Complex networks and data mining: toward a new perspective for the understanding of complex systems

Complex systems, i.e. systems composed of a large set of elements interacting in a non-linear way, are constantly found all around us. In the last decades, different approaches have been proposed toward their understanding, one of the most interesting being the Complex Network perspective. This legacy of the 18th century mathematical concepts proposed by Leonhard Euler is still current, and more and more relevant in real-world problems. In recent years, it has been demonstrated that network-based representations can yield relevant knowledge about complex systems. In spite of that, several problems have been detected, mainly related to the degree of subjectivity involved in the creation and evaluation of such network structures. In this Thesis, we propose addressing these problems by means of different data mining techniques, thus obtaining a novel hybrid approximation intermingling complex networks and data mining. Results indicate that such techniques can be effectively used to i) enable the creation of novel network representations, ii) reduce the dimensionality of analyzed systems by pre-selecting the most important elements, iii) describe complex networks, and iv) assist in the analysis of different network topologies. The soundness of such approach is validated through different validation cases drawn from actual biomedical problems, e.g. the diagnosis of cancer from tissue analysis, or the study of the dynamics of the brain under different neurological disorders.

The role of qualitative data and systems thinking in addressing service decline in market towns

Retail services are a main contributor to municipal budget and are an activity that affects perceived quality-of-life, especially for those with mobility difficulties (e.g. the elderly, low income citizens). However, there is evidence of a decline in some of the services market towns provide to their citizens. In market towns, this decline has been reported all over the western world, from North America to Australia. The aim of this research was to understand retail decline and enlighten on some ways of addressing this decline, using a case study, Thornbury, a small town in the Southwest of England. Data collected came from two participatory approaches: photo-surveys and multicriteria mapping. The interpretation of data came from using participants as analysts, but also, using systems thinking (systems diagramming and social trap theory) for theory building. This research moves away from mainstream economic and town planning perspectives by making use of different methods and concepts used in anthropology and visual sociology (photo-surveys), decision-making and ecological economics (multicriteria mapping and social trap theory). In sum, this research has experimented with different methods, out of their context, to analyse retail decline in a small town. This research developed a conceptual model for retail decline and identified the existence of conflicting goals and interests and their implications for retail decline, as well as causes for these. Most of the potential causes have had little attention in the literature. This research also identified that some of the measures commonly used for dealing with retail decline may be contributing to the causes of retail decline itself. Additionally, this research reviewed some of the measures that can be used to deal with retail decline, implications for policy-making and reflected on the use of the data collection and analysis methods in the context of small to medium towns.

Epidemiology of the viral hepatitis B and C in female prisoners of Metropolitan Regional Prison Complex in the State of Goiás, Central Brazil

INTRODUCTION: Little information regarding hepatitis B virus (HBV) and hepatitis C virus (HCV) infections among Brazilian female prisoners exists. This study investigated the prevalence and risk factors associated with HBV and HCV infections and identified viral genotypes among female prisoners in Goiás, Central Brazil. METHODS: Women incarcerated in the largest prison in the State of Goiás were invited to participate in the study. All female prisoners were interviewed and tested for the detection of hepatitis B surface antigen (HBsAg), antibodies against HBsAg (anti-HBs), against hepatitis B core antigen (anti-HBc), and antibody against HCV (anti-HCV) by ELISA. HBsAg and anti-HCV positive samples were tested for HBV DNA and HCV RNA and genotyped, respectively. RESULTS: Participants (n=148; 98.6%) completed the study with an overall HBV prevalence of 18.9%. Age >30 years, a low education level, sex with a sexually transmitted diseases carrier, and a male sexual partner serving in the same penitentiary were associated with HBV infections. Only 24% of the women were anti-HBs positive suggesting previous HBV vaccination. Nine female prisoners (6.1%) were anti-HCV positive. Age >40 years, injecting drug use and length of incarceration were statistically associated with anti-HCV antibodies. Five samples were HCV RNA positive and classified as genotypes 1 (subtypes 1a; n=3 and 1b; n=1) and 3 (subtype 3a; n=1). The HBsAg-reactive sample was HBV DNA positive and genotype A. CONCLUSIONS: These findings highlight the necessity of public policies to control hepatitis B and C infections and emphasize the importance of hepatitis B vaccination in prison environments.

