Immunohistochemical molecular phenotypes of gastric cancer based on SOX2 and CDX2 predict patient outcome

Background Gastric cancer remains a serious health concern worldwide. Patients would greatly benefit from the discovery of new biomarkers that predict outcome more accurately and allow better treatment and follow-up decisions. Here, we used a retrospective, observational study to assess the expression and prognostic value of the transcription factors SOX2 and CDX2 in gastric cancer. Methods SOX2, CDX2, MUC5AC and MUC2 expression were assessed in 201 gastric tumors by immunohistochemistry. SOX2 and CDX2 expression were crossed with clinicopathological and follow-up data to determine their impact on tumor behavior and outcome. Moreover, SOX2 locus copy number status was assessed by FISH (N = 21) and Copy Number Variation Assay (N = 62). Results SOX2 was expressed in 52% of the gastric tumors and was significantly associated with male gender, T stage and N stage. Moreover, SOX2 expression predicted poorer patient survival, and the combination with CDX2 defined two molecular phenotypes, SOX2+CDX2- versus SOX2-CDX2+, that predict the worst and the best long-term patients’ outcome. These profiles combined with clinicopathological parameters stratify the prognosis of patients with intestinal and expanding tumors and in those without signs of venous invasion. Finally, SOX2 locus copy number gains were found in 93% of the samples reaching the amplification threshold in 14% and significantly associating with protein expression. Conclusions We showed, for the first time, that SOX2 combined with CDX2 expression profile in gastric cancer segregate patients into different prognostic groups, complementing the clinicopathological information. We further demonstrate a molecular mechanism for SOX2 expression in a subset of gastric cancer cases.

Transgenerational Inheritance of Paternal Neurobehavioral Phenotypes: Stress, Addiction, Ageing and Metabolism

Epigenetic modulation is found to get involved in multiple neurobehavioral processes. It is believed that different types of environmental stimuli could alter the epigenome of the whole brain or related neural circuits, subsequently contributing to the long-lasting neural plasticity of certain behavioral phenotypes. While the maternal influence on the health of offsprings has been long recognized, recent findings highlight an alternative way for neurobehavioral phenotypes to be passed on to the next generation, i.e., through the male germ line. In this review, we focus specifically on the transgenerational modulation induced by environmental stress, drugs of abuse, and other physical or mental changes (e.g., ageing, metabolism, fear) in fathers, and recapitulate the underlying mechanisms potentially mediating the alterations in epigenome or gene expression of offsprings. Together, these findings suggest that the inheritance of phenotypic traits through male germ-line epigenome may represent the unique manner of adaptation during evolution. Hence, more attention should be paid to the paternal health, given its equivalently important role in affecting neurobehaviors of descendants.

Prevalência de resistência a antimicrobianos em isolados ambientais de Escherichia coli e enterococos

