Algorithmes de construction et correction d'arbres de gènes par la réconciliation

Les gènes, qui servent à encoder les fonctions biologiques des êtres vivants, forment l'unité moléculaire de base de l'hérédité. Afin d'expliquer la diversité des espèces que l'on peut observer aujourd'hui, il est essentiel de comprendre comment les gènes évoluent. Pour ce faire, on doit recréer le passé en inférant leur phylogénie, c'est-à-dire un arbre de gènes qui représente les liens de parenté des régions codantes des vivants. Les méthodes classiques d'inférence phylogénétique ont été élaborées principalement pour construire des arbres d'espèces et ne se basent que sur les séquences d'ADN. Les gènes sont toutefois riches en information, et on commence à peine à voir apparaître des méthodes de reconstruction qui utilisent leurs propriétés spécifiques. Notamment, l'histoire d'une famille de gènes en terme de duplications et de pertes, obtenue par la réconciliation d'un arbre de gènes avec un arbre d'espèces, peut nous permettre de détecter des faiblesses au sein d'un arbre et de l'améliorer. Dans cette thèse, la réconciliation est appliquée à la construction et la correction d'arbres de gènes sous trois angles différents: 1) Nous abordons la problématique de résoudre un arbre de gènes non-binaire. En particulier, nous présentons un algorithme en temps linéaire qui résout une polytomie en se basant sur la réconciliation. 2) Nous proposons une nouvelle approche de correction d'arbres de gènes par les relations d'orthologie et paralogie. Des algorithmes en temps polynomial sont présentés pour les problèmes suivants: corriger un arbre de gènes afin qu'il contienne un ensemble d'orthologues donné, et valider un ensemble de relations partielles d'orthologie et paralogie. 3) Nous montrons comment la réconciliation peut servir à "combiner'' plusieurs arbres de gènes. Plus précisément, nous étudions le problème de choisir un superarbre de gènes selon son coût de réconciliation.

Chasing butterflies: The Conception of the Soul in Plutarch’s Works

When first approaching a topic such as the concept of material or natural soul in Greek literature, the researcher might be puzzled. While in diverse contemporary cultures, numerous theriomorphic figures (bears, ravens, mice, wasps, bees, dragonflies, and dung-beetles) serve to represent the human soul in its transmigration from life to death, this is not the case in Greek culture. At least, this is what one may conclude from the monograph written by the Dutch scholar J. Bremmer, The early Greek Concept of the Soul: "importunely, there are no other indications of a possible connection between the butterfly and the soul of the living and the dead" (1987: 64). Given Plutarch’s great interest in the soul, which can be seen in a variety of texts referring to its generation, form, internal dichotomy, material substance, origin and destination, etc., the question arises as to whether Plutarch also includes such a representation of the soul when departing from the dead body. Does the corpus plutarcheum preserve and transmit such conception of the human soul? And if it does, are we dealing with survival of ancestral beliefs or motifs or is it a simple metaphor by means of which ancients intended to express the departing of the life-breath? In the following pages I will focus on three texts that allegedly include the butterfly-motif to represent the human soul, to wit, Table Talks 636C, Consolation to his Wife 611F, and the fragment 177 Sandbach.

Accurate Treatment of Large Supramolecular Complexes by Double-Hybrid Density Functionals Coupled with Nonlocal van der Waals Corrections

In this work, we present a thorough assessment of the performance of some representative double-hybrid density functionals (revPBE0-DH-NL and B2PLYP-NL) as well as their parent hybrid and GGA counterparts, in combination with the most modern version of the nonlocal (NL) van der Waals correction to describe very large weakly interacting molecular systems dominated by noncovalent interactions. Prior to the assessment, an accurate and homogeneous set of reference interaction energies was computed for the supramolecular complexes constituting the L7 and S12L data sets by using the novel, precise, and efficient DLPNO-CCSD(T) method at the complete basis set limit (CBS). The correction of the basis set superposition error and the inclusion of the deformation energies (for the S12L set) have been crucial for obtaining precise DLPNO-CCSD(T)/CBS interaction energies. Among the density functionals evaluated, the double-hybrid revPBE0-DH-NL and B2PLYP-NL with the three-body dispersion correction provide remarkably accurate association energies very close to the chemical accuracy. Overall, the NL van der Waals approach combined with proper density functionals can be seen as an accurate and affordable computational tool for the modeling of large weakly bonded supramolecular systems.

