Scaling In-Memory databases on multicores

Current computer systems have evolved from featuring only a single processing unit and limited RAM, in the order of kilobytes or few megabytes, to include several multicore processors, o↵ering in the order of several tens of concurrent execution contexts, and have main memory in the order of several tens to hundreds of gigabytes. This allows to keep all data of many applications in the main memory, leading to the development of inmemory databases. Compared to disk-backed databases, in-memory databases (IMDBs) are expected to provide better performance by incurring in less I/O overhead. In this dissertation, we present a scalability study of two general purpose IMDBs on multicore systems. The results show that current general purpose IMDBs do not scale on multicores, due to contention among threads running concurrent transactions. In this work, we explore di↵erent direction to overcome the scalability issues of IMDBs in multicores, while enforcing strong isolation semantics. First, we present a solution that requires no modification to either database systems or to the applications, called MacroDB. MacroDB replicates the database among several engines, using a master-slave replication scheme, where update transactions execute on the master, while read-only transactions execute on slaves. This reduces contention, allowing MacroDB to o↵er scalable performance under read-only workloads, while updateintensive workloads su↵er from performance loss, when compared to the standalone engine. Second, we delve into the database engine and identify the concurrency control mechanism used by the storage sub-component as a scalability bottleneck. We then propose a new locking scheme that allows the removal of such mechanisms from the storage sub-component. This modification o↵ers performance improvement under all workloads, when compared to the standalone engine, while scalability is limited to read-only workloads. Next we addressed the scalability limitations for update-intensive workloads, and propose the reduction of locking granularity from the table level to the attribute level. This further improved performance for intensive and moderate update workloads, at a slight cost for read-only workloads. Scalability is limited to intensive-read and read-only workloads. Finally, we investigate the impact applications have on the performance of database systems, by studying how operation order inside transactions influences the database performance. We then propose a Read before Write (RbW) interaction pattern, under which transaction perform all read operations before executing write operations. The RbW pattern allowed TPC-C to achieve scalable performance on our modified engine for all workloads. Additionally, the RbW pattern allowed our modified engine to achieve scalable performance on multicores, almost up to the total number of cores, while enforcing strong isolation

FEW phone file system

Trabalho apresentado no âmbito do Mestrado em Engenharia Informática, como requisito parcial para obtenção do grau de Mestre em Engenharia InformáticaThe evolution of mobile phones has made these devices more than just simple mobile communication devices. Current mobile phones include such features as built-in digital cameras, the ability to play and record multimedia contents and also the possibility of playing games. Most of these devices have support for Java developed applications, as well as multiple wireless technologies (e.g. GSM/GPRS, UMTS, Bluetooth, and Wi-Fi). All these features have been made possible due to technological evolution that led to the improvement of computational power, storage capacity, and communication capabilities of these devices. This thesis presents a distributed data management system, based on optimistic replication,named FEW Phone File System. This system takes advantage of the storage capacity and wireless communication capabilities of current mobile phones, by allowing users to carry their personal data “in” their mobile phones, and to access it in any workstation, as if they were files in the local file system. The FEW Phone File System is based on a hybrid architecture that merges the client/server model with peer-to-peer replication, that relies on periodic reconciliation to maintain consistency between replicas. The system’s server side runs on the mobile phone, and the client on a workstation. The communication between the client and the server can be supported by one of multiple network technologies, allowing the FEW Phone File System to dynamically adapt to the available network connectivity. The presented system addresses the mobile phone’s storage and power limitations by allowing multimedia contents to be adapted to the device’s specifications, thus reducing the volume of data transferred to the mobile phone, allowing for more user’s data to be stored. The FEW Phone File System also integrates mechanisms that maintain information about the existence of other copies of the stored files (e.g. WWW), avoiding the transfer of those files from the mobile device whenever accessing those copies is advantageous. Due to the increasing number of on-line storage resources (e.g. CVS/SVN, Picasa), this approach allows for those resources to be used by the FEW Phone File System to obtain the stored copies of the user’s files

Conhecimento, Responsabilidade, Visão e Futuro: bases programáticas da Lista F para o 3.º mandato do Conselho Geral da Universidade de Évora 2016-20

O presente documento inclui o programa de acção e os elementos de campanha da Lista F, candidata ao 3.º mandato do Conselho Geral da Universidade de Évora (2016-20)

Aspectos relacionados com a positividade para a esquistossomose: estudo transversal em área de baixa prevalência do estado de Alagoas, 2020

