Federated architecture for biomedical data integration

The last decades have been characterized by a continuous adoption of IT solutions in the healthcare sector, which resulted in the proliferation of tremendous amounts of data over heterogeneous systems. Distinct data types are currently generated, manipulated, and stored, in the several institutions where patients are treated. The data sharing and an integrated access to this information will allow extracting relevant knowledge that can lead to better diagnostics and treatments. This thesis proposes new integration models for gathering information and extracting knowledge from multiple and heterogeneous biomedical sources. The scenario complexity led us to split the integration problem according to the data type and to the usage specificity. The first contribution is a cloud-based architecture for exchanging medical imaging services. It offers a simplified registration mechanism for providers and services, promotes remote data access, and facilitates the integration of distributed data sources. Moreover, it is compliant with international standards, ensuring the platform interoperability with current medical imaging devices. The second proposal is a sensor-based architecture for integration of electronic health records. It follows a federated integration model and aims to provide a scalable solution to search and retrieve data from multiple information systems. The last contribution is an open architecture for gathering patient-level data from disperse and heterogeneous databases. All the proposed solutions were deployed and validated in real world use cases.

New tools for cognitive and motor rehabilitation: development and clinical validation

Nervous system disorders are associated with cognitive and motor deficits, and are responsible for the highest disability rates and global burden of disease. Their recovery paths are vulnerable and dependent on the effective combination of plastic brain tissue properties, with complex, lengthy and expensive neurorehabilitation programs. This work explores two lines of research, envisioning sustainable solutions to improve treatment of cognitive and motor deficits. Both projects were developed in parallel and shared a new sensible approach, where low-cost technologies were integrated with common clinical operative procedures. The aim was to achieve more intensive treatments under specialized monitoring, improve clinical decision-making and increase access to healthcare. The first project (articles I – III) concerned the development and evaluation of a web-based cognitive training platform (COGWEB), suitable for intensive use, either at home or at institutions, and across a wide spectrum of ages and diseases that impair cognitive functioning. It was tested for usability in a memory clinic setting and implemented in a collaborative network, comprising 41 centers and 60 professionals. An adherence and intensity study revealed a compliance of 82.8% at six months and an average of six hours/week of continued online cognitive training activities. The second project (articles IV – VI) was designed to create and validate an intelligent rehabilitation device to administer proprioceptive stimuli on the hemiparetic side of stroke patients while performing ambulatory movement characterization (SWORD). Targeted vibratory stimulation was found to be well tolerated and an automatic motor characterization system retrieved results comparable to the first items of the Wolf Motor Function Test. The global system was tested in a randomized placebo controlled trial to assess its impact on a common motor rehabilitation task in a relevant clinical environment (early post-stroke). The number of correct movements on a hand-to-mouth task was increased by an average of 7.2/minute while the probability to perform an error decreased from 1:3 to 1:9. Neurorehabilitation and neuroplasticity are shifting to more neuroscience driven approaches. Simultaneously, their final utility for patients and society is largely dependent on the development of more effective technologies that facilitate the dissemination of knowledge produced during the process. The results attained through this work represent a step forward in that direction. Their impact on the quality of rehabilitation services and public health is discussed according to clinical, technological and organizational perspectives. Such a process of thinking and oriented speculation has led to the debate of subsequent hypotheses, already being explored in novel research paths.

Intervenção socioeducativa: investigação-ação participativa com trabalhadoras do sexo de rua e uma equipa de outreach

