Effective squark/chargino/neutralino couplings: MadGraph implementation

We have included the effective description of squark interactions with charginos/neutralinos in the MadGraph MSSM model. This effective description includes the effective Yukawa couplings, and another logarithmic term which encodes the supersymmetry-breaking. We have performed an extensive test of our implementation analyzing the results of the partial decay widths of squarks into charginos and neutralinos obtained by using FeynArts/FormCalc programs and the new model file in MadGraph. We present results for the cross-section of top-squark production decaying into charginos and neutralinos.

Rapid LC-MS/MS quantification of the major benzodiazepines and their metabolites on dried blood spots using a simple and cost-effective sample pretreatment.

BACKGROUND: Dried blood spots (DBS) sampling has gained popularity in the bioanalytical community as an alternative to conventional plasma sampling, as it provides numerous benefits in terms of sample collection and logistics. The aim of this work was to show that these advantages can be coupled with a simple and cost-effective sample pretreatment, with subsequent rapid LC-MS/MS analysis for quantitation of 15 benzodiazepines, six metabolites and three Z-drugs. For this purpose, a simplified offline procedure was developed that consisted of letting a 5-µl DBS infuse directly into 100 µl of MeOH, in a conventional LC vial. RESULTS: The parameters related to the DBS pretreatment, such as extraction time or internal standard addition, were investigated and optimized, demonstrating that passive infusion in a regular LC vial was sufficient to quantitatively extract the analytes of interest. The method was validated according to international criteria in the therapeutic concentration ranges of the selected compounds. CONCLUSION: The presented strategy proved to be efficient for the rapid analysis of the selected drugs. Indeed, the offline sample preparation was reduced to a minimum, using a small amount of organic solvent and consumables, without affecting the accuracy of the method. Thus, this approach enables simple and rapid DBS analysis, even when using a non-DBS-dedicated autosampler, while lowering the costs and environmental impact.

Mate availability and male dispersal in the Argentine ant Linepithema humile (Mayr) (=Iridomyrmex humilis)

In the Argentine ant Linepithema humile (=Iridomyrmex humilis) only males disperse whereas female sexuals (unmated winged queens) stay in their mother nest where they mate. This study investigated (1) whether dispersing males are accepted into foreign colonies, (2) whether they can mate with resident female sexuals, and (3) whether the propensity of males to disperse is affected by the expectation of mating in their mother nest. Field experiments demonstrated that males were accepted into foreign colonies only when these colonies contained female sexuals or queen pupae. Before and after the time of (sic) female sexuals, workers attacked and killed most of the foreign males. Laboratory experiments snowed that males that successfully enter foreign colonies can mate with resident female sexuals. The propensity of males to disperse was significantly influenced by the presence of female sexuals in their nest. Males were more likely to fly out from colonies containing no female sexuals than from those with them. These results are consistent with males preferentially dispersing when there is little or no opportunity to mate in their mother nest. Thus there are two mating strategies available for males: staying in their mother nest when an opportunity to mate arises or dispersing and attempting to mate in a foreign nest when there are no female sexuals in their mother nest. This latter behaviour could mediate gene flow between colonies and account for the lack of significant inbreeding previously documented in this species.

Ancient dispersal of the human fungal pathogen Cryptococcus gattii from the Amazon rainforest

Over the past two decades, several fungal outbreaks have occurred, including the high-profile 'Vancouver Island' and 'Pacific Northwest' outbreaks, caused by Cryptococcus gattii, which has affected hundreds of otherwise healthy humans and animals. Over the same time period, C. gattii was the cause of several additional case clusters at localities outside of the tropical and subtropical climate zones where the species normally occurs. In every case, the causative agent belongs to a previously rare genotype of C. gattii called AFLP6/VGII, but the origin of the outbreak clades remains enigmatic. Here we used phylogenetic and recombination analyses, based on AFLP and multiple MLST datasets, and coalescence gene genealogy to demonstrate that these outbreaks have arisen from a highly-recombining C. gattii population in the native rainforest of Northern Brazil. Thus the modern virulent C. gattii AFLP6/VGII outbreak lineages derived from mating events in South America and then dispersed to temperate regions where they cause serious infections in humans and animals.