A água é um recurso escasso e indispensável à vida, podendo ser um importante veículo de microrganismos patogénicos com origem fecal. A matéria fecal é também uma fonte de microrganismos resistentes a antimicrobianos e contribui para a sua disseminação e dos seus genes de resistência no ambiente e entre as comunidades microbianas comensais e microrganismos patogénicos humanos e animais. A qualidade microbiológica da água é monitorizada recorrendo à utilização de bioindicadores como Escherichia coli, enterococos e microrganismos totais. O presente estudo apresentou como principal objetivo determinar a prevalência de ESBLs e AmpCs e ainda avaliar a prevalência de estirpes de enterococos com resistência à vancomicina (VRE) em águas do rio Douro e da orla costeira da cidade do Porto. As amostragens de água foram realizadas em quatro locais localizados no estuário do rio Douro e orla costeira da cidade do Porto entre o mês de Abril e Julho. A deteção e quantificação dos bioindicadores foram realizadas pelo método de filtração por membrana. A suscetibilidade das estirpes de E. coli e enterococos foi testada pelo método de difusão em disco relativamente a várias classes de antimicrobianos. As contagens microbianas mais elevadas foram determinadas entre Abril e Junho e em amostras de água doce. Foram isoladas 62 estirpes de E. coli e 49 estirpes de enterococos que apresentaram prevalências de resistência a antimicrobianos de 90,3% (56/62) e 83,7% (41/49), respetivamente. As estirpes de E. coli apresentaram altas frequências de resistência à ampicilina (74,2%) e tetraciclina (61,3%). Nestas estirpes verificou-se ainda fenótipos associados a multirresistência a um mínimo de três classes de antimicrobianos em 56,5% (35/62) dos isolados. Verificou-se que as estirpes de enterococos apresentaram altos níveis de resistência à rifampicina (34,7%) e azitromicina (40,8%), detetando-se ainda a manifestação de fenótipo de resistência à vancomicina em 26,5% das estirpes. Observou-se uma prevalência de 36,7% (18/49) de estirpes de enterococos associadas a fenómenos de multirresistência antimicrobiana. Ana Martins vi Os resultados obtidos sugerem que o rio Douro e orla costeira, bem como os ambientes aquáticos, constituem reservatórios de bactérias e genes de resistência a antimicrobianos e possuem um papel preponderante na sua disseminação.

Biochemical and structural characterization of β-lactamases tem-180 and tem-201

With the constant development of new antibiotics, selective pressure is a force to reckon when investigating antibiotic resistance. Although advantageous for medical treatments, it leads to increasing resistance. It is essential to use more potent and toxic antibiotics. Enzymes capable of hydrolyzing antibiotics are among the most common ways of resistance and TEM variants have been detected in several resistant isolates. Due to the rapid evolution of these variants, complex phenotypes have emerged and the need to understand their biological activity becomes crucial. To investigate the biochemical properties of TEM-180 and TEM-201 several computational methodologies have been used, allowing the comprehension of their structure and catalytic activity, which translates into their biological phenotype. In this work we intent to characterize the interface between these proteins and the several antibiotics used as ligands. We performed explicit solvent molecular dynamics (MD) simulations of these complexes and studied a variety of structural and energetic features. The interfacial residues show a distinct behavior when in complex with different antibiotics. Nevertheless, it was possible to identify some common Hot Spots among several complexes – Lys73, Tyr105 and Glu166. The structural changes that occur during the Molecular Dynamic (MD) simulation lead to the conclusion that these variants have an inherent capacity of adapting to the various antibiotics. This capability might be the reason why they can hydrolyze antibiotics that have not been described until now to be degraded by TEM variants. The results obtained with computational and experimental methodologies for the complex with Imipenem have shown that in order to this type of enzymes be able to acylate the antibiotics, they need to be capable to protect the ligand from water molecules.

Responsabilidade ambiental: análise das divulgações ambientais das empresas do PSI-20 comparativamente com empresas não cotadas

Orientador: Mestre, António Pinto Marques

Intelligent decision making in electricity markets: simulated annealing Q-Learning

Electricity markets are complex environments, involving a large number of different entities, playing in a dynamic scene to obtain the best advantages and profits. MASCEM is a multi-agent electricity market simulator to model market players and simulate their operation in the market. Market players are entities with specific characteristics and objectives, making their decisions and interacting with other players. MASCEM is integrated with ALBidS, a system that provides several dynamic strategies for agents’ behavior. This paper presents a method that aims at enhancing ALBidS competence in endowing market players with adequate strategic bidding capabilities, allowing them to obtain the higher possible gains out of the market. This method uses a reinforcement learning algorithm to learn from experience how to choose the best from a set of possible actions. These actions are defined accordingly to the most probable points of bidding success. With the purpose of accelerating the convergence process, a simulated annealing based algorithm is included.