The Smart Paradox : Stimulate the deployment of Smart grids with effective regulatory instruments

The concept of SG (Smart Grids) encompasses a set of technologies that raise the intelligence of the electrical networks, such as smart meters or instruments of communication, sensing and auto-correction of networks. Nevertheless, the cost is still an important obstacle for the transformation of the current electricity system into a smarter one. Regulation can have an important role in setting up a favorable framework that fosters investments. However, the novelty with SG is the disembodied character of the technology, which may change the incentives of the regulated network companies to invest, affecting the effectiveness of the regulatory instruments (“cost plus” or “price cap”). This paper demonstrates that the solution to this “Smart” paradox requires strong incentive regulation mechanisms able to stimulate the adoption of SG technologies. Moreover, the regulation should not jeopardize conventional investments that are unable to be substituted by SG. Thus, a combination of performance regulation and efficiency obligations may be necessary.

Hilbert Space Valued Signal Plus Noise Models: Analysis of Structural Breaks under High Dimensionality and Temporal Dependence

This thesis is concerned with change point analysis for time series, i.e. with detection of structural breaks in time-ordered, random data. This long-standing research field regained popularity over the last few years and is still undergoing, as statistical analysis in general, a transformation to high-dimensional problems. We focus on the fundamental »change in the mean« problem and provide extensions of the classical non-parametric Darling-Erdős-type cumulative sum (CUSUM) testing and estimation theory within highdimensional Hilbert space settings. In the first part we contribute to (long run) principal component based testing methods for Hilbert space valued time series under a rather broad (abrupt, epidemic, gradual, multiple) change setting and under dependence. For the dependence structure we consider either traditional m-dependence assumptions or more recently developed m-approximability conditions which cover, e.g., MA, AR and ARCH models. We derive Gumbel and Brownian bridge type approximations of the distribution of the test statistic under the null hypothesis of no change and consistency conditions under the alternative. A new formulation of the test statistic using projections on subspaces allows us to simplify the standard proof techniques and to weaken common assumptions on the covariance structure. Furthermore, we propose to adjust the principal components by an implicit estimation of a (possible) change direction. This approach adds flexibility to projection based methods, weakens typical technical conditions and provides better consistency properties under the alternative. In the second part we contribute to estimation methods for common changes in the means of panels of Hilbert space valued time series. We analyze weighted CUSUM estimates within a recently proposed »high-dimensional low sample size (HDLSS)« framework, where the sample size is fixed but the number of panels increases. We derive sharp conditions on »pointwise asymptotic accuracy« or »uniform asymptotic accuracy« of those estimates in terms of the weighting function. Particularly, we prove that a covariance-based correction of Darling-Erdős-type CUSUM estimates is required to guarantee uniform asymptotic accuracy under moderate dependence conditions within panels and that these conditions are fulfilled, e.g., by any MA(1) time series. As a counterexample we show that for AR(1) time series, close to the non-stationary case, the dependence is too strong and uniform asymptotic accuracy cannot be ensured. Finally, we conduct simulations to demonstrate that our results are practically applicable and that our methodological suggestions are advantageous.

Journal of Architecture and Urbanism - Rethinking Le Corbusier: Urban Design and History

This is much more than a mere compilation of texts about Corbusian architecture. The articles gathered here focus on Le Corbusier’s reflections about the public space of earlier times and its influence upon his own output, the relationship of his designs with the pre-existing city, and other subjects drawn from all periods of his career and training that clarify the affinity that he established with the past through urban design. They are very heterogeneous, pointing off in different directions and marking the most diverse interests. But at the same time they are interconnected, in that they seek to shed light on the affinity that Le Corbusier established with the past from the point of view of urban design, and open up new perspectives about the public space in his work and its controversial relationship with history. This special issue thus bears witness once again to Le Corbusier’s inexhaustible legacy, but also to the usefulness of research on his work and thought – a subject about which it seemed that everything had already been said when, paradoxically, we now know that there is still almost everything left to say.

