Molecular epidemiology of methicillin-resistant Staphylococcus aureus in Switzerland: sampling only invasive isolates does not allow a representative description of the local diversity of clones.

We conducted a molecular study of MRSA isolated in Swiss hospitals, including the first five consecutive isolates recovered from blood cultures and the first ten isolates recovered from other sites in newly identified carriers. Among 73 MRSA isolates, 44 different double locus sequence typing (DLST) types and 32 spa types were observed. Most isolates belonged to the NewYork/Japan, the UK-EMRSA-15, the South German and the Berlin clones. In a country with a low to moderate MRSA incidence, inclusion of non-invasive isolates allowed a more accurate description of the diversity.

A Local DLP-GIS-LP system for geographically decentralized wood procurement planning and decision making

Summary

Multiscale descriptions of density-driven flow instabilities in porous media

Les instabilités engendrées par des gradients de densité interviennent dans une variété d'écoulements. Un exemple est celui de la séquestration géologique du dioxyde de carbone en milieux poreux. Ce gaz est injecté à haute pression dans des aquifères salines et profondes. La différence de densité entre la saumure saturée en CO2 dissous et la saumure environnante induit des courants favorables qui le transportent vers les couches géologiques profondes. Les gradients de densité peuvent aussi être la cause du transport indésirable de matières toxiques, ce qui peut éventuellement conduire à la pollution des sols et des eaux. La gamme d'échelles intervenant dans ce type de phénomènes est très large. Elle s'étend de l'échelle poreuse où les phénomènes de croissance des instabilités s'opèrent, jusqu'à l'échelle des aquifères à laquelle interviennent les phénomènes à temps long. Une reproduction fiable de la physique par la simulation numérique demeure donc un défi en raison du caractère multi-échelles aussi bien au niveau spatial et temporel de ces phénomènes. Il requiert donc le développement d'algorithmes performants et l'utilisation d'outils de calculs modernes. En conjugaison avec les méthodes de résolution itératives, les méthodes multi-échelles permettent de résoudre les grands systèmes d'équations algébriques de manière efficace. Ces méthodes ont été introduites comme méthodes d'upscaling et de downscaling pour la simulation d'écoulements en milieux poreux afin de traiter de fortes hétérogénéités du champ de perméabilité. Le principe repose sur l'utilisation parallèle de deux maillages, le premier est choisi en fonction de la résolution du champ de perméabilité (grille fine), alors que le second (grille grossière) est utilisé pour approximer le problème fin à moindre coût. La qualité de la solution multi-échelles peut être améliorée de manière itérative pour empêcher des erreurs trop importantes si le champ de perméabilité est complexe. Les méthodes adaptatives qui restreignent les procédures de mise à jour aux régions à forts gradients permettent de limiter les coûts de calculs additionnels. Dans le cas d'instabilités induites par des gradients de densité, l'échelle des phénomènes varie au cours du temps. En conséquence, des méthodes multi-échelles adaptatives sont requises pour tenir compte de cette dynamique. L'objectif de cette thèse est de développer des algorithmes multi-échelles adaptatifs et efficaces pour la simulation des instabilités induites par des gradients de densité. Pour cela, nous nous basons sur la méthode des volumes finis multi-échelles (MsFV) qui offre l'avantage de résoudre les phénomènes de transport tout en conservant la masse de manière exacte. Dans la première partie, nous pouvons démontrer que les approximations de la méthode MsFV engendrent des phénomènes de digitation non-physiques dont la suppression requiert des opérations de correction itératives. Les coûts de calculs additionnels de ces opérations peuvent toutefois être compensés par des méthodes adaptatives. Nous proposons aussi l'utilisation de la méthode MsFV comme méthode de downscaling: la grille grossière étant utilisée dans les zones où l'écoulement est relativement homogène alors que la grille plus fine est utilisée pour résoudre les forts gradients. Dans la seconde partie, la méthode multi-échelle est étendue à un nombre arbitraire de niveaux. Nous prouvons que la méthode généralisée est performante pour la résolution de grands systèmes d'équations algébriques. Dans la dernière partie, nous focalisons notre étude sur les échelles qui déterminent l'évolution des instabilités engendrées par des gradients de densité. L'identification de la structure locale ainsi que globale de l'écoulement permet de procéder à un upscaling des instabilités à temps long alors que les structures à petite échelle sont conservées lors du déclenchement de l'instabilité. Les résultats présentés dans ce travail permettent d'étendre les connaissances des méthodes MsFV et offrent des formulations multi-échelles efficaces pour la simulation des instabilités engendrées par des gradients de densité. - Density-driven instabilities in porous media are of interest for a wide range of applications, for instance, for geological sequestration of CO2, during which CO2 is injected at high pressure into deep saline aquifers. Due to the density difference between the C02-saturated brine and the surrounding brine, a downward migration of CO2 into deeper regions, where the risk of leakage is reduced, takes place. Similarly, undesired spontaneous mobilization of potentially hazardous substances that might endanger groundwater quality can be triggered by density differences. Over the last years, these effects have been investigated with the help of numerical groundwater models. Major challenges in simulating density-driven instabilities arise from the different scales of interest involved, i.e., the scale at which instabilities are