limitations on telemetry volume. SO/PHI overcomes these restrictions through on-board instrument calibration and science data reduction, using dedicated firmware in FPGAs. This contribution analyses the accuracy of a data processing pipeline by comparing the results obtained with SO/PHI hardware to a reference from a ground computer. The results show that for the analyzed pipeline the error introduced by the firmware implementation is well below the requirements of SO/PHI.Workframe: International Max Planck Research School (IMPRS) for Solar System Science. Solar Orbiter: ESA, NASA. Support grants: DLR 50 OT 1201, Spanish Research Agency ESP2016-77548-05, European FEDER. Data: NASA/SDO HMI science team

Staphylococcus aureus Bacteremia in Children of Rural Areas of The Gambia, 2008–2015

Staphylococcus aureus bacteremia is a substantial cause of childhood disease and death, but few studies have described its epidemiology in developing countries. Using a population-based surveillance system for pneumonia, sepsis, and meningitis, we estimated S. aureus bacteremia incidence and the case-fatality ratio in children <5 years of age in 2 regions in the eastern part of The Gambia during 2008–2015. Among 33,060 children with suspected pneumonia, sepsis, or meningitis, we performed blood culture for 27,851; of 1,130 patients with bacteremia, 198 (17.5%) were positive for S. aureus. S. aureus bacteremia incidence was 78 (95% CI 67–91) cases/100,000 person-years in children <5 years of age and 2,080 (95% CI 1,621–2,627) cases/100,000 person-years in neonates. Incidence did not change after introduction of the pneumococcal conjugate vaccine. The case-fatality ratio was 14.1% (95% CI 9.6%–19.8%). Interventions are needed to reduce the S. aureus bacteremia burden in The Gambia, particularly among neonates

Autonomous on-board data processing and instrument calibration software for the Polarimetric and Helioseismic Imager on-board the Solar Orbiter mission

This is an open access article. Published by SPIE under a Creative Commons Attribution 4.0 Unported License. Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI.A frequent problem arising for deep space missions is the discrepancy between the amount of data desired to be transmitted to the ground and the available telemetry bandwidth. A part of these data consists of scientific observations, being complemented by calibration data to help remove instrumental effects. We present our solution for this discrepancy, implemented for the Polarimetric and Helioseismic Imager on-board the Solar Orbiter mission, the first solar spectropolarimeter in deep space. We implemented an on-board data reduction system that processes calibration data, applies them to the raw science observables, and derives science-ready physical parameters. This process reduces the raw data for a single measurement from 24 images to five, thus reducing the amount of downlinked data, and in addition, renders the transmission of the calibration data unnecessary. Both these on-board actions are completed autonomously. © The Authors. Published by SPIE under a Creative Commons Attribution 4.0 Unported License. Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI.This work was carried out in the framework of the International Max Planck Research School for Solar System Science at the Max Planck Institute for Solar System Research. Solar Orbiter is a mission led by the European Space Agency with contribution from the National Aeronautics and Space Administration (NASA). The Polarimetric and Helioseismic Imager instrument is supported by the German Aerospace Center (DLR) under grant Nos. 50 OT 1201 and 50 OT 1901. The Spanish contribution has been partly funded by the Spanish Research Agency under projects under grant Nos. ESP2016-77548-C5 and RTI2018-096886-B-C5, partially including European FEDER funds. IAA-CSIC members acknowledge and funds from the Spanish Ministry of Science and Innovation “Centro de Excelencia Severo Ochoa” Program under grant No. SEV-2017-0709. The solar data used in the tests are the courtesy of NASA/SDO HMI science team. Parts of the work shown in this paper have been introduced at the SPIE Astronomical Telescopes + Instrumentation conference.42 EditorialPeer reviewe

Oral saliva swab reverse transcription PCR for Covid-19 in the paediatric population

8Pág. Centro de Investigación en Sanidad Animal (CISA)To evaluate the performance of oral saliva swab (OSS) reverse transcription PCR (RT-PCR) compared with RT-PCR and antigen rapid diagnostic test (Ag-RDT) on nasopharyngeal swabs (NPS) for SARS-CoV-2 in children.The study was funded by: Project PI20/00095, from the Instituto de Salud Carlos III (Ministry of Economy, Industry and Competitiveness) and cofounded by the European Regional Development Fund, by Infanta Sofia University Hospital and Henares University Hospital Foundation for Biomedical Research and Innovation (FIIB HUIS HHEN), and by SERMAS-Fundación para la Investigación Biomédica del Hospital 12 de Octubre. EC-C is supported by the Spanish Society of Paediatrics (Asociación Española de Pediatría); Grant COVID-19 EPICO-AEP 2020. JMM is funded by SERMAS-Fundación para la Investigación Biomédica del Hospital Infanta Sofía y del Henares and by Universidad Europea de Madrid, Spain. MdlS is funded by Grant Cantera de Investigación Santander, Fundación Universidad Europea de Madrid, Spain. ED is funded by the Juan de la Cierva–Incorporación granted by the Spanish Ministry of Science and Innovation. DB-G is funded by the Spanish Ministry of Science and Innovation—Instituto de Salud Carlos III and Fondos FEDER by ’Contratos para la intensificación de la actividad investigadora en el Sistema Nacional de Salud, 2020 (INT20/00086)’.Peer reviewe

Estimating the burden of antimicrobial resistance: a systematic literature review.

