Social network analysis applied to knowledge creation and transfer in the portuguese agricultural R&D field: an exploratory study

Paper presented at the 9th European Conference on Knowledge Management, Southampton Solent University, Southampton, UK, 4-5 Sep. 2008. URL: http://academic-conferences.org/eckm/eckm2008/eckm08-home.htm

Open innovation and social network analysis

The present article is based on the report for the Doctoral Conference of the PhD programme in Technology Assessment, held at FCT-UNL Campus, Monte de Caparica, July 9th, 2012. The PhD thesis has the supervision of Prof. Cristina Sousa (ISCTE-IUL), and co-supervision of Prof. José Cardoso e Cunha (FCT-UNL).

Otimização da anisotropia fronto-calosa e ressonância magnética [1,5T] no idoso normal e com risco cérebro-vascular

RESUMO: Os mais recentes métodos de neuro imagem tal como a Ressonância Magnética (RM) permitiram obter imagens detalhadas do cérebro humano in vivo. Essas imagens revelam, muitas vezes, achados imprevistos face ao padrão normal, com elevada propensão para os indivíduos idosos e franca coexistência com fatores de risco vascular, como característica dum processo de envelhecimento normal. Embora na última década tenham surgido várias publicações sobre este assunto, ele continua ainda pouco explicado. Um pouco por todo o mundo têm emergido os programas de prevenção da doença e promoção da saúde desenvolvidos pela Saúde Pública suportadas sobretudo pelo avanço das tecnologias médicas que resultaram, entre outros impactos, num crescimento da população idosa. Estima-se, em 2030, uma composição demográfica com 20% de indivíduos acima dos 65 anos. Neste contexto, a doença microvascular cerebral é a causa mais frequente de comprometimento cognitivo vascular no idoso sendo as características senescentes na imagem por RM do tipo lesões isquémicas da Substância Branca (Leukoaraiosis) e enfartes lacunares (Status lacunar), atrofia cerebral, gliose e acumulação excessiva de ferro nos núcleos da base. Esta tese, considerando a linha de investigação de que deriva – Ciências da Vida - especialização em Medicina Clinica - Biotecnologia, reúne e reflete sobre três vertentes ligadas à RM e interdependentes em relação a uma problemática comum. A primeira trata da caracterização da Tecnologia por Ressonância Magnética existente em Portugal, a qual inclui uma avaliação exploratória da aplicação da técnica de Difusão Anisotrópica nos estudos cerebrais. As dimensões analíticas estudadas foram a Tecnológica, Sociodemográfica e Económica. Na recolha de dados recorreu-se a várias fontes de informação e a uma metodologia exploratória faseada, validada pela triangulação dos resultados. A sua análise obedeceu a critérios de estratificação e agrupamento segundo as mesmas dimensões analíticas. Otimização da anisotropia fronto-calosa e [RM 1,5T] no idoso normal e com risco cérebro-vascular A segunda descreve o estudo anátomo – radiológico que recaiu sobre parâmetros de quantificação assente na temática do cérebro do idoso em cadáver segundo uma metodologia experimental aplicada às métricas da difusão por RM. Na terceira, e última, é apresentado o estudo técnico - radiológico para avaliação e otimização da imagem ponderada em difusão em estudos clínicos associados ao cérebro do idoso “The Usual Brain Aging” ou Envelhecimento Cerebral Normal, com base metodológica assente nos critérios e indicadores estabelecidos pelo Estudo de Imagem de Roterdão (Rotterdam Scan Study - RSS). Como principais resultados obteve-se que não existem em Portugal estruturas para avaliação dos equipamentos pesados ou Agência de Avaliação das Tecnologias da Saúde para desenvolver o importante papel da produção de estudos comparativos entre os equipamentos disponíveis no mercado, a relação preço-qualidade e a sua afetação às necessidades clínico-epidemiológicas. Constatou-se que a implementação de equipamentos de RM está fortemente assente em critérios económicos carecendo de recomendações e diretivas para o uso racionalizado destas tecnologias. Quanto a dados quantitativos concluímos que a maioria dos equipamentos está instalada em instituições privadas (80,2%); a intensidade de campo magnético mais frequente é [1,5T] com 119 equipamentos; os equipamentos estão instalados maioritariamente nos distritos de Lisboa (55 unidades) e do Porto (39 unidades); o rácio médio de equipamentos por habitante em Portugal é de 1 para 65 195 habitantes; a amplitude de gradientes com maior expressão na amostra é 30-39mT/m; a maioria dos equipamentos foi instalada no intervalo temporal [2009-2012] com 59 equipamentos; apenas 6 instituições desenvolvem investigação clinica e a maioria das bobinas para estudos de crânio são do tipo Array. O estudo de otimização da técnica da difusão revelou, quanto à avaliação dos valoresb, que os mais baixos (b=500 s/mm2 e b=1000 s/mm2), apresentam maior IS e SNR sendo esta uma boa medida referente à qualidade de imagem, no entanto, os valores-b mais elevados (b=2000 s/mm2) apresentam maior CNR e CR, face aos anteriores, o Otimização da anisotropia fronto-calosa e [RM 1,5T] no idoso normal e com risco cérebro-vascular que apesar de proporcionar inferior detalhe anatómico e consequentemente inferior qualidade de imagem, num encéfalo normal, pode auxiliar na interpretação e apresentar vantagens na identificação de lesões microvasculares sempre que persistirem dúvidas em relação ao diagnóstico diferencial de doença microvascular do tipo status lacunar ou Hiperintensidades da Substância Branca. As alterações deste parâmetro são particularmente refletidas nas diferenças da avaliação da qualidade de imagem na região fronto-calos Concluímos da avaliação quantitativa da concentração média de ferro (26Fe) em todas as faixas etárias que os núcleos da base que apresentam maior concentração são, por ordem decrescente: Substância Nigra, Globus Pallidus, Putamen, Tálamo, Núcleo