Development and application of computational methodologies in qualitative modeling

La présente thèse s'intitule "Développent et Application des Méthodologies Computationnelles pour la Modélisation Qualitative". Elle comprend tous les différents projets que j'ai entrepris en tant que doctorante. Plutôt qu'une mise en oeuvre systématique d'un cadre défini a priori, cette thèse devrait être considérée comme une exploration des méthodes qui peuvent nous aider à déduire le plan de processus regulatoires et de signalisation. Cette exploration a été mue par des questions biologiques concrètes, plutôt que par des investigations théoriques. Bien que tous les projets aient inclus des systèmes divergents (réseaux régulateurs de gènes du cycle cellulaire, réseaux de signalisation de cellules pulmonaires) ainsi que des organismes (levure à fission, levure bourgeonnante, rat, humain), nos objectifs étaient complémentaires et cohérents. Le projet principal de la thèse est la modélisation du réseau de l'initiation de septation (SIN) du S.pombe. La cytokinèse dans la levure à fission est contrôlée par le SIN, un réseau signalant de protéines kinases qui utilise le corps à pôle-fuseau comme échafaudage. Afin de décrire le comportement qualitatif du système et prédire des comportements mutants inconnus, nous avons décidé d'adopter l'approche de la modélisation booléenne. Dans cette thèse, nous présentons la construction d'un modèle booléen étendu du SIN, comprenant la plupart des composantes et des régulateurs du SIN en tant que noeuds individuels et testable expérimentalement. Ce modèle utilise des niveaux d'activité du CDK comme noeuds de contrôle pour la simulation d'évènements du SIN à différents stades du cycle cellulaire. Ce modèle a été optimisé en utilisant des expériences d'un seul "knock-out" avec des effets phénotypiques connus comme set d'entraînement. Il a permis de prédire correctement un set d'évaluation de "knock-out" doubles. De plus, le modèle a fait des prédictions in silico qui ont été validées in vivo, permettant d'obtenir de nouvelles idées de la régulation et l'organisation hiérarchique du SIN. Un autre projet concernant le cycle cellulaire qui fait partie de cette thèse a été la construction d'un modèle qualitatif et minimal de la réciprocité des cyclines dans la S.cerevisiae. Les protéines Clb dans la levure bourgeonnante présentent une activation et une dégradation caractéristique et séquentielle durant le cycle cellulaire, qu'on appelle communément les vagues des Clbs. Cet évènement est coordonné avec la courbe d'activation inverse du Sic1, qui a un rôle inhibitoire dans le système. Pour l'identification des modèles qualitatifs minimaux qui peuvent expliquer ce phénomène, nous avons sélectionné des expériences bien définies et construit tous les modèles minimaux possibles qui, une fois simulés, reproduisent les résultats attendus. Les modèles ont été filtrés en utilisant des simulations ODE qualitatives et standardisées; seules celles qui reproduisaient le phénotype des vagues ont été gardées. L'ensemble des modèles minimaux peut être utilisé pour suggérer des relations regulatoires entre les molécules participant qui peuvent ensuite être testées expérimentalement. Enfin, durant mon doctorat, j'ai participé au SBV Improver Challenge. Le but était de déduire des réseaux spécifiques à des espèces (humain et rat) en utilisant des données de phosphoprotéines, d'expressions des gènes et des cytokines, ainsi qu'un réseau de référence, qui était mis à disposition comme donnée préalable. Notre solution pour ce concours a pris la troisième place. L'approche utilisée est expliquée en détail dans le dernier chapitre de la thèse. -- The present dissertation is entitled "Development and Application of Computational Methodologies in Qualitative Modeling". It encompasses the diverse projects that were undertaken during my time as a PhD student. Instead of a systematic implementation of a framework defined a priori, this thesis should be considered as an exploration of the methods that can help us infer the blueprint of regulatory and signaling processes. This exploration was driven by concrete biological questions, rather than theoretical investigation. Even though the projects involved divergent systems (gene regulatory networks of cell cycle, signaling networks in lung cells), as well as organisms (fission yeast, budding yeast, rat, human), our goals were complementary and coherent. The main project of the thesis is the modeling of the Septation Initiation Network (SIN) in S.pombe. Cytokinesis in fission yeast is controlled by the SIN, a protein kinase signaling network that uses the spindle pole body as scaffold. In order to describe the qualitative behavior of the system and predict unknown mutant behaviors we decided to adopt a Boolean modeling approach. In this thesis, we report the construction of an extended, Boolean model of the SIN, comprising most SIN components and regulators as individual, experimentally testable nodes. The model uses CDK activity levels as control nodes for the simulation of SIN related events in different stages of the cell cycle. The model was optimized using single knock-out experiments of known phenotypic effect as a training set, and was able to correctly predict a double knock-out test set. Moreover, the model has made in silico predictions that have been validated in vivo, providing new insights into the regulation and hierarchical organization of the SIN. Another cell cycle related project that is part of this thesis was to create a qualitative, minimal model of cyclin interplay in S.cerevisiae. CLB proteins in budding yeast present a characteristic, sequential activation and decay during the cell cycle, commonly referred to as Clb waves. This event is coordinated with the inverse activation curve of Sic1, which has an inhibitory role in the system. To generate minimal qualitative models that can explain this phenomenon, we selected well-defined experiments and constructed all possible minimal models that, when simulated, reproduce the expected results. The models were filtered using standardized qualitative ODE simulations; only the ones reproducing the wave-like phenotype were kept. The set of minimal models can be used to suggest regulatory relations among the participating molecules, which will subsequently be tested experimentally. Finally, during my PhD I participated in the SBV Improver Challenge. The goal was to infer species-specific (human and rat) networks, using phosphoprotein, gene expression and cytokine data and a reference network provided as prior knowledge. Our solution to the challenge was selected as in the final chapter of the thesis.

