Network signatures based on gene pair expression ratios improve classification and the analysis of muscle-invasive urothelial cancer

Urothelial cancer (UC) is highly recurrent and can progress from non-invasive (NMIUC) to a more aggressive muscle-invasive (MIUC) subtype that invades the muscle tissue layer of the bladder. We present a proof of principle study that network-based features of gene pairs can be used to improve classifier performance and the functional analysis of urothelial cancer gene expression data. In the first step of our procedure each individual sample of a UC gene expression dataset is inflated by gene pair expression ratios that are defined based on a given network structure. In the second step an elastic net feature selection procedure for network-based signatures is applied to discriminate between NMIUC and MIUC samples. We performed a repeated random subsampling cross validation in three independent datasets. The network signatures were characterized by a functional enrichment analysis and studied for the enrichment of known cancer genes. We observed that the network-based gene signatures from meta collections of proteinprotein interaction (PPI) databases such as CPDB and the PPI databases HPRD and BioGrid improved the classification performance compared to single gene based signatures. The network based signatures that were derived from PPI databases showed a prominent enrichment of cancer genes (e.g., TP53, TRIM27 and HNRNPA2Bl). We provide a novel integrative approach for large-scale gene expression analysis for the identification and development of novel diagnostical targets in bladder cancer. Further, our method allowed to link cancer gene associations to network-based expression signatures that are not observed in gene-based expression signatures.

Identity of a Tilapia Pheromone Released by Dominant Males that Primes Females for Reproduction

Knowledge of the chemical identity and role of urinary pheromones in fish is scarce, yet it is necessary in order to understand the integration of multiple senses in adaptive responses and the evolution of chemical communication [1]. In nature, Mozambique tilapia (Oreochromis mossambicus) males form hierarchies, and females mate preferentially with dominant territorial males, which they visit in aggregations or leks [2]. Dominant males have thicker urinary bladder muscular walls than subordinates or females and store large volumes of urine, which they release at increased frequency in the presence of subordinate males or preovulatory, but not postspawned, females [3–5]. Females exposed to dominant-male urine augment their release of the oocyte maturation-inducing steroid 17α,20β-dihydroxypregn-4-en-3-one (17,20β-P) [6]. Here we isolate and identify a male Mozambique tilapia urinary sex pheromone as two epimeric (20α- and 20β-) pregnanetriol 3-glucuronates. We show that both males and females have high olfactory sensitivity to the two steroids, which cross-adapt upon stimulation. Females exposed to both steroids show a rapid, 10-fold increase in production of 17,20β-P. Thus, the identified urinary steroids prime the female endocrine system to accelerate oocyte maturation and possibly promote spawning synchrony. Tilapia are globally important as a food source but are also invasive species, with devastating impact on local freshwater ecosystems [7, 8]. Identifying the chemical cues that mediate reproduction may lead to the development of tools for population control [9–11].

Mitochondrial plasticity in pathophysiological conditions

Both skeletal and cardiac muscles daily burn tremendous amounts of ATP to meet the energy requirements for contraction. So, it is not surprising that the maintenance of mitochondrial morphology, number, distribution and functionality in striated muscle are important for muscle homeostasis. In these tissues mitochondria present the added dimension of two populations, the intermyofibrillar (IMF) and the subsarcolemmal (SS) mitochondria, being IMF the most abundant one. In the present thesis, the molecular mechanisms harboured in mitochondria of striated muscles were studied using animal models, to better comprehend the role of mitochondrial plasticity in several pathophysiological conditions such as aging, diabetes mellitus and bladder cancer. The comparative analysis of IMF and SS populations isolated from heart evidenced a higher respiratory chain activity of mitochondria interspersed in the contractile apparatus. The higher susceptible of SS respiratory chain complexes subunits to carbonylation, but not to nitration, seems to justify the lower respiratory chain activity observed in this mitochondrial population. Our results showed that in heart from aged mice there is an accumulation of dysfunctional mitochondria. The age-related decrease of oxidative phosphorylation activity seems to be justified, at least partially, by the increased proneness of mitochondrial proteins as OXPHOS subunits and MnSOD to oxidative modifications. Moreover, a sedentary lifestyle seems to worsen the functional consequences of aging in heart by increasing mitochondrial proteins susceptibility to nitration. In skeletal muscle from rats with type 1 diabetes mellitus induced by streptozotocin administration, we verified the accumulation of dysfunctional mitochondria due, at least in part, to the impairment of PQC system. Indeed, the decreased activity of AAA proteases was accompanied by the accumulation of oxidatively modified mitochondrial proteins with impact in respiratory chain activity. The diminishing of mitochondria activity also underlies cancer-induced muscle wasting. Indeed, using a rat model of chemically induced urothelial carcinoma we verified that the loss of gastrocnemius mass was related to mitochondrial dysfunction due to, at least partially, the down-regulation of PQC system involving the mitochondrial proteases paraplegin and Lon. PQC impairment resulted in the accumulation of oxidatively modified mitochondrial proteins. In overall, regardless the pathophysiological stimuli that promote mitochondrial alterations, there are similarities in the pattern of disease-related mitochondrial plasticity. The diminished capacity for ATP production in striated muscle seems to be due to increased oxidative damage of mitochondrial proteins, namely subunits of respiratory chain complexes, metabolic proteins and MnSOD. Our data highlighted, for the first time, the impact of mitochondrial PQC system impairment in the accumulation of oxidized proteins, exacerbating the dysfunction of this organelle in striated muscle in several pathophysiological conditions.