Background: Accurate estimates of the burden of antimicrobial resistance (AMR) are needed to establish the magnitude of this global threat in terms of both health and cost, and to paramaterise cost-effectiveness evaluations of interventions aiming to tackle the problem. This review aimed to establish the alternative methodologies used in estimating AMR burden in order to appraise the current evidence base. Methods: MEDLINE, EMBASE, Scopus, EconLit, PubMed and grey literature were searched. English language studies evaluating the impact of AMR (from any microbe) on patient, payer/provider and economic burden published between January 2013 and December 2015 were included. Independent screening of title/abstracts followed by full texts was performed using pre-specified criteria. A study quality score (from zero to one) was derived using Newcastle-Ottawa and Philips checklists. Extracted study data were used to compare study method and resulting burden estimate, according to perspective. Monetary costs were converted into 2013 USD. Results: Out of 5187 unique retrievals, 214 studies were included. One hundred eighty-seven studies estimated patient health, 75 studies estimated payer/provider and 11 studies estimated economic burden. 64% of included studies were single centre. The majority of studies estimating patient or provider/payer burden used regression techniques. 48% of studies estimating mortality burden found a significant impact from resistance, excess healthcare system costs ranged from non-significance to $1 billion per year, whilst economic burden ranged from$21,832 per case to over $3 trillion in GDP loss. Median quality scores (interquartile range) for patient, payer/provider and economic burden studies were 0.67 (0.56-0.67), 0.56 (0.46-0.67) and 0.53 (0.44-0.60) respectively. Conclusions: This study highlights what methodological assumptions and biases can occur dependent on chosen outcome and perspective. Currently, there is considerable variability in burden estimates, which can lead in-turn to inaccurate intervention evaluations and poor policy/investment decisions. Future research should utilise the recommendations presented in this review. Trial registration: This systematic review is registered with PROSPERO (PROSPERO CRD42016037510)

High performance scientific computing on FPGA aboard the solar orbiter PHI instrument

SO/PHI (Solar Orbiter Polarimetric and Helioseismic Imager) is a filtergraph-based, solar magnetograph aimed at mapping the vector magnetic field and the line-of-sight (LOS) velocity of the solar photospheric plasma. It belongs to the scientific payload of the European Space Agency’s Solar Orbiter mission which will orbit the Sun at 0.28 astronomical units. The limited telemetry rate combined with the large amount of scientific information retrieved by the SO/PHI instrument demand a sophisticated on-board data reduction and scientific analysis through the study of the polarization state of a specific spectral line. The main aim is to perform the complicated algorithm needed to translate the polarization state of the light spectrum in terms of some specific solar parameters like the magnetic field vector and velocity. Technically speaking, the inference of the solar physical quantities through a spectropolarimetric study is based on the inversion of the Radiative Transfer Equation (RTE) and these tasks require the processing of a huge quantity of data in parallel. The RTE inverter is the core of the on-board scientific data analysis and, probably, one of the most innovative parts of the instrument. Due to the unavailability of qualified for space processors, DSPs, or GPGPUs that fulfil the stringent computational requirements with the limited room and power consumption allocated to the instrument, a specifically designed hardware device has been implemented in SO/PHI. This device is in charge of inverting the RTE aboard Solar Orbiter under narrow time and power constraints. The main aim of this thesis is to design, build, and test such a hardware device for SO/PHI. With that goal in mind, we propose two different high-performance computing architectures for carrying out the RTE inversion using FPGA devices embedded in the SO/PHI instrument. The first of these proposals is a distributed-memory MIMD multiprocessor architecture on a Virtex-5 FPGA that exploits the functional and data fine parallelism. It uses a pipelined execution based on a novel MIMD programming method. The processors within the architecture are simplified for saving resources but they are able of eliminating latency and exploiting the computing power that the FPGA provides. The synchronization and the communication network between processors have been simplified using this proposal. The second proposal consists of a SIMD multiprocessor architecture to reach high performance in floating point operations. This architecture on a Virtex-4 FPGA squeezes the FPGA resources in order to reach the time constraints. It is focused in exploiting the data parallelism using several processors working together and using different data streams. One of the most important contributions of this architecture is the ability of saving resources allocating operation cores in a shared operation block, which is accessed by every processor. Some details for extending the architecture to other problems are pointed out. A study of how the radiation induced errors affect each block of the architecture is detailed, and two fault mitigation strategies are described. We also present a novel software tool, which automates the entire design process and system settings from an input C-like pseudo-code. This tool uses advanced techniques of software pipelining and parallelizing scientific algorithms in multicore systems. A compiler within the tool makes it easier the use and programming of the proposed MIMD and SIMD architectures. As a byproduct of our development, a specific, novel Singular Value Decomposition (SVD) architecture within the SIMD architecture is proposed as well. SVD is one of the steps in the RTE inversion but can be of interest to other developments as is a fairly common mathematical tool. The achieved FPGA systems improve the time and power consumption of ground-based systems based on commercial CPUs. The final system is tested using synthetic and real data. It satisfies the scientific precision requirements and the engineering computing time and power consumption requirements.Tesis Univ. Granada. Programa Oficial de Doctorado en: Ciencias de la Computación y Tecnología informátic

