High-resolution numerical modelling of flow-vegetation interactions

In this paper, we present and apply a new three-dimensional model for the prediction of canopy-flow and turbulence dynamics in open-channel flow. The approach uses a dynamic immersed boundary technique that is coupled in a sequentially staggered manner to a large eddy simulation. Two different biomechanical models are developed depending on whether the vegetation is dominated by bending or tensile forces. For bending plants, a model structured on the Euler-Bernoulli beam equation has been developed, whilst for tensile plants, an N-pendula model has been developed. Validation against flume data shows good agreement and demonstrates that for a given stem density, the models are able to simulate the extraction of energy from the mean flow at the stem-scale which leads to the drag discontinuity and associated mixing layer.

A research agenda for malaria eradication: vaccines.

Vaccines could be a crucial component of efforts to eradicate malaria. Current attempts to develop malaria vaccines are primarily focused on Plasmodium falciparum and are directed towards reducing morbidity and mortality. Continued support for these efforts is essential, but if malaria vaccines are to be used as part of a repertoire of tools for elimination or eradication of malaria, they will need to have an impact on malaria transmission. We introduce the concept of "vaccines that interrupt malaria transmission" (VIMT), which includes not only "classical" transmission-blocking vaccines that target the sexual and mosquito stages but also pre-erythrocytic and asexual stage vaccines that have an effect on transmission. VIMT may also include vaccines that target the vector to disrupt parasite development in the mosquito. Importantly, if eradication is to be achieved, malaria vaccine development efforts will need to target other malaria parasite species, especially Plasmodium vivax, where novel therapeutic vaccines against hypnozoites or preventive vaccines with effect against multiple stages could have enormous impact. A target product profile (TPP) for VIMT is proposed and a research agenda to address current knowledge gaps and develop tools necessary for design and development of VIMT is presented.

Quality of care after acute coronary syndromes in a prospective cohort with reasons for non-prescription of recommended medications.

BACKGROUND: Adherence to guidelines is associated with improved outcomes of patients with acute coronary syndrome (ACS). Clinical registries developed to assess quality of care at discharge often do not collect the reasons for non-prescription for proven efficacious preventive medication in Continental Europe. In a prospective cohort of patients hospitalized for an ACS, we aimed at measuring the rate of recommended treatment at discharge, using pre-specified quality indicators recommended in cardiologic guidelines and including systematic collection of reasons for non-prescription for preventive medications. METHODS: In a prospective cohort with 1260 patients hospitalized for ACS, we measured the rate of recommended treatment at discharge in 4 academic centers in Switzerland. Performance measures for medication at discharge were pre-specified according to guidelines, systematically collected for all patients and included in a centralized database. RESULTS: Six hundred and eighty eight patients(54.6%) were discharged with a main diagnosis of STEMI, 491(39%) of NSTEMI and 81(6.4%) of unstable angina. Mean age was 64 years and 21.3% were women. 94.6% were prescribed angiotensin converting enzyme inhibitors/angiotensin II receptor blockers at discharge when only considering raw prescription rates, but increased to 99.5% when including reasons non-prescription. For statins, rates increased from 98% to 98.6% when including reasons for non-prescription and for beta-blockers, from 82% to 93%. For aspirin, rates further increased from 99.4% to 100% and from to 99.8% to 100% for P2Y12 inhibitors. CONCLUSIONS: We found a very high adherence to ACS guidelines for drug prescriptions at discharge when including reasons for non-prescription to drug therapy. For beta-blockers, prescription rates were suboptimal, even after taking into account reason for non-prescription. In an era of improving quality of care to achieve 100% prescription rates at discharge unless contra-indicated, pre-specification of reasons for non-prescription for cardiovascular preventive medication permits to identify remaining gaps in quality of care at discharge. TRIAL REGISTRATION: ClinicalTrials.gov NCT01000701.