Essays on bounded rationality: Individual decision and strategic interaction

Economics is a social science which, therefore, focuses on people and on the decisions they make, be it in an individual context, or in group situations. It studies human choices, in face of needs to be fulfilled, and a limited amount of resources to fulfill them. For a long time, there was a convergence between the normative and positive views of human behavior, in that the ideal and predicted decisions of agents in economic models were entangled in one single concept. That is, it was assumed that the best that could be done in each situation was exactly the choice that would prevail. Or, at least, that the facts that economics needed to explain could be understood in the light of models in which individual agents act as if they are able to make ideal decisions. However, in the last decades, the complexity of the environment in which economic decisions are made and the limits on the ability of agents to deal with it have been recognized, and incorporated into models of decision making in what came to be known as the bounded rationality paradigm. This was triggered by the incapacity of the unboundedly rationality paradigm to explain observed phenomena and behavior. This thesis contributes to the literature in three different ways. Chapter 1 is a survey on bounded rationality, which gathers and organizes the contributions to the field since Simon (1955) first recognized the necessity to account for the limits on human rationality. The focus of the survey is on theoretical work rather than the experimental literature which presents evidence of actual behavior that differs from what classic rationality predicts. The general framework is as follows. Given a set of exogenous variables, the economic agent needs to choose an element from the choice set that is avail- able to him, in order to optimize the expected value of an objective function (assuming his preferences are representable by such a function). If this problem is too complex for the agent to deal with, one or more of its elements is simplified. Each bounded rationality theory is categorized according to the most relevant element it simplifes. Chapter 2 proposes a novel theory of bounded rationality. Much in the same fashion as Conlisk (1980) and Gabaix (2014), we assume that thinking is costly in the sense that agents have to pay a cost for performing mental operations. In our model, if they choose not to think, such cost is avoided, but they are left with a single alternative, labeled the default choice. We exemplify the idea with a very simple model of consumer choice and identify the concept of isofin curves, i.e., sets of default choices which generate the same utility net of thinking cost. Then, we apply the idea to a linear symmetric Cournot duopoly, in which the default choice can be interpreted as the most natural quantity to be produced in the market. We find that, as the thinking cost increases, the number of firms thinking in equilibrium decreases. More interestingly, for intermediate levels of thinking cost, an equilibrium in which one of the firms chooses the default quantity and the other best responds to it exists, generating asymmetric choices in a symmetric model. Our model is able to explain well-known regularities identified in the Cournot experimental literature, such as the adoption of different strategies by players (Huck et al. , 1999), the inter temporal rigidity of choices (Bosch-Dom enech & Vriend, 2003) and the dispersion of quantities in the context of di cult decision making (Bosch-Dom enech & Vriend, 2003). Chapter 3 applies a model of bounded rationality in a game-theoretic set- ting to the well-known turnout paradox in large elections, pivotal probabilities vanish very quickly and no one should vote, in sharp contrast with the ob- served high levels of turnout. Inspired by the concept of rhizomatic thinking, introduced by Bravo-Furtado & Côrte-Real (2009a), we assume that each per- son is self-delusional in the sense that, when making a decision, she believes that a fraction of the people who support the same party decides alike, even if no communication is established between them. This kind of belief simplifies the decision of the agent, as it reduces the number of players he believes to be playing against { it is thus a bounded rationality approach. Studying a two-party first-past-the-post election with a continuum of self-delusional agents, we show that the turnout rate is positive in all the possible equilibria, and that it can be as high as 100%. The game displays multiple equilibria, at least one of which entails a victory of the bigger party. The smaller one may also win, provided its relative size is not too small; more self-delusional voters in the minority party decreases this threshold size. Our model is able to explain some empirical facts, such as the possibility that a close election leads to low turnout (Geys, 2006), a lower margin of victory when turnout is higher (Geys, 2006) and high turnout rates favoring the minority (Bernhagen & Marsh, 1997).