triggered and the aquifer scale over which long-term processes take place. An accurate numerical reproduction is possible, only if the finest scale is captured. For large aquifers, this leads to problems with a large number of unknowns. Advanced numerical methods are required to efficiently solve these problems with today's available computational resources. Beside efficient iterative solvers, multiscale methods are available to solve large numerical systems. Originally, multiscale methods have been developed as upscaling-downscaling techniques to resolve strong permeability contrasts. In this case, two static grids are used: one is chosen with respect to the resolution of the permeability field (fine grid); the other (coarse grid) is used to approximate the fine-scale problem at low computational costs. The quality of the multiscale solution can be iteratively improved to avoid large errors in case of complex permeability structures. Adaptive formulations, which restrict the iterative update to domains with large gradients, enable limiting the additional computational costs of the iterations. In case of density-driven instabilities, additional spatial scales appear which change with time. Flexible adaptive methods are required to account for these emerging dynamic scales. The objective of this work is to develop an adaptive multiscale formulation for the efficient and accurate simulation of density-driven instabilities. We consider the Multiscale Finite-Volume (MsFV) method, which is well suited for simulations including the solution of transport problems as it guarantees a conservative velocity field. In the first part of this thesis, we investigate the applicability of the standard MsFV method to density- driven flow problems. We demonstrate that approximations in MsFV may trigger unphysical fingers and iterative corrections are necessary. Adaptive formulations (e.g., limiting a refined solution to domains with large concentration gradients where fingers form) can be used to balance the extra costs. We also propose to use the MsFV method as downscaling technique: the coarse discretization is used in areas without significant change in the flow field whereas the problem is refined in the zones of interest. This enables accounting for the dynamic change in scales of density-driven instabilities. In the second part of the thesis the MsFV algorithm, which originally employs one coarse level, is extended to an arbitrary number of coarse levels. We prove that this keeps the MsFV method efficient for problems with a large number of unknowns. In the last part of this thesis, we focus on the scales that control the evolution of density fingers. The identification of local and global flow patterns allows a coarse description at late times while conserving fine-scale details during onset stage. Results presented in this work advance the understanding of the Multiscale Finite-Volume method and offer efficient dynamic multiscale formulations to simulate density-driven instabilities. - Les nappes phréatiques caractérisées par des structures poreuses et des fractures très perméables représentent un intérêt particulier pour les hydrogéologues et ingénieurs environnementaux. Dans ces milieux, une large variété d'écoulements peut être observée. Les plus communs sont le transport de contaminants par les eaux souterraines, le transport réactif ou l'écoulement simultané de plusieurs phases non miscibles, comme le pétrole et l'eau. L'échelle qui caractérise ces écoulements est définie par l'interaction de l'hétérogénéité géologique et des processus physiques. Un fluide au repos dans l'espace interstitiel d'un milieu poreux peut être déstabilisé par des gradients de densité. Ils peuvent être induits par des changements locaux de température ou par dissolution d'un composé chimique. Les instabilités engendrées par des gradients de densité revêtent un intérêt particulier puisque qu'elles peuvent éventuellement compromettre la qualité des eaux. Un exemple frappant est la salinisation de l'eau douce dans les nappes phréatiques par pénétration d'eau salée plus dense dans les régions profondes. Dans le cas des écoulements gouvernés par les gradients de densité, les échelles caractéristiques de l'écoulement s'étendent de l'échelle poreuse où les phénomènes de croissance des instabilités s'opèrent, jusqu'à l'échelle des aquifères sur laquelle interviennent les phénomènes à temps long. Etant donné que les investigations in-situ sont pratiquement impossibles, les modèles numériques sont utilisés pour prédire et évaluer les risques liés aux instabilités engendrées par les gradients de densité. Une description correcte de ces phénomènes repose sur la description de toutes les échelles de l'écoulement dont la gamme peut s'étendre sur huit à dix ordres de grandeur dans le cas de grands aquifères. Il en résulte des problèmes numériques de grande taille qui sont très couteux à résoudre. Des schémas numériques sophistiqués sont donc nécessaires pour effectuer des simulations précises d'instabilités hydro-dynamiques à grande échelle. Dans ce travail, nous présentons différentes méthodes numériques qui permettent de simuler efficacement et avec précision les instabilités dues aux gradients de densité. Ces nouvelles méthodes sont basées sur les volumes finis multi-échelles. L'idée est de projeter le problème original à une échelle plus grande où il est moins coûteux à résoudre puis de relever la solution grossière vers l'échelle de départ. Cette technique est particulièrement adaptée pour résoudre des problèmes où une large gamme d'échelle intervient et évolue de manière spatio-temporelle. Ceci permet de réduire les coûts de calculs en limitant la description détaillée du problème aux régions qui contiennent un front de concentration mobile. Les aboutissements sont illustrés par la simulation de phénomènes tels que l'intrusion d'eau salée ou la séquestration de dioxyde de carbone.

