BioRePortAP, an electronic clinical record coupled with a database : an example of its use in a single

Aims: To evaluate the efficacy and safety of the treatment of psoriatic arthritis (PsA) patients with tumor necrosis factor (TNF) antagonists in the Rheumatology Department of Hospital de Santa Maria using the BioRePortAP. Methods: The Portuguese Society of Rheumatology (SPR) developed an electronic medical chart coupled with a database for the follow up of PsA patients, the BioRePortAP, which was launched in May 2009. This evaluation was based on all the PsA patients that were on active treatment with TNF antagonists in September 2009 and were registered in the BioRePortAP. All the previous data on these patients were introduced in BioRePortAP using the prospective paper based follow up protocol that this Department was using since 1999. Only patients with more than 9 months of treatment were analyzed. Results: Forty-two patients with PsA, actively treated with anti-TNF agents in September 2009, for at least 9 months, were analyzed in BioRePortAP. Twenty-three patients were male (55%) and nineteen were female (45%). The average age of these patients was 49.8±10.9 years old, the average disease duration was of 10.7±5.6 years and the mean duration of biological therapy was of 37.8±27.8 months. For the 81% of patients with peripheral joint disease there was a mean reduction of more than 80% in the swollen and tender joint counts, and almost 50% in the health assessment questionnaire (HAQ) value. In the 19% of the patients with axial involvement the reduction of BASDAI and BASFI was not statistically significative. On top of that, PASI score suffered a reduction of 64%. Fourteen patients (33.3%) had to switch their TNF antagonist treatment. 58.8% of the switches were due to adverse effects and 41.2% due to therapy failure. Regarding the 56 adverse reactions registered, only one was a severe reaction. The remaining adverse reactions were not severe and 67% of them were due to infections. Discussion: The results of this first report of the use of the BioRePortAP in clinical practice confirm the efficacy and safety of TNF antagonist treatment in PsA. The results shown here elucidate the potential applications of BioRePortAP as a tool for efficacy and safety assessment of PsA patients treated with biotechnological drugs

The portuguese self-administered computerised 24-hour dietary recall

Copyright © 2015 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.Rationale: Measuring the diets of school-aged children is a challenging process. Technology offers the opportunity to automate more accurate methods of dietary assessment, making them less expensive, easier to use and an alternative to nutritionist interviews.info:eu-repo/semantics/publishedVersio

Tuning pipelined scientific data analyses for efficient multicore execution

Scientific data analyses often apply a pipelined sequence of computational tasks to independent datasets. Each task in the pipeline captures and processes a dataset element, may be dependent on other tasks in the pipeline, may have a different computational complexity and may be filtered out from progressing in the pipeline. The goal of this work is to develop an efficient scheduler that automatically (i) manages a parallel data reading and an adequate data structure creation, (ii) adaptively defines the most efficient order of pipeline execution of the tasks, considering their inter-dependence and both the filtering out rate and the computational weight, and (iii) manages the parallel execution of the computational tasks in a multicore system, applied to the same or to different dataset elements. A real case study data analysis application from High Energy Physics (HEP) was used to validate the efficiency of this scheduler. Preliminary results show an impressive performance improvement of the pipeline tuning when compared to the original sequential HEP code (up to a 35x speedup in a dual 12-core system), and also show significant performance speedups over conventional parallelization approaches of this case study application (up to 10x faster in the same system).Project Search-ON2 (NORTE-07-0162- FEDER-000086), co-funded by the North Portugal Regional Operational Programme (ON.2 - O Novo Norte), under the National Strategic Reference Framework, through the European Regional Development Fund

HEP-Frame: A software engineered framework to aid the development and efficient multicore execution of scientific code

This communication presents an evolutionary soft- ware prototype of a user-centered Highly Efficient Pipelined Framework, HEP-Frame, to aid the development of sustainable parallel scientific code with a flexible pipeline structure. HEP- Frame is the result of a tight collaboration between computational scientists and software engineers: it aims to improve scientists coding productivity, ensuring an efficient parallel execution on a wide set of multicore systems, with both HPC and HTC techniques. Current prototype complies with the requirements of an actual scientific code, includes desirable sustainability features and supports at compile time additional plugin interfaces for other scientific fields. The porting and development productivity was assessed and preliminary efficiency results are promising.This work was supported by FCT (Fundação para a Ciência e Tecnologia) within Project Scope (UID/CEC/00319/2013), by LIP (Laboratório de Instrumentação e Física Experimental de Partículas) and by Project Search-ON2 (NORTE-07-0162- FEDER-000086), co-funded by the North Portugal Regional Operational Programme (ON.2 - O Novo Norte), under the National Strategic Reference Framework, through the European Regional Development Fund

Tangerines cultivated on Madeira Island: a high throughput natural source of bioactive compounds