Digital Literacy: an analysis of social practices in cyberspace from the accessibility and frequency of use

This paper discusses the Digital Literacy and the importance of social practices of reading and writing nowadays. The research aims to analyze the accessibility of Digital Literacy of the residents from the satellite cities in Distrito Federal and the frequency of use of cyberspace to conduct reading and writing activities. According to Levy (1999), the transmutation of various means of communication (telephone, printed newspapers and post office, for example, in chat, digital newspapers and email, respectively) enabled the synchronous communication, interactivity and sharing of information between people from different places in the world, whether in oral form - as in video conferencing and telepresencial classroom - either in writing - as in most digital genres. It is this latter method - the writing, and hence the reading on the Internet - which has guided our discussion. According to Soares (2002), we live in a era of changes in the practices of reading and writing due to new forms of interaction between reader, author and text provided by the communication in the global computer network. Nothing better, therefore, than investigating how the user handles literacy in this new environment. The Digital Literacy, according to Xavier (2005), requires new ways of reading and writing. This means that time-honored practices of literacy, for example, should be rethought and reformulated in order to insert new ways of understanding the learning process - from handling the text to your perception, through the reading of written texts, engravings and icons linked to the electronic sphere. In this sense, the Digital Literacy, associated with multimodal genres, is present in the daily lives of several people from different social classes - particularly in large urban centers. So, facing this situation, we investigate if the residents of the satellite cities of DF have easy access to digital literacy and how often they make use of texts in cyberspace.

Comparative study of the lexicon of speakers of different religious

This work is part of the studies of Lexical Semantics and aims to compare the speakers lexicon of four different religions in four different types of texts. It starts from the assumption that religious speaker tends to keep its religious lexicon as a way of maintaining belief and block new doctrines. Thus, in addition to make use of a specific lexicon, the speaker tends to spreads it to other contexts of use. This shows how lexical and social reality are closely linked. For this research, were adopted as theoretical assumptions Structural Semantics, with an emphasis on Lexical Field Theory, Social Lexicology and Corpus Linguistics. The analyzed data confirmed the initial hypothesis that these speakers go beyond the religious context and make use of the religious lexicon in nonreligious contexts, specifically in not overtly religious texts. In addition, they showed that there is an approximation between churches of similar doctrines in some contexts, but, surprisingly, also doctrinally distinct churches in other contexts.

Dialogical-reflective meetings on reading practices and literacy (s) in a public school: report of research

This article is part of a research that investigated the practices of reading and literacy of students from a public school in Rondonópolis, Mato Grosso, and promote reflective meetings with teachers to know their views and practices regarding the teaching and learning of reading, searching contribute to the critical reflection on these practices. Thus, the proposed work was guided by reading theories and critical literacy, combined with the Bakhtin’s language theory and Vygotsky’s learning theory and human development. The data revealed that students participate in a variety of literacy practices  out of school contexts, however the context of school literacy uncovers centralization of activities in traditional tasks in school, especially copy of texts and activities of the blackboard. In the first meetings with the teachers, their perceptions about these practices were marked by uncertainty, not understanding what to do with some school problems. As the meetings were going on, the discourses could reveal critical reflection moments.