La gestion des services environnementaux: entre règles et régulation négociée. Six études de cas de services forestiers pour la production d'eau potable dans trois pays

Cette thèse est construite en quatre parties : trois annexes qui présentent six études de cas (env. 800 pages), précédées par une analyse transversale, plus synthétique (env. 150 pages), dont traite ce résumé. Chaque annexe contient une synthèse détaillée des études de cas. Cette thèse aborde la « gestion des ressources naturelles » en affirmant d'emblée que l'appellation est inappropriée, car ce ne sont pas les ressources qui sont gérées, mais leurs usages. Il s'agit donc d'identifier et d'analyser ce qui influence les comportements humains en lien avec la ressource. Cette affirmation fonde la perspective des sciences sociales sur la gestion des ressources naturelles, dans laquelle s'inscrit cette thèse. L'approche néo-institutionnaliste considère que les usages sont influencés par des institutions, qui sont elles-mêmes influencées par les usagers. Ces institutions sont des constructions humaines qui composent le contexte institutionnel dans lequel les acteurs décident de leurs usages (abattre un arbre, prélever de l'eau, etc.). Les usages des ressources ne sont donc jamais libres et il s'agit de comprendre comment ces règles du jeu influencent les pratiques. Elles sont nombreuses, interdépendantes et forment la trame sur laquelle se décident les usages. Pour saisir cette complexité, l'auteur applique le cadre d'analyse des régimes institutionnels des ressources (RIR) qui se limite à l'analyse de deux types de droits d'usages : ceux issues des règles de la propriété (titres de propriété, servitudes, etc.) et ceux issus des politiques publiques (lois, ordonnances, etc.). Le RIR permet d'identifier un « régime institutionnel », spécifique à la ressource étudiée, dont les évolutions peuvent être comparées dans le temps ou entre plusieurs lieux. Dans cette recherche, ce cadre d'analyse a été appliqué au même objet - la gestion forestière dans les zones de captage d'eau souterraine destinée au réseau public - dans trois pays : en France, en Suisse et en Indonésie. Trois années de recherche de terrain ont permis à l'auteur de s'intéresser non seulement aux règles prédéterminées (la réglementation), mais aussi aux règles effectivement activées sur le terrain (la régulation) par les acteurs rencontrés. Les études de cas montrent que les règles prévues sont inégalement activées et que les acteurs privilégient parfois la négociation directe pour résoudre leurs rivalités d'usages, à la place d'invoquer leurs droits acquis. Ce constat conduit l'auteur à proposer un élargissement de la focale du RIR, qui constitue le coeur de sa thèse. On ne s'intéresse plus seulement à ce qui « est » régulé, mais aussi à ce qui ne l'« est pas » et qui échappe à l'application classique du RIR. Ce renversement de perspective est crucial pour comprendre les usages concrets des ressources dans les régimes peu intégrés, où les pratiques s'expliquent davantage par la marge de manoeuvre laissée aux acteurs que par les règles prédéterminées. Cette relecture, testée avec succès dans cette thèse, permet d'intégrer la marge de manoeuvre à l'analyse au moyen du RIR. Elle se concrétise par l'identification des lacunes et incohérences dans les régimes institutionnels étudiés. Le champ d'application du RIR s'en trouve élargi et sa vulgarisation pour des non-spécialistes est facilitée, notamment pour les environnementalistes. La complémentarité entre les approches s'en trouve renforcée. Les résultats montrent deux choses : premièrement les acteurs disposent toujours d'une marge de manoeuvre pour négocier des régulations ponctuelles, qui sont autant d'alternatives à l'application des règles prévues. Deuxièmement, la conclusion d'accords issus de la négociation bi-/multilatérale dépend directement de la marge de manoeuvre laissée par le contexte institutionnel. Ceci explique pourquoi la négociation entre les propriétaires forestiers et les exploitants de captages s'imposent en Indonésie, est envisageable en France, mais n'aboutit pas en Suisse. Les nombreuses tentatives infructueuses de mise en oeuvre de solutions négociées, notamment sous forme de paiements pour services environnementaux (PSE), trouvent ici une explication. - This thesis (written in French) is built in four parts: three annexes that present six case studies (approx. 