The establishment of communication systems depends on the scale of competition

How communication systems emerge and remain stable is an important question in both cognitive science and evolutionary biology. For communication to arise, not only must individuals cooperate by signaling reliable information, but they must also coordinate and perpetuate signals. Most studies on the emergence of communication in humans typically consider scenarios where individuals implicitly share the same interests. Likewise, most studies on human cooperation consider scenarios where shared conventions of signals and meanings cannot be developed de novo. Here, we combined both approaches with an economic experiment where participants could develop a common language, but under different conditions fostering or hindering cooperation. Participants endeavored to acquire a resource through a learning task in a computer-based environment. After this task, participants had the option to transmit a signal (a color) to a fellow group member, who would subsequently play the same learning task. We varied the way participants competed with each other (either global scale or local scale) and the cost of transmitting a signal (either costly or noncostly) and tracked the way in which signals were used as communication among players. Under global competition, players signaled more often and more consistently, scored higher individual payoffs, and established shared associations of signals and meanings. In addition, costly signals were also more likely to be used under global competition; whereas under local competition, fewer signals were sent and no effective communication system was developed. Our results demonstrate that communication involves both a coordination and a cooperative dilemma and show the importance of studying language evolution under different conditions influencing human cooperation.

Improving Searching and Browsing Capabilities of Learning Object Repositories

Learning object repositories are a basic piece of virtual learning environments used for content management. Nevertheless, learning objects have special characteristics that make traditional solutions for content management ine ective. In particular, browsing and searching for learning objects cannot be based on the typical authoritative meta-data used for describing content, such as author, title or publicationdate, among others. We propose to build a social layer on top of a learning object repository, providing nal users with additional services fordescribing, rating and curating learning objects from a teaching perspective. All these interactions among users, services and resources can be captured and further analyzed, so both browsing and searching can be personalized according to user pro le and the educational context, helping users to nd the most valuable resources for their learning process. In this paper we propose to use reputation schemes and collaborative filtering techniques for improving the user interface of a DSpace based learning object repository.

Extending Learning Objects by Means of Social Networking

Learning objects have been the promise of providing people with high quality learning resources. Initiatives such as MIT Open-CourseWare, MERLOT and others have shown the real possibilities of creating and sharing knowledge through Internet. Thousands of educational resources are available through learning object repositories. We indeed live in an age of content abundance, and content can be considered as infrastructure for building adaptive and personalized learning paths, promoting both formal and informal learning. Nevertheless, although most educational institutions are adopting a more open approach, publishing huge amounts of educational resources, the reality is that these resources are barely used in other educational contexts. This paradox can be partly explained by the dificulties in adapting such resources with respect to language, e-learning standards and specifications and, finally, granularity. Furthermore, if we want our learners to use and take advantage of learning object repositories, we need to provide them with additional services than just browsing and searching for resources. Social networks can be a first step towards creating an open social community of learning around a topic or a subject. In this paper we discuss and analyze the process of using a learning object repository and building a social network on the top of it, with respect to the information architecture needed to capture and store the interaction between learners and resources in form of learning object metadata.

Relationships between users, resources and services in learning object repositories

In this paper we describe a proposal for defining the relationships between resources, users and services in a digital repository. Nowadays, virtual learning environments are widely used but digital repositories are not fully integrated yet into the learning process. Our final goal is to provide final users with recommendation systems and reputation schemes that help them to build a true learning community around the institutional repository, taking into account their educational context (i.e. the courses they are enrolled into) and their activity (i.e. system usage by their classmates and teachers). In order to do so, we extend the basic resource concept in a traditional digital repository by adding all the educational context and other elements from end-users' profiles, thus bridging users, resources and services, and shifting from a library-centered paradigm to a learning-centered one.

Multi-scale systems analysis of plant development : beyond cellular signaling and tissue morphodynamics