Importancia de la heterogeneidad y cantidad de recursos en la riqueza y redundancia funcional de hormigas arbóreas

Submitted by Luciana Ferreira ([email protected]) on 2015-01-13T10:49:47Z No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Dissertação - Vidal Angel Cobos Carrascosa - 2014.pdf: 972757 bytes, checksum: 55272ad11bc2ab41f00a44966fab6cea (MD5)Approved for entry into archive by Luciana Ferreira ([email protected]) on 2015-01-13T10:52:40Z (GMT) No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Dissertação - Vidal Angel Cobos Carrascosa - 2014.pdf: 972757 bytes, checksum: 55272ad11bc2ab41f00a44966fab6cea (MD5)Made available in DSpace on 2015-01-13T10:52:40Z (GMT). No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Dissertação - Vidal Angel Cobos Carrascosa - 2014.pdf: 972757 bytes, checksum: 55272ad11bc2ab41f00a44966fab6cea (MD5) Previous issue date: 2014-06-03Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPqAbiotic and biotic factors determine the species diversity along environmental gradients, but are not yet determined how these factors modulate changes in richness and ecological (functional) characteristics of communities along environmental gradients related to heterogeneity and amount of resources. There are studies which support that resources heterogeneity and/or resources amount influence the variations of animal diversity, but often, these studies do not distinguish clearly between these effects. On the other hand, species and ecological characteristics that coexist along environmental gradients should be affected by competition, niche overlap and/or environmental filters that influence the richness and functional redundancy (FR) of communities, and a greater niches heterogeneity and amount should promote functional differentiation among species. Because of their importance in ecosystems, their high diversity and close evolutionary relationship with plants at the Neotropics; I chose the arboreal ants as an object of study to test: 1) There is an increase in arboreal ants richness linked to an increase in the heterogeneity and amount of food and structural niches 2) The arboreal ants FR decreases with increasing heterogeneity and decreases with quantity of niches.Samples were taken in 42 plots of 100 m2 forming a heterogeneity and amount of resources gradient at Emas National Park, Mineiros, GO. After sampling and identification of organisms - plants and ants – I take nine functional characteristics measures for ants and a team of experts measured six variables of the community of woody plants. From the plots sampling, I got the ant richness and FR, and described biotic parameters related to heterogeneity and quantity of resources from the characteristics of the vegetation. Using the technique of PCA, I calculated the principal axes of environmental variables for the heterogeneity and amount of resources. These axes were related to arboreal ant richness and FR employing the Akaike criterion. Once the effect of heterogeneity and amount of resources was separated, the richness of ants was explained by the resources amount and the FR by the resources heterogeneity and amount. A greater amount of food and structural niches may encourage the coexistence of a large number of ant species possibly by a decreasing competitive exclusion and an improved distribution of resources among species. An increase in habitat heterogeneity and a decrease in food resources quantity may enable ant species to distinguished functionally, this may cause a decrease in FR; little diversification of structural resources and higheramount of food may promote that environment and competitive exclusion diminish the variety of functional features present in the community.Os fatores abióticos e bióticos determinam a diversidade de espécies ao longo de gradientes ambientais, porém ainda não está determinado como esses fatores modulam as mudanças da riqueza e características ecológicas (funcionais) das comunidades ao longo de gradientes de heterogeneidade e quantidade de recursos. Existem estudos que apoiam que a heterogeneidade e/ou quantidade recursos influenciam as variações da diversidade animal, mas com frequência, estes estudos não separam com nitidez estes efeitos. Por outro lado, as espécies e características ecológicas que coexistem ao longo de gradientes ambientais devem ser afetadas pela competição, sobreposição de nichos e/ou filtros ambientais que influenciam a riqueza e redundância funcional (RF) das comunidades, e uma maior heterogeneidade e menor quantidadede nichos deve promover a diferenciação funcional das espécies. Devido sua importância nos ecossistemas, sua alta diversidade e a estreita relação evolutiva com as plantas nos Neotrópicos, escolhi as formigas arborícolas como objeto de estudo para testar se: 1) Existe um aumento da riqueza de formigas arborícolas ligado a um aumento na heterogeneidade e quantidade de nichos alimentares e estruturais 2) A RF das formigas arborícolas diminui conforme aumenta a heterogeneidade e diminui a quantidade nichos.Amostrei 42 parcelas de 100 m2que formam um gradiente de heterogeneidade e quantidade de recursosno Parque Nacional das Emas, Mineiros, GO. Após a amostragem e identificação dos organismos - plantas e formigas -, mensureinove características funcionais para as formigas e uma equipe de especialistas mensurou seis variáveis da comunidade das plantas lenhosas. A partir da amostragem das parcelas obtive a riqueza e RF das formigas, e descrevi parâmetros bióticos de heterogeneidade e quantidade de recursos a partir das características da vegetação. Usando a técnica da PCA, calculei os eixos principais das variáveis ambientais para a heterogeneidade e quantidade de recursos. Estes eixos foram relacionados com a riqueza e RF das formigasarborícolas mediante o critério Akaike. Uma vez separado o efeito da heterogeneidade e quantidade de recursos, a riqueza das formigas foi explicada pela quantidade de recursos e a RF pela heterogeneidade e quantidade de recursos. Uma maior quantidade de nichos alimentares e estruturais deve fomentar a coexistência de um maior número de espécies de formigas possivelmente por uma diminuição da exclusão competitiva e uma melhor divisão dos recursos entre as espécies. Um aumento na heterogeneidade do habitat e diminuição da quantidade de recurso alimentar deve permitirque as espécies de formigas se diferenciem funcionalmente, isto pode provocaruma diminuição da RF; pouca diversificação dos recursos estruturais e maior quantidade de alimento pode fomentar que o ambiente e a exclusão competitiva diminuam a variedade de características funcionais presentes na comunidade