Nos últimos anos, assistimos ao crescimento do conhecimento sobre o trabalho sexual e os seus atores. No entanto, poucos estudos envolvem os/as trabalhadores/as do sexo (TS) como participantes ativos. Esta tese apresenta uma pesquisa de investigação-ação participativa (IAP) composta por dois estudos que, de forma complementar, pretendem contribuir para o desenvolvimento de uma proposta socioeducativa de intervenção centrada nos direitos e necessidades dos/as TS. O estudo preliminar pretende refletir sobre os discursos institucionais produzidos em torno do trabalho sexual e dar a conhecer as práticas socioeducativas empreendidas pelas instituições que dirigem serviços a TS, em Portugal. O segundo estudo apresenta o processo e os resultados de uma IAP, com TS de rua e uma equipa de outreach. O propósito do segundo estudo consistiu em identificar as necessidades e as vontades das TS e de uma equipa de outreach, com a finalidade de encorajar os/as participantes na construção de um modelo socioeducativo de intervenção. O estudo preliminar foi efetuado junto das 23 instituições que, à data deste estudo (de outubro de 2012 a março de 2013), prestavam apoio a TS. Concluímos que os serviços são bastante similares, focados na redução de riscos decorrentes do trabalho sexual, sobretudo a nível da promoção e educação para a saúde, assumindo uma intervenção tradicional centrada na epidemiologia. De forma menos expressiva, encontrámos instituições que se centram no apoio ao abandono da atividade. Todas assumem um papel fundamental no debate social e político sobre a prostituição enquanto trabalho ou opressão. Estes resultados conduziram-nos à formulação das seguintes questões: 1) Os serviços tradicionais centrados na epidemiologia reforçam inadvertidamente o estigma do/a TS?; 2) Quais são as preocupações, necessidades e vontades reais dos/as TS?; 3) O que pensam sobre serem envolvidos/as no desenho, implementação e avaliação de projetos que lhes dizem respeito? Assim, identificámos uma falta de participação dos/as TS em projetos a si dirigidos, corroborada pela literatura científica. O segundo estudo foi desenvolvido, de setembro de 2012 a junho de 2015, através de três ciclos de planificação-ação-reflexão com TS de rua e uma equipa de outreach, em Coimbra, tendo envolvido 28 participantes formais. Através de entrevistas e da reinterpretação conjunta dos resultados das mesmas, verificámos a existência de preocupações comuns, designadamente no que se refere à saúde e segurança ocupacionais, mas pouca coesão entre as TS. As iniciativas de conscientização, desenvolvidas no âmbito da IAP, providenciaram um sentido de controlo, mas a transformação da subjetividade em ação coletiva continua a ser premente. Por tal, propomos um modelo de intervenção socioeducativa com TS, segundo uma abordagem centrada na relação e na prática reflexiva, através do recurso a métodos e à filosofia da IAP. Propomos, ainda, algumas recomendações em torno da educação/formação dos profissionais de proximidade, das/os TS e, a um nível macro, iniciativas educativas centrada na desconstrução social do género.

Study and development of UV photodetectors envisaging COMPASS RICH-1 upgrade and applications

COMPASS is an experiment at CERN’s SPS whose goal is to study hadron structure and spectroscopy. The experiment includes a wide acceptance RICH detector, operating since 2001 and subject to a major upgrade of the central region of its photodetectors in 2006. The remaining 75% of the photodetection area are still using MWPCs from the original design, who suffer from limitations in gain due to aging of the photocathodes from ion bombardment and due to ion-induced instabilities. Besides the mentioned limitations, the increased luminosity conditions expected for the upcoming years of the experiment make an upgrade to the remaining detectors pertinent. This upgrade should be accomplished in 2016, using hybrid detectors composed of ThGEMs and MICROMEGAS. This work presents the study, development and characterization of gaseous photon detectors envisaging the foreseen upgrade, and the progress in production and evaluation techniques necessary to reach increasingly larger area detectors with the performances required. It includes reports on the studies performed under particle beam environment of such detectors. MPGD structures can also be used in a variety of other applications, of which nuclear medical imaging is a notorious example. This work includes, additionally, the initial steps in simulating, assembling and characterizing a prototype of a gaseous detector for application as a Compton Camera.

Design of experiments to optimized the determination of TDIs in agglomerated cork stoppers