Molecular identification and antifungal susceptibility profiles of Candida parapsilosis complex species isolated from culture collection of clinical samples

AbstractINTRODUCTION:Candida parapsilosis is a common yeast species found in cases of onychomycosis and candidemia associated with infected intravascular devices. In this study, we differentiated Candida parapsilosis sensu stricto, Candida orthopsilosis , and Candida metapsilosis from a culture collection containing blood and subungual scraping samples. Furthermore, we assessed the in vitro antifungal susceptibility of these species to fluconazole, itraconazole, voriconazole, posaconazole, amphotericin B, and caspofungin.METHODS:Differentiation of C. parapsilosis complex species was performed by amplification of the secondary alcohol dehydrogenase (SADH) gene and digestion by the restriction enzyme Ban I. All isolates were evaluated for the determination of minimal inhibitory concentrations using Etest, a method for antifungal susceptibility testing.RESULTS:Among the 87 isolates, 78 (89.7%) were identified as C. parapsilosis sensu stricto , five (5.7%) were identified as C. orthopsilosis , and four (4.6%) were identified as C. metapsilosis . Analysis of antifungal susceptibility showed that C. parapsilosis sensu strictoisolates were less susceptible to amphotericin B and itraconazole. One C. parapsilosis sensu stricto isolate was resistant to amphotericin B and itraconazole. Moreover, 10.2% of C. parapsilosis sensu stricto isolates were resistant to caspofungin. Two C. parapsilosis sensu strictoisolates and one C. metapsilosis isolate were susceptible to fluconazole in a dose-dependent manner.CONCLUSIONS:We reported the first molecular identification of C. parapsilosiscomplex species in State of Goiás, Brazil. Additionally, we showed that although the three species exhibited differences in antifungal susceptibility profiles, the primary susceptibility of this species was to caspofungin.

Production and characterization of Chitin-Glucan Complex by Komagataella pastoris

This thesis was focused on the production, extraction and characterization of chitin:β-glucan complex (CGC). In this process, glycerol byproduct from the biodiesel industry was used as carbon source. The selected CGC producing yeast was Komagataella pastoris (formerly known as Pichia pastoris), due the fact that to achieved high cell densities using as carbon source glycerol from the biodiesel industry. Firstly, a screening of K. pastoris strains was performed in shake flask assays, in order to select the strain of K. pastoris with better performance, in terms of growth, using glycerol as a carbon source. K. pastoris strain DSM 70877 achieved higher final cell densities (92-97 g/l), using pure glycerol (99%, w/v) and in glycerol from the biodiesel industry (86%, w/v), respectively, compared to DSM 70382 strain (74-82 g/l). Based on these shake flask assays results, the wild type DSM 70877 strain was selected to proceed for cultivation in a 2 l bioreactor, using glycerol byproduct (40 g/l), as sole carbon source. Biomass production by K. pastoris was performed under controlled temperature and pH (30.0 ºC and 5.0, respectively). More than 100 g/l biomass was obtained in less than 48 h. The yield of biomass on a glycerol basis was 0.55 g/g during the batch phase and 0.63 g/g during the fed-batch phase. In order to optimize the downstream process, by increasing extraction and purification efficiency of CGC from K. pastoris biomass, several assays were performed. It was found that extraction with 5 M NaOH at 65 ºC, during 2 hours, associated to neutralization with HCl, followed by successive washing steps with deionised water until conductivity of ≤20μS/cm, increased CGC purity. The obtained copolymer, CGCpure, had a chitin:glucan molar ratio of 25:75 mol% close to commercial CGC samples extracted from A. niger mycelium, kiOsmetine from Kitozyme (30:70 mol%). CGCpure was characterized by solid-state Nuclear Magnetic Resonance (NMR) spectroscopy and Differential Scanning Calorimetry (DCS), revealing a CGC with higher purity than a CGC commercial (kiOsmetine). In order to optimize CGC production, a set of batch cultivation experiments was performed to evaluate the effect of pH (3.5–6.5) and temperature (20–40 ºC) on the specific cell growth rate, CGC production and polymer composition. Statistical tools (response surface methodology and central composite design) were used. The CGC content in the biomass and the volumetric productivity (rp) were not significantly affected within the tested pH and temperature ranges. In contrast, the effect of pH and temperature on the CGC molar ratio was more pronounced. The highest chitin: β-glucan molar ratio (> 14:86) was obtained for the mid-range pH (4.5-5.8) and temperatures (26–33 ºC). The ability of K. pastoris to synthesize CGC with different molar ratios as a function of pH and temperature is a feature that can be exploited to obtain tailored polymer compositions.(...)