Les plantes sont essentielles pour les sociétés humaines. Notre alimentation quotidienne, les matériaux de constructions et les sources énergétiques dérivent de la biomasse végétale. En revanche, la compréhension des multiples aspects développementaux des plantes est encore peu exploitée et représente un sujet de recherche majeur pour la science. L'émergence des technologies à haut débit pour le séquençage de génome à grande échelle ou l'imagerie de haute résolution permet à présent de produire des quantités énormes d'information. L'analyse informatique est une façon d'intégrer ces données et de réduire la complexité apparente vers une échelle d'abstraction appropriée, dont la finalité est de fournir des perspectives de recherches ciblées. Ceci représente la raison première de cette thèse. En d'autres termes, nous appliquons des méthodes descriptives et prédictives combinées à des simulations numériques afin d'apporter des solutions originales à des problèmes relatifs à la morphogénèse à l'échelle de la cellule et de l'organe. Nous nous sommes fixés parmi les objectifs principaux de cette thèse d'élucider de quelle manière l'interaction croisée des phytohormones auxine et brassinosteroïdes (BRs) détermine la croissance de la cellule dans la racine du méristème apical d'Arabidopsis thaliana, l'organisme modèle de référence pour les études moléculaires en plantes. Pour reconstruire le réseau de signalement cellulaire, nous avons extrait de la littérature les informations pertinentes concernant les relations entre les protéines impliquées dans la transduction des signaux hormonaux. Le réseau a ensuite été modélisé en utilisant un formalisme logique et qualitatif pour pallier l'absence de données quantitatives. Tout d'abord, Les résultats ont permis de confirmer que l'auxine et les BRs agissent en synergie pour contrôler la croissance de la cellule, puis, d'expliquer des observations phénotypiques paradoxales et au final, de mettre à jour une interaction clef entre deux protéines dans la maintenance du méristème de la racine. Une étude ultérieure chez la plante modèle Brachypodium dystachion (Brachypo- dium) a révélé l'ajustement du réseau d'interaction croisée entre auxine et éthylène par rapport à Arabidopsis. Chez ce dernier, interférer avec la biosynthèse de l'auxine mène à la formation d'une racine courte. Néanmoins, nous avons isolé chez Brachypodium un mutant hypomorphique dans la biosynthèse de l'auxine qui affiche une racine plus longue. Nous avons alors conduit une analyse morphométrique qui a confirmé que des cellules plus anisotropique (plus fines et longues) sont à l'origine de ce phénotype racinaire. Des analyses plus approfondies ont démontré que la différence phénotypique entre Brachypodium et Arabidopsis s'explique par une inversion de la fonction régulatrice dans la relation entre le réseau de signalisation par l'éthylène et la biosynthèse de l'auxine. L'analyse morphométrique utilisée dans l'étude précédente exploite le pipeline de traitement d'image de notre méthode d'histologie quantitative. Pendant la croissance secondaire, la symétrie bilatérale de l'hypocotyle est remplacée par une symétrie radiale et une organisation concentrique des tissus constitutifs. Ces tissus sont initialement composés d'une douzaine de cellules mais peuvent aisément atteindre des dizaines de milliers dans les derniers stades du développement. Cette échelle dépasse largement le seuil d'investigation par les moyens dits 'traditionnels' comme l'imagerie directe de tissus en profondeur. L'étude de ce système pendant cette phase de développement ne peut se faire qu'en réalisant des coupes fines de l'organe, ce qui empêche une compréhension des phénomènes cellulaires dynamiques sous-jacents. Nous y avons remédié en proposant une stratégie originale nommée, histologie quantitative. De fait, nous avons extrait l'information contenue dans des images de très haute résolution de sections transverses d'hypocotyles en utilisant un pipeline d'analyse et de segmentation d'image à grande échelle. Nous l'avons ensuite combiné avec un algorithme de reconnaissance automatique des cellules. Cet outil nous a permis de réaliser une description quantitative de la progression de la croissance secondaire révélant des schémas développementales non-apparents avec une inspection visuelle classique. La formation de pôle de phloèmes en structure répétée et espacée entre eux d'une longueur constante illustre les bénéfices de notre approche. Par ailleurs, l'exploitation approfondie de ces résultats a montré un changement de croissance anisotropique des cellules du cambium et du phloème qui semble en phase avec l'expansion du xylème. Combinant des outils génétiques et de la modélisation biomécanique, nous avons démontré que seule la croissance plus rapide des tissus internes peut produire une réorientation de l'axe de croissance anisotropique des tissus périphériques. Cette prédiction a été confirmée par