Expression and purification of the immunogenically active fragment B of the Park Williams 8 Corynebacterium diphtheriae strain toxin

The construction of a hexahistidine-tagged version of the B fragment of diphtheria toxin (DTB) represents an important step in the study of the biological properties of DTB because it will permit the production of pure recombinant DTB (rDTB) in less time and with higher yields than currently available. In the present study, the genomic DNA of the Corynebacterium diphtheriae Park Williams 8 (PW8) vaccine strain was used as a template for PCR amplification of the dtb gene. After amplification, the dtb gene was cloned and expressed in competent Escherichia coli M15™ cells using the expression vector pQE-30™. The lysate obtained from transformed E. coli cells containing the rDTB PW8 was clarified by centrifugation and purified by affinity chromatography. The homogeneity of the purified rDTB PW8 was confirmed by immunoblotting using mouse polyclonal anti-diphtheria toxoid antibodies and the immune response induced in animals with rDTB PW8 was evaluated by ELISA and dermonecrotic neutralization assays. The main result of the present study was an alternative and accessible method for the expression and purification of immunogenically reactive rDTB PW8 using commercially available systems. Data also provided preliminary evidence that rabbits immunized with rDTB PW8 are able to mount a neutralizing response against the challenge with toxigenic C. diphtheriae.

Gene trio signatures as molecular markers to predict response to doxorubicin cyclophosphamide neoadjuvant chemotherapy in breast cancerpatients

In breast cancer patients submitted to neoadjuvant chemotherapy (4 cycles of doxorubicin and cyclophosphamide, AC), expression of groups of three genes (gene trio signatures) could distinguish responsive from non-responsive tumors, as demonstrated by cDNA microarray profiling in a previous study by our group. In the current study, we determined if the expression of the same genes would retain the predictive strength, when analyzed by a more accessible technique (real-time RT-PCR). We evaluated 28 samples already analyzed by cDNA microarray, as a technical validation procedure, and 14 tumors, as an independent biological validation set. All patients received neoadjuvant chemotherapy (4 AC). Among five trio combinations previously identified, defined by nine genes individually investigated (BZRP, CLPTM1,MTSS1, NOTCH1, NUP210, PRSS11, RPL37A, SMYD2, and XLHSRF-1), the most accurate were established by RPL37A, XLHSRF-1based trios, with NOTCH1 or NUP210. Both trios correctly separated 86% of tumors (87% sensitivity and 80% specificity for predicting response), according to their response to chemotherapy (82% in a leave-one-out cross-validation method). Using the pre-established features obtained by linear discriminant analysis, 71% samples from the biological validation set were also correctly classified by both trios (72% sensitivity; 66% specificity). Furthermore, we explored other gene combinations to achieve a higher accuracy in the technical validation group (as a training set). A new trio, MTSS1, RPL37 and SMYD2, correctly classified 93% of samples from the technical validation group (95% sensitivity and 80% specificity; 86% accuracy by the cross-validation method) and 79% from the biological validation group (72% sensitivity and 100% specificity). Therefore, the combined expression of MTSS1, RPL37 and SMYD2, as evaluated by real-time RT-PCR, is a potential candidate to predict response to neoadjuvant doxorubicin and cyclophosphamide in breast cancer patients.

Photodynamic antimicrobial chemotherapy (PACT) for the treatment of malaria, leishmaniasis and trypanosomiasis

A photodynamic effect occurs when photosensitiser molecules absorb light and dissipate the absorbed energy by transferring it to biological acceptors (usually oxygen), generating an excess of reactive species that are able to force cells into death pathways. Several tropical diseases present physiopathological aspects that are accessible to the application of a photosensitiser and local illumination. In addition, disease may be transmitted through infected blood donations, and many of the aetiological agents associated with tropical diseases have been shown to be susceptible to the photodynamic approach. However, there has been no systematic investigation of the application of photoantimicrobial agents in the various presentations, whether to human disease or to the disinfection of blood products or even as photo-insecticides. We aim in this review to report the advances in the photoantimicrobial approach that are beneficial to the field of anti-parasite therapy and also have the potential to facilitate the development of low-cost/high-efficiency protocols for underserved populations.

Citations to papers from Brazilian institutions: a more effective indicator to assess productivity and the impact of research in graduate programs

A recent assessment of 4400 postgraduate courses in Brazil by CAPES (a federal government agency dedicated to the improvement of the quality of and research at the postgraduate level) stimulated a large amount of manifestations in the press, scientific journals and scientific congresses. This gigantic effort to classify 16,400 scientific journals in order to provide indicators for assessment proved to be puzzling and methodologically erroneous in terms of gauging the institutions from a metric point of view. A simple algorithm is proposed here to weigh the scientometric indicators that should be considered in the assessment of a scientific institution. I conclude here that the simple gauge of the total number of citations accounts for both the productivity of scientists and the impact of articles. The effort spent in this exercise is relatively small, and the sources of information are fully accessible. As an exercise to estimate the value of the methodology, 12 institutions of physics (10 from Brazil, one from the USA and one from Italy) have been evaluated.