800 pages), preceded by a transverse, more conceptual analysis (approx. 150 pages), which this summary is about. Each annexe contains a detailed summary of the case studies. 'Natural resource management' is an inappropriate designation because it is not the resources that are managed but the uses made of them, therefore this thesis addresses the identification and analysis of the influences on human behaviour in relation to the resource. This statement roots the social sciences perspective on the management of natural resources, in which this thesis fits. A neoinstitutionalist approach considers that the uses are influenced by institutions, which are themselves influenced by users. These institutions are human constructions that form the institutional context in which the actors decide on the use of resources (felling a tree, collecting water, etc.). Thus, the uses of resources are never independent from institutional influences and it becomes necessary to understand how these rules of the game affect practices. They are numerous, interrelated and form the basis for the uses of resources. To understand this complexity, the author applies the institutional regime resource framework (IRR) which limits the analysis to two types of use rights: those resulting from the property rights (deeds, easements, etc.) and those from public policies (laws, ordinances, etc.). The IRR identifies an 'institutional regime', specific to the resource, from which developments can be compared over time or between several places. In this research, this analytical framework has been applied to the same topic - forest management in the recharging areas of groundwater piped for public supply - in three countries: France, Switzerland and Indonesia. Three years of field research allow the author to look not only at predetermined rules (rules), but also at regulations that are actually activated on the ground (rules-in-use). The case studies show that the predetermined rules are unevenly applied and that sometimes actors favour direct negotiation to resolve their rivalry of uses, instead of invoking their vested rights. From this observation the author proposes an enlargement of the IRR's scope, forming the core of his thesis. The interest covers not only what 'is' regulated, but what 'is not' and so is beyond the classical application of the IRR. This shift in perspective is crucial to understand the concrete uses of resources in poorly integrated regimes, where practices are explained by the margin of manoeuvre left to the actors rather than predetermined rules. This reinterpretation, tested successfully in this research, allows the margin of manoeuvre to be integrated in the analysis using the IRR and is made concrete by the identification of gaps and inconsistencies in the investigated institutional context. The new interpretation of the IRR in this thesis complements and enhances its classical application. In particular, its use and understanding by non-specialists, especially environmentalists, is facilitated. The results show two things: first the actors always have leeway to negotiate ad hoc regulations, which are alternatives to the application of the predefined rules. Second, the conclusion of bi/multilateral negotiated agreements depends directly on the leeway left by the institutional context. This explains why the negotiation between forest owners and operators of water catchments is needed in Indonesia, is possible in France, but does not succeed in Switzerland. This offers an explanation for many unsuccessful attempts to implement negotiated solutions, notably payments for environmental services (PES).

