A relational algebra approach to ETL modeling

The MAP-i Doctoral Programme in Informatics, of the Universities of Minho, Aveiro and Porto

Perchlorate and chlorate reduction by the Crenarchaeon Aeropyrum pernix and two thermophilic Firmicutes

This study reports the ability of one hyperthermophile and two thermophilic microorganisms to grow anaerobically by the reduction of chlorate and perchlorate. Physiological, genomic and proteome analyses suggest that the Crenarchaeon Aeropyrum pernix reduces perchlorate with a periplasmic enzyme related to nitrate reductases, but that it lacks a functional chlorite-disproportionating enzyme (Cld) to complete the pathway. A. pernix, previously described as a strictly aerobic microorganism, seems to rely on the chemical reactivity of reduced sulfur compounds with chlorite, a mechanism previously reported for perchlorate-reducing Archaeoglobus fulgidus. The chemical oxidation of thiosulfate (in excessive amounts present in the medium) and the reduction of chlorite result in the release of sulfate and chloride, which are the products of a biotic-abiotic perchlorate reduction pathway in A. pernix. The apparent absence of Cld in two other perchlorate-reducing microorganisms, Carboxydothermus hydrogenoformans and Moorella glycerini strain NMP, and their dependence on sulfide for perchlorate reduction is consistent with observations made on A. fulgidus. Our findings suggest that microbial perchlorate reduction at high temperature differs notably from the physiology of perchlorate- and chlorate-reducing mesophiles and that it is characterized by the lack of a chlorite dismutase and is enabled by a combination of biotic and abiotic reactions.

Reconstructing transcriptional regulatory networks using data integration and text mining

Transcriptional Regulatory Networks (TRNs) are powerful tool for representing several interactions that occur within a cell. Recent studies have provided information to help researchers in the tasks of building and understanding these networks. One of the major sources of information to build TRNs is biomedical literature. However, due to the rapidly increasing number of scientific papers, it is quite difficult to analyse the large amount of papers that have been published about this subject. This fact has heightened the importance of Biomedical Text Mining approaches in this task. Also, owing to the lack of adequate standards, as the number of databases increases, several inconsistencies concerning gene and protein names and identifiers are common. In this work, we developed an integrated approach for the reconstruction of TRNs that retrieve the relevant information from important biological databases and insert it into a unique repository, named KREN. Also, we applied text mining techniques over this integrated repository to build TRNs. However, was necessary to create a dictionary of names and synonyms associated with these entities and also develop an approach that retrieves all the abstracts from the related scientific papers stored on PubMed, in order to create a corpora of data about genes. Furthermore, these tasks were integrated into @Note, a software system that allows to use some methods from the Biomedical Text Mining field, including an algorithms for Named Entity Recognition (NER), extraction of all relevant terms from publication abstracts, extraction relationships between biological entities (genes, proteins and transcription factors). And finally, extended this tool to allow the reconstruction Transcriptional Regulatory Networks through using scientific literature.

Roteiro metodológico para o estudo dos moinhos e aproveitamentos hidráulicos no concelho de Lousada

A Agência Portuguesa do Ambiente é possuidora de um valioso arquivo, resultante da atividade centenária desenvolvida pelos diferentes organismos com tutela sobre a gestão da água e o planeamento dos recursos hídricos, que importa conhecer e divulgar. O Arquivo Histórico dos Serviços Hidráulicos é um dos mais ricos acervos locais do País, reunindo um conjunto de milhares de documentos, que vão do século XIX à atualidade, constituindo um repositório documental com características ímpares e um testemunho da identidade, memória e história dos Serviços Hidráulicos. Os processos arquivados contam casos de estudo que percorrem os usos das águas públicas para diferentes fins e as modalidades da sua utilização, das quais queremos destacar os aproveitamentos hidráulicos e a laboração de moinhos. Com este artigo, pretendemos apresentar um roteiro metodológico para o estudo das formas de organização dos processos existentes no arquivo sobre os moinhos e aproveitamentos hidráulicos, no concelho de Lousada, no que respeita aos documentos e peças anexas, bem como aos modelos administrativos subjacentes.

Modelos de simulação de processos por junção de componentes

Dissertação de mestrado integrado em Engenharia e Gestão de Sistemas de Informação

Concise server-wide causality management for eventually consistent data stores

Large scale distributed data stores rely on optimistic replication to scale and remain highly available in the face of net work partitions. Managing data without coordination results in eventually consistent data stores that allow for concurrent data updates. These systems often use anti-entropy mechanisms (like Merkle Trees) to detect and repair divergent data versions across nodes. However, in practice hash-based data structures are too expensive for large amounts of data and create too many false conflicts. Another aspect of eventual consistency is detecting write conflicts. Logical clocks are often used to track data causality, necessary to detect causally concurrent writes on the same key. However, there is a nonnegligible metadata overhead per key, which also keeps growing with time, proportional with the node churn rate. Another challenge is deleting keys while respecting causality: while the values can be deleted, perkey metadata cannot be permanently removed without coordination. Weintroduceanewcausalitymanagementframeworkforeventuallyconsistentdatastores,thatleveragesnodelogicalclocks(BitmappedVersion Vectors) and a new key logical clock (Dotted Causal Container) to provides advantages on multiple fronts: 1) a new efficient and lightweight anti-entropy mechanism; 2) greatly reduced per-key causality metadata size; 3) accurate key deletes without permanent metadata.

