A rede GÉANT e as tendências de desenvolvimento das novas redes de comunicação em fibra óptica

Trabalho realizado sob orientação do Prof. António Brandão Moniz para a disciplina “Factores Sociais da Inovação” do Mestrado Engenharia Informática realizado na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa (Portugal).

Tensor regression based on linked multiway parameter analysis

Classical regression methods take vectors as covariates and estimate the corresponding vectors of regression parameters. When addressing regression problems on covariates of more complex form such as multi-dimensional arrays (i.e. tensors), traditional computational models can be severely compromised by ultrahigh dimensionality as well as complex structure. By exploiting the special structure of tensor covariates, the tensor regression model provides a promising solution to reduce the model’s dimensionality to a manageable level, thus leading to efficient estimation. Most of the existing tensor-based methods independently estimate each individual regression problem based on tensor decomposition which allows the simultaneous projections of an input tensor to more than one direction along each mode. As a matter of fact, multi-dimensional data are collected under the same or very similar conditions, so that data share some common latent components but can also have their own independent parameters for each regression task. Therefore, it is beneficial to analyse regression parameters among all the regressions in a linked way. In this paper, we propose a tensor regression model based on Tucker Decomposition, which identifies not only the common components of parameters across all the regression tasks, but also independent factors contributing to each particular regression task simultaneously. Under this paradigm, the number of independent parameters along each mode is constrained by a sparsity-preserving regulariser. Linked multiway parameter analysis and sparsity modeling further reduce the total number of parameters, with lower memory cost than their tensor-based counterparts. The effectiveness of the new method is demonstrated on real data sets.

Studies on the biosynthesis of taxol: the taxane carbon skeleton is not of mevalonoid origin.

A cell culture of Taxus chinensis was established to produce the diterpene 2alpha,5alpha,10beta,14beta-tetra-acetoxy4 ++ +(20),11-taxadiene (taxuyunnanine C) in 2.6% (dry weight) yield. The incorporation of [U-13C6]glucose, [1-13C]glucose, and [1,2-13C2]acetate into this diterpene was analyzed by NMR spectroscopy. Label from [1,2-13C2]acetate was diverted to the four acetyl groups of taxuyunnanine C, but not to the taxane ring system. Label from [1-13C]glucose and [U-13C6]glucose was efficiently incorporated into both the taxane ring system and the acetyl groups. The four isoprenoid moieties of the diterpene showed identical labeling patterns. The analysis of long-range 13C13C couplings in taxuyunnanine C obtained from an experiment with [U-13C6]glucose documents the involvement of an intramolecular rearrangement in the biosynthesis of the isoprenoid precursor. The labeling patterns are inconsistent with the mevalonate pathway. The taxoid data share important features with the alternative pathway of isoprenoid biosynthesis operating in certain eubacteria Rohmer, M., Knani, M., Simonin, P., Sutter, B. & Sahm, H. (1993) Biochem. J. 295, 517-524].

Using Blogs to Share and Discuss Experimental Data - Cameron Neylon

This is one of a series of short case studies describing how academic tutors at the University of Southampton have made use of learning technologies to support their students.

Development and implementation of a S/W platform to automatically receive and share satellite data

Relazione del lavoro di creazione e implementazione della piattaforma software che sviluppa l’archivio del progetto SATNET. I satelliti universitari hanno un tempo di vista della propria Stazione di Terra di pochi minuti al giorno: SATNET risponde all’esigenza di comunicare con un satellite universitario in orbita bassa per più dei pochi minuti al giorno che una singola Stazione di Terra permette. Questo avviene grazie a una rete di Stazioni di Terra Satellitari collegate da specifiche missioni comuni che mettono in condivisione dati ricevuti da uno o più satelliti, aumentando il rendimento dati/giorno di questi e permettendo una migliore fruizione delle Stazioni di Terra stesse. Il network sfrutta Internet come canale di connessione, e prevede la presenza di un archivio nel quale memorizzare i dati ricevuti, per poi renderne possibile la consultazione e il recupero. Oggetto di questo lavoro di tesi è stato lo sviluppo e l’implementazione di tale archivio: utilizzando un sito web dinamico, il software risponde a tutte le richieste evidenziate nel paragrafo precedente, permettendo a utenti autenticati di inserire dati e ad altri di poterne avere accesso. Il software è completo e funzionante ma non finito, in quanto manca la formulazione di alcune richieste; per esempio non è stato specificato il tipo di informazioni che è possibile caricare in upload, né il tipo di campi richiesti nel modulo di registrazione dei vari utenti. In questi casi sono stati inseriti campi generici, lasciando all’utente la possibilità di modificarli in seguito. Il software è stato dunque concepito come facilmente personalizzabile e modificabile anche da utenti inesperti grazie alla sola lettura della tesi, che rappresenta quindi una vera e propria guida per l’utilizzo, l’installazione, la personalizzazione e la manutenzione della piattaforma software. La tesi evidenzia gli obiettivi e le richieste, mostrando l’aspetto del sito web e le sue funzionalità, e spiega passo per passo il procedimento per la modifica dell’aspetto delle pagine e di alcuni parametri di configurazione. Inoltre, qualora siano necessarie modifiche sostanziali al progetto, introduce i vari linguaggi di programmazione necessari allo sviluppo e alla programmazione web e aiuta l’utente nella comprensione della struttura del software. Si conclude con alcuni suggerimenti su eventuali modifiche, attuabili solo a seguito di un lavoro di definizione degli obiettivi e delle specifiche richieste. In futuro ci si aspetta l’implementazione e la personalizzazione del software, nonché l’integrazione dell’archivio all’interno del progetto SATNET, con l’obiettivo di migliorare e favorire la diffusione e la condivisione di progetti comuni tra diverse Università Europee ed Extra-Europee.