Molecular tools in the diagnostic and epidemiology of infections caused by members of Mycobacterium avium Complex

Mycobacterium avium Complex (MAC) comprises microorganisms that affect a wide range of animals including humans. The most relevant are Mycobacterium avium subspecies hominissuis (Mah) with a high impact on public health affecting mainly immunocompromised individuals and Mycobacterium avium subspecies paratuberculosis (Map) causing paratuberculosis in animals with a high economic impact worldwide. In this work, we characterized 28 human and 67 porcine Mah isolates and evaluated the relationship among them by Multiple-Locus Variable number tandem repeat Analysis (MLVA). We concluded that Mah population presented a high genetic diversity and no correlations were inferred based on geographical origin, host or biological sample. For the first time in Portugal Map strains, from asymptomatic bovine faecal samples were isolated highlighting the need of more reliable and rapid diagnostic methods for Map direct detection. Therefore, we developed an IS900 nested real time PCR with high sensitivity and specificity associated with optimized DNA extraction methodologies for faecal and milk samples. We detected 83% of 155 faecal samples from goats, cattle and sheep, and 26% of 98 milk samples from cattle, positive for Map IS900 nested real time PCR. A novel SNPs (single nucleotide polymorphisms) assay to Map characterization based on a Whole Genome Sequencing analysis was developed to elucidate the genetic relationship between strains. Based on sequential detection of 14 SNPs and on a decision tree we were able to differentiate 14 phylogenetic groups with a higher discriminatory power compared to other typing methods. A pigmented Map strain was isolated and characterized evidencing for the first time to our knowledge the existence of pigmented Type C strains. With this work, we intended to improve the ante mortem direct molecular detection of Map, to conscientiously aware for the existence of Map animal infections widespread in Portugal and to contribute to the improvement of Map and Mah epidemiological studies.

On the function of the floccular complex of the vertebrate cerebellum: implications in paleoneuroanatomy

The cerebellum floccular complex lobes (FCLs) are housed in the FCL fossa of the periotic complex. There is experimental evidence indicating that the FCLs integrate visual and vestibular information, responsible for the vestibulo-ocular reflex, vestibulo-collic reflex, smooth pursuit and gaze holding. Thus, the behavior of extinct animals has been correlated with FCLs dimension in multiple paleoneuroanatomy studies. Here I analyzed braincase endocasts of a representative sample of Mammalia (48 species) and Aves (59 species) rendered using tomography and image segmentation and tested statistical correlations between the floccular complex volume, ecological and behavioral traits to assess various previously formulated paleobiological speculations. My results demonstrate: 1) there is no significant correlation between relative FCL volume and body mass; 2) there is no significant correlation between relative FCL and optic lobes size in birds; 3) average relative FCL size is larger in diurnal than in nocturnal birds but there is no statistically significant difference in mammals; 4) feeding strategies are related with different FCL size patterns in birds, but not in mammals; 5) locomotion type is not related with relative FCL size in mammals; 6) agility is not significantly correlated with FCL size in mammals. I conclude that, despite the apparent relation between FCL size and ecology in birds, the cerebellum of tetrapods is a highly plastic structure and may be adapted to control different functions across different taxonomic levels. For example, the european mole (Talpa europaea) which is fossorial and practically blind, has a FCL fossae relative size larger than those of bats, which are highly maneuverable. Therefore, variation in FCL size may be better explained by a combination of multiple factors with relation to anatomical and phylogenetic evolutionary constraints.