A detailed description of an economical setup for electroporation of chick embryos in ovo

One of the challenges of the postgenomic era is characterizing the function and regulation of specific genes. For various reasons, the early chick embryo can easily be adopted as an in vivo assay of gene function and regulation. The embryos are robust, accessible, easily manipulated, and maintained in the laboratory. Genomic resources centered on vertebrate organisms increase daily. As a consequence of optimization of gene transfer protocols by electroporation, the chick embryo will probably become increasingly popular for reverse genetic analysis. The challenge of establishing chick embryonic electroporation might seem insurmountable to those who are unfamiliar with experimental embryological methods. To minimize the cost, time, and effort required to establish a chick electroporation assay method, we describe and illustrate in great detail the procedures involved in building a low-cost electroporation setup and the basic steps of electroporation.

Novel control, haptic and calibration methods for teleoperated electrohydraulic servo systems

The aim of this thesis is to propose a novel control method for teleoperated electrohydraulic servo systems that implements a reliable haptic sense between the human and manipulator interaction, and an ideal position control between the manipulator and the task environment interaction. The proposed method has the characteristics of a universal technique independent of the actual control algorithm and it can be applied with other suitable control methods as a real-time control strategy. The motivation to develop this control method is the necessity for a reliable real-time controller for teleoperated electrohydraulic servo systems that provides highly accurate position control based on joystick inputs with haptic capabilities. The contribution of the research is that the proposed control method combines a directed random search method and a real-time simulation to develop an intelligent controller in which each generation of parameters is tested on-line by the real-time simulator before being applied to the real process. The controller was evaluated on a hydraulic position servo system. The simulator of the hydraulic system was built based on Markov chain Monte Carlo (MCMC) method. A Particle Swarm Optimization algorithm combined with the foraging behavior of E. coli bacteria was utilized as the directed random search engine. The control strategy allows the operator to be plugged into the work environment dynamically and kinetically. This helps to ensure the system has haptic sense with high stability, without abstracting away the dynamics of the hydraulic system. The new control algorithm provides asymptotically exact tracking of both, the position and the contact force. In addition, this research proposes a novel method for re-calibration of multi-axis force/torque sensors. The method makes several improvements to traditional methods. It can be used without dismantling the sensor from its application and it requires smaller number of standard loads for calibration. It is also more cost efficient and faster in comparison to traditional calibration methods. The proposed method was developed in response to re-calibration issues with the force sensors utilized in teleoperated systems. The new approach aimed to avoid dismantling of the sensors from their applications for applying calibration. A major complication with many manipulators is the difficulty accessing them when they operate inside a non-accessible environment; especially if those environments are harsh; such as in radioactive areas. The proposed technique is based on design of experiment methodology. It has been successfully applied to different force/torque sensors and this research presents experimental validation of use of the calibration method with one of the force sensors which method has been applied to.

Show me your brain! Stories of interdisciplinary knowledge creation in practice. Experiences and observations from Aalto Design Factory, Finland.

This dissertation centres on the themes of knowledge creation, interdisciplinarity and knowledge work. My research approaches interdisciplinary knowledge creation (IKC) as practical situated activity. I argue that by approaching IKC from the practice-based perspective makes it possible to “deconstruct” how knowledge creation actually happens, and demystify its strong intellectual, mentalistic and expertise-based connotations. I have rendered the work of the observed knowledge workers into something ordinary, accessible and routinized. Consequently this has made it possible to grasp the pragmatic challenges as well the concrete drivers of such activity. Thus the effective way of organizing such activities becomes a question of organizing and leading effective everyday practices. To achieve that end, I have conducted ethnographic research of one explicitly interdisciplinary space within higher education, Aalto Design Factory in Helsinki, Finland, where I observed how students from different disciplines collaborated in new product development projects. I argue that IKC is a multi-dimensional construct that intertwines a particular way of doing; a way of experiencing; a way of embodied being; and a way of reflecting on the very doing itself. This places emphasis not only the practices themselves, but also on the way the individual experiences the practices, as this directly affects how the individual practices. My findings suggest that in order to effectively organize and execute knowledge creation activities organizations need to better accept and manage the emergent diversity and complexity inherent in such activities. In order to accomplish this, I highlight the importance of understanding and using a variety of (material) objects, the centrality of mundane everyday practices, the acceptance of contradictions and negotiations well as the role of management that is involved and engaged. To succeed in interdisciplinary knowledge creation is to lead not only by example, but also by being very much present in the very everyday practices that make it happen.