Amlodipine and valsartan as components of a rational and effective fixed-dose combination.

Pharmacological treatment of hypertension is effective in preventing cardiovascular and renal complications. Calcium antagonists and blockers of the renin-angiotensin system are widely used today to initiate antihypertensive therapy but, when given as monotherapy, do not suffice in most patients to normalize blood pressure. Combining the two types of agents considerably increases the antihypertensive efficacy, but not at the expense of a deterioration of tolerability. This is exemplified by the experience accumulated with the recently developed fixed dose combination containing the AT(1)-receptor blocker valsartan (160 mg) and the dihydropyridine amlodipine (5 or 10 mg). In a randomized trial, an 8-week treatment normalized blood pressure (<140/90 mmHg) within 8 weeks in a large fraction of hypertensive patients (78.4% and 85.2% using the 5/160 [n = 371] and 10/160 mg [n = 377] dosage, respectively). Like all AT(1)-receptor blockers valsartan has a placebo-like tolerability. Valsartan prevents to a large extent the occurrence amlodipine-induced peripheral edema. Both amlodipine and valsartan have beneficial effects on cardiovascular morbidity and mortality, as well as protective effects on renal function. The co-administration of these two agents is therefore very attractive, as it enables a rapid and sustained blood pressure control in hypertensive patients. The availability of a fixed-dose combination based on amlodipine and valsartan is expected therefore to facilitate the management of hypertension, to improve long-term adherence with antihypertensive therapy and, ultimately, to have a positive impact on cardiovascular and renal outcomes.

Multilocus phylogeography of the common lizard Zootoca vivipara at the Ibero-Pyrenean suture zone reveals lowland barriers and high-elevation introgression.

BACKGROUND: The geographic distribution of evolutionary lineages and the patterns of gene flow upon secondary contact provide insight into the process of divergence and speciation. We explore the evolutionary history of the common lizard Zootoca vivipara (= Lacerta vivipara) in the Iberian Peninsula and test the role of the Pyrenees and the Cantabrian Mountains in restricting gene flow and driving lineage isolation and divergence. We also assess patterns of introgression among lineages upon secondary contact, and test for the role of high-elevation trans-mountain colonisations in explaining spatial patterns of genetic diversity. We use mtDNA sequence data and genome-wide AFLP loci to reconstruct phylogenetic relationships among lineages, and measure genetic structure RESULTS: The main genetic split in mtDNA corresponds generally to the French and Spanish sides of the Pyrenees as previously reported, in contrast to genome-wide AFLP data, which show a major division between NW Spain and the rest. Both types of markers support the existence of four distinct and geographically congruent genetic groups, which are consistent with major topographic barriers. Both datasets reveal the presence of three independent contact zones between lineages in the Pyrenean region, one in the Basque lowlands, one in the low-elevation mountains of the western Pyrenees, and one in the French side of the central Pyrenees. The latter shows genetic evidence of a recent, high-altitude trans-Pyrenean incursion from Spain into France. CONCLUSIONS: The distribution and age of major lineages is consistent with a Pleistocene origin and a role for both the Pyrenees and the Cantabrian Mountains in driving isolation and differentiation of Z. vivipara lineages at large geographic scales. However, mountain ranges are not always effective barriers to dispersal, and have not prevented a recent high-elevation trans-Pyrenean incursion that has led to asymmetrical introgression among divergent lineages. Cytonuclear discordance in patterns of genetic structure and introgression at contact zones suggests selection may be involved at various scales. Suture zones are important areas for the study of lineage formation and speciation, and our results show that biogeographic barriers can yield markedly different phylogeographic patterns in different vertebrate and invertebrate taxa.