Cooperative scheduling system with emergent swarm based behavior

This paper presents a Swarm based Cooperation Mechanism for scheduling optimization. We intend to conceptualize real manufacturing systems as interacting autonomous entities in order to support decision making in agile manufacturing environments. Agents coordinate their actions automatically without human supervision considering a common objective – global scheduling solution taking advantages from collective behavior of species through implicit and explicit cooperation. The performance of the cooperation mechanism will be evaluated consider implicit cooperation at first stage through ACS, PSO and ABC algorithms and explicit through cooperation mechanism application.

Adaptive learning in multiagent systems: a forecasting methodology based on error analysis

Electricity markets are complex environments, involving a large number of different entities, playing in a dynamic scene to obtain the best advantages and profits. MASCEM is a multi-agent electricity market simu-lator to model market players and simulate their operation in the market. Market players are entities with specific characteristics and objectives, making their decisions and interacting with other players. MASCEM pro-vides several dynamic strategies for agents’ behaviour. This paper presents a method that aims to provide market players strategic bidding capabilities, allowing them to obtain the higher possible gains out of the market. This method uses an auxiliary forecasting tool, e.g. an Artificial Neural Net-work, to predict the electricity market prices, and analyses its forecasting error patterns. Through the recognition of such patterns occurrence, the method predicts the expected error for the next forecast, and uses it to adapt the actual forecast. The goal is to approximate the forecast to the real value, reducing the forecasting error.

Cost dependent strategy for electricity markets bidding based on adaptive reinforcement learning

Electricity markets are complex environments, involving a large number of different entities, playing in a dynamic scene to obtain the best advantages and profits. MASCEM is a multi-agent electricity market simulator to model market players and simulate their operation in the market. Market players are entities with specific characteristics and objectives, making their decisions and interacting with other players. MASCEM provides several dynamic strategies for agents’ behavior. This paper presents a method that aims to provide market players with strategic bidding capabilities, allowing them to obtain the higher possible gains out of the market. This method uses a reinforcement learning algorithm to learn from experience how to choose the best from a set of possible bids. These bids are defined accordingly to the cost function that each producer presents.

Seller, buyer and VPP agents behavior on a simulated electricity market

Competitive electricity markets are complex environments, involving a large number of different entities, playing in a dynamic scene to obtain the best advantages and profits. MASCEM is an electricity market simulator able to model market players and simulate their operation in the market. As market players are complex entities, having their characteristics and objectives, making their decisions and interacting with other players, a multi-agent architecture is used and proved to be adequate. MASCEM players have learning capabilities and different risk preferences. They are able to refine their strategies according to their past experience (both real and simulated) and considering other agents’ behavior. Agents’ behavior is also subject to its risk preferences.

Self-organization for scheduling in agile manufacturing

Agility refers to the manufacturing system ability to rapidly adapt to market and environmental changes in efficient and cost-effective ways. This paper addresses the development of self-organization methods to enhance the operations of a scheduling system, by integrating scheduling system, configuration and optimization into a single autonomic process requiring minimal manual intervention to increase productivity and effectiveness while minimizing complexity for users. We intend to conceptualize real manufacturing systems as interacting autonomous entities in order to build future Decision Support Systems (DSS) for Scheduling in agile manufacturing environments.

ISEM: a multi-agent system that simulates competitive electronic marketplaces

With the increasing importance of large commerce across the Internet it is becoming increasingly evident that in a few years the Iternet will host a large number of interacting software agents. a vast number of them will be economically motivated, and will negociate a variety of goods and services. It is therefore important to consider the economic incentives and behaviours of economic software agents, and to use all available means to anticipate their collective interactions. This papers addresses this concern by presenting a multi-agent market simulator designed for analysing agent market strategies based on a complete understanding of buyer and seller behaviours, preference models and pricing algorithms, consideting risk preferences. The system includes agents that are capable of increasing their performance with their own experience, by adapting to the market conditions. The results of the negotiations between agents are analysed by data minig algorithms in order to extract rules that give agents feedback to imprive their strategies.