A single LC-tandem mass spectrometry method for the simultaneous determination of 14 antimalarial drugs and their metabolites in human plasma.

Among the various determinants of treatment response, the achievement of sufficient blood levels is essential for curing malaria. For helping us at improving our current understanding of antimalarial drugs pharmacokinetics, efficacy and toxicity, we have developed a liquid chromatography-tandem mass spectrometry method (LC-MS/MS) requiring 200mul of plasma for the simultaneous determination of 14 antimalarial drugs and their metabolites which are the components of the current first-line combination treatments for malaria (artemether, artesunate, dihydroartemisinin, amodiaquine, N-desethyl-amodiaquine, lumefantrine, desbutyl-lumefantrine, piperaquine, pyronaridine, mefloquine, chloroquine, quinine, pyrimethamine and sulfadoxine). Plasma is purified by a combination of protein precipitation, evaporation and reconstitution in methanol/ammonium formate 20mM (pH 4.0) 1:1. Reverse-phase chromatographic separation of antimalarial drugs is obtained using a gradient elution of 20mM ammonium formate and acetonitrile both containing 0.5% formic acid, followed by rinsing and re-equilibration to the initial solvent composition up to 21min. Analyte quantification, using matrix-matched calibration samples, is performed by electro-spray ionization-triple quadrupole mass spectrometry by selected reaction monitoring detection in the positive mode. The method was validated according to FDA recommendations, including assessment of extraction yield, matrix effect variability, overall process efficiency, standard addition experiments as well as antimalarials short- and long-term stability in plasma. The reactivity of endoperoxide-containing antimalarials in the presence of hemolysis was tested both in vitro and on malaria patients samples. With this method, signal intensity of artemisinin decreased by about 20% in the presence of 0.2% hemolysed red-blood cells in plasma, whereas its derivatives were essentially not affected. The method is precise (inter-day CV%: 3.1-12.6%) and sensitive (lower limits of quantification 0.15-3.0 and 0.75-5ng/ml for basic/neutral antimalarials and artemisinin derivatives, respectively). This is the first broad-range LC-MS/MS assay covering the currently in-use antimalarials. It is an improvement over previous methods in terms of convenience (a single extraction procedure for 14 major antimalarials and metabolites reducing significantly the analytical time), sensitivity, selectivity and throughput. While its main limitation is investment costs for the equipment, plasma samples can be collected in the field and kept at 4 degrees C for up to 48h before storage at -80 degrees C. It is suited to detecting the presence of drug in subjects for screening purposes and quantifying drug exposure after treatment. It may contribute to filling the current knowledge gaps in the pharmacokinetics/pharmacodynamics relationships of antimalarials and better define the therapeutic dose ranges in different patient populations.