Objective: To analyze aspects related to positivity for schistosomiasis in an area of ​​low prevalence in Brazil. Methods: Cross-sectional study, carried out in the first half of 2020, where proportion of positivity was analyzed according to the number of Kato-Katz slides, the diagnostic performance of the test and the creation of a positivity estimation factor from the data of the Information from the Schistosomiasis Surveillance and Control Program (SISPCE). Results: 2,088 slides from 348 individuals were analyzed, with proportion of positivity of 11.8%, 26.7% and 31.0% for 1, 4 and 6 slides analyzed, respectively. There was excellent agreement (Kappa = 0.91) between the reading of 4 and 6 slides. An underreporting of 2.1 times was estimated in the SISPCE data. Conclusion: Increasing the number of blades increased the positivity of Kato-Katz, which can contribute to maximize the control of the disease as a public health problem.Objetivo: Analisar aspectos relacionados com a positividade para esquistossomose em área de baixa prevalência, no Brasil. Métodos: Estudo transversal, realizado no primeiro semestre de 2020, quando foram analisadas a proporção de positividade, em função do número de lâminas de Kato-Katz, o desempenho diagnóstico do teste e a estimação da positividade a partir dos dados do Sistema de Informação do Programa de Vigilância e Controle da Esquistossomose (SISPCE). Resultados: Foram analisadas 2.088 lâminas de 348 indivíduos, sendo a proporção de positividade de 11,8%, 26,7% e 31,0% para 1, 4 e 6 lâminas analisadas, respectivamente. Houve concordância excelente (índice Kappa = 0,91) na comparação entre as leituras de 4 e 6 lâminas. Foi estimada subnotificação de 2,1 vezes nos dados do SISPCE. Conclusão: Ampliar o número de lâminas aumentou a positividade do Kato-Katz, o que pode contribuir para maximizar o controle da doença enquanto problema de Saúde Pública

SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARSCoV-2 introductions and early dissemination in Portugal. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.We gratefully acknowledge to Sara Hill and Nuno Faria (University of Oxford) and Joshua Quick and Nick Loman (University of Birmingham) for kindly providing us with the initial sets of Artic Network primers for NGS; Rafael Mamede (MRamirez team, IMM, Lisbon) for developing and sharing a bioinformatics script for sequence curation (https://github.com/rfm-targa/BioinfUtils); Philippe Lemey (KU Leuven) for providing guidance on the implementation of the phylodynamic models; Joshua L. Cherry (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health) for providing guidance with the subsampling strategies; and all authors, originating and submitting laboratories who have contributed genome data on GISAID (https://www.gisaid.org/) on which part of this research is based. The opinions expressed in this article are those of the authors and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government. This study is co-funded by Fundação para a Ciência e Tecnologia and Agência de Investigação Clínica e Inovação Biomédica (234_596874175) on behalf of the Research 4 COVID-19 call. Some infrastructural resources used in this study come from the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).info:eu-repo/semantics/publishedVersio

New rhizobia strains isolated from the Amazon region fix atmospheric nitrogen in symbiosis with cowpea and increase its yield

ABSTRACT Studies in the Amazon indicate a wide diversity of rhizobia with the ability for biological nitrogen fixation (BNF), which could expand the number of strains approved for cowpea. Thus, the aim of this field study was to evaluate the agronomic performance in cowpea of the several strains isolated from the soils of the Brazilian states Acre and Rondônia, and to compare them withstrains approved by the Ministry of Agriculture (MAPA) and withnon-inoculated controls (without and with mineral nitrogen fertilizer). The inoculants performed well. Though less effective than the other strains, the UFLA 03-36 strain also was prominent with respect to grain yield. Because of the positive response of the UFLA 03-129 strain, which led to yield increases greater than the obtained from the control without inoculation plus mineral-N, it can be recommended as an inoculum for cowpea. Further investigations should be carried out to obtain MAPA’s approval for their use. Other experiments involving this strain and several cultivars are being carried out on other types of soil and environmental conditions of the state of Minas Gerais

5) Comportamento de clones primários de seringueira (Hevea spp), da série Pé-franco-Açailândia (PFA), em Belém-Pa, e estudo da viabilidade da seleção precoce.