Amblyopia treatment : an evidence-based approach to maximising treatment outcome

The basis of treatment for amblyopia (poor vision due to abnormal visual experience early in life) for 250 years has been patching of the unaffected eye for extended times to ensure a period of use of the affected eye. Over the last decade randomised controlled treatment trials have provided some evidence on how to tailor amblyopia therapy more precisely to achieve the best visual outcome with the least negative impact on the patient and the family. This review highlights the expansion of knowledge regarding treatment for amblyopia and aims to provide optometrists with a summary of research evidence to enable them to better treat amblyopia. Treatment for amblyopia is effective, as it reduces overall prevalence and severity of visual loss in this population. Correction of refractive error alone significantly improves visual acuity, sometimes to the point where further amblyopia treatment is not required. Atropine penalisation and patch occlusion are effective in treating amblyopia. Lesser amounts of occlusion or penalisation have been found to be just as effective as greater amounts. Recent evidence has highlighted that occlusion or penalisation in amblyopia treatment can create negative changes in behaviour in children and impact on family life. These complications should be considere when prescribing treatment because they can negatively affect compliance. Studies investigating the maximum age at which treatment of amblyopia can still be effective and the importance of near activities during occlusion are ongoing.

Humanistic science education : moves from within and challenges from without

For a number of years now it has been evident that the major issue facing science educators in the more developed countries of the world is the quantitative decline in enrolments in the senior secondary sciences, particularly the physical sciences, and in the number of higher achieving students applying for places in universities to undertake further studies in science. The deep malaise in school science to which these quantitative measures point has been elucidated by more qualitative studies of the students’ experience of studying science in secondary school in several of these countries (Sweden, Lindahl (2003); England, Simon and Osborne (2002); and Australia, Lyons (2005)). Remarkably concordant descriptions of these experiences can be summarized as: School science is: • transmission of knowledge from the teacher or the textbook to the students. • about content that is irrelevant and boring to our lives. • difficult to learn in comparison with other subjects Incidentally, the Australian study only involved consistently high achieving students; but even so, most of them found science more difficult than other more interesting subjects, and concluded that further science studies should be avoided unless they were needed for some career purpose. Other more representative confirmations of negative evaluations of the science curricula across Australia (and in particular states) are now available in Australia, from the large scale reviews of Goodrum, Hackling and Rennie (2001) and from the TIMSS (2002). The former reported that well under half of secondary students find the science at school relevant to my future, useful ion everyday life, deals with things I am concerned with and helps me make decisions about my health.. TIMSS found that 62 and 65 % of females and males in Year 4 agree with I like learning science, but by Year 8 only 26 and 33 % still agree. Students in Japan have been doubly notably because of (a) their high performance in international measures of science achievement like TIMSS and PISA and (b) their very low response to items in these studies which relate to interest in science. Ogura (2003) reported an intra-national study of students across Years 6-9 (upper primary through Junior High); interest in a range of their subjects (including science) that make up that country’s national curriculum. There was a steady decline in interest in all these subjects which might have indicated an adolescent reaction against schooling generally. However, this study went on to ask the students a further question that is very meaningful in the Japanese context, If you discount the importance of this subject for university entrance, is it worth studying? Science and mathematics remained in decline while all the other subjects were seen more positively. It is thus ironic, at a time when some innovations in curriculum and other research-based findings are suggesting ways that these failures of school science might be corrected, to find school science under a new demands that come from quite outside science education, and which certainly do not have the correction of this malaise as a priority. The positive curricular and research findings can be characterized as moves from within science education, whereas the new demands are moves that come from without science education. In this paper I set out these two rather contrary challenges to the teaching of science as it is currently practised, and go on to suggest a way forward that could fruitfully combine the two.

A gendered educational agenda : what's wrong with 10 Things I Hate About You?

Both William Shakespeare's play The Taming of the Shrew (1593) and the film 10 thing I hate About You (Gil Junger, 1999) contain tropes of gender and education and gendered education, and both represent and perform 'education'. That is, they depict characters undergoing a range of educational experiences and in turn educate their audience about what it means to be educated appropriately. It seems fitting then that these pairng of texts has been popular with high school teachers who, more often than not, use them as ways into teaching Shakespeare to contemporary adolescents. I suggest that the play-film pairing can be more productively introduced into the classroom as texts that offer critical readers the opportunity to contest the values of education and gender contatined within them, rather than as tools to reintroduce outdated notions of gendered agency and cultural authority. Indeed it is precisely because 10 Things is unequivocally a romantic comedy that aims to work within the audience's comfort zone that we must seriously interrogate the cultural politics of gender and education it promotes.