The rate of outpatient cataract surgery in ten European countries: an analysis using data from the SHARE survey

BACKGROUND: The aim of this study was to determine the rates of outpatient cataract surgery (ROCS) in ten European countries and to find country-specific health indicators explaining the differences. METHODS: Using data from the Survey of Health, Ageing and Retirement in Europe (SHARE), 251 eligible respondents were identified for which cataract surgery was the last surgical procedure. The ROCS of ten countries were compared using logistic regression. The influence of the public expenditure on health as per cent of the total expenditure on health, of the number of acute care beds per 1,000 population, and of the number of practicing physicians per 1,000 population, was studied by multiple logistic regression. Additional information was obtained from country-specific opinion leaders in the field of cataract surgery. RESULTS: The ROCS differed significantly between the ten analysed European countries where Denmark had the highest (100%) and Austria the lowest (0%) rate of day care surgery. A decrease in the density of acute care beds (p < 0.0000001) and in the density of practicing physicians (p < 0.05) and an increase in the public expenditure on health as per cent of the total health expenditure (p < 0.01) lead to an increase in the ROCS. According to the opinion leaders, regulations and financial incentives also have a strong influence on the ROCS. CONCLUSIONS: The outpatient rate of cataract surgery in the ten European countries was mainly influenced by the acute-care beds density, but also by the density of practicing physicians, and by the public expenditure on health.

Waiting times for cataract surgery in ten European countries: an analysis using data from the SHARE survey

AIMS: To assess waiting times for cataract surgery and their acceptance in European countries, and to find explanatory, country-specific health indicators. METHODS: Using data from the survey of health, ageing and retirement in Europe (SHARE), waiting times for cataract surgery of 245 respondents in ten countries were analysed with the help of linear regression. The influence of four country specific health indicators on waiting times was studied by multiple linear regression. The influence of waiting time and country on the wish to have surgery performed earlier was determined through logistic regression. Additional information was obtained for each country from opinion leaders in the field of cataract surgery. RESULTS: Waiting times differed significantly (p<0.001) between the ten analysed European countries. The length of wait was significantly influenced by the total expenditure on health (p<0.01) but not by the other country specific health indicators. The wish to have surgery performed earlier was determined by the length of wait (p<0.001) but not by the country where surgery was performed. CONCLUSION: The length of wait is influenced by the total expenditure on health, but not by the rate of public expenditure on health, by the physician density or by the acute bed density. The wish to have surgery performed earlier depends on the length of wait for surgery and is not influenced by the country.

Highway user fees: updated data needed to determine whether all users pay their fair share.

Mode of access: Internet.

Patient data sharing for the improvement of healthcare and medical research: towards a moral duty of patients to share health-related data?

The project answers to the following central research question: ‘How would a moral duty of patients to transfer (health) data for the benefit of health care improvement, research, and public health in the eHealth sector sit within the existing confidentiality, privacy, and data protection legislations?’. The improvement of healthcare services, research, and public health relies on patient data, which is why one might raise the question concerning a potential moral responsibility of patients to transfer data concerning health. Such a responsibility logically would have subsequent consequences for care providers concerning the further transferring of health data with other healthcare providers or researchers and other organisations (who also possibly transfer the data further with others and other organisations). Otherwise, the purpose of the patients’ moral duty, i.e. to improve the care system and research, would be undermined. Albeit the arguments that may exist in favour of a moral responsibility of patients to share health-related data, there are also some moral hurdles that come with such a moral responsibility. Furthermore, the existing European and national confidentiality, privacy and data protection legislations appear to hamper such a possible moral duty, and they may need to be reconsidered to unlock the full use of data for healthcare and research.