Tangerines (Citrus reticulata) are popular fruits worldwide, being rich in many bioactive metabolites. The setubalense variety cultivated on Madeira Island has an intense aroma easily distinguishable from other tangerines, being traditionally used to enrich several foods and beverages. Nonetheless, setubalense volatile composition has never been characterized, and we aimed to unveil the bioactive potential of peels and juices of setubalense tangerines and compare them with the murcott variety grown in Portugal mainland. Using headspace solid-phase microextraction coupled to gas chromatography mass spectrometry (HS-SPME/GC-MS), we identified a total of 128 volatile organic metabolites (VOMs) in the juice and peels, with d-limonene, γ-terpinene, β-myrcene, α- and β-pinene, o-cymene, and terpinolene, the most dominant in both cultivars. In contrast, setubalense juices are richer in terpenes, many of them associated with health protection. Discriminant analysis revealed a pool of VOMs, including β-caryophyllene and E-ocimene, with bioactive properties able to differentiate among tangerines according to variety and sample type (peel vs. juice). This is the first report on the volatile composition of setubalense tangerines grown on Madeira Island revealing that its pungent aroma is constituted by secondary metabolites with specific aroma notes and health properties. This is strong evidence of the higher nutraceutical value of such fruit for the human diet.info:eu-repo/semantics/publishedVersio

Removing inefficiencies from scientific code : the study of the Higgs boson couplings to top quarks

Publicado em "Computational science and its applications – ICCSA 2014 : proceedings", Series : Lecture notes in computer science, vol. 8582This paper presents a set of methods and techniques to remove inefficiencies in a data analysis application used in searches by the ATLAS Experiment at the Large Hadron Collider. Profiling scientific code helped to pinpoint design and runtime inefficiencies, the former due to coding and data structure design. The data analysis code used by groups doing searches in the ATLAS Experiment contributed to clearly identify some of these inefficiencies and to give suggestions on how to prevent and overcome those common situations in scientific code to improve the efficient use of available computational resources in a parallel homogeneous platform.This work is funded by National Funds through the FCT - Fundaçãoo para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) within project PEst-OE/EEI/UI0752/2014, by LIP (Laborat ́orio de Instrumentação e Física Experimental de Partículas), and the SeARCH cluster (REEQ/443/EEI/2005)

Modelação matemática da produção primária em zonas costeiras

O estudo da dinâmica de produção primária apresenta um interesse especial quando realizado em zonas costeiras utilizadas de forma intensiva para a aquicultura, como é o caso da Ria de Arosa. Nesta ria, a cadeia alimentar é dominada pelas elevadas taxas de produção primária sustentadas pelo afloramento de águas oceânicas ricas em nutrientes, resultando em elevadas quantidades de fitoplâncton que, por sua vez, servem de sustento às culturas de mexilhão em bateas. Neste artigo apresenta-se um modelo da cadeia alimentar proposto para a Ria de Arosa. Procede-se à apresentação das principais variáveis de estado seleccionadas e à caracterização das cinéticas que lhes estão associadas, evidenciando-se ainda as principais potencialidades de um modelo deste tipo na avaliação e previsão de cenários de funcionamento da cadeia alimentar

Contribution to the preservation of healthy coastal ecosystems

The release of pollutants into coastal zones from municipal and/or industrial drainage systems is a problem with a considerable environmental impact. In order to minimize the contamination of coastal waters in certain places (e.g., along beaches and in aquacultures), solutions based on the construction of submarine sewer outfalls have been proposed. In order to ascertain the optimal conditions for the release of an emissary, in particular the place of release, it is necessary to characterize the hydrodynamic transport processes that govern the evolution and mixture of pollutants in the area of interest. Circulation in the coastal zone is complicated, given that it is determined by a set of forcing mechanisms of diverse origins (meteorological, astronomical, large-scale ocean circulation, etc.) that endow it with a considerable space-time variation. Wastewater plume behaviour and characteristics depend both on the receiving water conditions and on the discharge characteristics. Accordingly, the implementation of a submarine outfall system requires a prior study of the site where the outfall is to be constructed, in order to achieve optimal rates of dilution of the pollutants released to the environment. Mathematical modelling appears to be a very useful tool for coastal zone environmental management either for continuous monitoring analysis or in accidental ecosystem rupture. This work presents some results and conclusions of two case studies. The first is a study of the pollutant cloud released at the São Jacinto submarine sewer outfall, located about 3 km offshore and 3 km north of an important coastal lagoon (NW Portugal). The main focus of this study was to establish the hydrodynamic conditions in which the pollutant release might affect the coastline (principally the existing beaches and lagoon). The second case presents some hydrodynamic results and water quality aspects of the Ria de Arosa (NW Spain), and also includes an assessment of the environmental impact of wastewater discharges from nine submarine outfalls considered in the sanitation plan of this bay. Results of faecal matter concentration distribution were used in the discussion on the outfall discharges’ impact on the natural water system for different hydrodynamic scenarios. In both cases, 3D numerical models were used