Application of mathematical models for the prediction of adsorption isotherms in solid mixture for mango powder refreshment

Solid mixtures for refreshment are already totally integrated to the Brazilian consumers' daily routine, because of their quick preparation method, yield and reasonable price - quite lower if compared to 'ready-to-drink' products or products for prompt consumption, what makes them economically more accessible to low-income populations. Within such a context, the aim of this work was to evaluate the physicochemical and mineral composition, as well as the hygroscopic behavior of four different brands of solid mixture for mango refreshment. The BET, GAB, Oswim and Henderson mathematical models were built through the adjustment of experimental data to the isotherms of adsorption. Results from the physiochemical evaluation showed that the solid mixtures for refreshments are considerable sources of ascorbic acid and reductor sugar; and regarding mineral compounds, they are significant sources of calcium, sodium and potassium. It was also verified that the solid mixtures for refreshments of the four studied brands are considered highly hygroscopic.

Energy evaluation of an evaporative cooling system using water driven ejector

The search for efficient and accessible cooling systems has increased worldwide. This study aims to build and evaluate an evaporative cooling system using a water driven ejector, allowing it to be installed in places with plenty of water. The system was investigated varying the flow rate and temperature of the circulating water, temperature of the replacement water, and coefficient of performance. The best vacuum obtained was 8.5 kPa at nominal operating conditions of 4.1 ± 0.1 m³/h and 5 ± 0.5 ºC for the circulating water reaching the temperature of 9.7 ± 0.5 ºC. The pulse-like disturbance generated by replacing the cooling water at different periods of times did not result in significant affect vacuum destabilization and the temperature rise in the cooling tank. The coefficient of performance of the system at the highest thermal power of 92.27 W was 0.077, which was underestimated due to possible problems related to pump efficiency. The system evaluated under the conditions proposed can be very efficient for cooling fluids at higher temperatures, and it can be complementary to main refrigeration systems.

Logiikka ja pelit

Tämä tutkielma käsittelee loogisia pelejä, etenkin pelaajien voittostrategioita loogisissa peleissä. Voittostrategia on strategia, jolla kahden pelaajan pelissä pelaaja voittaa pelasipa toinen pelaaja millaisia siirtoja tahansa. Tutkielman alkupuolella todistetaan, että missä tahansa kahden pelaajan äärellisessä pelissä Gn(A;W) toisella pelaajista on voittostrategia. Pääpaino on esittää logiikan ja pelien välinen yhteys. Tämä yhteys on nimeltään logiikan strateginen tasapaino, ja se muodostuu kolmesta loogisesta pelistä. Tutkielmassa esitellään tarkasti näiden pelien kulku, ja tarkastellaan milloin toisella pelaajista on voittostrategia kyseisissä loogisissa peleissä. Tutkielma mukailee Jouko Väänäsen teosta Models and Games ja osittain L.Kirbyn ja J.Parisin artikkelia Accessible Independence Results for Peano Arithmetic.

Opus Sylvanum : Selim Palmgren ja Paavo Heininen vedenjakajan maisemissa

Konsertissa esiintyvät pianistit: Elisa Järvi, Annikka Konttori-Gustafsson, Tuomas Mali, Maria Männikkö, Anu Vehviläinen.

Challenges for virtual teams in voluntary organizations

This research concerns virtual teams in the field of volunteer work. The developments in the area of information and communication technology have decreased their costs and made them easily accessible. As a result, it seems natural that also the voluntary organizations have adopted online tools and virtual teams as a part of their work modes. However, virtual teams have not received much research in this context, and one of the goals of this study was to begin closing that gap. The research had two main focus areas: the challenges that the volunteers face in the teams, and the leadership that the teams have. The study used a qualitative approach and semi-structured interviews. The interviews were conducted over Skype and email and included members from six different teams. The case organization was a European-wide student organization that widely utilized virtual teams in its work. The study identified three critical issues for managing the virtual teams. The first challenge was creating common ground for teamwork through electronic communication. Secondly, volunteering created challenges for the teams through variations in the level of commitment of the members, as some left the organization during the term of the team. Lastly, knowledge transfer was a challenge that came from changing the team members regularly each year. As for the second key topic, leadership in the teams was spread among the team members unevenly. The teams had a formal leader, but they exhibited signs of shared leadership, and the team members were able to influence the team through their own level of involvement. Especially the experience that a member had contributed the amount of influence she held. All in all, the challenges that the volunteers faced were similar to those of normal virtual teams. Volunteering brought additional challenges through the varying levels of commitment and the changing of the team members. Additionally, the role of the team leader was not as firm. The results of the study can be applied to other volunteer organizations that utilize virtual teams.