Resistance to β-lactams in bacteria isolated from different types of Portuguese cheese

The purpose of this study was to investigate the presence of beta-lactam-resistant bacteria in six different types of Portuguese cheese. The numbers of ampicillin resistant (AMP(r)) bacteria varied from 4.7 x 10(2) to 1.5 x 10(7) CFU/g. Within 172 randomly selected beta-lactam-resistant bacteria, 44 resistant phenotypes were found and 31.4% were multidrug resistant. The majority (85%) of the isolates identified belonged to the Enterobacteriaceae family. The presence of the bla(TEM) gene was detected in 80.9% of the tested isolates. The results suggest that without thermal processing of the milk and good hygienic practices, cheese may act as a vehicle of transfer of beta-lactam-resistant bacteria to the gastrointestinal tract of consumers.

Antibiotic resistance in enterobacteriaceae isolated from Portuguese deli meats

This study aimed to identify the presence of β-lactam-resistant bacteria in different types of Portuguese deli meats. The numbers of ampicillin resistant bacteria varied from negative in 25 g to 1.0 × 108colony-forming units/g. Within 78 randomly selected β-lactam-resistant bacteria, 24 different resistant phenotypes were found and 35.9% were multidrug resistant (MDR). The majority (87.2%) of the isolates identified belonged to the Enterobacteriaceae family. The presence of the blaTEM gene was detected in 23 out of 67 isolates (34.3%) and 16 of them presented MDR phenotypes. Four Klebsiella oxytoca isolates (6%) harbored a gene for the CTX-M/OXY-type enzyme. The direct sequencing of their purified amplicons confirmed the presence of three types of blaOXYgenes (blaOXY-1, blaOXY-2 and blaOXY-5). These results suggest that without good hygienic practices, deli meats may act as a vehicle of transfer of β-lactam-resistant bacteria to the gastrointestinal tract of consumers.

Corporate brand identity management – proposal of a new framework

The term “corporate brand” has been widely used in literature since the eighties. According to Balmer (1998) this concept tends to be used as an alternative to the concept of corporate identity. The author argues that the use of branding principles to discuss corporate identity has tended to align the area more closely with marketing. However, the literature on brand management (Aaker, 1991; Kapferer, 1991 and de Chernatony and McDonald, 1992), gives little attention to the corporate brand” (p. 985). Based on the concepts of corporate brand, brand identity and B2B relationship, the authors are interested in eliminating this gap in literature by designing a framework of corporate brand identity management. The aim of this investigation is to investigate the impact of B2B relationships in corporate brand identity management. The methodology used is quantitative analysis of surveys and scale development. The originality of this paper is to investigate the influence of the relationship between brands in corporate brand identity. This investigation is very important to help the decisions of the corporate brand managers and academics. According to literature, namely on corporate brands (Balmer 2002b, Hatch and Schultz, 2001, 2003) and on brand identity (Kapferer, 1991, 2008, Aaker, 1996, de Chernatony, 1999) the authors developed a corporate brand identity management framework considering relationships between brands a context variable with definite impact on identity management as stated by Hakansson and Snehota (1989, 1995). These authors consider that organisations´ identity management is pursued under a relational perspective with impact on identity management. Most researchers on identity and corporate brand emphasise the importance of external influences (Kennedy, 1977; King, 1991; de Chernatony, 1999; Balmer and Gray, 2000; Balmer, 2002a). Those influences concern legislation, concurrence, political issues... and stakeholders’ perceptions and reputations (due to the holistic approach demanded by corporate brands). In this context the authors claim the importance of another influence: B2B relationships. This decision is inspired in sociological studies (Mannheim, 1950; and Tajfel and Turner, 1979) regarding individual identity. These authors claim that individuals form their personality by interacting in the social field. The authors argue that corporate brand identity also develops itself under a relational approach. The relationships selected to pursue this investigation are the ones that are developed by Portuguese universities and investigation centres that cooperate by developing investigation. Those centres are administrative and financially autonomous