Isocyanates are included into a class with an extreme commercial importance because their use in the manufacture of polyurethanes. Polyurethanes are used in several applications such as adhesives, coatings, foams, thermoplastics resins, printing inks, foundry moulds and rubbers. Agglomerated cork stoppers are currently used for still wines, semi-sparkle and gaseous wines, beer and cider. Methylene diphenyl diisocyanate (MDI) is presently the isocyanate used in the production of polyurethane based adhesive in use due to its lowest toxicity comparing with toluene diisocyanate (TDI) previously employed. However, free monomeric TDI or MDI, depending on the based polyurethane, can migrate from agglomerated cork stoppers to beverages therefore it needs to be under control. The presence of these compounds are usually investigated by HPLC with Fluorescence or UV-Vis detector depending on the derivatising agent. Ultra Performance Liquid Chromatography with Diode Array Detector (UPLC-DAD) method is replacing HPLC. The objective of this study is to determine which method is better to analyze isocyanates from agglomerated cork stoppers, essentially TDI to quantify its monomer. A Design of Experiments (DOE) with three factors, column temperature, flow and solvent, at two levels was done. Eight experiments with three replications and two repetitions were developed. Through an ANOVA the significance of the factors was evaluated and the best level’s factors were selected. As the TDI has two isomers and in this method these two isomers were not always separated an ANOVA with results of resolution between peaks was performed. The Design of Experiments reveals to be a suitable statistical tool to determine the best conditions to quantified free isocyanates from agglomerated cork stoppers to real foodstuff. The best level’s factors to maximize area was column temperature at 30ºC, flow to 0,3 mL/min and solvent 0,1% Ammonium Acetate, to maximize resolution was the same except the solvent that was 0,01% Ammonium Acetate.

Scalable semantic aware context storage

The number of connected devices collecting and distributing real-world information through various systems, is expected to soar in the coming years. As the number of such connected devices grows, it becomes increasingly difficult to store and share all these new sources of information. Several context representation schemes try to standardize this information, but none of them have been widely adopted. In previous work we addressed this challenge, however our solution had some drawbacks: poor semantic extraction and scalability. In this paper we discuss ways to efficiently deal with representation schemes' diversity and propose a novel d-dimension organization model. Our evaluation shows that d-dimension model improves scalability and semantic extraction.

Remoção de hidrocarbonetos aromáticos policíclicos em águas utilizando subprodutos da indústria da cortiça

Os Hidrocarbonetos Aromáticos Policíclicos (HAPs) são contaminantes persistentes em meio aquoso. Estes compostos são conhecidos pelas suas propriedades carcinogénicas, mutagénicas e genotóxicas. O principal objetivo deste trabalho consistiu na avaliação das potencialidades de subprodutos da indústria corticeira, como adsorventes alternativos para a remoção de cinco HAPs em meio aquoso: benzo(a)pireno, benzo(ghi)perileno, benzo(b)fluoranteno, benzo(k)fluoranteno e indeno(1,2,3-cd)pireno. A metodologia analítica para quantificar os HAPs envolveu a preparação das amostras, através da técnica de extração em fase sólida (SPE), e a quantificação dos compostos analisados por cromatografia líquida com detetor de fluorescência (LC-FLD). O método foi otimizado e validado, obtendo-se limites de quantificação de 0,004 μg/L para todos os HAPs. Os estudos incidiram na utilização de uma amostra de cortiça, pó de aglomerado de cortiça expandida (PACE), obtida por aglutinação de cortiça em condições hidrotérmicas, a qual nos estudos preliminares revelou desempenho semelhante aos carvões ativados. Com exceção do benzo(ghi)perileno, os resultados mostram que o processo de adsorção dos HAPs na amostra PACE segue uma cinética de pseudo-segunda ordem e as isotérmicas ajustam-se ao modelo de Langmuir.

Wild Morchella conica Pers. from different origins: a comparative study of nutritional and bioactive properties

Morchella conica Pers. is a species of fungus that belongs to the Morchellaceae family and was studied in order to obtain more information about this species, by comparing Portuguese and Serbian wild samples. Free sugars, fatty acids, tocopherols, organic and phenolic acids were analysed by chromatographic techniques. M. conica methanolic extracts were tested regarding antioxidant and antimicrobial properties. The absence of hepatotoxicity was confirmed in porcine liver primary cells.