Phthalocyanines : interaction with carbon structures and as PDT agents

This dissertation describes the synthesis and characterization of different phthalocyanine (Pc) derivatives, as well as some porphyrins (Pors), for supramolecular interaction with different carbon nanostructures, to evaluate their potential application in electronic nanodevices. Likewise, it is also reported the preparation and biological evaluation of interesting phthalocyanine conjugates for cancer photodynamic therapy (PDT) and microorganisms photodynamic inactivation (PDI). The phthalonitrile precursors were prepared from commercial phthalonitriles by nucleophilic substitution of -NO2, -Cl, or -F groups, present in the phthalonitrile core, by thiol or pyridyl units. After the synthesis of these phthalonitriles, the corresponding Pcs were prepared by ciclotetramerization using a metallic salt as template at high temperatures. A second strategy involved the postfunctionalization of hexadecafluorophthalocyaninato zinc(II) through the adequate substituents of mercaptopyridine or cyclodextrin units on the macrocycle periphery. The different compounds were structurally characterized by diverse spectroscopic techniques, namely 1H, 13C and 19F nuclear magnetic resonance spectroscopies (attending the elemental composition of each structure); absorption and emission spectroscopy, and mass spectrometry. For the specific photophysical studies were also used electrochemical characterization, femtosecond and raman spectroscopy, transmission electron and atomic force microscopy. It was highlighted the noncovalent derivatisation of carbon nanostructures, mainly single wall carbon nanotubes (SWNT) and graphene nanosheets with the prepared Pc conjugates to study the photophysical properties of these supramolecular nanoassemblies. Also, from pyridyl-Pors and ruthenium phthalocyanines (RuPcs) were performed Por-RuPcs arrays via coordination chemistry. The results obtained of the novel supramolecular assemblies showed interesting electron donor-acceptor interactions and might be considered attractive candidates for nanotechnological devices. On the other hand, the amphiphilic phthalocyanine-cyclodextrin (Pc-CD) conjugates were tested in biological trials to assess their ability to inhibit UMUC- 3 human bladder cancer cells. The results obtained demonstrated that these photoactive conjugates are highly phototoxic against human bladder cancer cells and could be applied as promising PDT drugs.