le calcul du ratio des taux de croissance du xylème et du phloème au cours de développement secondaire ; des ratios élevés sont effectivement observés et concomitant à l'établissement progressif et tangentiel du cambium. Ces résultats suggèrent un mécanisme d'auto-organisation établi par un gradient de division méristématique qui génèrent une distribution de contraintes mécaniques. Ceci réoriente la croissance anisotropique des tissus périphériques pour supporter la croissance secondaire. - Plants are essential for human society, because our daily food, construction materials and sustainable energy are derived from plant biomass. Yet, despite this importance, the multiple developmental aspects of plants are still poorly understood and represent a major challenge for science. With the emergence of high throughput devices for genome sequencing and high-resolution imaging, data has never been so easy to collect, generating huge amounts of information. Computational analysis is one way to integrate those data and to decrease the apparent complexity towards an appropriate scale of abstraction with the aim to eventually provide new answers and direct further research perspectives. This is the motivation behind this thesis work, i.e. the application of descriptive and predictive analytics combined with computational modeling to answer problems that revolve around morphogenesis at the subcellular and organ scale. One of the goals of this thesis is to elucidate how the auxin-brassinosteroid phytohormone interaction determines the cell growth in the root apical meristem of Arabidopsis thaliana (Arabidopsis), the plant model of reference for molecular studies. The pertinent information about signaling protein relationships was obtained through the literature to reconstruct the entire hormonal crosstalk. Due to a lack of quantitative information, we employed a qualitative modeling formalism. This work permitted to confirm the synergistic effect of the hormonal crosstalk on cell elongation, to explain some of our paradoxical mutant phenotypes and to predict a novel interaction between the BREVIS RADIX (BRX) protein and the transcription factor MONOPTEROS (MP),which turned out to be critical for the maintenance of the root meristem. On the same subcellular scale, another study in the monocot model Brachypodium dystachion (Brachypodium) revealed an alternative wiring of auxin-ethylene crosstalk as compared to Arabidopsis. In the latter, increasing interference with auxin biosynthesis results in progressively shorter roots. By contrast, a hypomorphic Brachypodium mutant isolated in this study in an enzyme of the auxin biosynthesis pathway displayed a dramatically longer seminal root. Our morphometric analysis confirmed that more anisotropic cells (thinner and longer) are principally responsible for the mutant root phenotype. Further characterization pointed towards an inverted regulatory logic in the relation between ethylene signaling and auxin biosynthesis in Brachypodium as compared to Arabidopsis, which explains the phenotypic discrepancy. Finally, the morphometric analysis of hypocotyl secondary growth that we applied in this study was performed with the image-processing pipeline of our quantitative histology method. During its secondary growth, the hypocotyl reorganizes its primary bilateral symmetry to a radial symmetry of highly specialized tissues comprising several thousand cells, starting with a few dozens. However, such a scale only permits observations in thin cross-sections, severely hampering a comprehensive analysis of the morphodynamics involved. Our quantitative histology strategy overcomes this limitation. We acquired hypocotyl cross-sections from tiled high-resolution images and extracted their information content using custom high-throughput image processing and segmentation. Coupled with an automated cell type recognition algorithm, it allows precise quantitative characterization of vascular development and reveals developmental patterns that were not evident from visual inspection, for example the steady interspace distance of the phloem poles. Further analyses indicated a change in growth anisotropy of cambial and phloem cells, which appeared in phase with the expansion of xylem. Combining genetic tools and computational modeling, we showed that the reorientation of growth anisotropy axis of peripheral tissue layers only occurs when the growth rate of central tissue is higher than the peripheral one. This was confirmed by the calculation of the ratio of the growth rate xylem to phloem throughout secondary growth. High ratios are indeed observed and concomitant with the homogenization of cambium anisotropy. These results suggest a self-organization mechanism, promoted by a gradient of division in the cambium that generates a pattern of mechanical constraints. This, in turn, reorients the growth anisotropy of peripheral tissues to sustain the secondary growth.

