Bacterial inter-species communication mediated by the autoinducer-2 signal

Dissertation presented to obtain the Ph.D degree in Biology by Universidade Nova de Lisboa, Instituto de Tecnologia Química e Biológica, Instituto Gulbenkian de Ciência.

Analysis of panoramio photo tags in order to extract land use information

In the recent past, hardly anyone could predict this course of GIS development. GIS is moving from desktop to cloud. Web 2.0 enabled people to input data into web. These data are becoming increasingly geolocated. Big amounts of data formed something that is called "Big Data". Scientists still don't know how to deal with it completely. Different Data Mining tools are used for trying to extract some useful information from this Big Data. In our study, we also deal with one part of these data - User Generated Geographic Content (UGGC). The Panoramio initiative allows people to upload photos and describe them with tags. These photos are geolocated, which means that they have exact location on the Earth's surface according to a certain spatial reference system. By using Data Mining tools, we are trying to answer if it is possible to extract land use information from Panoramio photo tags. Also, we tried to answer to what extent this information could be accurate. At the end, we compared different Data Mining methods in order to distinguish which one has the most suited performances for this kind of data, which is text. Our answers are quite encouraging. With more than 70% of accuracy, we proved that extracting land use information is possible to some extent. Also, we found Memory Based Reasoning (MBR) method the most suitable method for this kind of data in all cases.

From e-voting to smart-voting : e-Tools in and for elections and direct democracy in Switzerland

To what extent do and could e-tools contribute to a democracy like Switzerland? This paper puts forward experiences and visions concerning the application of e-tools for the most traditional democratic processes- elections and, of special importance in Switzerland, direct-democratic votes.Having the particular voting behaviour of the Swiss electorate in mind (low voter turnout - especially among the youngest age group, low political knowledge, etc.) we believe that e-tools which provide information in the forefront of elections or direct-democratic votes offer an enormous service to the voter. As soon as e-voting will be possible in Switzerland (as planned by the government), those e-tools for gathering information online will become indispensable and will gain power enormously. Therefore political scientists should not only focus on potential effects of e-voting itself but rather on the combination of (connected)e-tools of the pre-voting and the voting sphere. In the case of Switzerland, we argue in this paper, the offer of VAAs such as smartvote for elections and direct-democratic votes can provide the voter with more balanced and qualitatively higher information and thereby make a valuable contribution to the Swiss democracy.

Deux approches de l'influence du discours économique sur les phénomènes sociaux

The influence of theoretical discourse on the corresponding field of investigation is an important feature of social science : social scientists shape the world by describing it. This phenomenon has been studied in several ways. Economic sociology has recently focused on the fact that the economy is embedded in the economics through which it is scrutinized. Great names of economic theory have focused on the effects of economists' discourse on agents' behaviours. This article aims to bring out the distinction between these two kinds of contributions which deal with the same object. Finally, it explains the analytical distinction by a difference in the initial problematic. Following trends in the French school of the economics of convention, the social influence of theoretical discourse is analyzed on the strategic side (in connection with economics) and on the interpretative side (in connection with sociology).

Conference scene: Immune signatures in the tumor and beyond.

Led by key opinion leaders in the field, the Cancer Immunotherapy Consortium of the Cancer Research Institute 2012 Scientific Colloquium included 179 participants who exchanged cutting-edge information on basic, clinical and translational cancer immunology and immunotherapy. The meeting revealed how rapidly this field is advancing. The keynote talk was given by Wolf H Fridman and it described the microenvironment of primary and metastatic human tumors. Participants interacted through oral presentations and panel discussions on topics that included host reactions in tumors, advances in imaging, monitoring therapeutic immune modulation, the benefit and risk of immunotherapy, and immune monitoring activities. In summary, the annual meeting gathered clinicians and scientists from academia, industry and regulatory agencies from around the globe to interact and exchange important scientific advances related to tumor immunobiology and cancer immunotherapy.

Pollution and pollutant transport in the geosphere - An introduction to the symposium

Environmental research in earth sciences is focused on the geosphere, i.e. (1) waters and sediments of rivers, lakes and oceans, and (2) soils and underlying shallow rock formations,both water-unsaturated and -saturated. The subsurface is studied down to greater depths at sites where waste repositories or tunnels are planned and mining activities exist. In recent years, earth scientists have become more and more involved in pollution problems related to their classical field of interest, e.g. groundwater, ore deposits, or petroleum and non-metal natural deposits (gravel, clay, cement precursors). Major pollutants include chemical substances, radioactive isotopes and microorganisms. Mechanisms which govern the transport of pollutants are of physical, chemical (dissolution, precipitation, adsorption), or microbiological (transformation) nature. Land-use planning must reflect a sustainable development and sound scientific criteria. Today's environmental pollution requires working teams with an interdisciplinary background in earth sciences, hydrology, chemistry, biology, physics as well as engineering. This symposium brought together for the first time in Switzerland earth and soil scientists, physicists and chemists, to present and discuss environmental issues concerning the geosphere.