Optimal network topologies for local search with congestion

The problem of searchability in decentralized complex networks is of great importance in computer science, economy, and sociology. We present a formalism that is able to cope simultaneously with the problem of search and the congestion effects that arise when parallel searches are performed, and we obtain expressions for the average search cost both in the presence and the absence of congestion. This formalism is used to obtain optimal network structures for a system using a local search algorithm. It is found that only two classes of networks can be optimal: starlike configurations, when the number of parallel searches is small, and homogeneous-isotropic configurations, when it is large.

Local size segregation in polydisperse hard sphere fluids

The structure of polydisperse hard sphere fluids, in the presence of a wall, is studied by the Rosenfeld density functional theory. Within this approach, the local excess free energy depends on only four combinations of the full set of density fields. The case of continuous polydispersity thereby becomes tractable. We predict, generically, an oscillatory size segregation close to the wall, and connect this, by a perturbation theory for narrow distributions, with the reversible work for changing the size of one particle in a monodisperse reference fluid.

Modelling the influence of change in fire regime on the local distribution of a Mediterranean pyrophytic plant species (Cistus salviifolius) at its northern range limit

Aims: To assess the potential distribution of an obligate seeder and active pyrophyte, Cistus salviifolius, a vulnerable species in the Swiss Red List; to derive scenarios by changing the fire return interval; and to discuss the results from a conservation perspective. A more general aim is to assess the impact of fire as a natural factor influencing the vegetation of the southern slopes of the Alps. Locations: Alps, southern Switzerland. Methods: Presence-absence data to fit the model were obtained from the most recent field mapping of C. salviifolius. The quantitative environmental predictors used in this study include topographic, climatic and disturbance (fire) predictors. Models were fitted by logistic regression and evaluated by jackknife and bootstrap approaches. Changes in fire regime were simulated by increasing the time-return interval of fire (simulating longer periods without fire). Two scenarios were considered: no fire in the past 15 years; or in the past 35 years. Results: Rock cover, slope, topographic position, potential evapotranspiration and time elapsed since the last fire were selected in the final model. The Nagelkerke R-2 of the model for C. salviifolius was 0.57 and the Jackknife area under the curve evaluation was 0.89. The bootstrap evaluation revealed model robustness. By increasing the return interval of fire by either up to 15 years, or 35 years, the modelled C. salviifolius population declined by 30-40%, respectively. Main conclusions: Although fire plays a significant role, topography and rock cover appear to be the most important predictors, suggesting that the distribution of C. salviifolius in the southern Swiss Alps is closely related to the availability of supposedly competition-free sites, such as emerging bedrock, ridge locations or steep slopes. Fire is more likely to play a secondary role in allowing C. salviifolius to extend its occurrence temporarily, by increasing germination rates and reducing the competition from surrounding vegetation. To maintain a viable dormant seed bank for C. salviifolius, conservation managers should consider carrying out vegetation clearing and managing wild fire propagation to reduce competition and ensure sufficient recruitment for this species.

The Foundational Significance of Leggett's Non-local Hidden-Variable Theories

