Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas

BACKGROUND: The bacterial flagellum is the most important organelle of motility in bacteria and plays a key role in many bacterial lifestyles, including virulence. The flagellum also provides a paradigm of how hierarchical gene regulation, intricate protein-protein interactions and controlled protein secretion can result in the assembly of a complex multi-protein structure tightly orchestrated in time and space. As if to stress its importance, plants and animals produce receptors specifically dedicated to the recognition of flagella. Aside from motility, the flagellum also moonlights as an adhesion and has been adapted by humans as a tool for peptide display. Flagellar sequence variation constitutes a marker with widespread potential uses for studies of population genetics and phylogeny of bacterial species. RESULTS: We sequenced the complete flagellin gene (flaA) in 18 different species and subspecies of Aeromonas. Sequences ranged in size from 870 (A. allosaccharophila) to 921 nucleotides (A. popoffii). The multiple alignment displayed 924 sites, 66 of which presented alignment gaps. The phylogenetic tree revealed the existence of two groups of species exhibiting different FlaA flagellins (FlaA1 and FlaA2). Maximum likelihood models of codon substitution were used to analyze flaA sequences. Likelihood ratio tests suggested a low variation in selective pressure among lineages, with an omega ratio of less than 1 indicating the presence of purifying selection in almost all cases. Only one site under potential diversifying selection was identified (isoleucine in position 179). However, 17 amino acid positions were inferred as sites that are likely to be under positive selection using the branch-site model. Ancestral reconstruction revealed that these 17 amino acids were among the amino acid changes detected in the ancestral sequence. CONCLUSION: The models applied to our set of sequences allowed us to determine the possible evolutionary pathway followed by the flaA gene in Aeromonas, suggesting that this gene have probably been evolving independently in the two groups of Aeromonas species since the divergence of a distant common ancestor after one or several episodes of positive selection. REVIEWERS: This article was reviewed by Alexey Kondrashov, John Logsdon and Olivier Tenaillon (nominated by Laurence D Hurst).

The Pursuit of Efficient Copyright Licensing : How Some Rights Reserved Attempts to Solve the Problems of All Rights Reserved

This dissertation analyses the growing pool of copyrighted works, which are offered to the public using Creative Commons licensing. The study consist of analysis of the novel licensing system, the licensors, and the changes of the "all rights reserved" —paradigm of copyright law. Copyright law reserves all rights to the creator until seventy years have passed since her demise. Many claim that this endangers communal interests. Quite often the creators are willing to release some rights. This, however, is very difficult to do and needs help of specialized lawyers. The study finds that the innovative Creative Commons licensing scheme is well suited for low value - high volume licensing. It helps to reduce transaction costs on several le¬vels. However, CC licensing is not a "silver bullet". Privacy, moral rights, the problems of license interpretation and license compatibility with other open licenses and collecting societies remain unsolved. The study consists of seven chapters. The first chapter introduces the research topic and research questions. The second and third chapters inspect the Creative Commons licensing scheme's technical, economic and legal aspects. The fourth and fifth chapters examine the incentives of the licensors who use open licenses and describe certain open business models. The sixth chapter studies the role of collecting societies and whether two institutions, Creative Commons and collecting societies can coexist. The final chapter summarizes the findings. The dissertation contributes to the existing literature in several ways. There is a wide range of prior research on open source licensing. However, there is an urgent need for an extensive study of the Creative Commons licensing and its actual and potential impact on the creative ecosystem.