Rubro e Núcleo Caudado; que existe uma predominância na concentração de ferro (26Fe) no hemisfério esquerdo e que os indivíduos do género masculino apresentam mais ferro (26Fe) que os do género feminino nas faixas etárias [30-40[, [40-50[ e [50-60[. Como principal conclusão do estudo da concentração média de ferro em relação à idade destacamos que a concentração média de ferro (26Fe) é superior nos grupos etários superiores, logo aumenta com a idade, sobretudo na Substância Nigra e no Núcleo Lenticular. No estudo técnico-radiológico encontrámos evidências do aumento da difusibilidade da água na substância branca subcortical dos sujeitos idosos comparativamente aos mais jovens. Uma relação idêntica foi avaliada nos tálamos. O aumento relacionado com a idade parece ser predominantemente observado em doentes com mais de 65 anos de idade o que pode refletir alterações estruturais ligeiras associados ao envelhecimento normal. Os resultados indicam que a análise quantitativa das imagens ponderadas em difusão fornece informações, sobre a estrutura do cérebro, as quai s não estão disponíveis apenas por inspeção visual, tanto nas imagens ponderadas em difusão como em outras sequências de aplicação clínica de rotina. Para fazer face às desvantagens dos sistemas de quantificação das HSB os quais são dispendiosos, complexos, requererem tecnologia e formação específicas, recomendamos que a aplicação automatizada GUIAL, desenvolvida ao longo do nosso trabalho é de utilização elementar e prática para que seja introduzida nos sistemas de aquisição de imagem por RM com o fim de integrar o processamento de imagem nos indivíduos portadores de fatores de risco vascular. A avaliação do ADC, nesta amostra, permitiu concluir que a variação desta variável é explicada estatisticamente pela existência da condição clínica de status lacunar em ambos os hemisférios ou por outras palavras, o status lacunar influencia o valor de ADC. Embora uma pequena percentagem da variação do ADC seja explicada pelo género, o ADC nos homens foi superior ao das mulheres o que não nos surpreende, pois são também os homens onde a frequência de doença microvascular se revelou mais expressiva. Os valores do ADC, globalmente, entre os hemisférios cerebrais não mostraram alterações exceto na SB entre os idosos e não idosos. A SB da região frontal mostrou valores diminuídos na anisotropia e isotropia face às restantes áreas anatómicas. Os estudos indicam que na idade avançada existe uma maior predisposição para suscetibilidades de estrutura com status de desconexão. A classificação das HSB foi superior em indivíduos mais velhos e com status lacunar, e em menor quantidade (inferior rating de classificação) nos indivíduos idosos sem status lacunar. As alterações volumétricas foram mais frequentes no homem do que na mulher, presumivelmente devido à associação com a elevada classificação de status lacunar. Um aumento do índice de Evan correspondeu, neste estudo, ao aumento das HSB, à diminuição do volume cerebral total, à expansão ventrículo-sulcal frontal e ao aumento da medida do ângulo caloso. Estes resultados foram agravados pela classificação elevada de status lacunar nos indivíduos que apresentaram indícios de doença de pequenos vasos, com manifesto aumento dos espaços de Virchow-Robin,enfartes lacunares ou HSB. Esses resultados foram mais expressivos no género masculino do que no feminino revelando uma maior vulnerabilidade sobretudo na atrofia frontal nos homens. Por sua vez as dimensões do Corpo Caloso tornaram-se reduzidas devido à compressão dos ventrículos laterais e terceiro ventrículo. Estes indicadores tiveram expressão particularmente nos indivíduos com mais de 65 anos. ---------------------------------------------------------------------------------------------ABSTRACT: The latest neuroimaging methods, such as Magnetic Resonance Imaging (MRI), have enabled detailed images of in vivo human brain. These images reveal often unexpected findings related to the normal pattern, with high predisposition for the elderly people with forthright coexistence with vascular risk factors such as characteristics of a normal aging process. Although it has been, in the last decade, several publications on this subject, it is still little explained. All over the world have emerged disease prevention programs and health promotion developed by the Public Health sector, supported mainly by the advancement of medical technologies that have resulted, among other impacts, in a growing of the elderly population. It is estimated, in 2030, a demographic composition with 20% o people over 65 years. In this context, microvascular disease is the most common cause of cognitive vascular impairment in the elderly and senescent characteristics in the MRI trough ischemic lesions of the white matter (Leukoaraiosis) and lacunar infarcts (lacunar status), cerebral atrophy, gliosis and iron accumulation in the basal ganglia in excess.This thesis, considering the research line that stems - Life Sciences - specialization in Clinical Medicine, Biotechnology, gathers and reflects on three aspects linked to MR, interdependent and related to a common problem. The first deals with the Magnetic Resonance Technology characterization in Portugal, which includes an exploratory evaluation of the implementation of Anisotropic Diffusion technique in brain studies. The analytical dimensions studied were the Technologic, Socio-demographic and Economics. Collecting data was supported by different sources of information and was applied an exploratory methodology whose results were validated by triangulation. The research method was grouped and stratified criteria under the same analytical dimensions. The second describes the anatomical study - which was focused on radiological measurement parameters, based on the brain’s specimen under an experimental methodology applied to MRI diffusion metrics. Radiological