Laudisa (Found. Phys. 38:1110-1132, 2008) claims that experimental research on the class of non-local hidden-variable theories introduced by Leggett is misguided, because these theories are irrelevant for the foundations of quantum mechanics. I show that Laudisa's arguments fail to establish the pessimistic conclusion he draws from them. In particular, it is not the case that Leggett-inspired research is based on a mistaken understanding of Bell's theorem, nor that previous no-hidden-variable theorems already exclude Leggett's models. Finally, I argue that the framework of Bohmian mechanics brings out the importance of Leggett tests, rather than proving their irrelevance, as Laudisa supposes.

Evolutionary dynamics of molecular markers during local adaptation: a case study in Drosophila subobscura

Background: Natural selection and genetic drift are major forces responsible for temporal genetic changes in populations. Furthermore, these evolutionary forces may interact with each other. Here we study the impact of an ongoing adaptive process at the molecular genetic level by analyzing the temporal genetic changes throughout 40 generations of adaptation to a common laboratory environment. Specifically, genetic variability, population differentiation and demographic structure were compared in two replicated groups of Drosophila subobscura populations recently sampled from different wild sources. Results: We found evidence for a decline in genetic variability through time, along with an increase in genetic differentiation between all populations studied. The observed decline in genetic variability was higher during the first 14 generations of laboratory adaptation. The two groups of replicated populations showed overall similarity in variability patterns. Our results also revealed changing demographic structure of the populations during laboratory evolution, with lower effective population sizes in the early phase of the adaptive process. One of the ten microsatellites analyzed showed a clearly distinct temporal pattern of allele frequency change, suggesting the occurrence of positive selection affecting the region around that particular locus. Conclusion: Genetic drift was responsible for most of the divergence and loss of variability between and within replicates, with most changes occurring during the first generations of laboratory adaptation. We also found evidence suggesting a selective sweep, despite the low number of molecular markers analyzed. Overall, there was a similarity of evolutionary dynamics at the molecular level in our laboratory populations, despite distinct genetic backgrounds and some differences in phenotypic evolution.

Water tanks as ecosystems. Local ecosystemic perception for integral management of water tanks in Tamil Nadu, South India

Water tanks offer from many centuries ago solutions in South India for several problems related with water scarcity. They are a traditional water harvesting system wide spread in this territory, allowing a potential decentralized and participatory management of the local population on their own resources. Although water tanks¿ main function is irrigation, they have many other uses, functions and natural resources associated, involving stakeholders in the villages apart from those farmers making use of the irrigation. Water tanks provide a variety of landscapes and biodiversity that creates a valuable heterogeneous territory. The complexity of such an ecosystem should be managed with an integral perspective, considering all the elements involved and their relations, and understanding that water tanks are not just water deposits. This multidisciplinary study tries to demonstrate the idea of water tanks as ecosystems, describing and analyzing deeply and in an unprecedentedly way the functions, uses, natural resources and stakeholders. The research also focuses in the assessment of the ecosystemic perception of the local population of some villages in Tamil Nadu, employing diverse anthropological methodology.