Optimization of ultrasound-assisted extraction to obtain mycosterols from Agaricus bisporus L. by response surface methodology and comparison with conventional Soxhlet extraction

Ergosterol, a molecule with high commercial value, is the most abundant mycosterol in Agaricus bisporus L. To replace common conventional extraction techniques (e.g. Soxhlet), the present study reports the optimal ultrasound-assisted extraction conditions for ergosterol. After preliminary tests, the results showed that solvents, time and ultrasound power altered the extraction efficiency. Using response surface methodology, models were developed to investigate the favourable experimental conditions that maximize the extraction efficiency. All statistical criteria demonstrated the validity of the proposed models. Overall, ultrasound-assisted extraction with ethanol at 375 W during 15 min proved to be as efficient as the Soxhlet extraction, yielding 671.5 ± 0.5mg ergosterol/100 g dw. However, with n-hexane extracts with higher purity (mg ergosterol/g extract) were obtained. Finally, it was proposed for the removal of the saponification step, which simplifies the extraction process and makes it more feasible for its industrial transference.

Cottage cheeses functionalized with fennel and chamomile extracts: comparative performance between free and microencapsulated forms

Globally, there is a trend for healthy food products, preferably incorporating natural bioactive ingredients, replacing synthetic additives. From previous screening studies, extracts of Foeniculum vulgare Mill. (fennel) and Matricaria recutita L. (chamomile) maintained nutritional properties and improved the antioxidant activity of cottage cheese. Nevertheless, this effect was limited to 7 days. Accordingly, aqueous extracts of these plants were microencapsulated in alginate and incorporated into cottage cheese to achieve an extended bioactivity. Plain cottage cheese, and cheese functionalized by direct addition of free decoctions, were prepared and compared. Independently of plant species, "functionalization type" factor did not show a significant effect on the nutritional parameters, as also confirmed in the linear discriminant analysis, where these parameters were not selected as discriminating variables. Furthermore, samples functionalized with microencapsulated extracts showed higher antioxidant activity after the 7th day, thereby demonstrating that the main purpose of this experimental work was achieved.

Extended use of gamma irradiation in wild mushrooms conservation: validation of 2 kGy dose to preserve their chemical characteristics

Irradiation is recognized by international organizations as a conservation technology, and its application to wild mushrooms has been tested in some species. Our research group evaluated the effectiveness of gamma irradiation to conserve different samples of highly appreciated species, particularly, Lactarius deliciosus, Macrolepiota procera, Boletus edulis and Hydnum repandum. From those results and considering also international recommendations on this subject, the 2 kGy dose was chosen for further studies. Therefore, the application of gamma irradiation at 2 kGy dose was extended to Boletus pinophilus Pilát & Dermek and Clitocybe subconnexa Murrill to validate the proposed technology. Considering the obtained results, some of the analysed chemical parameters (specially sugars and fatty acids), as well as the antioxidant activity, showed significant changes after irradiation treatment, particularly in B. pinophillus, probably due to its higher water content. Nevertheless, the obtained differences did not seem to be sufficient to change the organoleptic characteristics of these mushrooms. Furthermore, the antioxidant activity was generally higher in irradiated samples. In conclusion, the detected chemical changes might be considered as acceptable, when considering the high advantages of gamma irradiation at decontamination and/or disinfestation level.

In vitro anti-Candida activity of Glycyrrhiza glabra L.

The severity and frequency of opportunistic fungal infections still growing, concomitantly to the increasing rates of antimicrobial drug’s resistance. Natural matrices have been used over years due to its multitude of health benefits, including antifungal potential. Thus, the present work aims to evaluate the anti-Candida potential of the phenolic extract and individual phenolic compounds of Glycyrrhiza glabra L. (licorice), by disc diffusion assay, followed by determination of the minimal inhibitory concentration (MIC) and minimal fungicidal concentration (MFC) for both planktonic cells and biofilms. Licorice extract evidenced inhibitory potential against the nineteen tested Candida strains, but no pronounced effect was observed by testing the most abundant individual phenolic compounds. Candida tropicalis strains were the most sensible, followed by Candida glabrata, Candida parapsilosis and, then, Candida albicans. Lower MIC and MFC values were achieved to C. glabrata and C. tropicalis, which confirms its susceptibility to licorice extract; however, for C. tropicalis strains a higher variability was observed. Anti-biofilm potential was also achieved, being most evident in some C. glabrata and C. tropicalis strains. In general, a twice concentration of the MIC was necessary for planktonic cells to obtain a similar potential to that one observed for biofilms. Thus, an upcoming approach for new antifungal agents, more effective and safer than the current ones, is stablished; notwithstanding, further studies are necessary in order to understand its mechanism of action, as also to assess kinetic parameters.