Retrospective research: What are the ethical and legal requirements?

Retrospective research is conducted on already available data and/or biologic material. Whether such research requires that patients specifically consent to the use of "their" data continues to stir controversy. From a legal and ethical point of view, it depends on several factors. The main criteria to be considered are whether the data or the sample is anonymous, whether the researcher is the one who collected it and whether the patient was told of the possible research use. In Switzerland, several laws delineate the procedure to be followed. The definition of "anonymous" is open to some interpretation. In addition, it is debatable whether consent waivers that are legally admissible for data extend to research involving human biological samples. In a few years, a new Swiss federal law on human research could clarify the regulatory landscape. Meanwhile, hospital-internal guidelines may impose stricter conditions than required by federal or cantonal law. Conversely, Swiss and European ethical texts may suggest greater flexibility and call for a looser interpretation of existing laws. The present article provides an overview of the issues for physicians, scientists, ethics committee members and policy makers involved in retrospective research in Switzerland. It aims at provoking more open discussions of the regulatory problems and possible future legal and ethical solutions.

Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes.

Research in autophagy continues to accelerate,(1) and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.(2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.

High-density lipoprotein, beta cells, and diabetes .

High-density lipoproteins (HDLs) exert a series of potentially beneficial effects on many cell types including anti-atherogenic actions on the endothelium and macrophage foam cells. HDLs may also exert anti-diabetogenic functions on the beta cells of the endocrine pancreas, notably by potently inhibiting stress-induced cell death and enhancing glucose-stimulated insulin secretion. HDLs have also been found to stimulate insulin-dependent and insulin-independent glucose uptake into skeletal muscle, adipose tissue, and liver. These experimental findings and the inverse association of HDL-cholesterol levels with the risk of diabetes development have generated the notion that appropriate HDL levels and functionality must be maintained in humans to diminish the risks of developing diabetes. In this article, we review our knowledge on the beneficial effects of HDLs in pancreatic beta cells and how these effects are mediated. We discuss the capacity of HDLs to modulate endoplasmic reticulum stress and how this affects beta-cell survival. We also point out the gaps in our understanding on the signalling properties of HDLs in beta cells. Hopefully, this review will foster the interest of scientists in working on beta cells and diabetes to better define the cellular pathways activated by HDLs in beta cells. Such knowledge will be of importance to design therapeutic tools to preserve the proper functioning of the insulin-secreting cells in our body.

A comparative study of ballpoint ink ageing parameters using GC/MS.

For more than a decade scientists tried to develop methods capable of dating ink by monitoring the loss of phenoxyethanol (PE) over time. While many methods were proposed in the literature, few were really used to solve practical cases and they still raise much concern within the scientific community. In fact, due to the complexity of ink drying processes it is particularly difficult to find a reliable ageing parameter to reproducibly follow ink ageing. Moreover, systematic experiments are required in order to evaluate how different factors actually influence the results over time. Therefore, this work aimed at evaluating the capacity of four different ageing parameters to reliably follow ink ageing over time: (1) the quantity of solvent PE in an ink line, (2) the relative peak area (RPA) normalising the PE results using stable volatile compounds present in the ink formulation, (3) the solvent loss ratio (R%) calculated from PE results obtained by the analyses of naturally and artificially aged samples, (4) a modified solvent loss ratio version (R%*) calculated from RPA results. After the determination of the limits of reliable measurements of the analytical method, the repeatability of the different ageing parameters was evaluated over time, as well as the influence of ink composition, writing pressure and storage conditions on the results. Surprisingly, our results showed that R% was not the most reliable parameter, as it showed the highest standard deviation. Discussion of the results in an ink dating perspective suggests that other proposed parameters, such as RPA values, may be more adequate to follow ink ageing over time.

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article.