Effect of olive oil on early and late events of colon carcinogenesis in rats: modulation of arachidonic acid metabolism and local prostaglandin E2 synthesis.

BACKGROUND Animal model studies have shown that the colon tumour promoting effect of dietary fat depends not only on the amount but on its fatty acid composition. With respect to this, the effect of n9 fatty acids, present in olive oil, on colon carcinogenesis has been scarcely investigated. AIMS To assess the effect of an n9 fat diet on precancer events, carcinoma development, and changes in mucosal fatty acid composition and prostaglandin (PG)E2 formation in male Sprague-Dawley rats with azoxymethane induced colon cancer. METHODS Rats were divided into three groups to receive isocaloric diets (5% of the energy as fat) rich in n9, n3, or n6 fat, and were administered azoxymethane subcutaneously once a week for 11 weeks at a dose rate of 7.4 mg/kg body weight. Vehicle treated groups received an equal volume of normal saline. Groups of animals were colectomised at weeks 12 and 19 after the first dose of azoxymethane or saline. Mucosal fatty acids were assessed at 12 and 19 weeks. Aberrant crypt foci and the in vivo intracolonic release of PGE2 were assessed at week 12, and tumour formation at week 19. RESULTS Rats on the n6 diet were found to have colonic aberrant crypt foci and adenocarcinomas more often than those consuming either the n9 or n3 diet. There were no differences between the rats on the n9 and n3 diets. On the other hand, administration of both n9 and n3 diets was associated with a decrease in mucosal arachidonate concentrations as compared with the n6 diet. Carcinogen treatment induced an appreciable increase in PGE2 formation in rats fed the n6 diet, but not in those fed the n3 and n9 diets. CONCLUSIONS Dietary olive oil prevented the development of aberrant crypt foci and colon carcinomas in rats, suggesting that olive oil may have chemopreventive activity against colon carcinogenesis. These effects may be partly due to modulation of arachidonic acid metabolism and local PGE2synthesis.

CPT-11 and concomitant hyperfractionated accelerated radiotherapy induce efficient local control in rectal cancer patients: results from a phase II.

Patients with rectal cancer are at high risk of disease recurrence despite neoadjuvant radiochemotherapy with 5-Fluorouracil (5FU), a regimen that is now widely applied. In order to develop a regimen with increased antitumour activity, we previously established the recommended dose of neoadjuvant CPT-11 (three times weekly 90 mg m(-2)) concomitant to hyperfractionated accelerated radiotherapy (HART) followed by surgery within 1 week. Thirty-three patients (20 men) with a locally advanced adenocarcinoma of the rectum were enrolled in this prospective phase II trial (1 cT2, 29 cT3, 3 cT4 and 21 cN+). Median age was 60 years (range 43-75 years). All patients received all three injections of CPT-11 and all but two patients completed radiotherapy as planned. Surgery with total mesorectal excision (TME) was performed within 1 week (range 2-15 days). The preoperative chemoradiotherapy was overall well tolerated, 24% of the patients experienced grade 3 diarrhoea that was easily manageable. At a median follow-up of 2 years no local recurrence occurred, however, nine patients developed distant metastases. The 2-year disease-free survival was 66% (95% confidence interval 0.48-0.83). Neoadjuvant CPT-11 and HART allow for excellent local control; however, distant relapse remains a concern in this patient population.

Local character of magnetic coupling in ionic solids

Magnetic interactions in ionic solids are studied using parameter-free methods designed to provide accurate energy differences associated with quantum states defining the Heisenberg constant J. For a series of ionic solids including KNiF3, K2NiF4, KCuF3, K2CuF4, and high- Tc parent compound La2CuO4, the J experimental value is quantitatively reproduced. This result has fundamental implications because J values have been calculated from a finite cluster model whereas experiments refer to infinite solids. The present study permits us to firmly establish that in these wide-gap insulators, J is determined from strongly local electronic interactions involving two magnetic centers only thus providing an ab initio support to commonly used model Hamiltonians.