The vacuum assisted closure of complex wounds: report of 3 cases

Treatment of wounds using conventional methods is frequently limited by inadequate local wound conditions, or by a poor systemic clinical situation. Vacuum system may promote faster granulation tissue formation, remove excessive exudate, increase blood flow in the wound, and attract the borders of the wound to the center, reducing its dimension. We present 3 cases of patients with difficult wounds, due to bad local conditions, or poor clinical situation, in whom we used a vacuum system to prepare the wound for the surgical closure. One patient had a pressure ulcer, another had a diabetic foot ulcer, and the third one had an open foot stump. In the 3 cases a significant improvement of the wound conditions was achieved after 7 to 8 days, allowing successful surgical treatment with flap or skin grafts.

Studies on the eucalyptus leaf disease complex in Portugal

Native from south eastern Australia, Eucalyptus globulus is the main species in eucalypts plantations in Portugal. The most serious foliar disease in eucalypt plantations is linked to Mycosphaerella senso lato, which affects young trees in the juvenile phase foliage causing leaf necrosis. This disease results in reduced growth rate of the host and lower wood volume, thus causing significant productivity losses. The most common name for this disease was Mycosphaerella Leaf Disease that became inappropriate when most of the pathogens on eucalypts were re-distributed into several genera. The term "Eucalyptus Leaf Disease Complex" is now more appropriate. The overall aim of this thesis was to investigate the Eucalyptus Leaf Disease Complex in Portugal, focusing on species diversity, taxonomy and the role played by each species in the disease complex on Eucalyptus globulus. Literature on the Eucalyptus Leaf Disease Complex was reviewed and the species were distributed into several genera. A survey based on symptomatic leaves collected from several Eucalyptus globulus plantations and characterized by morphological and molecular tools provided an overview of species incidence and of the most frequent species in the disease complex. The present work reveals additional species of Mycosphaerella senso lato associated with eucalypt plantations in Portugal. Thus, five new records of Teratosphaeria and phylogenetically related species were added to the Iberian Peninsula, namely, Neodevriesia hilliana, for the first time on Myrtaceae; Quasiteratosphaeria mexicana, Teratosphaericola pseudoafricana, Teratosphaeria pluritubularis and Teratosphaeria lusitanica, a new species. Furthermore, new anamorphic structures were found and two new combinations were made. Regarding other genera, some species were observed for the first time, such as Cladosporium cladosporioides, Fusicladium eucalypti, Mycosphaerella madeirae, in the mainland. In addition to leave diseases, Teratosphaeria gauchensis was found causing a severe stem and trunk canker on Eucalyptus globulus. The aggressiveness of several species was compared to evaluate each species individually in the complex, permitting to distinguish different behaviours, from primary to secondary pathogens. Cladosporium cladosporioides, M. communis and M. lateralis, appeared to be more aggressive than Teratosphaeria nubilosa. In fact, contrary to the prevailing views on this disease complex, Teratosphaeria nubilosa is not the only species responsible for the disease, which clearly involves a complex of species acting together.