Adaptive changes in a radial maze task: Efficient selection of baited arms with reduced foraging in senescent hooded rats

Qualitative differences in strategy selection during foraging in a partially baited maze were assessed in young and old rats. The baited and non-baited arms were at a fixed position in space and marked by a specific olfactory cue. The senescent rats did more re-entries during the first four-trial block but were more rapid than the young rats in selecting the reinforced arms during the first visits. Dissociation between the olfactory spatial cue reference by rotating the maze revealed that only few old subjects relied on olfactory cues to select the baited arms and the remainder relied mainly on the visuo-spatial cues.

Information System ProcessInnovation Adoption, Adaptation, Learning, and Unlearning: A Longitudinal Case Study

This thesis examines the history and evolution of information system process innovation (ISPI) processes (adoption, adaptation, and unlearning) within the information system development (ISD) work in an internal information system (IS) department and in two IS software house organisations in Finland over a 43-year time-period. The study offers insights into influential actors and their dependencies in deciding over ISPIs. The research usesa qualitative research approach, and the research methodology involves the description of the ISPI processes, how the actors searched for ISPIs, and how the relationships between the actors changed over time. The existing theories were evaluated using the conceptual models of the ISPI processes based on the innovationliterature in the IS area. The main focus of the study was to observe changes in the main ISPI processes over time. The main contribution of the thesis is a new theory. The term theory should be understood as 1) a new conceptual framework of the ISPI processes, 2) new ISPI concepts and categories, and the relationships between the ISPI concepts inside the ISPI processes. The study gives a comprehensive and systematic study on the history and evolution of the ISPI processes; reveals the factors that affected ISPI adoption; studies ISPI knowledge acquisition, information transfer, and adaptation mechanisms; and reveals the mechanismsaffecting ISPI unlearning; changes in the ISPI processes; and diverse actors involved in the processes. The results show that both the internal IS department and the two IS software houses sought opportunities to improve their technical skills and career paths and this created an innovative culture. When new technology generations come to the market the platform systems need to be renewed, and therefore the organisations invest in ISPIs in cycles. The extent of internal learning and experiments was higher than the external knowledge acquisition. Until the outsourcing event (1984) the decision-making was centralised and the internalIS department was very influential over ISPIs. After outsourcing, decision-making became distributed between the two IS software houses, the IS client, and itsinternal IT department. The IS client wanted to assure that information systemswould serve the business of the company and thus wanted to co-operate closely with the software organisations.

On Modelling, System Identification and Control of Servo-Systems with a Flexible Load

The present study was done with two different servo-systems. In the first system, a servo-hydraulic system was identified and then controlled by a fuzzy gainscheduling controller. The second servo-system, an electro-magnetic linear motor in suppressing the mechanical vibration and position tracking of a reference model are studied by using a neural network and an adaptive backstepping controller respectively. Followings are some descriptions of research methods. Electro Hydraulic Servo Systems (EHSS) are commonly used in industry. These kinds of systems are nonlinearin nature and their dynamic equations have several unknown parameters.System identification is a prerequisite to analysis of a dynamic system. One of the most promising novel evolutionary algorithms is the Differential Evolution (DE) for solving global optimization problems. In the study, the DE algorithm is proposed for handling nonlinear constraint functionswith boundary limits of variables to find the best parameters of a servo-hydraulic system with flexible load. The DE guarantees fast speed convergence and accurate solutions regardless the initial conditions of parameters. The control of hydraulic servo-systems has been the focus ofintense research over the past decades. These kinds of systems are nonlinear in nature and generally difficult to control. Since changing system parameters using the same gains will cause overshoot or even loss of system stability. The highly non-linear behaviour of these devices makes them ideal subjects for applying different types of sophisticated controllers. The study is concerned with a second order model reference to positioning control of a flexible load servo-hydraulic system using fuzzy gainscheduling. In the present research, to compensate the lack of dampingin a hydraulic system, an acceleration feedback was used. To compare the results, a pcontroller with feed-forward acceleration and different gains in extension and retraction is used. The design procedure for the controller and experimental results are discussed. The results suggest that using the fuzzy gain-scheduling controller decrease the error of position reference tracking. The second part of research was done on a PermanentMagnet Linear Synchronous Motor (PMLSM). In this study, a recurrent neural network compensator for suppressing mechanical vibration in PMLSM with a flexible load is studied. The linear motor is controlled by a conventional PI velocity controller, and the vibration of the flexible mechanism is suppressed by using a hybrid recurrent neural network. The differential evolution strategy and Kalman filter method are used to avoid the local minimum problem, and estimate the states of system respectively. The proposed control method is firstly designed by using non-linear simulation model built in Matlab Simulink and then implemented in practical test rig. The proposed method works satisfactorily and suppresses the vibration successfully. In the last part of research, a nonlinear load control method is developed and implemented for a PMLSM with a flexible load. The purpose of the controller is to track a flexible load to the desired position reference as fast as possible and without awkward oscillation. The control method is based on an adaptive backstepping algorithm whose stability is ensured by the Lyapunov stability theorem. The states of the system needed in the controller are estimated by using the Kalman filter. The proposed controller is implemented and tested in a linear motor test drive and responses are presented.