A hybrid feature selection approach for the early diagnosis of Alzheimer's disease

Objective. Recently, significant advances have been made in the early diagnosis of Alzheimer’s disease from EEG. However, choosing suitable measures is a challenging task. Among other measures, frequency Relative Power and loss of complexity have been used with promising results. In the present study we investigate the early diagnosis of AD using synchrony measures and frequency Relative Power on EEG signals, examining the changes found in different frequency ranges. Approach. We first explore the use of a single feature for computing the classification rate, looking for the best frequency range. Then, we present a multiple feature classification system that outperforms all previous results using a feature selection strategy. These two approaches are tested in two different databases, one containing MCI and healthy subjects (patients age: 71.9 ± 10.2, healthy subjects age: 71.7 ± 8.3), and the other containing Mild AD and healthy subjects (patients age: 77.6 ± 10.0; healthy subjects age: 69.4± 11.5). Main Results. Using a single feature to compute classification rates we achieve a performance of 78.33% for the MCI data set and of 97.56 % for Mild AD. Results are clearly improved using the multiple feature classification, where a classification rate of 95% is found for the MCI data set using 11 features, and 100% for the Mild AD data set using 4 features. Significance. The new features selection method described in this work may be a reliable tool that could help to design a realistic system that does not require prior knowledge of a patient's status. With that aim, we explore the standardization of features for MCI and Mild AD data sets with promising results.

Assembly Methods of Permanent Magnets for Synchronous Generators

This thesis examines and explains the procedure used to redesign the attachment of permanent magnets to the surface of the rotor of a synchronous generator. The methodology followed to go from the actual assembly to converge to the final purposed innovation was based on the systematic approach design. This meant that first a series of steps had to be predefined as a frame of reference later to be used to compare and select proposals, and finally to obtain the innovation that was sought. Firstly, a series of patents was used as the background for the upcoming ideas. To this end, several different patented assemblies had been found and categorized according the main element onto which this thesis if focused, meaning the attachment element or method. After establishing the technological frame of reference, a brainstorm was performed to obtain as many ideas as possible. Then these ideas were classified, regardless of their degree of complexity or usability, since at this time the quantity of the ideas was the important issue. Subsequently, they were compared and evaluated from different points of view. The comparison and evaluation in this case was based on the use of a requirement list, which established the main needs that the design had to fulfill. Then the selection could be done by grading each idea in accordance with these requirements. In this way, one was able to obtain the idea or ideas that best fulfilled these requirements. Once all of the ideas were compared and evaluated, the best or most suitable idea or ideas were separated. Finally, the selected idea or ideas was/were analyzed in extension and a number of improvements were made. Consequently, a final idea was refined and made more suitable at its performance, manufacture, and life cycle assessment. Therefore, in the end, the design process gave a solution to the problem pointed out at the beginning.

Lo que no es nuevo puede ser actual: hacia distintos puntos de mira de la didáctica del arte What is not new can be current - towards different approaches of the didactics of art

With this article we want to present a state of affairs of the didactics of art in our context, and at the same time we want todiscuss on its pluri- and interdisciplinary construction. We check the different disciplines that configure it and we analysethe paradigm of artistic education as a discipline (DBAE) and its passage to post-modernity. This example focuses thediscussion about the opportunity of adapting holistic educative models and the transition of the current educativeinnovation towards skill models

Ciência como cultura: paradigmas e implicações epistemológicas na educação científica escolar

"Science as culture" is based on the assumption that science is a valuable component of human culture. We therefore have to build the bridge, in cultural terms, from the scientific community to the common citizen. Teaching science as culture requires the co-construction of knowledge and citizenship. Ways of articulating science/technology with society are invoked, pondering on the ethical ambivalence of such connections. The goals of this reflection are to think about: a) epistemological obstacles that, in favouring the logic of monoculture, oppose the implantation of the science as culture; b) epistemological strategies that point towards a diversity of cultural practices and "constellations" of knowledge leading to the reconfiguration of the being through knowledge; c) imperatives that force us to (re)think the epistemological bases suited to the paradigmatic changes and which translate the dynamics and complexity of the evolution of the frameworks that currently sustain science and school scientific education.