Activity-Based Costing Model for a Vendor Managed Inventory Service

Uusien paperikoneiden kysyntä on vähentynyt ja jälkimarkkinointipalveluiden, kuten huoltojen ja varaosamyyntien, merkittävyys paperikoneliiketoiminnassa on kasvanut entisestään viime aikoina. Uudentyyppisiä palveluja kilpailuedun lisäämiseksi kehitellään jatkuvasti. Esimerkki tällaisesta palvelusta on sopimusperusteinen varastointipalvelu, jossa osat ovat myyjän varastossa kunnes asiakas ottaa ne käyttöön. Diplomityön tavoite on rakentaa malli varastoinnin kustannuslaskentaan ja laskea sen avulla varastointipalvelun kustannukset. Perinteinen toimitusketju monine varastoineen ei nykykäsityksen mukaan ole enää kustannustehokas. Yhä useammat yritykset kaupan ja teollisuuden aloilla ovat ryhtyneet soveltamaan VMI (Vendor Managed Inventory) teoriaa toimitusketjuissaan. Varastot ovat tällöin keskitettyjä, tiedonkulku toimitusketjun portaiden välillä on nopeaa ja kysyntään pystytään vastaamaan lyhyemmällä viiveellä sen ennakoitavuuden paranemisen takia. Työn tuloksena on toimintolaskentaan pohjautuva kustannuslaskentamalli, jota voidaan hyödyntää myös hinnoittelupäätöksiä tehtäessä. Työssä esitellään mallin soveltaminen eri tapauksiin ja ehdotetaan jatkotoimenpiteitä.

Projeccions de canvi climatic per a Catalunya (NE Península Ibèrica). Part II: sintetitzant diverses metodologies = Climate change projections for Catalonia (NE Iberian Peninsula). Part II: Integrating several methodologies

The publication of the fourth IPCC report, as well as the number of research results reported in recent years about the regionalization of climate projections, were the driving forces to justify the update of the report on climate change in Catalonia. Specifically, the new IPCC report contains new climate projections at global and continental scales, while several international projects (especially European projects PRUDENCE and ENSEMBLES) have produced continental-scale climate projections, which allow for distinguishing between European regions. For Spain, some of these results have been included in a document commissioned by the“State Agency of Meteorology”. In addition, initiatives are being developed within Catalonia (in particular, by the Meteorological Service of Catalonia) to downscale climate projections in this area. The present paper synthesizes results of these and other previously published studies, as well as our own analysis of results of the ENSEMBLES project. The aim is to propose scenarios of variation in temperature and rainfall in Catalonia during the 21st Century. Thus, by the middle of this century temperatures could rise up to 2 C compared with that of the late 20th Century. These increases would probably be higher in summer than in winter, generalized across the territory but less pronounced in coastal areas. Rainfall, however, would not change much, but it could slightly decrease. Towards the end of the 21st Century, temperatures could rise to about 5 C above that of the last century, while the average rainfall could decrease by more than 10%. Increases in temperature would be higher in summer and in areas further from the coast. Rainfall would decrease especially during the summer, while it could even increase in winter in mountainous areas such as the Pyrenees.