Identifying quantitative operation principles in metabolic pathways: a systematic method for searching feasible enzyme activity patterns leading to cellular adaptive responses

Background: Optimization methods allow designing changes in a system so that specific goals are attained. These techniques are fundamental for metabolic engineering. However, they are not directly applicable for investigating the evolution of metabolic adaptation to environmental changes. Although biological systems have evolved by natural selection and result in well-adapted systems, we can hardly expect that actual metabolic processes are at the theoretical optimum that could result from an optimization analysis. More likely, natural systems are to be found in a feasible region compatible with global physiological requirements. Results: We first present a new method for globally optimizing nonlinear models of metabolic pathways that are based on the Generalized Mass Action (GMA) representation. The optimization task is posed as a nonconvex nonlinear programming (NLP) problem that is solved by an outer- approximation algorithm. This method relies on solving iteratively reduced NLP slave subproblems and mixed-integer linear programming (MILP) master problems that provide valid upper and lower bounds, respectively, on the global solution to the original NLP. The capabilities of this method are illustrated through its application to the anaerobic fermentation pathway in Saccharomyces cerevisiae. We next introduce a method to identify the feasibility parametric regions that allow a system to meet a set of physiological constraints that can be represented in mathematical terms through algebraic equations. This technique is based on applying the outer-approximation based algorithm iteratively over a reduced search space in order to identify regions that contain feasible solutions to the problem and discard others in which no feasible solution exists. As an example, we characterize the feasible enzyme activity changes that are compatible with an appropriate adaptive response of yeast Saccharomyces cerevisiae to heat shock Conclusion: Our results show the utility of the suggested approach for investigating the evolution of adaptive responses to environmental changes. The proposed method can be used in other important applications such as the evaluation of parameter changes that are compatible with health and disease states.

Interoperability of learning objects copyright in the LUISA semantic learning management system

Semantic Web technology is able to provide the required computational semantics for interoperability of learning resources across different Learning Management Systems (LMS) and Learning Object Repositories (LOR). The EU research project LUISA (Learning Content Management System Using Innovative Semantic Web Services Architecture) addresses the development of a reference semantic architecture for the major challenges in the search, interchange and delivery of learning objects in a service-oriented context. One of the key issues, highlighted in this paper, is Digital Rights Management (DRM) interoperability. A Semantic Web approach to copyright management has been followed, which places a Copyright Ontology as the key component for interoperability among existing DRM systems and other licensing schemes like Creative Commons. Moreover, Semantic Web tools like reasoners, rule engines and semantic queries facilitate the implementation of an interoperable copyright management component in the LUISA architecture.

Adaptive Protocol Stacks for Mobile Devices

Tulevaisuudessa siirrettävät laitteet, kuten matkapuhelimet ja kämmenmikrot, pystyvät muodostamaan verkkoyhteyden käyttäen erilaisia yhteysmenetelmiä eri tilanteissa. Yhteysmenetelmillä on toisistaan poikkeavat viestintäominaisuudet mm. latenssin, kaistanleveyden, virhemäärän yms. suhteen. Langattomille yhteysmenetelmille on myös ominaista tietoliikenneyhteyden ominaisuuksien voimakas muuttuminen ympäristön suhteen. Parhaan suorituskyvyn ja käytettävyyden saavuttamiseksi, on siirrettävän laitteen pystyttävä mukautumaan käytettyyn viestintämenetelmään ja viestintäympäristössä tapahtuviin muutoksiin. Olennainen osa tietoliikenteessä ovat protokollapinot, jotka mahdollistavat tietoliikenneyhteyden järjestelmien välillä tarjoten verkkopalveluita päätelaitteen käyttäjäsovelluksille. Jotta protokollapinot pystyisivät mukautumaan tietyn viestintäympäristön ominaisuuksiin, on protokollapinon käyttäytymistä pystyttävä muuttamaan ajonaikaisesti. Perinteisesti protokollapinot ovat kuitenkin rakennettu muuttumattomiksi niin, että mukautuminen tässä laajuudessa on erittäin vaikeaa toteuttaa, ellei jopa mahdotonta. Tämä diplomityö käsittelee mukautuvien protokollapinojen rakentamista käyttäen komponenttipohjaista ohjelmistokehystä joka mahdollistaa protokollapinojen ajonaikaisen muuttamisen. Toteuttamalla esimerkkijärjestelmän, ja mittaamalla sen suorituskykyä vaihtelevassa tietoliikenneympäristössä, osoitamme, että mukautuvat protokollapinot ovat mahdollisia rakentaa ja ne tarjoavat merkittäviä etuja erityisesti tulevaisuuden siirrettävissä laitteissa.