Implicit methods for qualitative modeling of gene regulatory networks.

Advancements in high-throughput technologies to measure increasingly complex biological phenomena at the genomic level are rapidly changing the face of biological research from the single-gene single-protein experimental approach to studying the behavior of a gene in the context of the entire genome (and proteome). This shift in research methodologies has resulted in a new field of network biology that deals with modeling cellular behavior in terms of network structures such as signaling pathways and gene regulatory networks. In these networks, different biological entities such as genes, proteins, and metabolites interact with each other, giving rise to a dynamical system. Even though there exists a mature field of dynamical systems theory to model such network structures, some technical challenges are unique to biology such as the inability to measure precise kinetic information on gene-gene or gene-protein interactions and the need to model increasingly large networks comprising thousands of nodes. These challenges have renewed interest in developing new computational techniques for modeling complex biological systems. This chapter presents a modeling framework based on Boolean algebra and finite-state machines that are reminiscent of the approach used for digital circuit synthesis and simulation in the field of very-large-scale integration (VLSI). The proposed formalism enables a common mathematical framework to develop computational techniques for modeling different aspects of the regulatory networks such as steady-state behavior, stochasticity, and gene perturbation experiments.

Global deployment of a short message gateway

Lyhytsanomiin perustuvat lisäarvopalvelut ovat viime vuosikymmenen lopulla kehittyneet nopeasti parhaimmin tuottaviksi mobiilin televerkon käyttötavoista. Nämä palvelut on monesti kehitetty nopeasti ottamatta huomioon mahdollisia siirrettävyysongelmia, joita palveluiden vieminen muihin kuin alkuperäiseen ympäristöön aiheuttaa. Tämän työn tarkoituksena on tutkia odotettavissa olevia teknisiä ongelmia vietäessä lyhytsanomapohjaisia palveluita kansainvälisille markkinoille. Ongelman ratkaisuna esitellään Intellitel Messaging Gateway (MGw) - yhdyskäytävä, joka tarjoaa mahdollisuuden avointen internet-protokollien kautta tarjottavaan lisäarvopalveluiden luontiin. Työn käytännön osuus koostuu valikoimasta pieniä suunnittelu- ja toteutustehtäviä, joiden tarkoituksena on korjata kansainvälistä verkkoonvientiä estäviä ominaisuuksia ja puutteita Intellitel MGw:ssä. Näistä ominaisuuksista tärkeimmät ovat merkistö-, osoitteistus- ja protokollayhteensopivuuden asettamat rajoitukset.

Statistical mechanics of multi-edge networks

Statistical properties of binary complex networks are well understood and recently many attempts have been made to extend this knowledge to weighted ones. There are, however, subtle yet important considerations to be made regarding the nature of the weights used in this generalization. Weights can be either continuous or discrete magnitudes, and in the latter case, they can additionally have undistinguishable or distinguishable nature. This fact has not been addressed in the literature insofar and has deep implications on the network statistics. In this work we face this problem introducing multiedge networks as graphs where multiple (distinguishable) connections between nodes are considered. We develop a statistical mechanics framework where it is possible to get information about the most relevant observables given a large spectrum of linear and nonlinear constraints including those depending both on the number of multiedges per link and their binary projection. The latter case is particularly interesting as we show that binary projections can be understood from multiedge processes. The implications of these results are important as many real-agent-based problems mapped onto graphs require this treatment for a proper characterization of their collective behavior.

Strategic Development of Electricity Distribution Networks – Concept and Methods

Strategic development of distribution networks plays a key role in the asset management in electricity distribution companies. Owing to the capital-intensive nature of the field and longspan operations of companies, the significance of a strategy is emphasised. A well-devised strategy combines awareness of challenges posed by the operating environment and the future targets of the distribution company. Economic regulation, ageing infrastructure, scarcity of resources and tightening supply requirements with challenges created by the climate change put a pressure on the strategy work. On the other hand, technology development related to network automation and underground cabling assists in answering these challenges. This dissertation aims at developing process knowledge and establishing a methodological framework by which key issues related to network development can be addressed. Moreover, the work develops tools by which the effects of changes in the operating environment on the distribution business can be analysed in the strategy work. To this end, the work discusses certain characteristics of the distribution business and describes the strategy process at a principle level. Further, the work defines the subtasks in the strategy process and presents the key elements in the strategy work and long-term network planning. The work delineates the factors having either a direct or indirect effect on strategic planning and development needs in the networks; in particular, outage costs constitute an important part of the economic regulation of the distribution business, reliability being thus a key driver in network planning. The dissertation describes the methodology and tools applied to cost and reliability analyses in the strategy work. The work focuses on determination of the techno-economic feasibility of different network development technologies; these feasibility surveys are linked to the economic regulation model of the distribution business, in particular from the viewpoint of reliability of electricity supply and allowed return. The work introduces the asset management system developed for research purposes and to support the strategy work, the calculation elements of the system and initial data used in the network analysis. The key elements of this asset management system are utilised in the dissertation. Finally, the study addresses the stages of strategic decision-making and compilation of investment strategies. Further, the work illustrates implementation of strategic planning in an actual distribution company environment.