Empirics of the international inequality in CO2 emissions intensity: explanatory factors according to complementary decomposition methodologies

This paper analyses the international inequalities in CO2 emissions intensity for the period 1971- 2009 and assesses explanatory factors. Multiplicative, group and additive methodologies of inequality decomposition are employed. The first allows us to clarify the separated role of the carbonisation index and the energy intensity in the pattern observed for inequalities in CO2 intensities; the second allows us to understand the role of regional groups; and the third allows us to investigate the role of different fossil energy sources (coal, oil and gas). The results show that, first, the reduction in global emissions intensity has coincided with a significant reduction in international inequality. Second, the bulk of this inequality and its reduction are attributed to differences between the groups of countries considered. Third, coal is the main energy source explaining these inequalities, although the growth in the relative contribution of gas is also remarkable. Fourth, the bulk of inequalities between countries and its decline are explained by differences in energy intensities, although there are significant differences in the patterns demonstrated by different groups of countries.

Analyzing the Background Information of an Activity-Based Costing System

The aim of this thesis was to analyze the background information of an activity-based costing system, which is being used in a domestic forest industry company. The reports produced by the system have not been reliable, and this has caused the utilization of the system to diminish. The study was initiated by examining the theory of activity-based costing. It was also discovered, that the system produces management accounting information and therefore also that theory was introduced briefly. Next the possible sources of errors were examined. The significance of these errors was evaluated and waste handling was chosen as a subject of further study. The problem regarding waste handling was that there is no waste compensation in current model. When paper or board machine produces waste, it can be used as raw material in the process. However, at the moment the product, which is being produced, at the time does not get any compensation. The use of compensation has not been possible due to not knowing the quantity of process waste. As a result of the study a calculatory model, which enables calculating the quantity of process waste based on the data from the mill system, was introduced. This, for one, enables starting to use waste compensation in the future.

Active teaching-learning methodologies: medical students' views of problem-based learning

The prevailing undergraduate medical training process still favors disconnection and professional distancing from social needs. The Brazilian Ministries of Education and Health, through the National Curriculum Guidelines, the Incentives Program for Changes in the Medical Curriculum (PROMED), and the National Program for Reorientation of Professional Training in Health (PRO-SAÚDE), promoted the stimulus for an effective connection between medical institutions and the Unified National Health System (SUS). In accordance to the new paradigm for medical training, the Centro Universitário Serra dos Órgãos (UNIFESO) established a teaching plan in 2005 using active methodologies, specifically problem-based learning (PBL). Research was conducted through semi-structured interviews with third-year undergraduate students at the UNIFESO Medical School. The results were categorized as proposed by Bardin's thematic analysis, with the purpose of verifying the students' impressions of the new curriculum. Active methodologies proved to be well-accepted by students, who defined them as exciting and inclusive of theory and practice in medical education.

Evaluating land-use related environmental impacts of biomass value chains for decision-support : Comparison and testing of methodologies proposed for environmental life cycle assessment

Life cycle assessment (LCA) is one of the most established quantitative tools for environmental impact assessment of products. To be able to provide support to environmentally-aware decision makers on environmental impacts of biomass value-chains, the scope of LCA methodology needs to be augmented to cover landuse related environmental impacts. This dissertation focuses on analysing and discussing potential impact assessment methods, conceptual models and environmental indicators that have been proposed to be implemented into the LCA framework for impacts of land use. The applicability of proposed indicators and impact assessment frameworks is tested from practitioners' perspective, especially focusing on forest biomass value chains. The impacts of land use on biodiversity, resource depletion, climate change and other ecosystem services is analysed and discussed and the interplay in between value choices in LCA modelling and the decision-making situations to be supported is critically discussed. It was found out that land use impact indicators are necessary in LCA in highlighting differences in impacts from distinct land use classes. However, many open questions remain on certainty of highlighting actual impacts of land use, especially regarding impacts of managed forest land use on biodiversity and ecosystem services such as water regulation and purification. The climate impact of energy use of boreal stemwood was found to be higher in the short term and lower in the long-term in comparison with fossil fuels that emit identical amount of CO2 in combustion, due to changes implied to forest C stocks. The climate impacts of energy use of boreal stemwood were found to be higher than the previous estimates suggest on forest residues and stumps. The product lifetime was found to have much higher influence on the climate impacts of woodbased value chains than the origin of stemwood either from thinnings or final fellings. Climate neutrality seems to be likely only in the case when almost all the carbon of harvested wood is stored in long-lived wooden products. In the current form, the land use impacts cannot be modelled with a high degree of certainty nor communicated with adequate level of clarity to decision makers. The academia needs to keep on improving the modelling framework, and more importantly, clearly communicate to decision-makers the limited certainty on whether land-use intensive activities can help in meeting the strict mitigation targets we are globally facing.