The impact of the law 10,267/2001 in the brazilian rural registration

The publication of the Law 10,267 of 08/28/2001 changed the paradigm of rural registration in Brazil, because this law known as the "Law of Georeferencing" has created the National Registration of Rural Property, that unifies in a common basis different registrations present in several government agencies, such as the National Institute for Colonization and Agrarian Reform (INCRA), the Secretariat of Federal Revenue, the Brazilian Institute of Environment and Natural Resources, and the National Indian Foundation. Also, this new registration system has a graphical component which has not existed until such date, where the boundaries of rural property are georeferenced to the Brazilian Geodetic System. This new paradigm has resulted in a standardization of the survey and its representation of rural properties according to the Technical Standard for Georeferencing of Rural Properties, published by INCRA in compliance with the new legislation. Due to the georeferencing, the creation of a public GIS of free access on the Internet was possible. Among the difficulties found it may be observed the great Brazilian territory, the need for specialized professionals, and especially the certification process that INCRA has to perform for each georeferenced property. It is hoped that this last difficulty is solved with the implementation of the Land Management System that will allow automated and online certification, making the process more transparent, agile and fast.

Strategic external deployment of intellectual assets

Globalization, pervasiveness of technology and ICT, and the buildup of information societies and policies have lead to a growing abundance of knowledge and highly educated labour supply that is distributed widely. These changes have shifted the foundation of competitiveness to valuable knowledge resources which are now distributed widely across the globe, across actors in the value chain and across educated individuals in multiple organizations. Against this backdrop, the paradigm of open innovation (OI) has emerged as a new response to managing the increased amount of boundary-spanning knowledge flows in and out of the innovation process. The outbound mode of open innovation, that is to say the external exploitation of knowledge assets outside of the firm’s own products and services, has been the less-researched aspect of the concept and so far typically seen as concerning the outlicensing of unused technological assets to generate additional revenue. Given that open innovation is essentially a framework for the holistic structuring and management of crossboundary knowledge flows to improve a firm’s innovative performance, a close integration to corporate strategy seems imperative in order to fully benefit from it. Integrating open innovation to strategy leads to elevating its role from a fringe activity to a central innovation management issue that needs to be systematically managed. Building a structure that allows effective management necessitates linking open innovation activities to each phase of the innovation process. Previously, the connection between outbound OI and the earlier stages of innovation has not been studied. The thesis finds that connecting outbound OI to the entire innovation process of the firm, including the fuzzy front end of innovation, is critical for attaining strategic objectives and to the successful implementation and management of the activity. The practical purpose for the research is to enable companies to fully utilize their potential for outbound open innovation and to be able to implement and manage it from a strategic standpoint.

Organisational learning and knowledge acquisition. A case study of internationalising manufacturers of wood-based prefabricated buildings

The study investigates organisational learning and knowledge acquisition of wood-based prefabricated building manufacturers. This certain group of case companies was chosen, because their management and their employees generally have a strong manufacturing and engineering background, while the housing sector is characterised by national norms, regulations, as well as local building styles. Considering this setting, it was investigated, how the case companies develop organisational learning capabilities, acquire and transfer knowledge for their internationalisation. The theoretical framework of this study constitutes the knowledge-based conceptualisation of internationalisation, which combines the traditional internationalisation process, as well as the international new venture perspective based on their commonalities in the knowledge-based view of the firm. Different theories of internationalisation, including the network-perspective, were outlined and a framework on organisational learning and knowledge acquisition was established. The empirical research followed a qualitative approach, deploying a multiple-case study with five case companies from Austria, Finland and Germany. In the study, the development of the wood-based prefabricated building industry and of the case companies are described, and the motives, facilitators and challenges for foreign expansion, as well as the companies’ internationalisation approaches are compared. Different methods of how companies facilitate the knowledge-exchange or learn about new markets are also outlined. Experience, market knowledge and personal contacts are considered essential for the internationalisation process. The major finding of the study is that it is not necessary to acquire the market knowledge internally in a slow process as proposed by the Uppsala model. In four cases companies engaged knowledge in symbiotic relations with local business partners. Thereby, the building manufacturers contribute their design and production capabilities, and in return, their local partners provide them with knowledge about the market and local regulations; while they manage the sales and construction operations. Thus, the study provides strong evidence for the propositions of network perspective. One case company developed the knowledge internally in a gradual process: it entered the market sequentially with several business lines, showing an increasing level of complexity. In both of the observed strategies, single-loop and double-loop learning processes occurred.