evaluation and optimization of the weighted image diffusion in clinical studies were associated with the brain of the elderly "The Usual Brain Aging" with methodological basis based on established criteria and indicators by Rotterdam Scan Study (RSS). The main results obtained reveal the inexistence frameworks in Portugal for evaluation of equipments or Agency of Health Technology to produce studies comparing the equipment available on the market, the value for money and its allocation to clinical and epidemiological needs. It was found that the implementation of MRI equipment is strongly based on economic criteria lacking recommendations and guidelines for the rationalized use of these technologies. As the quantitative data we conclude that most of the scanners are located in private clinical institutions (80,2%); the most frequent magnetic field intensity is [1.5T] with 119 scanners; the scanners are mainly installed in Lisbon (55 units) and Porto (39 units) districts; the average ratio of equipment per capita in Portugal is 1 to 65 195 people; the gradient power with higher expression in the sample is 30-39mT / m;most of the scanners were installed in the years range [2009-2012 years] with 59 equipment; only 6 clinical placements develop clinical research and the most coils for brain studies are of Array type. The optimization study of diffusion technique revealed, as the assessment of the bvalues, the lower (b = 500 s / mm2 and b = 1000 s / mm 2), promotes an increase in the SI and SNR being this measure related to a higher image quality, however the highest b values (b = 2000 s / mm 2) have a higher CNR (Contrast to Noise-Ratio) and CR (Contrast Ratio), compared to the previous ones. This may provide less anatomical details and, thus, ower image quality, of a normal brain, however can help the interpretation and have advantages in identifying microvascular injuries when doubts persist regarding the differential diagnosis of microvascular disease of lacunar or WMH (White Matter Hyperintensities) status type. Changes on this parameter are Otimização da anisotropia fronto-calosa e [RM 1,5T] no idoso normal e com risco cérebro-vascular particularly reflected in the differences of image quality evaluation in the frontocallosum anatomical area. We conclude from the quantitative assessment of the average concentration of iron (26Fe), in all age groups to the basal ganglia, that the higher concentrations are, in descending order: Nigral Substantia, Globus pallidus, Putamen, Thalamus, Rubio nucleus and Caudate nucleus; that there is a predominance in the concentration of iron (26Fe) in the left hemisphere and that male gender show higher iron (26Fe) level tha females, in the age groups [30-40 [[40-50 [and [50- 60 [. Regarding a main conclusion of the mean concentration study of iron, in terms of age we point out that the average concentration of iron (26Fe) is higher among older groups and increases with age, especially in Nigral Substantia and Lenticular Nucleus. On the technical and radiological study we found evidence of an increased in water /diffusivity in the ubcortical white matter of the elderly compared with younger subjects. A similar relationship was assessed in the Thalamus. The increase agerelated seems to be predominantly observed in patients over 65 years which may reflect minor structural changes associated with normal aging. The results indicate that quantitative analysis of diffusion weighted imaging can provide information about the structure of the brain which is not reached only by visual inspection or standard sequences applied in clinical routine. To address the disadvantages the systems of quantification of WMH which the authors state that are costly, complex, require specific technology and training, we recommend that the automated application GUIAL, developed over our work is basic and practical to use and to be introduced in MR image systems acquisition in order to integrate image processing in patients with vascular risk factors. The evaluation of the ADC showed that its variation is statistically explained by the existence of the medical condition of lacunar status, in both hemispheres, or in other words, the lacunar status influences the ADC value. Although a small percentage of the ADC variation is explained by gender, the ADC in men was higher than women which Otimização da anisotropia fronto-calosa e [RM 1,5T] no idoso normal e com risco cérebro-vascular do not surprise us, since they are also men where the frequency of microvasculardisease has proved more significant. The values of ADC, overall, between the cerebral hemispheres showed no changes but were different in WM among the elderly and non-elderly subjects.The WM's forehead showed decreased values in anisotropy and isotropy face the other anatomical areas. The studies indicate that in old age there is a greater tendency to higher susceptibility to disconnection- status framework. The classification of WMH was higher in elderly people and lacunar status, and fewer (lower classification rating) in the elderly without lacunar status. volumetric changes were more frequent in men than in women, most probably because of its association with high lacunar status rating. An increase of Evan index corresponded, in this study, to an increase in WMH, to a decreased of total brain volume, to a ventricle sulcal frontal and callous angle expansion. These results were wound up by high ranking of lacunar status in subjects who had small vessel disease, clear increase in spaces of Virchow-Robin, lacunar infarctions or WMH. These results were more significant in males than in females revealing vulnerability particularly in the frontal atrophy in men. In turn the size of Corpus Callosum because reduced due to the compression of the lateral and third ventricles. These indicators had expression particularly in individuals over 65 years.