Exploring Adaptive Implementation of On-Chip Networks

As technology geometries have shrunk to the deep submicron regime, the communication delay and power consumption of global interconnections in high performance Multi- Processor Systems-on-Chip (MPSoCs) are becoming a major bottleneck. The Network-on- Chip (NoC) architecture paradigm, based on a modular packet-switched mechanism, can address many of the on-chip communication issues such as performance limitations of long interconnects and integration of large number of Processing Elements (PEs) on a chip. The choice of routing protocol and NoC structure can have a significant impact on performance and power consumption in on-chip networks. In addition, building a high performance, area and energy efficient on-chip network for multicore architectures requires a novel on-chip router allowing a larger network to be integrated on a single die with reduced power consumption. On top of that, network interfaces are employed to decouple computation resources from communication resources, to provide the synchronization between them, and to achieve backward compatibility with existing IP cores. Three adaptive routing algorithms are presented as a part of this thesis. The first presented routing protocol is a congestion-aware adaptive routing algorithm for 2D mesh NoCs which does not support multicast (one-to-many) traffic while the other two protocols are adaptive routing models supporting both unicast (one-to-one) and multicast traffic. A streamlined on-chip router architecture is also presented for avoiding congested areas in 2D mesh NoCs via employing efficient input and output selection. The output selection utilizes an adaptive routing algorithm based on the congestion condition of neighboring routers while the input selection allows packets to be serviced from each input port according to its congestion level. Moreover, in order to increase memory parallelism and bring compatibility with existing IP cores in network-based multiprocessor architectures, adaptive network interface architectures are presented to use multiple SDRAMs which can be accessed simultaneously. In addition, a smart memory controller is integrated in the adaptive network interface to improve the memory utilization and reduce both memory and network latencies. Three Dimensional Integrated Circuits (3D ICs) have been emerging as a viable candidate to achieve better performance and package density as compared to traditional 2D ICs. In addition, combining the benefits of 3D IC and NoC schemes provides a significant performance gain for 3D architectures. In recent years, inter-layer communication across multiple stacked layers (vertical channel) has attracted a lot of interest. In this thesis, a novel adaptive pipeline bus structure is proposed for inter-layer communication to improve the performance by reducing the delay and complexity of traditional bus arbitration. In addition, two mesh-based topologies for 3D architectures are also introduced to mitigate the inter-layer footprint and power dissipation on each layer with a small performance penalty.

Development of capacitive sensor for measuring soil water content

The irrigation management based on the monitoring of the soil water content allows for the minimization of the amount of water applied, making its use more efficient. Taking into account these aspects, in this work, a sensor for measuring the soil water content was developed to allow real time automation of irrigation systems. This way, problems affecting crop yielding such as irregularities in the time to turn on or turn off the pump, and excess or deficit of water can be solved. To develop the sensors were used stainless steel rods, resin, and insulating varnish. The sensors measuring circuit was based on a microcontroller, which gives its output signal in the digital format. The sensors were calibrated using soil of the type “Quartzarenic Neosoil”. A third order polynomial model was fitted to the experimental data between the values of water content corresponding to the field capacity and the wilting point to correlate the soil water content obtained by the oven standard method with those measured by the electronic circuit, with a coefficient of determination of 93.17%, and an accuracy in the measures of ±0.010 kg kg-1. Based on the results, it was concluded that the sensor and its implemented measuring circuit can be used in the automation process of irrigation systems.

Seasonality of net radiation in two sub-basins of Paracatu by the use of modis sensor products

The net radiation (Rn) represents the main source of energy for physical and chemical processes that occur in the surface-atmosphere interface, and it is used for air and soil heating, water transfer, in the form of vapor from the surface to the atmosphere, and for the metabolism of plants, especially photosynthesis. If there is no record of net radiation in certain areas, the use of information is important to help determine it. Among them we can highlight those provided by remote sensing. In this context, this work aims to estimate the net radiation, with the use of products of MODIS sensor, in the sub-basins of Entre Ribeiros creek and Preto River, located between the Brazilian states of Goiás and Minas Gerais. The SEBAL (Surface Energy Balance Algorithm for Land) was used to obtain the Rn in four different days in the period of July to October, 2007. The Rn results obtained were consistent with others cited in the literature and are important because the orbital information can help determine the Rn in areas where there are not automatic weather stations to record the net radiation.