Assessment of a novel Cu (II) complex as a potential anticancer agent

Widely used in cancer treatment, chemotherapy still faces hindering challenges, ranging from severe induced toxicity to drug resistance acquisition. As means to overcome these setbacks, newly synthetized compounds have recently come into play with the basis of improved pharmacokinetic/pharmacodynamic properties. With this mind-set, this project aimed towards the antiproliferative potential characterization of a group of metallic compounds. Additionally the incorporation of the compounds within a nanoformulation and within new combination strategies with commercial chemotherapeutic drugs was also envisaged. Cell viability assays presented copper (II) compound (K4) as the most promising, presenting an IC50 of 6.10 μM and 19.09 μM for HCT116 and A549 cell line respectively. Exposure in fibroblasts revealed a 9.18 μM IC50. Hoechst staining assays further revealed the compound’s predisposition to induce chromatin condensation and nuclear fragmentation in HCT116 upon exposure to K4 which was later demonstrated by flow cytometry and annexin V-FITC/propidium iodide double staining analysis (under 50 % cell death induction). The compound further revealed the ability to interact with major macromolecules such as DNA (Kb = 2.17x105 M-1), inducing structural brakes and retardation, and further affecting cell cycle progression revealing delay in S-phase. Moreover BSA interactions were also visible however not conclusive. Proteome profiling revealed overexpression of proteins involved in metabolic activity and underexpression of proteins involved in apoptosis thus corroborating Hoechst and apoptosis flow cytometry data. K4 nanoformulation suffered from several hindrances and was ill succeeded in part due to K4’s poor solubility in aqueous buffers. Other approaches were considered in this regard. Combined chemotherapy assays revealed high cytotoxicity for afatinib and lapatinib strategies. Lapatinib and K4 proteome profiling further revealed high apoptosis rates, high metabolic activity and activation of redundant proteins as part of compensatory mechanisms.

The Simaba guianensis complex in northers South America

With additional data from specimens not studied by previous workers, the confusing Simaba guianensis compex was re-analized. Simaba polyphylla is recognized as a distinct species and two subspecies of S. guianensis are maintained. Simaba polyphylla, S. guianensis ssp. guianensis, and S. guianensis ssp. ecaudata are keyed, described, and illustrated and specimens examined are cited for each. Specimens of S. guianensis ssp. ecaudata show great morphological diversity but can be separeted into three groups. Further collecting may provide information that shows these groups to be worthy of separate taxonomic status.

Taxonomy of the Oenocarpus-Jessenia (Palmae) complex in Brazil

Two genera, Oenocarpus and Jessenia are recognized in this complex of Neotropical palms. They are well represented in Brasil, Oenocarpus with seven species (O. distinchus, O. discolar, O. tarampabo, O. bacaba, O. macrocalyx, O. mapora and O. minor, and Jessenia with one species, J. bataua). Many of these taza are poorly know and under-represented in herbaria, both in Brazil and elsewhere. A great deal of fieldwork is needed to betther undestand the basic biology and extent of variation in the populations of these palms.

Gestão em saúde

RESUMO - As organizações de saúde, para além de muito complexas, sofrem a influência de importantes mudanças em curso nos sistemas de saúde, em que se integram, e que constituem novos desafios, com reflexos na sua gestão. Por isso se espera, cada vez mais, dos seus gestores uma atitude proactiva e inovadora, o que exige que o processo educativo conducente à formação dos gestores nesta área valorize, para além de conhecimentos técnicos aprofundados, outras dimensões de um futuro exercício: desde a capacidade de liderança em organizações em mudança, em cenários instáveis, à disponibilidade para suscitar a colaboração dos profissionais prestadores, passando pela faculdade de criação de coligações que facilitem processos de integração multidisciplinar e plurinstitucional, pela sensibilidade à relação qualidade/custo em ambientes de constrangimento financeiro e pela promoção da inovação. O presente artigo analisa duas questões subjacentes a um bom exercício e que atravessam a concepção de qualquer processo formativo em gestão: • A competência, que deverá ser o objectivo maior da formação em gestão; • A integração da aprendizagem enquanto elemento condicionante da angariação das aptidões necessárias.

The mixed impact of design thinking on business collaborations

The present work project investigates the implications of design thinking on an interbusiness collaborative project, unveiling both the benefits and fragilities that derive from the use of such methodology within the mentioned context. The study is organized in two parts. The first one starts with a literature review on the two relevant frames of reference – design thinking and business collaboration. It proceeds to the creation of a conceptual framework to assess the potential value of the design-based approach. The second part focuses on the practical application of to the newly developed instrument to the inTRAIN project – R&D for railway interiors.