A five factor model of grief : a q-methodological study /

Q-methodology permitted 41 people to communicate their perspective of grief. In an attempt to clarify the research to date and to allow those who have experienced this human journey to direct the scientists, 80 statements were chosen to present to the participants based on the research from academic and counselling sources. Five different perspectives emerged from the Q-sorts and factor analysis. Each perspective was valuable for the understanding of different groups of mourners. They were interpreted using questionnaire data and interview information. They are as follows: Factor 1- Growth Optimism; Factor 2 - Schema Destruction and Negative Affect; Factor 3- Identification with the Deceased Person; Factor 4- Intact World view with High Clarity and High Social Support; Factor 5- Schema Destruction with High Preoccupation and Attention to Emotion. Some people grow in the face of grief, others hold on to essentially the same schemas and others are devastated by their loss. The different perspectives reported herein supply clues to the sources of these differing outcomes. From examination of Factor 1, it appears that a healthy living relationship helps substantially in the event of loss. An orientation toward emotions that encourages clarity, exemplified by Factor 4, without hyper-vigilance to emotion may be helpful as well. Strategies for maintaining schematic representations of the world with little alteration include: identification with the values of the deceased person, as in Factor 3 and reliance on social support and/or God as demonstrated by Factor 4. When the relationship had painful periods, social support may be accessed to benefit some mourners. When the person's frame of reference or higher order schemas are assaulted by the events of loss, the people most at risk for traumatic grief seem to be those with difficult relationships as indicated by Factor 5 individuals. When low social support, high attention to emotion with low clarity and little belief that feelings can be altered for the better are also attributes of the mourner devastating grief can result. In the end, there are groups of people who are forced to endure the entire process of schema destruction and devastation. Some appear to recover in part and others appear to stay in a form of purgatory for many years. The results of this study suggest that, those who experience devastating grief may be in the minority. In the future interventions could be more specifically addressed if these perspectives are replicated in a larger, more detailed study.

Motivational differences in science course enrolment shown by males and females in grades 9 through OAC

A sample of 1,345 students enrolled in advanced-level science courses from Grades 9 through OAe was surveyed in order to gain perspective into the existence of motivational differences attributing to science course enrolment by gender. Records of enrolment were examined in order to detect patterns and trends. A questionnaire was devised and piloted. It measured five motivational variables - demographics, science and science-related experiences, science ability and attitudes, impressions about women in science, and importance of science and science-related skills. The students also provided some impressions about the image of scientists. Results of the questionnaire were analyzed for frequency of responses and for significant gender differences using the chi-square. Differences were found to exist in the areas of science anxiety as it relates to testing and oral participation; in motivation generated by the performance of extra-curricular science and science-related activities, and by the classroom environment; in impressions of women in science; in the importance of science skills, and in the area of teacher influence. The study also showed a differential enrolment of females, with an emphasis on biology and chemistry. The males were enrolled in courses of physics and chemistry. The findings lead to numerous suggested strategies and programs for encouraging the participation of females in science education and careers.

Medicalization and women : O, the Oprah Magazine diagnosed through critical discourse analysis

This thesis uses critical discourse analysis (COAl to explore and examine direct-toconsumer (OTC) pharmaceutical drug advertisements appearing in four issues of 0, The Oprah Magazine in 2006. The theoretical underpinnings of this thesis emerge from social scientists and feminists analyses regarding the medicalization of everyday life. The findings of this study highlight three types of discourses used by pharmaceutical companies. First, I explore the use of historical and contemporary gender norms to seJi pharmacological products; second, J examine discourses which normalize the use of chemical solutions as the first line of defense to address a wide range of everyday problems; and finally, I assess how phannaceutical advertisements provide an illusion of autonomy by responsibilizing individuals as patients, at the same time as they suggest that real independence can only be achieved with medication. My discussion of these themes also includes an analysis of why 0 Magazine, which explicitly promotes women's empowerment through holistic approaches to health and personal growthmight support such advertising. Thus I explore: how does OTC advertising benefit both pharmaceutical companies and 0 Magazine itself? I conclude through a brief discussion of the larger implications of OTC advertising for women's health.

RelMDD-A Library for Manipulating Relations Based on MDDs

Relation algebras is one of the state-of-the-art means used by mathematicians and computer scientists for solving very complex problems. As a result, a computer algebra system for relation algebras called RelView has been developed at Kiel University. RelView works within the standard model of relation algebras. On the other hand, relation algebras do have other models which may have different properties. For example, in the standard model we always have L;L=L (the composition of two (heterogeneous) universal relations yields a universal relation). This is not true in some non-standard models. Therefore, any example in RelView will always satisfy this property even though it is not true in general. On the other hand, it has been shown that every relation algebra with relational sums and subobjects can be seen as matrix algebra similar to the correspondence of binary relations between sets and Boolean matrices. The aim of my research is to develop a new system that works with both standard and non-standard models for arbitrary relations using multiple-valued decision diagrams (MDDs). This system will implement relations as matrix algebras. The proposed structure is a library written in C which can be imported by other languages such as Java or Haskell.