Application of NMR RDC’s, relaxation and self-diffusion for the study of dynamic processes of small molecules in solution

Spin-lattice Relaxation, self-Diffusion coefficients and Residual Dipolar Couplings (RDC’s) are the basis of well established Nuclear Magnetic Resonance techniques for the physicochemical study of small molecules (typically organic compounds and natural products with MW < 1000 Da), as they proved to be a powerful and complementary source of information about structural dynamic processes in solution. The work developed in this thesis consists in the application of the earlier-mentioned NMR techniques to explore, analyze and systematize patterns of the molecular dynamic behavior of selected small molecules in particular experimental conditions. Two systems were chosen to investigate molecular dynamic behavior by these techniques: the dynamics of ion-pair formation and ion interaction in ionic liquids (IL) and the dynamics of molecular reorientation when molecules are placed in oriented phases (alignment media). The application of NMR spin-lattice relaxation and self-diffusion measurements was applied to study the rotational and translational molecular dynamics of the IL: 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF4]. The study of the cation-anion dynamics in neat and IL-water mixtures was systematically investigated by a combination of multinuclear NMR relaxation techniques with diffusion data (using by H1, C13 and F19 NMR spectroscopy). Spin-lattice relaxation time (T1), self-diffusion coefficients and nuclear Overhauser effect experiments were combined to determine the conditions that favor the formation of long lived [BMIM][BF4] ion-pairs in water. For this purpose and using the self-diffusion coefficients of cation and anion as a probe, different IL-water compositions were screened (from neat IL to infinite dilution) to find the conditions where both cation and anion present equal diffusion coefficients (8% water fraction at 25 ºC). This condition as well as the neat IL and the infinite dilution were then further studied by 13C NMR relaxation in order to determine correlation times (c) for the molecular reorientational motion using a mathematical iterative procedure and experimental data obtained in a temperature range between 273 and 353 K. The behavior of self-diffusion and relaxation data obtained in our experiments point at the combining parameters of molar fraction 8 % and temperature 298 K as the most favorable condition for the formation of long lived ion-pairs. When molecules are subjected to soft anisotropic motion by being placed in some special media, Residual Dipolar Couplings (RDCs), can be measured, because of the partial alignment induced by this media. RDCs are emerging as a powerful routine tool employed in conformational analysis, as it complements and even outperforms the approaches based on the classical NMR NOE or J3 couplings. In this work, three different alignment media have been characterized and evaluated in terms of integrity using 2H and 1H 1D-NMR spectroscopy, namely the stretched and compressed gel PMMA, and the lyotropic liquid crystals CpCl/n-hexanol/brine and cromolyn/water. The influence that different media and degrees of alignment have on the dynamic properties of several molecules was explored. Different sized sugars were used and their self-diffusion was determined as well as conformation features using RDCs. The results obtained indicate that no influence is felt by the small molecules diffusion and conformational features studied within the alignment degree range studied, which was the 3, 5 and 6 % CpCl/n-hexanol/brine for diffusion, and 5 and 7.5 % CpCl/n-hexanol/brine for conformation. It was also possible to determine that the small molecules diffusion verified in the alignment media presented close values to the ones observed in water, reinforcing the idea of no conditioning of molecular properties in such media.