Ministério da Educação, Faculdade de Ciências Agrárias do Pará, Serviço de Documentação e Informação e Superintendência do Desenvolvimento da Amazônia - SUDAM.1) Foi avaliado o desempenho de três linhagens formadas na Faculdade de Ciências Agrárias do Pará a partir das raças Red Cornish e New Hampshire. Foram utilizadas 210 aves/Cobb e Shaver Starbor (marcas), FCAP-1, FCAP-2 e FCAP-3 (linhagens) e Recí Cornish e New Hampshire (raças), sendo 30 de cada, distribuídas em três blocos casualizados. Os resultados obtidos revelaram que o consumo de ração esteve compatível com o desempenho apresentado pelas aves, isto é, quando melhor o seu desempenho maior a quantidade de ração consumida. Também o ganho de peso médio diário acompanhou o grau de melhoramento das aves envolvidas na pesquisa, influindo positivamente no peso final alcançado aos 56 dias. A conversão alimentar tendeu a corresponder ao grau de melhoramento das aves, tendo no entanto as linhagens FCAP-1, FCAP-2 e FCAP-3 se revelado estatisticamente iguais às marcas comerciais, tendendo, no caso da FCAP-3 a suplantar a marca Shaver Starbor. Apesar de terem revelado resultados que não as credenciem ainda a competir no mercado em igualdade de condições, as linhagens obtidas na Faculdade de Ciências Agrárias do Pará, de imediato poderão ser aproveitadas no meio rural, especialmente para os pequenos avicultores em função dos resultados nitidamente superiores às raças matrizes, evidenciados no presente trabalho.2) As informações bibliográficas sobre o posicionamento e a morfologia das glândulas sexuais acessórias do bovino (Bos indicus Lin.) são restritas e contraditórias, principalmente no que se refere ao sistema de desembocadura dos duetos excretores e aos conhecimentos de alguns detalhes estruturais desses órgãos. A investigação anatômica de exemplares da espécie permitiu observar aspectos morfológicos importantes, relacionados com a presença e a maneira de drenagem do dueto ejaculador, com a disposição do complexo prostático e das glândulas bulbo-uretrais, com seus mecanismos excretores e com a existência de elementos histológicos, antes não mencionados.3) O experimento foi conduzido em Belém-PA, no período de abril a julho de 1984. Avaliou-se, para duas formas de aplicação da calda enraizante (em toda extensão da pivotante e apenas no terço inferior), a produção e distribuição de raízes laterais em tocos enxertados de seringueira, plantados em sacos plásticos. Utilizou-se os fitohormônios alfa-naftaleno acetato de sódio (ANA) e o ácido indolbutírico (AIB). O delineamento experimental foi o bloco casualizado com 3 repetições, num esquema fatorial 2 x 2 x 3, mais um tratamento adicional, a testemunha, sem aplicação da calda. Os fatores foram: dois tipos de fitohormônios; duas formas de aplicação da calda e três posições na pivotante de produção de raízes laterais (terço inferior, médio e superior). Os resultados do peso-seco total de raízes laterais. 75 dias após a aplicação da calda, apontaram a superioridade dos tratamentos em que foram utilizados os fitohormônios. Houve uma tendência de distribuição mais uniforme das raízes laterais ao longo da pivotante, quando se aplicou a calda em toda a extensão da raiz.4) Em maio de 1984, na região doMojü-PA, efetuou-se um levantamento com o objetivo de identificar as espécies de vaquinhas que estavam atacando viveiro de seringueira e seringais recém implantados. Foram determinados quatro espécies: Diabrotica speciosa, Diabrotica atromaculata, Diabrotica sinuata e Cerotoma arcuata, sendo a incidência destas três últimas espécies registrada pela primeira vez na cultura da seringueira. A espécie de maior ocorrência foi D. speciosa, apresentando índices que variaram de 72% a 96,6% do total de insetos capturados.5) O trabalho objetivou estudar o desempenho de 16 clones primários de seringueira nas condições ecológicas de Belém-PA, e verificar a confiabilidade de efetuar a seleção do material nos dois primeiros anos de idade. As matrizes dos clones primários foram selecionados em Açailãndia-MA e o ensaio clonal foi instalado em 1982 no campo experimental da FCAP, em Belém-PA. O elineamento experimental, em blocos casualizados com 18 tratamentos e três repetições, envolveu, além dos 16 clones primários, as testemunhas IAN 717 e IAN 3087. A produção de borracha foi avaliada pelo miniteste de produção (MTP) e Hamaker-Morris-Mann modificado (HMM-m), no primeiro e segundo ano, respectivamente. Os clones PFA 622, 715, 617 e 599 destacaram-se como os mais produtivos no primeiro ano, enquanto IAN 717, PFA 768, IAN 3087 e PFA 617 tiveram o melhor desempenho com dois anos de idade. Foram constatadas grandes alterações no comportamento dos clones nos dois anos de ensaio. O estudo de correlação entre produção nas fases jovem (clones) e adulta (matrizes) indicou que a seleção não será eficiente caso praticada naquela fase, indicando que será necessário repetir a avaliação dos clones em anos posteriores.1) Was appraised the performance of three lineages of chicken goíten from the races Red Cornish and New Hampshire. 