Diet-induced thermogenesis in chronic obstructive pulmonary disease.

Increased resting energy expenditure and malnutrition are frequently observed in patients with COPD. The aim of this study was to examine the possible contribution of an increased diet-induced thermogenesis (DIT) to weight loss. Eleven patients with COPD in stable clinical state and 11 healthy control subjects were studied. Resting energy expenditure (REE) was measured by standard methods of indirect calorimetry, using a ventilated canopy. Premeal REE was measured after an overnight fast. All subjects then received a balanced liquid test meal with a caloric content that was 0.3 times their REE extrapolated to 24 h. Diet-induced thermogenesis was measured over 130 min. Premeal REE was 109.9 +/- 11.7% of predicted values in the COPD group and 97.5 +/- 9.6% of predicted in the control group (p < 0.01). Seventy minutes after the test meal, REE had increased by 18.8 +/- 8.5% in the COPD group and by 15.1 +/- 5.8% in the control group (NS). After 130 min, REE had increased by 16.4 +/- 7.1% in the COPD group and by 12.4 +/- 5.3% in the control group (NS). The DIT expressed as a percentage of the caloric content of the meal was 4.3 +/- 1.6% in the COPD group and 3.3 +/- 1.4% in the control group (NS). We conclude that patients with stable COPD, although hypermetabolic at rest, do not show an increased DIT.

Sex determination: why so many ways of doing it?

Sexual reproduction is an ancient feature of life on earth, and the familiar X and Y chromosomes in humans and other model species have led to the impression that sex determination mechanisms are old and conserved. In fact, males and females are determined by diverse mechanisms that evolve rapidly in many taxa. Yet this diversity in primary sex-determining signals is coupled with conserved molecular pathways that trigger male or female development. Conflicting selection on different parts of the genome and on the two sexes may drive many of these transitions, but few systems with rapid turnover of sex determination mechanisms have been rigorously studied. Here we survey our current understanding of how and why sex determination evolves in animals and plants and identify important gaps in our knowledge that present exciting research opportunities to characterize the evolutionary forces and molecular pathways underlying the evolution of sex determination.

NanoImpactNet - Stakeholders' knowledge needs for research on the health and environmental impact of nanomaterials

NanoImpactNet (NIN) is a multidisciplinary European Commission funded network on the environmental, health and safety (EHS) impact of nanomaterials. The 24 founding scientific institutes are leading European research groups active in the fields of nanosafety, nanorisk assessment and nanotoxicology. This 4−year project is the new focal point for information exchange within the research community. Contact with other stakeholders is vital and their needs are being surveyed. NIN is communicating with 100s of stakeholders: businesses; internet platforms; industry associations; regulators; policy makers; national ministries; international agencies; standard−setting bodies and NGOs concerned by labour rights, EHS or animal welfare. To improve this communication, internet research, a questionnaire distributed via partners and targeted phone calls were used to identify stakeholders' interests and needs. Knowledge gaps and the necessity for further data mentioned by representatives of all stakeholder groups in the targeted phone calls concerned: potential toxic and safety hazards of nanomaterials throughout their lifecycles; fate and persistence of nanoparticles in humans, animals and the environment; risks associated to nanoparticle exposure; participation in the preparation of nomenclature, standards, methodologies, protocols and benchmarks; development of best practice guidelines; voluntary schemes on responsibility; databases of materials, research topics and themes. Findings show that stakeholders and NIN researchers share very similar knowledge needs, and that open communication and free movement of knowledge will benefit both researchers and industry. Consequently NIN will encourage stakeholders to be active members. These survey findings will be used to improve NIN's communication tools to further build on interdisciplinary relationships towards a healthy future with nanotechnology.