Transport mechanism in ionic liquid membranes and the study of thiomersal biodegradation

The initial goal of this work was the development of a supported liquid membrane (SLM) bioreactor for the remediation of vaccine production effluents contaminated with a highly toxic organomercurial – thiomersal. Therefore, two main aspects were focused on: 1) the development of a stable supported liquid membrane – using room temperature ionic liquids (RTILs) – for the selective transport of thiomersal from the wastewater to a biological compartment, 2) study of the biodegradation kinetics of thiomersal to metallic mercury by a Pseudomonas putida strain. The first part of the work focused on the evaluation of the physicochemical properties of ionic liquids and on the SLMs’ operational stability. The results obtained showed that, although it is possible to obtain a SLM with a high stability, water possesses nonnegligible solubility in the RTILs studied. The formation of water clusters inside the hydrophobic ionic liquid was identified and found to regulate the transport of water and small ions. In practical terms, this meant that, although it was possible to transport thiomersal from the vaccine effluent to the biological compartment, complete isolation of the microbial culture could not be guaranteed and the membrane might ultimately be permeable to other species present in the aqueous vaccine wastewater. It was therefore decided not to operate the initially targeted integrated system but, instead, the biological system by itself. Additionally, attention was given to the development of a thorough understanding of the transport mechanisms involved in the solubilisation and transport of water through supported liquid membranes with RTILs as well as to the evaluation of the effect of water uptake by the SLM in the transport mechanisms of water-soluble solutes and its effect on SLM performance. The results obtained highlighted the determinant role played by water – solubilised inside the ionic liquids – on the transport mechanism. It became clear that the transport mechanism of water and water-soluble solutes through SLMs with [CnMIM][PF6] RTILs was regulated by the dynamics of water clusters inside the RTIL, rather than by molecular diffusion through the bulk of the ionic liquid. Although the stability tests vi performed showed that there were no significant losses of organic phase from the membrane pores, the formation of water clusters inside the ionic liquid, which constitute new, non-selective environments for solute transport, leads to a clear deterioration of SLM performance and selectivity. Nevertheless, electrical impedance spectroscopy characterisation of the SLMs showed that the formation of water clusters did not seem to have a detrimental effect on the SLMs’ electrical characteristics and highlighted the potential of using this type of membranes in electrochemical applications with low resistance requirements. The second part of the work studied the kinetics of thiomersal degradation by a pure culture of P. putida spi3 strain, in batch culture and using a synthe tic wastewater. A continuous ly stirred tank reactor fed with the synthetic wastewater was also operated and the bioreactor’s performance and robustness, when exposed to thiomersal shock loads, were evaluated. Finally, a bioreactor for the biological treatment of a real va ccine production effluent was set up and operated at different dilution rates. Thus it was possible to treat a real thiomersal-contaminated effluent, lowering the outlet mercury concentration to values below the European limit for mercury effluent discharges.