The third transformation of Japan: An institutional narrative on agglomeration economies in abenomics

Objective of the study The aim of this study is to understand the institutional implications in Abenomics in a spatial context, the contemporary economic reform taking place in Japan, which is to finally end over two decades of economic malaise. For theoretical perspective of choice, this study explores a synthesis of institutionalism as the main approach, complemented by economies of agglomeration in spatial economics, or New Economic Geography (NEG). The outcomes include a narrative with implications for future research, as well as possible future implications for the economy of Japan, itself. The narrative seeks to depict the dialogue between public discourse and governmental communication in order to create a picture of how this phenomenon is being socially constructed. This is done by studying the official communications by the Cabinet along with public media commentary on respective topics. The reform is studied with reference to historical socio-cultural, economic evolution of Japan, which in turn, is explored through a literature review. This is to assess the unique institutional characteristics of Japan pertinent to reform. Research method This is a social and exploratory qualitative study – an institutional narrative case study. The methodological approach was kept practical: in addition to literature review, a narrative, thematic content analysis with structural emphasis was used to construct the contemporary narrative based on the Cabinet communication. This was combined with practical analytic tools borrowed from critical discourse analysis, which were utilized to assess the implicit intertextual agenda within sources. Findings What appears to characterize the discourse is status quo bias that comes in multiple forms. The bias is also coded in the institutions surrounding the reform, wherein stakeholders have vested interests in protecting the current state of affairs. This correlates with uncertainty avoidance characteristic to Japan. Japan heeds the international criticism to deregulate on a rhetorical level, but consistent with history, the Cabinet solutions appear increasingly bureaucratic. Hence, the imposed western information-age paradigm of liberal cluster agglomeration seems ill-suited to Japan which lacks risk takers and a felicitous entrepreneur culture. The Japanese, however, possess vast innovative potential ascribed to some institutional practices and traits, but restrained by others. The derived conclusion is to study the successful intrapreneur cases in Japanese institutional setting as a potential benchmark for Japan specific cluster agglomeration, and a solution to its structural problems impeding growth.

Evaluation of two experimental models of hepatic encephalopathy in rats

The serious neuropsychological repercussions of hepatic encephalopathy have led to the creation of several experimental models in order to better understand the pathogenesis of the disease. In the present investigation, two possible causes of hepatic encephalopathy, cholestasis and portal hypertension, were chosen to study the behavioral impairments caused by the disease using an object recognition task. This working memory test is based on a paradigm of spontaneous delayed non-matching to sample and was performed 60 days after surgery. Male Wistar rats (225-250 g) were divided into three groups: two experimental groups, microsurgical cholestasis (N = 20) and extrahepatic portal hypertension (N = 20), and a control group (N = 20). A mild alteration of the recognition memory occurred in rats with cholestasis compared to control rats and portal hypertensive rats. The latter group showed the poorest performance on the basis of the behavioral indexes tested. In particular, only the control group spent significantly more time exploring novel objects compared to familiar ones (P < 0.001). In addition, the portal hypertension group spent the shortest time exploring both the novel and familiar objects (P < 0.001). These results suggest that the existence of portosystemic collateral circulation per se may be responsible for subclinical encephalopathy.