Integration and visualization of systems biology data in context of the genome

Background: High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results: The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions: Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment.

Affected and non-affected skin fibroblasts from systemic sclerosis patients share a gene expression profile deviated from the one observed in healthy individuals

Objectives To evaluate the gene expression profile of fibroblasts from affected and non-affected skin of systemic sclerosis (SSc) patients and from controls. Materials and methods Labeled cDNA from fibroblast cultures from forearm (affected) and axillary (non-affected) skin from six diffuse SSc patients, from three normal controls, and from MOLT-4/HEp-2/normal fibroblasts (reference pool) was probed in microarrays generated with 4193 human cDNAs from the IMAGE Consortium. Microarray images were converted into numerical data and gene expression was calculated as the ratio between fibroblast cDNA (Cy5) and reference pool cDNA (Cy3) data and analyzed by R environment/Aroma, Cluster, Tree View, and SAM softwares. Differential expression was confirmed by real time PCR for a set of selected genes. Results Eighty-eight genes were up- and 241 genes down-regulated in SSc fibroblasts. Gene expression correlation was strong between affected and non-affected fibroblast samples from the same patient (r>0.8), moderate among fibroblasts from all patients (r=0.72) and among fibroblasts from all controls (r=0.70), and modest among fibroblasts from patients and controls (r=0.55). The differential expression was confirmed by real time PCR for all selected genes. Conclusions Fibroblasts from affected and non-affected skin of SSc patients shared a similar abnormal gene expression profile, suggesting that the widespread molecular disturbance in SSc fibroblasts is more sensitive than histological and clinical alterations. Novel molecular elements potentially involved in SSc pathogenesis were identified.

Share GFS – Games, Films & Series: sistema de recomendação

Esta dissertação incide sobre o estudo e análise de uma solução para a criação de um sistema de recomendação para uma comunidade de consumidores de media e no consequente desenvolvimento da mesma cujo âmbito inicial engloba consumidores de jogos, filmes e/ou séries, com o intuito de lhes proporcionar a oportunidade de partilharem experiências, bem como manterem um registo das mesmas. Com a informação adquirida, o sistema reúne condições para proceder a sugestões direcionadas a cada membro da comunidade. O sistema atualiza a sua informação mediante as ações e os dados fornecidos pelos membros, bem como pelo seu feedback às sugestões. Esta aprendizagem ao longo do tempo permite que as sugestões do sistema evoluam juntamente com a mudança de preferência dos membros ou se autocorrijam. O sistema toma iniciativa de sugerir mediante determinadas ações, mas também pode ser invocada uma sugestão diretamente pelo utilizador, na medida em que este não precisa de esperar por sugestões, podendo pedir ao sistema que as forneça num determinado momento. Nos testes realizados foi possível apurar que o sistema de recomendação desenvolvido forneceu sugestões adequadas a cada utilizador específico, tomando em linha de conta as suas ações prévias. Para além deste facto, o sistema não forneceu qualquer sugestão quando o histórico destas tinha provado incomodar o utilizador.

An Approach To Publish a Data Warehouse Content as Linked Data

Mestrado em Engenharia Informática - Área de Especialização em Tecnologias do Conhecimento e Decisão

Sistema de Recomendação: Share GFS Games, Films & Series

Esta dissertação incide sobre o estudo e análise de uma solução para a criação de um sistema de recomendação para uma comunidade de consumidores de media e no consequente desenvolvimento da mesma cujo âmbito inicial engloba consumidores de jogos, filmes e/ou séries, com o intuito de lhes proporcionar a oportunidade de partilharem experiências, bem como manterem um registo das mesmas. Com a informação adquirida, o sistema reúne condições para proceder a sugestões direccionadas a cada membro da comunidade. O sistema actualiza a sua informação mediante as acções e os dados fornecidos pelos membros, bem como pelo seu feedback às sugestões. Esta aprendizagem ao longo do tempo permite que as sugestões do sistema evoluam juntamente com a mudança de preferência dos membros ou se autocorrijam. O sistema toma iniciativa de sugerir mediante determinadas acções, mas também pode ser invocada uma sugestão directamente pelo utilizador, na medida em que este não precisa de esperar por sugestões, podendo pedir ao sistema que as forneça num determinado momento. Nos testes realizados foi possível apurar que o sistema de recomendação desenvolvido forneceu sugestões adequadas a cada utilizador específico, tomando em linha de conta as suas acções prévias. Para além deste facto, o sistema não forneceu qualquer sugestão quando o histórico destas tinha provado incomodar o utilizador.