“Who is steering the ship and which constellation guides the way? Exploring transparency in the European Central Bank during the time of crisis”

This paper explores transparency in the decision-making of the European Central Bank (ECB). According to ECB´s definition, transparency means that the central bank provides the general public with all relevant information on its strategy, assessments and policy decisions as well as its procedures in an open, clear and timely manner. In this paper, however, the interpretation of transparency is somewhat broader: Information is freely available and directly accessible to those who will be affected by the decisions. Moreover, the individuals shall be able to master this material. ECB´s negative attitude towards publication of documents has demonstrated central bank´s reluctance to strive towards more extensive transparency. By virtue of the definition adopted by the ECB the bank itself is responsible for determining what is considered as relevant information. On the grounds of EU treaties, this paper assesses ECB`s accountability concentrating especially on transparency by employing principal-agent theory and constitutional approach. Traditionally, the definite mandate and the tenet of central bank independence have been used to justify the limited accountability. The de facto competence of the ECB has, however, considerably expanded as the central bank has decisively resorted to non-standard measures in order to combat the economic turbulences facing Europe. It is alleged that non-standard monetary policy constitutes a grey zone occasionally resembling economic policy or fiscal policy. Notwithstanding, the European Court of Justice has repeatedly approved these measures. This dynamic interpretation of the treaties seems to allow temporarily exceptions from the central bank´s primary objective during extraordinary times. Regardless, the paper suggests that the accountability nexus defined in the treaties is not sufficient in order to guarantee the accountability of the ECB after the adoption of the new, more active role. Enhanced transparency would help the ECB to maintain its credibility. Investing in the quality of monetary dialogue between the Parliament and the ECB appears to constitute the most adequate and practicable method to accomplish this intention. As a result of upgraded transparency the legitimacy of the central bank would not solely rest on its policy outputs.

Challenges for virtual teams in voluntary organizations

This research concerns virtual teams in the field of volunteer work. The developments in the area of information and communication technology have decreased their costs and made them easily accessible. As a result, it seems natural that also the voluntary organizations have adopted online tools and virtual teams as a part of their work modes. However, virtual teams have not received much research in this context, and one of the goals of this study was to begin closing that gap. The research had two main focus areas: the challenges that the volunteers face in the teams, and the leadership that the teams have. The study used a qualitative approach and semi-structured interviews. The interviews were conducted over Skype and email and included members from six different teams. The case organization was a European-wide student organization that widely utilized virtual teams in its work. The study identified three critical issues for managing the virtual teams. The first challenge was creating common ground for teamwork through electronic communication. Secondly, volunteering created challenges for the teams through variations in the level of commitment of the members, as some left the organization during the term of the team. Lastly, knowledge transfer was a challenge that came from changing the team members regularly each year. As for the second key topic, leadership in the teams was spread among the team members unevenly. The teams had a formal leader, but they exhibited signs of shared leadership, and the team members were able to influence the team through their own level of involvement. Especially the experience that a member had contributed the amount of influence she held. All in all, the challenges that the volunteers faced were similar to those of normal virtual teams. Volunteering brought additional challenges through the varying levels of commitment and the changing of the team members. Additionally, the role of the team leader was not as firm. The results of the study can be applied to other volunteer organizations that utilize virtual teams.

Measuring software security from the design of software

The vast majority of our contemporary society owns a mobile phone, which has resulted in a dramatic rise in the amount of networked computers in recent years. Security issues in the computers have followed the same trend and nearly everyone is now affected by such issues. How could the situation be improved? For software engineers, an obvious answer is to build computer software with security in mind. A problem with building software with security is how to define secure software or how to measure security. This thesis divides the problem into three research questions. First, how can we measure the security of software? Second, what types of tools are available for measuring security? And finally, what do these tools reveal about the security of software? Measuring tools of these kind are commonly called metrics. This thesis is focused on the perspective of software engineers in the software design phase. Focus on the design phase means that code level semantics or programming language specifics are not discussed in this work. Organizational policy, management issues or software development process are also out of the scope. The first two research problems were studied using a literature review while the third was studied using a case study research. The target of the case study was a Java based email server called Apache James, which had details from its changelog and security issues available and the source code was accessible. The research revealed that there is a consensus in the terminology on software security. Security verification activities are commonly divided into evaluation and assurance. The focus of this work was in assurance, which means to verify one’s own work. There are 34 metrics available for security measurements, of which five are evaluation metrics and 29 are assurance metrics. We found, however, that the general quality of these metrics was not good. Only three metrics in the design category passed the inspection criteria and could be used in the case study. The metrics claim to give quantitative information on the security of the software, but in practice they were limited to evaluating different versions of the same software. Apart from being relative, the metrics were unable to detect security issues or point out problems in the design. Furthermore, interpreting the metrics’ results was difficult. In conclusion, the general state of the software security metrics leaves a lot to be desired. The metrics studied had both theoretical and practical issues, and are not suitable for daily engineering workflows. The metrics studied provided a basis for further research, since they pointed out areas where the security metrics were necessary to improve whether verification of security from the design was desired.