Impact of exercise training on cancer-induced cardiac dysfunction

Cachexia is a complex syndrome characterized by severe weight loss frequently observed in cancer patients and associated with poor prognosis. Cancer cachexia is also related to modifications in cardiac muscle structure and metabolism leading to cardiac dysfunction. In order to better understand the cardiac remodeling induced by bladder cancer and the impact of exercise training after diagnosis on its regulation, we used an animal model of bladder cancer induced by exposition to N-butyl-N-(4-hydroxybutyl)-nitrosamine (BBN) in the drinking water. Healthy animals and previously BBN exposed animals were submitted to a training program in a treadmill at a speed of 20m/min, 60 min/day, 5 days/week during 13 weeks. At the end of the protocol, animals exposed to BBN presented a significant decrease of body weight, in comparison with control groups, supporting the presence of cancer cachexia. Morphological analysis of the cardiac muscle sections revealed the presence of fibrosis and a significant decrease of cardiomyocyte’s cross-sectional area, suggesting the occurrence of cardiac dysfunction associated with bladder cancer. These modifications were accompanied by heart metabolic remodeling characterized by a decreased fatty acid oxidation given by diminished levels of ETFDH and of complex II subunit  from the respiratory chain. Exercise training promoted an increment of connexin 43, a protein involved in cardioprotection, and of c-kit, a protein present in cardiac stem cells. These results suggest an improved heart regenerative capacity induced by exercise training. In conclusion, endurance training seems an attractive non-pharmacological therapeutic option for the management of cardiac dysfunction in cancer cachexia.

Does this case hold the answer to one of the worse types of pain in medicine--that of loin pain haematuria syndrome (LPHS)

A patient with loin pain haematuria syndrome suffering chronic throbbing pulsing pain overlaid with prolonged periods of incapacitating colic and overnight vomiting was presented 10 months following diagnosis. Ultrasound was normal. No renal or ureteral stones, or filling defects were seen on CT. At cytoscopy, bladder and urethra were normal, and bloody urine effluxed from the left ureteric orifice. The ureters were normal at diagnosis, and developed new abutting non‐penetrating calcifications by 8 months. Pain episodes of complete incapacitating intensity of 2–4 h duration were reduced to 10 min with 5 mg crushed tadalafil administered at onset. If tadalafil was delayed to after onset, the original course of agony resulted. Daily tadalafil reduced loin pain intensity, but not the exacerbations. Tadalafil efficacy may indicate that the pain exacerbations are due to spasm of ureter smooth muscle. 5 mg tadalafil taken at onset alleviated severe loin pain exacerbations in this case of loin pain haematuria syndrome.

Efeito de um concentrado de microalgas liofilizadas na larvicultura de dourada, Sparus aurata

Dissesrtação de Mestrado, Biologia Marinha, Especialização em Pescas e Aquacultura, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2009

Organic-walled dinoflagellate cysts in recent sediments from the Guadiana river estuary, South-East Portugal

Dissertação de Mestrado, Biologia Marinha, Faculdade de Ciências do Mar e do Ambiente, Universidade do Algarve, 2007

The role of papyrus plants (Cyperus papyrus) and internal waves in the nutrient balance of Lake Victoria, East Africa

Dissertação mest., Gestão da água e da costa, Universidade do Algarve, 2007

Hydrodynamic and sediment fluxes through the inlets of the Ria Formosa

Tese de dout., Ciências do Mar, da Terra e do Ambiente (Ciências do Mar-Oceanografia Física), Faculdade de Ciências e Tecnologia, Univ. do Algarve, 2011

Formas, estruturas e modelos de Governance: o caso do Parque Enxerim

O presente projeto apresentado visa estudar à luz da informação disponível as formas e estruturas societárias assim como os possíveis modelos de Governance aplicados a um centro comercial: O caso do Parque Enxerim. Na metodologia apresentada é definido o modelo do centro comercial selecionado: Factory Outlet Center. A orientação deste projeto encontra-se exposta na revisão de literatura, sendo os objetivos principais, ao longo desta revisão, estudar quais as possibilidades societárias, com ou sem personalidade jurídica, para implementar o desenvolvimento do Factory Outlet Center. As sociedades anónimas e os fundos de investimento imobiliário tornam-se o objeto de estudo como veículos para a implementação do projeto do centro comercial. Como contribuição para a escolha da estrutura, sociedade anónima versus fundo de investimento imobiliário, a eficiência fiscal foi um dos temas primordiais a ter em conta. Os modelos de Corporate Govenance conduzem, em última instância, à maximização do valor acionista a longo prazo. Os resultados obtidos permitem concluir que, consoante a origem dos fundos para a concretização do projeto assim se optará pelo tipo de organização e o modelo societário. A relação entre gastos e rendimentos deverá também ser equacionada atendendo à dimensão da estrutura, em termos fiscais e de Corporate Governance.