Free-living amoebae: Biological by-passes in water treatment.

Free-living amoebae constitute reservoirs for many bacteria including not only well-known pathogens but also emerging pathogens responsible for respiratory diseases, and contribute to the protection, survival and dissemination of these bacteria in water systems, despite the application of disinfection or thermal treatments. In this article we review the available information on the presence of free-living amoebae and amoebae-resisting bacteria in drinking water systems, on the factors that contribute to their presence in the water and/or the biofilms, on the possible control measures and their effectiveness, and we identify some gaps in current knowledge needing further research.

Treeline and climate change : analyzing and modeling patterns and shifts in the Swiss Alps

Summary: Global warming has led to an average earth surface temperature increase of about 0.7 °C in the 20th century, according to the 2007 IPCC report. In Switzerland, the temperature increase in the same period was even higher: 1.3 °C in the Northern Alps anal 1.7 °C in the Southern Alps. The impacts of this warming on ecosystems aspecially on climatically sensitive systems like the treeline ecotone -are already visible today. Alpine treeline species show increased growth rates, more establishment of young trees in forest gaps is observed in many locations and treelines are migrating upwards. With the forecasted warming, this globally visible phenomenon is expected to continue. This PhD thesis aimed to develop a set of methods and models to investigate current and future climatic treeline positions and treeline shifts in the Swiss Alps in a spatial context. The focus was therefore on: 1) the quantification of current treeline dynamics and its potential causes, 2) the evaluation and improvement of temperaturebased treeline indicators and 3) the spatial analysis and projection of past, current and future climatic treeline positions and their respective elevational shifts. The methods used involved a combination of field temperature measurements, statistical modeling and spatial modeling in a geographical information system. To determine treeline shifts and assign the respective drivers, neighborhood relationships between forest patches were analyzed using moving window algorithms. Time series regression modeling was used in the development of an air-to-soil temperature transfer model to calculate thermal treeline indicators. The indicators were then applied spatially to delineate the climatic treeline, based on interpolated temperature data. Observation of recent forest dynamics in the Swiss treeline ecotone showed that changes were mainly due to forest in-growth, but also partly to upward attitudinal shifts. The recent reduction in agricultural land-use was found to be the dominant driver of these changes. Climate-driven changes were identified only at the uppermost limits of the treeline ecotone. Seasonal mean temperature indicators were found to be the best for predicting climatic treelines. Applying dynamic seasonal delimitations and the air-to-soil temperature transfer model improved the indicators' applicability for spatial modeling. Reproducing the climatic treelines of the past 45 years revealed regionally different attitudinal shifts, the largest being located near the highest mountain mass. Modeling climatic treelines based on two IPCC climate warming scenarios predicted major shifts in treeline altitude. However, the currently-observed treeline is not expected to reach this limit easily, due to lagged reaction, possible climate feedback effects and other limiting factors. Résumé: Selon le rapport 2007 de l'IPCC, le réchauffement global a induit une augmentation de la température terrestre de 0.7 °C en moyenne au cours du 20e siècle. En Suisse, l'augmentation durant la même période a été plus importante: 1.3 °C dans les Alpes du nord et 1.7 °C dans les Alpes du sud. Les impacts de ce réchauffement sur les écosystèmes - en particuliers les systèmes sensibles comme l'écotone de la limite des arbres - sont déjà visibles aujourd'hui. Les espèces de la limite alpine des forêts ont des taux de croissance plus forts, on observe en de nombreux endroits un accroissement du nombre de jeunes arbres s'établissant dans les trouées et la limite des arbres migre vers le haut. Compte tenu du réchauffement prévu, on s'attend à ce que ce phénomène, visible globalement, persiste. Cette thèse de doctorat visait à développer un jeu de méthodes et de modèles pour étudier dans un contexte spatial la position présente et future de la limite climatique des arbres, ainsi que ses déplacements, au sein des Alpes suisses. L'étude s'est donc focalisée sur: 1) la quantification de la dynamique actuelle de la limite des arbres et ses causes potentielles, 2) l'évaluation et l'amélioration des indicateurs, basés sur la température, pour la limite des arbres et 3) l'analyse spatiale et la projection de la position climatique passée, présente et future de la limite des arbres et des déplacements altitudinaux de cette position. Les méthodes utilisées sont une combinaison de mesures de température sur le terrain, de modélisation statistique et de la modélisation spatiale à l'aide d'un système d'information géographique. Les relations de voisinage entre parcelles de forêt ont été analysées à l'aide d'algorithmes utilisant des fenêtres mobiles, afin de mesurer les déplacements de la limite des arbres et déterminer leurs causes. Un modèle de transfert de température air-sol, basé sur les modèles de régression sur séries temporelles, a été développé pour calculer des indicateurs thermiques de la limite des arbres. Les indicateurs ont ensuite été appliqués spatialement pour délimiter la limite climatique des arbres, sur la base de données de températures interpolées. L'observation de la dynamique forestière récente dans l'écotone de la limite des arbres en Suisse a montré que les changements étaient principalement dus à la fermeture des trouées, mais aussi en partie à des déplacements vers des altitudes plus élevées. Il a été montré que la récente déprise agricole était la cause principale de ces changements. Des changements dus au climat n'ont été identifiés qu'aux limites supérieures de l'écotone de la limite des arbres. Les indicateurs de température moyenne saisonnière se sont avérés le mieux convenir pour prédire la limite climatique des arbres. L'application de limites dynamiques saisonnières et du modèle de transfert de température air-sol a amélioré l'applicabilité des indicateurs pour la modélisation spatiale. La reproduction des limites climatiques des arbres durant ces 45 dernières années a mis en évidence des changements d'altitude différents selon les régions, les plus importants étant situés près du plus haut massif montagneux. La modélisation des limites climatiques des arbres d'après deux scénarios de réchauffement climatique de l'IPCC a prédit des changements majeurs de l'altitude de la limite des arbres. Toutefois, l'on ne s'attend pas à ce que la limite des arbres actuellement observée atteigne cette limite facilement, en raison du délai de réaction, d'effets rétroactifs du climat et d'autres facteurs limitants.