Texting while driving : psychosocial influences on young people’s texting intentions and behaviour

Despite the dangers and illegality, there is a continued prevalence of texting while driving amongst young Australian drivers. The present study tested an extended theory of planned behaviour (TPB) to predict young drivers’ (17 to 24 years) intentions to [1] send and [2] read text messages while driving. Participants (N = 169 university students) completed measures of attitudes, subjective norm, perceived behavioural control, intentions, and the additional social influence measures of group norm and moral norm. One week later, participants reported on the number of texts sent and read while driving in the previous week. Attitude predicted intentions to both send and read texts while driving, and subjective norm and perceived behavioural control determined sending, but not reading, intentions. Further, intention, but not perceptions of control, predicted both texting behaviours 1 week later. In addition, both group norm and moral norm added predictive ability to the model. These findings provide support for the TPB in understanding students’ decisions to text while driving as well as the inclusion of additional normative influences within this context, suggesting that a multi-strategy approach is likely to be useful in attempts to reduce the incidence of these risky driving behaviours.

Axial length charges during accommodation in myopes and emmetropes

Purpose: To investigate the influence of accommodation upon axial length (and a comprehensive range of ocular biometric parameters), in populations of young adult myopic and emmetropic subjects. Methods: Forty young adult subjects had ocular biometry measured utilizing a non-contact optical biometer (Lenstar LS 900) based upon the principle of optical low coherence reflectometry, under three different accommodation demands (0 D, 3 D and 6 D). Subjects were classified as emmetropes (n=19) or myopes (n=21) based upon their spherical equivalent refraction (mean emmetropic refraction -0.05 ± 0.27DS and mean myopic refraction -1.82 ± 0.84 DS). Results: Axial length changed significantly with accommodation, with a mean increase of 11.9 ± 12.3 µm and 24.1 ± 22.7 µm for the 3 D and 6 D accommodation stimuli respectively. A significant axial elongation associated with accommodation was still evident even following correction of the axial length data for potential error due to lens thickness change. The mean ‘corrected’ increase in axial length was 5.2 ± 11.2 µm, and 7.4 ± 18.9 µm for the 3 D and 6 D stimuli respectively. There was no significant difference between the myopic and emmetropic populations in terms of the magnitude of change in axial length with accommodation, regardless of whether the data were corrected or not. A number of other ocular biometric parameters, such as anterior chamber depth, lens thickness and vitreous chamber depth also exhibited significant change with accommodation. The myopic and emmetropic populations also exhibited no significant difference in the magnitude of change in these parameters with accommodation. Conclusions: The eye undergoes a significant axial elongation associated with a brief period of accommodation, and the magnitude of this change in eye length increases for larger accommodation demands, however there is no significant difference in the magnitude of eye elongation in myopic and emmetropic subjects.

Towards a unified method for the knowledge based urban development framework

Purpose–The growing debate in the literature indicates that the initiative to implement Knowledge Based Urban Development (KBUD) approaches in urban development process is neither simple nor quick. Many research efforts has therefore, been put forward to the development of appropriate KBUD framework and KBUD practical approaches. But this has lead to a fragmented and incoherent methodological approach. This paper outlines and compares a few most popular KBUD frameworks selected from the literature. It aims to identify some key and common features in the effort to achieve a unified method of KBUD framework. Design/methodology/approach–This paper reviews, examines and identifies various popular KBUD frameworks discussed in the literature from urban planners’ viewpoint. It employs a content analysis technique i.e. a research tool used to determine the presence of certain words or concepts within texts or sets of texts. Originality/value–The paper reports on the key and common features of a few selected most popular KBUD frameworks. The synthesis of the results is based from a perspective of urban planners. The findings which encompass a new KBUD framework incorporating the key and common features will be valuable in setting a platform to achieve a unified method of KBUD. Practical implications –The discussion and results presented in this paper should be significant to researchers and practitioners and to any cities and countries that are aiming for KBUD. Keywords – Knowledge based urban development, Knowledge based urban development framework, Urban development and knowledge economy