Influence of distance, geometry and number of control stations on quality of local geodetic networks for the purpose of georeferencing of rural properties

The implementation of local geodetic networks for georeferencing of rural properties has become a requirement after publication of the Georeferencing Technical Standard by INCRA. According to this standard, the maximum distance of baselines to GNSS L1 receivers is of 20 km. Besides the length of the baseline, the geometry and the number of geodetic control stations are other factors to be considered in the implementation of geodetic networks. Thus, this research aimed to examine the influence of baseline lengths higher than the regulated limit of 20 km, the geometry and the number of control stations on quality of local geodetic networks for georeferencing, and also to demonstrate the importance of using specific tests to evaluate the solution of ambiguities and on the quality of the adjustment. The results indicated that the increasing number of control stations has improved the quality of the network, the geometry has not influenced on the quality and the baseline length has influenced on the quality; however, lengths higher than 20 km has not interrupted the implementation, with GPS L1 receiver, of the local geodetic network for the purpose of georeferencing. Also, the use of different statistical tests, both for the evaluation of the resolution of ambiguities and for the adjustment, have enabled greater clearness in analyzing the results, which allow that unsuitable observations may be eliminated.

Application of artificial neural networks as an alternative to volumetric water balance in drip irrigation management in watermelon crop

Precision irrigation seeks to establish strategies which achieve an efficient ratio between the volume of water used (reduction in input) and the productivity obtained (increase in production). There are several studies in the literature on strategies for achieving this efficiency, such as those dealing with the method of volumetric water balance (VWB). However, it is also of great practical and economic interest to set up versatile implementations of irrigation strategies that: (i) maintain the performance obtained with other implementations, (ii) rely on few computational resources, (iii) adapt well to field conditions, and (iv) allow easy modification of the irrigation strategy. In this study, such characteristics are achieved when using an Artificial Neural Network (ANN) to determine the period of irrigation for a watermelon crop in the Irrigation Perimeter of the Lower Acaraú, in the state of Ceará, Brazil. The Volumetric Water Balance was taken as the standard for comparing the management carried out with the proposed implementation of ANN. The statistical analysis demonstrates the effectiveness of the proposed management, which is able to replace VWB as a strategy in automation.

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.

Potential of built environment interventions involving deployment of public bicycles to increase utilitarian cycling : the case of BIXI in Montreal, Quebec

Contexte : Les interventions sur l'environnement bâti reliées au transport peuvent contribuer à l'augmentation de la pratique de l'activité physique. En tant qu’intervention, les programmes de vélos en libre-service (PVLS) peuvent contribuer à l’utilisation du vélo. BIXI© (nom qui fusionne les mots BIcyclette et taXI) est un programme de vélos en libre-service implanté à Montréal, au Canada, en mai 2009. Le programme BIXI© met à la disposition des gens 5050 vélos à 405 bornes d’ancrage. Objectif : L'objectif général de cette thèse est d'étudier l'impact d'un programme de vélos en libre-service sur l’utilisation du vélo. Les objectifs spécifiques de la thèse sont de : 1) Estimer la prévalence populationnelle et identifier des variables environnementales, sociodémographiques et comportementales associées à l’utilisation des vélos en libre-service. 2) Estimer l’impact populationnel de l’implantation des vélos en libre-service sur l’utilisation du vélo et les contributions respectives de l’utilisation du vélo pour des fins utilitaires et récréatives à l’utilisation totale du vélo. 3) Estimer l’impact local de l’implantation des vélos en libre-service sur l’utilisation du vélo. Méthodes : Un devis populationnel transversal avec mesures répétées. Des enquêtes ont été réalisées au moment du lancement du programme de vélos en libre-service (4 mai au 10 juin, 2009), à la fin de la première année d’implantation (8 octobre au 12 décembre, 2009), et à la fin de la deuxième année d’implantation (8 novembre au 12 décembre, 2010). Les échantillons se composaient de 2001 (âge moyen = 49,4 années, 56,7 % de femmes), 2502 (âge moyen = 47,8 ans, 61,8 % de femmes) et 2509 (âge moyen = 48,9 années, 59,0 % de femmes) adultes à chaque période de mesure respectivement. Résultats : Globalement, les résultats démontrent le potentiel des PVLS pour augmenter l’utilisation du vélo. Les résultats suggèrent que près de 128 744 habitants ou 8,1 % de la population adulte ont utilisé les vélos BIXI© au moins une fois dans la première saison. Après deux ans d’implantation, ceux qui sont exposés à BIXI© dans leur milieu résidentiel avaient une probabilité significativement plus élevée d’utiliser le vélo par rapport à ceux non exposés. Par contre, il n'y avait aucun impact local de l’implantation du programme BIXI© sur l’utilisation du vélo. Conclusions : L’implantation d'un PVLS à Montréal a augmenté la probabilité d’utiliser le vélo chez les individus habitant près d'une borne d'ancrage. Mots clés : programme de vélos en libre-service, expérience naturelle, santé des populations.