Optimisation de la cryo microscopie électronique pour les études des minicercles d'ADN

RESUME : Bien que les propriétés physiques de la structure de l'ADN aient été intensivement étudiées pendant plus de 50 ans il y a encore beaucoup de questions importantes qui attendent des réponses. Par exemple, qu'arrive-t-il à la structure de la double hélice d'ADN nue (sans protéines liées) lorsqu'elle est fortement courbée, de la même manière que dans les nucléosomes? Cet ADN nu est-il facilement plié (il reste dans le régime élastique) ou réduit-il la contrainte de flexion en formant des sites hyperflexibles «kinks» (il sort du régime élastique en cassant l'empilement des paires de bases à certains endroits) ? La microscopie électronique peut fournir une réponse à cette question par visualisation directe des minicercles d'ADN de la longueur d'un tour de nucléosome (environ 90 paires de bases). Pour que la réponse soit scientifiquement valide, on doit observer les molécules d'ADN lorsqu'elles sont en suspension dans la solution d'intérêt et sans que des colorations, produits chimiques ou fixatifs n'aient été ajoutés, étant donné que ceux-ci peuvent changer les propriétés de l'ADN. La technique de la cryo-microscopie électronique (cryo-EM) développée par le groupe de Jacques Dubochet au début des années 80, permet la visualisation directe des molécules d'ADN suspendues dans des couche minces vitrifiées de solutions aqueuses. Toutefois, le faible contraste qui caractérise la cryo-EM combinée avec la très petite taille des minicercles d'ADN rendent nécessaire l'optimisation de plusieurs étapes, aussi bien dans la préparation des échantillons que dans le processus d'acquisition d'images afin d'obtenir deux clichés stéréo qui permettent la reconstruction 3-D des minicercles d'ADN. Dans la première partie de ma thèse, je décris l'optimisation de certains paramètres pour la cryoEM et des processus d'acquisition d'image utilisant comme objets de test des plasmides et d'autres molécules d'ADN. Dans la deuxième partie, je .décris comment j'ai construit les minicercles d'ADN de 94 bp et comment j'ai introduit des modifications structurelles comme des coupures ou des lacunes. Dans la troisième partie, je décris l'analyse des reconstructions des rninicercles d'ADN. Cette analyse, appuyée par des tests biochimiques, indique fortement que des molécules d'ADN sont capables de former de petites molécules circulaires de 94 bp sans dépasser les limites d'élasticité, indiquant que les minicercles adoptent une forme circulaire régulière où la flexion est redistribuée le long la molécule. ABSTRACT : Although physical properties of DNA structure have been intensively studied for over 50 years there are still many important questions that need to be answered. For example, what happens to protein-free double-stranded DNA when it is strongly bent, as in DNA forming nucleosomes? Is such protein-free DNA smoothly bent (i.e. it remains within elastic limits of DNA rigidity) or does it release its bending stress by forming sharp kinks (i.e. it exits the elastic regime and breaks the stacking between neighbouring base-pairs in localized regions)? Electron microscopy can provide an answer to this question by directly visualizing DNA minicircles that have the size of nucleosome gyres (ca 90 bp). For the answer to be scientifically valid, one needs to observe DNA molecules while they are still suspended in the solution of interest and no staining chemicals or fixatives have been added since these can change the properties of the DNA. CryoEM techniques developed by Jacques Dubochet's group beginning in the 1980's permit direct visualization of DNA molecules suspended in cryo-vitrified layers of aqueous solutions. However, a relatively weak contrast of cryo-EM preparations combined with the very small size of the DNA minicircles made it necessary to optimize many of the steps and parameters of the cryo-EM specimen preparation and image acquisition processes in order to obtain stereo-pairs of images that permit the 3-D reconstruction of the observed DNA minicircles. In the first part of my thesis I describe the optimization of the cryo-EM preparation and the image acquisition processes using plasmid size DNA molecules as a test object. In the second part, I describe how I formed the 94 by DNA minicircles and how I introduced structural modifications like nicks or gaps. In the third part, I describe the cryo-EM analysis of the constructed DNA minicircles. That analysis, supported by biochemical tests, strongly indicates that DNA minicircles as small as 94 by remain within the elastic limits of DNA structure, i.e. the minicircles adopt a regular circular shape where bending is redistributed along the molecules.

Energy balance in elderly patients after surgery for a femoral neck fracture.

To study energy and protein balances in elderly patients after surgery, spontaneous energy and protein intake and resting energy expenditure (REE) were measured in 20 elderly female patients with a femoral neck fracture (mean age 81 +/- 4, SD, range 74-87 years; weight 53 +/- 8, range 42-68 kg) during a 5-6 day period following surgery. REE, measured over 20-40 min by indirect calorimetry using a ventilated canopy, averaged 0.98 +/- 0.15 kcal/min on day 3 and decreased to 0.93 +/- 0.15 kcal/min on day 8-9 postsurgery (p less than 0.02). REE was positively correlated with body weight (r = 0.69, p less than 0.005). Mean REE extrapolated to 24 hr (24-REE) was 1283 +/- 194 kcal/day. Mean daily food energy intake measured over the 5-day follow-up period was 1097 +/- 333 kcal/day and was positively correlated with 24-REE (r = 0.50, p less than 0.05). Daily energy balance was -235 +/- 351 kcal/day on day 3 (p less than 0.01 vs zero) and -13 +/- 392 kcal/day on day 8-9 postsurgery (NS vs zero) with a mean over the study period of -185 +/- 289 kcal/day (p less than 0.01 vs zero). When an extra 100 kcal/day was allowed for the energy cost of physical activity, mean daily energy balance over the 5-day study period was calculated to be -285 +/- 289 kcal/day (p less than 0.01 vs zero). Measurements of total 24-hr urinary nitrogen (N) excretion were obtained in a subgroup of 14 patients.(ABSTRACT TRUNCATED AT 250 WORDS)

Lesion bypass by the Escherichia coli DNA polymerase V requires assembly of a RecA nucleoprotein filament.

