Objectives and motivations of small-scale forest owners : theoretical modelling and qualitative assessment

Abstract

Place branding : a conceptual and theoretical framework

Within the context of rising competition between territories, identity has become the most important element of recognition, differentiation and commodification in the communicative process within which cities, regions and countries position themselves. Geographical spaces thus compete in terms of this identity, which is then subjected to fierce comparison and competition (Nogué, 1999; Anholt, 2007a). The territorial brand thus entails the reinvention of places through a process of brand construction (branding) based on the promotion of the individual and collective identities of geographical spaces; these identities, in turn, are imbued with the intangible factors associated with their respective territorial identities.

PixFRET, an ImageJ plug-in for FRET calculation that can accommodate variations in spectral bleed-throughs.

Fluorescence resonance energy transfer (FRET) allows the user to investigate interactions between fluorescent partners. One crucial issue when calculating sensitized emission FRET is the correction for spectral bleed-throughs (SBTs), which requires to calculate the ratios between the intensities in the FRET and in the donor or acceptor settings, when only the donor or acceptor are present. Theoretically, SBT ratios should be constant. However, experimentally, these ratios can vary as a function of fluorophore intensity, and assuming constant values may hinder precise FRET calculation. One possible cause for such a variation is the use of a microscope set-up with different photomultipliers for the donor and FRET channels, a set-up allowing higher speed acquisitions on very dynamic fluorescent molecules in living cells. Herein, we show that the bias introduced by the differential response of the two PMTs can be circumvented by a simple modeling of the SBT ratios as a function of fluorophore intensity. Another important issue when performing FRET is the localization of FRET within the cell or a population of cells. We hence developed a freely available ImageJ plug-in, called PixFRET, that allows a simple and rapid determination of SBT parameters and the display of normalized FRET images. The usefulness of this modeling and of the plug-in are exemplified by the study of FRET in a system where two interacting nuclear receptors labeled with ECFP and EYFP are coexpressed in living cells.

Application of theoretical models to financial innovation

The present paper is aimed at providing a general strategic overview of the existing theoretical models that have applications in the field of financial innovation. Whereas most financialdevelopments have relied upon traditional economic tools, a new stream of research is defining a novel paradigm in which mathematical models from diverse scientific disciplines are being applied to conceptualize and explain economic and financial behavior. Indeed, terms such as ‘econophysics’ or ‘quantum finance’ have recently appeared to embrace efforts in this direction. As a first contact with such research, the project will present a brief description of some of the main theoretical models that have applications in finance and economics, and will try to present, if possible, potential new applications to particular areas in financial analysis, or new applicable models. As a result, emphasiswill be put on the implications of this research for the financial sector and its future dynamics.