Production unit’s overhead cost allocation with activity-based costing in food industry enterprise

The main objective of this Master’s thesis is to develop a cost allocation model for a leading food industry company in Finland. The goal is to develop an allocation method for fixed overhead expenses produced in a specific production unit and create a plausible tracking system for product costs. The second objective is to construct an allocation model and modify the created model to be suited for other units as well. Costs, activities, drivers and appropriate allocation methods are studied. This thesis is started with literature review of existing theory of ABC, inspecting cost information and then conducting interviews with officials to get a general view of the requirements for the model to be constructed. The familiarization of the company started with becoming acquainted with the existing cost accounting methods. The main proposals for a new allocation model were revealed through interviews, which were utilized in setting targets for developing the new allocation method. As a result of this thesis, an Excel-based model is created based on the theoretical and empiric data. The new system is able to handle overhead costs in more detail improving the cost awareness, transparency in cost allocations and enhancing products’ cost structure. The improved cost awareness is received by selecting the best possible cost drivers for this situation. Also the capacity changes are taken into consideration, such as usage of practical or normal capacity instead of theoretical is suggested to apply. Also some recommendations for further development are made about capacity handling and cost collection.

Comparison of methodologies for moisture determination on dried bee pollen samples

Bee pollen moisture value is one of the quality parameters for this product. Some countries such as Argentina, Brazil, Bulgaria, Poland and Switzerland have bee pollen regulations on quality parameters, but these are not clear regarding which method should be used for moisture determination. The aim of this paper was to compare six methods of moisture determination in dried bee pollen samples. The methods were: conventional oven at 100 °C, vacuum oven at 70 °C, desiccator with sulfuric acid, drying out process with infrared light at 85 °C, lyophilization and Karl Fisher's method. Based on the results, the best methods for moisture determination of bee pollen were the drying process with infrared and the lyophilization, since these have shown lower moisture values.

Chemical profile of sugarcane spirits produced by double distillation methodologies in rectifying still

The objective of this study was to determine the chemical profile of sugarcane spirits produced by different double distillation methodologies in rectifying still. Fermented sugarcane juice was distilled in rectifying still according to three double distillation methodologies: the methodology used for cognac production; the methodology used for whisky production; and the 10-80-10 percentage composition methodology, referring to the volumes of head, heart and tail of the distillate fractions from the second distillation. For comparison purposes, a simple distilled spirit was also produced. The distillates were analyzed for concentrations of ethanol, copper, volatile acidity, furfural and hydroxymethylfurfural, aldehydes, esters, methanol and higher alcohols. The spirits were also evaluated on the sensory attributes of aroma, taste and preference. Compared to simple distillation, double distillation improved the chemical quality of the spirits, since it has reduced the concentrations of acids, aldehydes, esters, methanol, higher alcohols and, consequently, their coefficient of congeners. Regardless of the methodology employed, the double distillation improved the sensory quality of the spirits since they obtained higher sensory acceptance in relation to spirits produced by simple distillation. Among double distilled spirits, the one produced according to whisky methodology obtained the best scores from appraisers on the aroma and flavor parameters and it was also the most preferred.

Osmotic priming methodologies in relation to the physiological performance of rangpur lime seeds (Citrus limonia Osbeck)

Several mechanisms have been used to promote rapid germination of citrus seeds and uniform seedling emergence. We evaluated the effects of osmotic priming on the physiological performance of Rangpur lime seeds (Citrus limonia Osbeck). Seeds were treated with 30 g of Captan and 10 g of Tecto 600 in 20-litre batches and stored, without drying, at 10 ºC and 50% relative humidity for periods of 3, 6 and 9 months. After each period, seeds were primed at 25 ºC, in the light, by immersion in Poliethylenoglicol (PEG 6000), potassium nitrate (KNO3) and 70% PEG 6000 plus 30% KNO3, all at an osmotic potential of -1.1MPa, for priming periods of 3, 6, 9 and 12 days. Percentage germination, tray emergence and the emergence rate index (ERI) were evaluated. Priming in PEG 6000 solution, independent of priming period, or in KNO3 or PEG 6000 plus KNO3 for up to 9 days, were efficient at improving the physiological performance of seeds stored for up to 3 months. Osmotic priming appears to be a promising technique for improving the physiological quality of Rangpur lemon seeds.