Translesion replication is carried out in Escherichia coli by the SOS-inducible DNA polymerase V (UmuC), an error-prone polymerase, which is specialized for replicating through lesions in DNA, leading to the formation of mutations. Lesion bypass by pol V requires the SOS-regulated proteins UmuD' and RecA and the single-strand DNA-binding protein (SSB). Using an in vitro assay system for translesion replication based on a gapped plasmid carrying a site-specific synthetic abasic site, we show that the assembly of a RecA nucleoprotein filament is required for lesion bypass by pol V. This is based on the reaction requirements for stoichiometric amounts of RecA and for single-stranded gaps longer than 100 nucleotides and on direct visualization of RecA-DNA filaments by electron microscopy. SSB is likely to facilitate the assembly of the RecA nucleoprotein filament; however, it has at least one additional role in lesion bypass. ATPgammaS, which is known to strongly increase binding of RecA to DNA, caused a drastic inhibition of pol V activity. Lesion bypass does not require stoichiometric binding of UmuD' along RecA filaments. In summary, the RecA nucleoprotein filament, previously known to be required for SOS induction and homologous recombination, is also a critical intermediate in translesion replication.

Conceptual models for designing information systems supporting the strategic analysis of technology environments

1 6 STRUCTURE OF THIS THESIS -Chapter I presents the motivations of this dissertation by illustrating two gaps in the current body of knowledge that are worth filling, describes the research problem addressed by this thesis and presents the research methodology used to achieve this goal. -Chapter 2 shows a review of the existing literature showing that environment analysis is a vital strategic task, that it shall be supported by adapted information systems, and that there is thus a need for developing a conceptual model of the environment that provides a reference framework for better integrating the various existing methods and a more formal definition of the various aspect to support the development of suitable tools. -Chapter 3 proposes a conceptual model that specifies the various enviromnental aspects that are relevant for strategic decision making, how they relate to each other, and ,defines them in a more formal way that is more suited for information systems development. -Chapter 4 is dedicated to the evaluation of the proposed model on the basis of its application to a concrete environment to evaluate its suitability to describe the current conditions and potential evolution of a real environment and get an idea of its usefulness. -Chapter 5 goes a step further by assembling a toolbox describing a set of methods that can be used to analyze the various environmental aspects put forward by the model and by providing more detailed specifications for a number of them to show how our model can be used to facilitate their implementation as software tools. -Chapter 6 describes a prototype of a strategic decision support tool that allow the analysis of some of the aspects of the environment that are not well supported by existing tools and namely to analyze the relationship between multiple actors and issues. The usefulness of this prototype is evaluated on the basis of its application to a concrete environment. -Chapter 7 finally concludes this thesis by making a summary of its various contributions and by proposing further interesting research directions.

Do voting advice applications have an effect on electoral participation and voter turnout ? : Evidence from the 2007 Swiss Federal Elections

Voting Advice Applications (VAAs) render a valuable platform for tackling one of democracy's central challenges: low voter turnout. Studies indicate that lack of information and cost-benefit considerations cause voters to abstain from voting. VAAs are online voting assistance tools which match own political preferences with those of candidates and parties in elections. By assisting voters in their decision-making process prior to casting their votes, VAAs not only rebut rational choice reasoning against voting but also narrow existing information gaps. In this paper we examine the impact of VAAs on participation and voter turnout. Specifically, we present results on how the Swiss VAA smartvote affected voter turnout in the 2007 federal elections. Our analyses suggest that smartvote does have a mobilizing capacity, especially among young voters who are usually underrepresented at polls. Moreover, the study demonstrates how VAAs such as smartvote do affect citizen's propensity to deal with politics in general.