210 fowls Cobb and Shaver Starbor^ (marks), FCAP-1, FCAP-2 and FCAP-3 (lineages) and Red Cornish and New Hampshire (races) were used, 30 of lach one, distributed in three randomired blocks. The results showed that the consumption of ration was compatible with the performance of the fowls, that is, the better their performance, the greater their consumptionof ration. The gain of médium weight by day followed the grade of improvement of the fowls involved withe the research, increasing the final weight golten in 56 days. The alimentary conversion tended to correspond to the grade of improvement of the fowls nevertheless the lineages FCAP-1, FCAP-2 and FCAP-3 have shwed to be statistically egral to the commonly sold commercial marks tendind to supplant the Sheiver Starbor, in the case of FCAP-3. Although they have showed results that still do not allow them to compete at the same levei in the market, the lineages gotten at Faculdade de Ciências Agrárias do Pará can be inmediateby available in the country, specially for the small aviarists, in accordance with the results clearly better tham the monld races, evidenced at the present research.2) The anatomic investigation of 50 male genital-urinary systems of Zebu (Bos indicus Lin) from Amazon region, killed in slaughter-houses near Belem, Para State, showed some important morfological aspects as; the presence of ejaculator duct formed by the confluence of the deferente duct with the duct of the vesicular gland; the isolation of the lobulos of the prostate's body and this one with the disseminated prostate as well as details of the excretor system of this complex; the presence of structural elements that were never mentioned in the bibliography, and also presented other caracteristics of position and anatomic relations of the constituents elements.3) The trial was conduced in Belém-PA, from April to July, 1984. The parameters analized for two methods of application of the phytormones (on ali extension of the taproot and on the inferior third part of it) were the production and distribution of new lateral roots on budded stumps planted in polybabs. The phytormones used were the sodium acetate alfa naphtalene (ANA) and the indolebutyric acid (IBA), in concentration of 2000 ppm. The experimental design was in causalized plots with three repetitions with fatorial 2 x 2 x 3 plus the control treatment, without application. The factors were two types of phytormones, two methods of application and three positions of new lateral roots production (one, two and three thirds). The results of total dry weght of lateral roots 75 days after application showed that the best treatments were those with phytormones. There was best uniformity on distribution of lateral roots on the tap root when the treatment was applied in ali extension of the root.4) A series of samples were taken at Mojú, Pará on May 1984 to determine the species of chrysomelidae that were attaking seedlings of rubber treee and hevea budded stumps. Four species were identified: Diabrotica speciosa, Diabrotica athromaculata, Diabrotica sinuata e Cerotoma arcuata. The last three species are mentioned for the first time on rubber tree. D. speciosa was the specie that presented the greatest occurence with indexes ranging from 72% to 96,6% of the specimens colleted for sample.5) The objective of this research was to study the performance of 16 rubber primary clones under the ecological conditions of Belém, State of Pará, Brazil. In addition, it was observed the confidence of the selection practiced among clones at age two years old. The mother trees that originated the clones were pre-selected in Açailândia (Maranhão State) and the experiment was established in 1982 in the experimental field at Belem, under FCAP agreement. A randomized complete block design with treatments and 3 replications was used. The clones IAN 717 and IAN 3087 were used as checks. Data were collected in plants at first and second years of age. Rubber yield was evaluated by the Mendes' early test (MTP) and modifíed HAMAKER-MORRISMANN early test (HMN-m) in the first and second year, respectively. The clones PFA 622, PFA 715, PFA 617 and PFA 599, showed to be most productive in the first year, whereas IAN 717, PFA 768 IAN 3087 and PFA 617, had the best performance in the second year. It was observed large variations in the clones in two years of study. Correlation studies between clones and mother trees for yield, revealed that selection at early stages was meffective, suggesting that evaluation should be performed m latter stages o tree development