A 3D computer assisted Orthopedic Surgery Planning approach based on planar radiography

Dissertação de mestrado integrado em Engenharia Biomédica (área de especialização em Informática Médica)

As mulheres com VIH-SIDA no discurso jornalístico: um estudo feminista sobre a activação ideológica dos estereótipos

Dissertação de mestrado em Ciências da Comunicação (área de especialização em Informação e Jornalismo)

A imprensa desportiva do papel ao online: o exemplo do jornal Record

Dissertação de mestrado em Ciências da Comunicação (área de especialização em Informação e Jornalismo)

Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data

The Supplementary Material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fmicb. 2016.00275

Pervasive adaptive data acquisition gateway for critical healthcare

The data acquisition process in real-time is fundamental to provide appropriate services and improve health professionals decision. In this paper a pervasive adaptive data acquisition architecture of medical devices (e.g. vital signs, ventilators and sensors) is presented. The architecture was deployed in a real context in an Intensive Care Unit. It is providing clinical data in real-time to the INTCare system. The gateway is composed by several agents able to collect a set of patients’ variables (vital signs, ventilation) across the network. The paper shows as example the ventilation acquisition process. The clients are installed in a machine near the patient bed. Then they are connected to the ventilators and the data monitored is sent to a multithreading server which using Health Level Seven protocols records the data in the database. The agents associated to gateway are able to collect, analyse, interpret and store the data in the repository. This gateway is composed by a fault tolerant system that ensures a data store in the database even if the agents are disconnected. The gateway is pervasive, universal, and interoperable and it is able to adapt to any service using streaming data.

Repositorios colectivos de e-información

Desde 1999, el Centre de Supercomputació de Catalunya (CESCA) promociona actividades para poner en acceso abierto contenido en internet, contribuyendo al avance de la e-Ciencia en nuestro país. Junto con el Consorci de Biblioteques Universitàries de Catalunya (CBUC) se han creado tres repositorios: Tesis Doctorales en Red (TDR), Dipòsit de la Recerca de Catalunya (RECERCAT) y Revistes Catalanes amb Accés Obert (RACO). En septiembre de 2006, la Biblioteca Nacional de Catalunya[6] ha puesto en marcha otro ambicioso repositorio en colaboración con el CESCA, Patrimoni Digital de Catalunya (PADICAT).

Catalan Policies and Experiences on Cooperative Repositories

The Centre de Supercomputació de Catalunya (CESCA) together with the Consorci de Biblioteques Universitàries de Catalunya (CBUC) started in 1999 a cooperative repository, named TDR, to file in digital format the full-text of the read thesis at the universities of our country to spread them worldwide in open access preserving the intellectual copyright of the authors. This became operational in 2001 and today it is a service fully consolidated not only among the Catalan universities, but also used by other Spanish universities. Since then, there are four additional cooperative repositories which have been created: RECERCAT, for research papers; RACO, for scientific, cultural and erudite Catalan magazines; PADICAT, for archiving Catalan web sites; and MDC, for Catalan digital collections of pictures, maps, posters, old magazines... These five repositories have some common characteristics: they are open access, that is, they are accessible on the internet for free; they mostly comply with the Open Archive Initiative interoperability protocol for facilitating the efficient dissemination of content; and they have been built in a cooperative manner so that it is easy to adopt common procedures and to share the repository developing and managing costs, it permits more visibility of the indexed documents throughout the search engines, and a better provision for long-term preservation can be made. In this paper we present the common policy established for the Catalan cooperative repositories, we describe the five of them briefly, and we comment on the results obtained of our 6-year experience since the first one became operational.

Estudi i implementació d'un arxivat de dades per a les plataformes SAP Enterprise 4.7 x 200 d'una gran empresa

En aquest projecte s'ha implementat un sistema de data archiving amb SAP-IXOS per a una empresa després que aquesta demanés consell a la nostra consultora per reduir espai en la base de dades, ja que només els quedava lliure un 14% de l'ocupació total, i d'aquesta forma millorar el rendiment del sistema. S'ha realitzat un estudi de la base de dades, ocupació en Mb i creixement mensual de les dades en les taules. S'han parametritzat objectes d'arxivat, creat i definits repositoris de contingut, fitxers lògics i s'han programat reports addicionals per arxivar les dades correctament. El resultat ha estat reduir la base de dades en un 22% sent posible l'entrada de noves dades obtenint una resposta més àgil del sistema.

Una infraestructura de metadades bibliogràfiques pel segle XXI

Aquest article tracta l'actual infraestructura bibliogràfica de les biblioteques que va ser creada en els inicis dels ordinadors – abans de la Web, XML, i de la varietat d'altres avenços tecnològics que en l'actualitat ofereixen noves oportunitats. Per una banda, s'identifiquen els requisits generals d'una infraestructura de metadades moderna per a les biblioteques incloent qualitats com: versatilitat, extensibilitat, granularitat i accessibilitat. Per l'altra banda, es proposa un nou tipus d'infraestructura de metadades que mostra, com a mínim, alguna d'aquestes qualitats. S'han identificat alguns temes clau que caldrà superar per tal d'implementar un canvi d'aquesta magnitud.