Maintenance of polymorphism : a theoretical approach using multilocus systems

Résumé La thématique de cette thèse peut être résumée par le célèbre paradoxe de biologie évolutive sur le maintien du polymorphisme face à la sélection et par l'équation du changement de fréquence gamétique au cours du temps dû, à la sélection. La fréquence d'un gamète xi à la génération (t + 1) est: !!!Equation tronquée!!! Cette équation est utilisée pour générer des données utlisée tout au long de ce travail pour 2, 3 et 4 locus dialléliques. Le potentiel de l'avantage de l'hétérozygote pour le maintien du polymorphisme est le sujet de la première partie. La définition commune de l'avantage de l'hétérozygote n'etant applicable qu'a un locus ayant 2 allèles, cet avantage est redéfini pour un système multilocus sur les bases de précédentes études. En utilisant 5 définitions différentes de l'avantage de l'hétérozygote, je montre que cet avantage ne peut être un mécanisme général dans le maintien du polymorphisme sous sélection. L'étude de l'influence de locus non-détectés sur les processus évolutifs, seconde partie de cette thèse, est motivée par les travaux moléculaires ayant pour but de découvrir le nombre de locus codant pour un trait. La plupart de ces études sous-estiment le nombre de locus. Je montre que des locus non-détectés augmentent la probabilité d'observer du polymorphisme sous sélection. De plus, les conclusions sur les facteurs de maintien du polymorphisme peuvent être trompeuses si tous les locus ne sont pas détectés. Dans la troisième partie, je m'intéresse à la valeur attendue de variance additive après un goulot d'étranglement pour des traits sélectionés. Une études précédente montre que le niveau de variance additive après goulot d'étranglement augmente avec le nombre de loci. Je montre que le niveau de variance additive après un goulot d'étranglement augmente (comparé à des traits neutres), mais indépendamment du nombre de loci. Par contre, le taux de recombinaison a une forte influence, entre autre en regénérant les gamètes disparus suite au goulot d'étranglement. La dernière partie de ce travail de thèse décrit un programme pour le logiciel de statistique R. Ce programme permet d'itérer l'équation ci-dessus en variant les paramètres de sélection, recombinaison et de taille de populations pour 2, 3 et 4 locus dialléliques. Cette thèse montre qu'utiliser un système multilocus permet d'obtenir des résultats non-conformes à ceux issus de systèmes rnonolocus (la référence en génétique des populations). Ce programme ouvre donc d'intéressantes perspectives en génétique des populations. Abstract The subject of this PhD thesis can be summarized by one famous paradox of evolu-tionary biology: the maintenance of polymorphism in the face of selection, and one classical equation of theoretical population genetics: the changes in gametic frequencies due to selection and recombination. The frequency of gamete xi at generation (t + 1) is given by: !!! Truncated equation!!! This equation is used to generate data on selection at two, three, and four diallelic loci for the different parts of this work. The first part focuses on the potential of heterozygote advantage to maintain genetic polymorphism. Results of previous studies are used to (re)define heterozygote advantage for multilocus systems, since the classical definition is for one diallelic locus. I use 5 different definitions of heterozygote advantage. And for these five definitions, I show that heterozygote advantage is not a general mechanism for the maintenance of polymorphism. The study of the influence of undetected loci on evolutionary processes (second part of this work) is motivated by molecular works which aim at discovering the loci coding for a trait. For most of these works, some coding loci remains undetected. I show that undetected loci increases the probability of maintaining polymorphism under selection. In addition, conclusions about the factor that maintain polymorphism can be misleading if not all loci are considered. This is, therefore, only when all loci are detected that exact conclusions on the level of maintained polymorphism or on the factor(s) that maintain(s) polymorphism could be drawn. In the third part, the focus is on the expected release of additive genetic variance after bottleneck for selected traits. A previous study shows that the expected release of additive variance increases with an increase in the number of loci. I show that the expected release of additive variance after bottleneck increases for selected traits (compared with neutral), but this increase is not a function of the number of loci, but function of the recombination rate. Finally, the last part of this PhD thesis is a description of a package for the statistical software R that implements the Equation given above. It allows to generate data for different scenario regarding selection, recombination, and population size. This package opens perspectives for the theoretical population genetics that mainly focuses on one locus, while this work shows that increasing the number of loci leads not necessarily to straightforward results.

Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population genetics

A workshop recently held at the Ecole Polytechnique Federale de Lausanne (EPFL, Switzerland) was dedicated to understanding the genetic basis of adaptive change, taking stock of the different approaches developed in theoretical population genetics and landscape genomics and bringing together knowledge accumulated in both research fields. Indeed, an important challenge in theoretical population genetics is to incorporate effects of demographic history and population structure. But important design problems (e.g. focus on populations as units, focus on hard selective sweeps, no hypothesis-based framework in the design of the statistical tests) reduce their capability of detecting adaptive genetic variation. In parallel, landscape genomics offers a solution to several of these problems and provides a number of advantages (e.g. fast computation, landscape heterogeneity integration). But the approach makes several implicit assumptions that should be carefully considered (e.g. selection has had enough time to create a functional relationship between the allele distribution and the environmental variable, or this functional relationship is assumed to be constant). To address the respective strengths and weaknesses mentioned above, the workshop brought together a panel of experts from both disciplines to present their work and discuss the relevance of combining these approaches, possibly resulting in a joint software solution in the future.

Probabilistic evidential assessment of gunshot residue particle evidence (Part I): likelihood ratio calculation and case pre-assessment using Bayesian networks

Well developed experimental procedures currently exist for retrieving and analyzing particle evidence from hands of individuals suspected of being associated with the discharge of a firearm. Although analytical approaches (e.g. automated Scanning Electron Microscopy with Energy Dispersive X-ray (SEM-EDS) microanalysis) allow the determination of the presence of elements typically found in gunshot residue (GSR) particles, such analyses provide no information about a given particle's actual source. Possible origins for which scientists may need to account for are a primary exposure to the discharge of a firearm or a secondary transfer due to a contaminated environment. In order to approach such sources of uncertainty in the context of evidential assessment, this paper studies the construction and practical implementation of graphical probability models (i.e. Bayesian networks). These can assist forensic scientists in making the issue tractable within a probabilistic perspective. The proposed models focus on likelihood ratio calculations at various levels of detail as well as case pre-assessment.

Validation des SCORES cliniques: notions théoriques et pratiques de base. [Validation of clinical scores: theoretical and practical basic notions].

Chaque jour, le médecin utilise dans sa pratique des scores cliniques. Ces scores sont souvent des aides à la décision médicale. Les étapes de validation des scores cliniques sont par contre souvent méconnues du médecin. Cette revue rappelle les bases théoriques de la validation d'un score clinique et propose des exercices pratiques. [Abstract] Physicians are using clinical scores on a regular basis. These scores are generally helpful in making medical decisions. However, the process of validation of clinical scores is often unknown to the physicians. This paper reviews the theory of validation of clinical scores and proposes practical exercises.