Évaluation prospective de l’état nutritionnel et risque de complications post-opératoires de la cystectomie radicale

La cystectomie radicale est le traitement de référence pour les cancers de la vessie infiltrant le muscle. Cette chirurgie entraine un taux élevé de complications et diminue la qualité de vie des patients à court et à long terme. Une revue de la littérature a d’abord été effectuée afin d’identifier les facteurs de l’état nutritionnel associés au risque de complications et de mortalité après la cystectomie radicale. L’hypoalbuminémie a été identifiée comme un prédicteur potentiel de la mortalité post-opératoire. Une étude de cohorte a ensuite été menée afin d’identifier des facteurs de l’état nutritionnel associés au risque de développer des complications après cette chirurgie. Un indice de masse corporelle élevé, une baisse de l’appétit, une perte de poids, une hypo-albuminémie et une hypo-préalbuminémie avant l’opération sont les facteurs qui ont été associés au développement de complications post-opératoires. Des analyses et des études supplémentaires doivent être menées dans l’optique développer des interventions qui pourraient diminuer le risque de complications après la cystectomie radicale.

Modeling and simulation of spray drying processes based on quality by design principles

Tese de doutoramento, Farmácia (Tecnologia Farmacêutica), Universidade de Lisboa, Faculdade de Farmácia, 2014

Assessing energy consumption in supply chains

The paper addresses the transport activities and associated energy consumption involved in the production and supply of two products: jeans and yoghurt. In the case of jeans, the analysis is from the locations in which cotton is grown, to retail outlets in the UK; in the case of yoghurt, the analysis is from the supply of milk on farms, to retail outlets in France. The results show that the transport stages from the point of jeans manufacture to UK port are responsible for the greatest proportion of transport energy use per kilogram of jeans in the UK supply chain. In the case of the French yoghurt supply chains, the results indicate that each of the three transport stages from farm to third-party distribution centre consume approximately the same proportion of total freight transport energy. The energy used on the transport stage for yoghurt from third-party distribution centre to retail outlet varies depending on the type of retail outlet served. Far greater quantities of energy are used in transporting jeans than yoghurts from farm/field to retail outlet. This is explained by the distances involved in the respective supply chains. Both case studies demonstrate that the energy used by consumers transporting goods to their homes by car can be as great as total freight transport energy used in the supply chain from farm/field to retail outlet (per kilogram of product transported).

Energy efficiency and greenhouse gas emissions of different supply chains: a comparison of French, UK and Belgian cases

Freight transportation system is critical to economic activity but it carries significant environmental costs, notably GHG emissions and climate change : energy use and corresponding CO2 emissions is increasing faster in freight transport than in other sectors and this increase is primarily the result of increased trade. This paper compares the transport activities, associated energy consumption and CO2 emissions of different supply chains for a range of products in three countries: Belgium, France and United Kingdom. Among the products considered are furniture and ‘fruits & vegetables’. For each of these products, different supply chains, involving more or less transport activity and associated energy consumption are analysed in each country. The comparison highlights some of the main factors that influence GHG emissions for different supply chains and illustrates how they vary according to product and country of final distribution. In more detail, the paper addresses the main differences between the supply chains of these products namely, the origin of their sourcing, the logistical organisation between production and retail and different types of retail outlet. The origin of the sourcing impact is mainly related to distance. The impact of the logistical organisation between raw material and retail on GHG emissions is linked to the mode and vehicle choice and to the load factor. As for retail, the consumer trip emissions, between his home and the retail outlet, are also an important part of the whole supply chain emissions. It is worthwhile to notice that our goal in this project is to consider the whole supply chain, from production to consumption. Therefore a particular focus is put on the mobility behaviours of consumers purchasing the studied products during their shopping and dropping back home activities related to these products. Especially a web based survey has been conducted and the gathered results offer an opportunity for drawing a more detailed picture of the associated CO2 emissions. This paper uses the results of an ongoing research on supply chain energy efficiency, funded by ADEME (the French Energy Agency) through the French program on transport research (PREDIT). This research is based on a comprehensive review of the various approaches to quantifying the environmental impacts of supply chains together with data collection from a range of organisations including manufacturers, retailers and transport companies. We will first present the developed methodologies, then the results corresponding to each studied product will be described. A discussion of the potential application of the research approach to the wider debate about the environmental impact of freight transport and the scope for GHG emissions reduction targets to be achieved will be included.