Exploring plant tissue culture to improve the production of phenolic compounds: A review

Plant tissue and organ culture has been extensively used from the beginning of the XX century for the study and comprehension of some primary biological mechanisms such as morphogenesis. However, with the increasing demand of the market for novel products derived from plants, in vitro culture became a reliable technique for the mass production of plant material. Moreover, the potential to use this technique for the production of some bioactive compounds, such as phenolic compounds, is immense since it allows the manipulation of the biosynthetic routes to increase the production and accumulation of specific compounds. This work intends to make a brief historical review of in vitro culture, highlighting its use for the production of bioactive compounds. Also, emphasizes the importance of phenolic compounds for the consumer as well reviews the metabolic pathways involved in its production in plant cells. Furthermore, it was carried out a comprehensive study on the work developed for the production of plant phenolic compounds in in vitro cultures, as well as on the type of elicitors used to increase of the same production; also a brief highlighting of the phenolic compounds which serve as elicitors. There are numerous reports directed to the production of phenolic extracts in in vitro plant cultures, however there is a lack in the production of individual phenolic compounds mainly due to the complexity of the biosynthetic routes and extraction procedures. Elicitation procedures are often used to increase the production of phenolics, archieving in most cases higher yields than in non-elicitated cultures. The increasing production of bioactive phenolic extracts/compounds allows for their further applicability, namely in the industry of functional foods or in pharmaceutical/medical fields.

Wild Roman chamomile extracts and phenolic compounds: enzymatic assays and molecular modelling studies with VEGFR-2 tyrosine kinase

Angiogenesis is a process by which new blood vessels are formed from the pre-existing vasculature, and it is a key process that leads to tumour development. Some studies have recognized phenolic compounds as chemopreventive agents; flavonoids, in particular, seem to suppress the growth of tumor cells modifying the cell cycle. Herein, the antiangiogenic activity of Roman chamomile (Chamaemelum nobile L.) extracts (methanolic extract and infusion) and the main phenolic compounds present (apigenin, apigenin-7-O-glucoside, caffeic acid, chlorogenic acid, luteolin, and luteolin-7-O-glucoside) was evaluated through enzymatic assays using the tyrosine kinase intracellular domain of the Vascular Endothelium Growth Factor Receptor-2 (VEGFR-2), which is a transmembrane receptor expressed fundamentally in endothelial cells involved in angiogenesis, and molecular modelling studies. The methanolic extract showed a lower IC50 value (concentration that provided 50% of VEGFR-2 inhibition) than the infusion, 269 and 301 μg mL(-1), respectively. Regarding phenolic compounds, luteolin and apigenin showed the highest capacity to inhibit the phosphorylation of VEGFR-2, leading us to believe that these compounds are involved in the activity revealed by the methanolic extract.

Improving bioactive compounds extractability of Amorphophallus paeoniifolius (Dennst.) Nicolson

Elephant foot yam (Amorphophallus paeoniifolius (Dennst.) Nicolson) is an underground, unbranched deciduous plant that produces a large tubercle (rhizome) with recognized health effects. In this study, the influence of solvent nature (water, water/etanol (1:1) and absolute ethanol) and processing type (fresh, lyophilized and boiled) on the antioxidant activity and bioactive compounds extractability of elephant foot yam was evaluated. Extracts were compared for their contents in total phenolics, flavonoids and tannins. Moreover, their antioxidant capacity was assessed by the ferric reducing antioxidant power (FRAP) and the 2,2-diphenyl-1-picrylhydrazyl radical (DPPH▪) scavenging capacity assays. Phenolics (154 mg GAE/L) and tannins (109 mg GAE/L) were maximized in lyophilized samples extracted with the hydroalcoholic solvent, which attained also the highest FRAP value (711 mg FSE/L). In turn, flavonoids reached the highest yields in lyophilized samples (95 mg ECE/L) extracted with pure ethanol, as well as the highest DPPH▪ scavenging activity. These findings might have practical applications to define the best processing methodology regarding the enhancement of elephant foot yam, either for prompt consumption, as well as to develop food supplements or pharmaceutical related products.