Cancer chronotherapeutics: experimental, theoretical, and clinical aspects.

The circadian timing system controls cell cycle, apoptosis, drug bioactivation, and transport and detoxification mechanisms in healthy tissues. As a consequence, the tolerability of cancer chemotherapy varies up to several folds as a function of circadian timing of drug administration in experimental models. Best antitumor efficacy of single-agent or combination chemotherapy usually corresponds to the delivery of anticancer drugs near their respective times of best tolerability. Mathematical models reveal that such coincidence between chronotolerance and chronoefficacy is best explained by differences in the circadian and cell cycle dynamics of host and cancer cells, especially with regard circadian entrainment and cell cycle variability. In the clinic, a large improvement in tolerability was shown in international randomized trials where cancer patients received the same sinusoidal chronotherapy schedule over 24h as compared to constant-rate infusion or wrongly timed chronotherapy. However, sex, genetic background, and lifestyle were found to influence optimal chronotherapy scheduling. These findings support systems biology approaches to cancer chronotherapeutics. They involve the systematic experimental mapping and modeling of chronopharmacology pathways in synchronized cell cultures and their adjustment to mouse models of both sexes and distinct genetic background, as recently shown for irinotecan. Model-based personalized circadian drug delivery aims at jointly improving tolerability and efficacy of anticancer drugs based on the circadian timing system of individual patients, using dedicated circadian biomarker and drug delivery technologies.

The environmental effectiviness of alternative agri-environmental policy reforms : theoretical and empirical analysis

Selostus: Maatalouden ympäristöpolitiikan reformien tehokkuus ravinnepäästöjen vähentämisessä - teoreettinen ja empiirinen analyysi

Tulologistiikan optimointi

Diplomityön tavoite jaettiin kahteen osaan, joista ensimmäinen oli laskentamallin rakentaminen tulologistiikkaan. Tavoitteen toinen osa muodostui optimaalisen ratkaisuehdotuksen tekemisestä työn tilaajana olevan yrityksen eräälle tuoteperheelle rakennettua laskentamallia hyödyntäen. Työn teoriaosuudessa esiteltiin keskeisiä tekijöitä, joilla on vaikutusta toimitusketjun sekä tulologistiikan hallintaan. Lisäksi teorian ja esimerkkilaskelmien avulla esiteltiin rakennetun laskentamallin kannalta keskeistä toimitusketjun varastojen laskentaa. Työn tuloksina esiteltiin rakennettua laskentamallia sekä yrityksen kahdelle valmistuspaikalle laskentamallilla tehtyjen tulologististen laskelmien keskeisiä tuloksia. Laskelmien yksityiskohtaiset tulokset eivät ole sisällytetty työhön. Tuoteperheen optimaaliset ratkaisuehdotukset valmistuspaikoittain muodostettiin laskelmien analysoinnin pohjalta.

Suunnittelun tunnusluvut

Diplomityön tavoitteena oli kehittää Andritzin Kuitulinja-divisioonalle tunnuslukuja, työkaluja sekä menetelmiä projektin johdon jasuunnittelun eri osa-alueiden arviointiin, hinnoitteluun ja seurantaan Työn teoriaosuudessa käsiteltiin projektiliiketoimintaa, suunnitteluaja sen hankintaa, tunnuslukuja sekä mittaamista projektiympäristössä. Työn pääpaino oli kuitenkin empiriaosuudella, jossa aluksi tutustuttiin yksityiskohtaisesti työssä tutkittaviin osa-alueisiin. Tiedonkeruuvaiheessa kerättiin suuri määrätunnuslukujen laskemiseksi tarvittavaa tietoa toteutetuista tai vielä hieman keskeneräisistä projekteista. Työn kirjallinen osuus ja kerätty numeerinen tieto yhdistettiin tunnuslukujen analysointivaiheessa, jossa tutkittiin eri tunnuslukujen soveltuvuutta mittaamiseen. Tunnusluvut soveltuivat hyvin joidenkin osa-alueiden kuten prosessi- ja putkistosuunnittelun mittaamiseen. Joidenkin osa-alueiden, kuten rakennussuunnittelun mittaaminen tunnuslukujen avulla oli vaikeampaa tunnuslukujen suuresta hajonnasta johtuen. Eri osa-alueille saatiin kuitenkin määritettyä parhaat tunnusluvut, projektien luokitteluperusteet ja standardiarvot. Työn lopputuloksina saatiin päätavoitteena ollut tunnuslukumittaristo sekä mittaamisen yhtenäistämiseksi luotu tiedonkeruulomake. Mittaamisen tehostamiseksi ja kehittämiseksi tehtiin useita jatkotutkimus- ja kehitysehdotuksia. Lisäksi työssä esitettiin uusi menetelmä projektinohjauksen ja resurssisuunnittelun tueksi.