Study of the comprehension of the scientific method by members of a university health research laboratory

In Brazil, scientific research is carried out mainly at universities, where professors coordinate research projects with the active participation of undergraduate and graduate students. However, there is no formal program for the teaching/learning of the scientific method. The objective of the present study was to evaluate the comprehension of the scientific method by students of health sciences who participate in scientific projects in an academic research laboratory. An observational descriptive cross-sectional study was conducted using Edgar Morin complexity as theoretical reference. In a semi-structured interview, students were asked to solve an abstract logical puzzle - TanGram. The collected data were analyzed using the hermeneutic-dialectic analysis method proposed by Minayo and discussed in terms of the theoretical reference of complexity. The students’ concept of the scientific method is limited to participation in projects, stressing the execution of practical procedures as opposed to scientific thinking. The solving of the TanGram puzzle revealed that the students had difficulties in understanding questions and activities focused on subjects and their processes. Objective answers, even when dealing with personal issues, were also reflected on the students’ opinions about the characteristics of a successful researcher. Students’ difficulties concerning these issues may affect their scientific performance and result in poorly designed experiments. This is a preliminary study that should be extended to other centers of scientific research.

Enabling and Measuring Complexity in Evolving Designs using Generative Representations for Artificial Architecture

As the complexity of evolutionary design problems grow, so too must the quality of solutions scale to that complexity. In this research, we develop a genetic programming system with individuals encoded as tree-based generative representations to address scalability. This system is capable of multi-objective evaluation using a ranked sum scoring strategy. We examine Hornby's features and measures of modularity, reuse and hierarchy in evolutionary design problems. Experiments are carried out, using the system to generate three-dimensional forms, and analyses of feature characteristics such as modularity, reuse and hierarchy were performed. This work expands on that of Hornby's, by examining a new and more difficult problem domain. The results from these experiments show that individuals encoded with those three features performed best overall. It is also seen, that the measures of complexity conform to the results of Hornby. Moving forward with only this best performing encoding, the system was applied to the generation of three-dimensional external building architecture. One objective considered was passive solar performance, in which the system was challenged with generating forms that optimize exposure to the Sun. The results from these and other experiments satisfied the requirements. The system was shown to scale well to the architectural problems studied.

Aggregations and Marginalization of GARCH and Stochastic Volatility Models

The GARCH and Stochastic Volatility paradigms are often brought into conflict as two competitive views of the appropriate conditional variance concept : conditional variance given past values of the same series or conditional variance given a larger past information (including possibly unobservable state variables). The main thesis of this paper is that, since in general the econometrician has no idea about something like a structural level of disaggregation, a well-written volatility model should be specified in such a way that one is always allowed to reduce the information set without invalidating the model. To this respect, the debate between observable past information (in the GARCH spirit) versus unobservable conditioning information (in the state-space spirit) is irrelevant. In this paper, we stress a square-root autoregressive stochastic volatility (SR-SARV) model which remains true to the GARCH paradigm of ARMA dynamics for squared innovations but weakens the GARCH structure in order to obtain required robustness properties with respect to various kinds of aggregation. It is shown that the lack of robustness of the usual GARCH setting is due to two very restrictive assumptions : perfect linear correlation between squared innovations and conditional variance on the one hand and linear relationship between the conditional variance of the future conditional variance and the squared conditional variance on the other hand. By relaxing these assumptions, thanks to a state-space setting, we obtain aggregation results without renouncing to the conditional variance concept (and related leverage effects), as it is the case for the recently suggested weak GARCH model which gets aggregation results by replacing conditional expectations by linear projections on symmetric past innovations. Moreover, unlike the weak GARCH literature, we are able to define multivariate models, including higher order dynamics and risk premiums (in the spirit of GARCH (p,p) and GARCH in mean) and to derive conditional moment restrictions well suited for statistical inference. Finally, we are able to characterize the exact relationships between our SR-SARV models (including higher order dynamics, leverage effect and in-mean effect), usual GARCH models and continuous time stochastic volatility models, so that previous results about aggregation of weak GARCH and continuous time GARCH modeling can be recovered in our framework.