Evaluación de la efectividad de un programa de higiene de manos sobre el absentismo escolar debido a infecciones respiratorias de vías altas y gastroenteritis en el distrito sanitario de atención primaria Almería y área de gestión sanitaria norte Almería

Las infecciones respiratorias de vías altas (IRVA) y gastrointestinales (GEA) tienen un gran impacto entre los alumnos y requiere visitas médicas, hospitalizaciones, medicación, además de ser una causa relevante de absentismo laboral debido a su alta incidencia y fácil transmisión, sobre todo en las escuelas. El lavado de manos es la medida más eficaz para evitar su transmisión. Objetivos: Evaluar la efectividad de un programa de higiene de manos sobre la disminución de IRVA y las GEA así como su relación con el absentismo escolar. Métodos: Se realizó un ensayo clínico controlado, abierto y aleatorizado en colegios públicos de localidades pertenecientes a la provincia de Almería en 1,640 alumnos escolarizados con edades comprendidas entre los 4-12 años. Los colegios fueron aleatorizados por cluster en grupo control (GC) y experimental (GE) usando como unidad de aleatorización los colegios de cada pueblo. Se incluyeron aquellos escolares con absentismo secundario a IRVA o GEA, sin enfermedades crónicas y cuyos padres firmaron el consentimiento informado. Resultados: se registraron 1.271 casos de absentismo secundario a IRVA y 446 debido a GEA. Los escolares del GE presentaron 0,72 (IC95%: 0,64-0,79) episodios de absentismo/niño/año escolar y en el GC 1,17 (IC95%: 1,8-1,25) episodios/niño/año escolar, con un NNT=2,21 (IC95%: 2,13-2,31) debido a IRVA. Los escolares del GE tenían un 36% de menos riesgo de absentismo por GEA (IRR: 0,64, IC95%: 0,52-0,78) y una disminución de episodios de absentismo de 0,13 episodios/niño/año académico (0,27 en GE y 0,40 en el GC, p<0,001). Los alumnos perdieron 2.734 días de clase debido a IRVA y 725 días de clase debido a GEA. Conclusiones: La aplicación correcta de un programa de higiene de manos asociado al gel hidroalcohólico es una medida eficaz para reducir tanto los días de absentismo como el número de episodios de absentismo escolar causados por IRVA y GEA.Tesis Univ. Granada. Departamento de Pediatrí