Revealing fungal activity in the presence of ionic liquids

Dissertation presented to obtain the Ph.D degree in Biochemistry

Study on solubility of pharmaceutical compounds in ionic liquids

Dissertation to obtain the degree of master in Chemical and Biochemical Engineering

Exploring ionic liquids′ unique stimuli to elucidate uncharacterised cellular and molecular mechanisms in filamentous fungi

The emergence of new fungal pathogens, either of plants or animals, and the increasing number of reported cases of resistant human pathogenic strains to the available antifungal drugs reinforces the need for better understanding the biology of filamentous fungi. Conventional drugs target components of the fungal membrane or cell wall, therefore identifying novel intracellular targets, yet unique to fungi, is a global priority.(...)

Design of bio-inspired ionic liquids for protein stabilisation

Ionic Liquids (ILs) consist in organic salts that are liquid at/or near room temperature. Since ILs are entirely composed of ions, the formation of ion pairs is expected to be one essential feature for describing solvation in ILs. In recent years, protein - ionic liquid (P-IL) interactions have been the subject of intensive studies mainly because of their capability to promote folding/unfolding of proteins. However, the ion pairs and their lifetimes in ILs in P-IL thematic is dismissed, since the action of ILs is therefore the result of a subtle equilibrium between anion-cation interaction, ion-solvent and ion-protein interaction. The work developed in this thesis innovates in this thematic, once the design of ILs for protein stabilisation was bio-inspired in the high concentration of organic charged metabolites found in cell milieu. Although this perception is overlooked, those combined concentrations have been estimated to be ~300 mM among the macromolecules at concentrations exceeding 300 g/L (macromolecular crowding) and transient ion-pair can naturally occur with a potential specific biological role. Hence the main objective of this work is to develop new bio-ILs with a detectable ion-pair and understand its effects on protein structure and stability, under crowding environment, using advanced NMR techniques and calorimetric techniques. The choline-glutamate ([Ch][Glu]) IL was synthesized and characterized. The ion-pair was detected in water solutions using mainly the selective NOE NMR technique. Through the same technique, it was possible to detect a similar ion-pair promotion under synthetic and natural crowding environments. Using NMR spectroscopy (protein diffusion, HSQC experiments, and hydrogen-deuterium exchange) and differential scanning calorimetry (DSC), the model protein GB1 (production and purification in isotopic enrichment media) it was studied in the presence of [Ch][Glu] under macromolecular crowding conditions (PEG, BSA, lysozyme). Under dilute condition, it is possible to assert that the [Ch][Glu] induces a preferential hydration by weak and non-specific interactions, which leads to a significant stabilisation. On the other hand, under crowding environment, the [Ch][Glu] ion pair is promoted, destabilising the protein by favourable weak hydrophobic interactions , which disrupt the hydration layer of the protein. However, this capability can mitigates the effect of protein crowders. Overall, this work explored the ion-pair existence and its consequences on proteins in conditions similar to cell milieu. In this way, the charged metabolites found in cell can be understood as key for protein stabilisation.