Case-based learning in VTLE: An effective strategy for improving learning design

This article presents preliminary research from an instructional design perspective on the design of the case method as an integral part of pedagogy and technology. Key features and benefitsusing this teaching and learning strategy in a Virtual Teaching and Learning Environment(VTLE) are identified, taking into account the requirements of the European Higher Education Area (EHEA) for a competence-based curricula design. The implications of these findings for alearning object approach exploring the possibilities of learning personalization, reusability and interoperability trough IMS LD, are also analyzed.

Effect of spatial processes on the evolution of ecological niches and dispersal in metacommunity systems

RésuméLa coexistence de nombreuses espèces différentes a de tout temps intrigué les biologistes. La diversité et la composition des communautés sont influencées par les perturbations et l'hétérogénéité des conditions environnementales. Bien que dans la nature la distribution spatiale des conditions environnementales soit généralement autocorrélée, cet aspect est rarement pris en compte dans les modèles étudiant la coexistence des espèces. Dans ce travail, nous avons donc abordé, à l'aide de simulations numériques, la coexistence des espèces ainsi que leurs caractéristiques au sein d'un environnement autocorrélé.Afin de prendre en compte cet élément spatial, nous avons développé un modèle de métacommunauté (un ensemble de communautés reliées par la dispersion des espèces) spatialement explicite. Dans ce modèle, les espèces sont en compétition les unes avec les autres pour s'établir dans un nombre de places limité, dans un environnement hétérogène. Les espèces sont caractérisées par six traits: optimum de niche, largeur de niche, capacité de dispersion, compétitivité, investissement dans la reproduction et taux de survie. Nous nous sommes particulièrement intéressés à l'influence de l'autocorrélation spatiale et des perturbations sur la diversité des espèces et sur les traits favorisés dans la métacommunauté. Nous avons montré que l'autocorrélation spatiale peut avoir des effets antagonistes sur la diversité, en fonction du taux de perturbations considéré. L'influence de l'autocorrélation spatiale sur la capacité de dispersion moyenne dans la métacommunauté dépend également des taux de perturbations et survie. Nos résultats ont aussi révélé que de nombreuses espèces avec différents degrés de spécialisation (i.e. différentes largeurs de niche) peuvent coexister. Toutefois, les espèces spécialistes sont favorisées en absence de perturbations et quand la dispersion est illimitée. A l'opposé, un taux élevé de perturbations sélectionne des espèces plus généralistes, associées avec une faible compétitivité.L'autocorrélation spatiale de l'environnement, en interaction avec l'intensité des perturbations, influence donc de manière considérable la coexistence ainsi que les caractéristiques des espèces. Ces caractéristiques sont à leur tour souvent impliquées dans d'importants processus, comme le fonctionnement des écosystèmes, la capacité des espèces à réagir aux invasions, à la fragmentation de l'habitat ou aux changements climatiques. Ce travail a permis une meilleure compréhension des mécanismes responsables de la coexistence et des caractéristiques des espèces, ce qui est crucial afin de prédire le devenir des communautés naturelles dans un environnement changeant.AbstractUnderstanding how so many different species can coexist in nature is a fundamental and long-standing question in ecology. Community diversity and composition are known to be influenced by heterogeneity in environmental conditions and disturbance. Though in nature the spatial distribution of environmental conditions is frequently autocorrelated, this aspect is seldom considered in models investigating species coexistence. In this work, we thus addressed several questions pertaining to species coexistence and composition in spatially autocorrelated environments, with a numerical simulations approach.To take into account this spatial aspect, we developed a spatially explicit model of metacommunity (a set of communities linked by dispersal of species). In this model, species are trophically equivalent, and compete for space in a heterogeneous environment. Species are characterized by six life-history traits: niche optimum, niche breadth, dispersal, competitiveness, reproductive investment and survival rate. We were particularly interested in the influence of environmental spatial autocorrelation and disturbance on species diversity and on the traits of the species favoured in the metacommunity. We showed that spatial autocorrelation can have antagonistic effects on diversity depending on disturbance rate. Similarly, spatial autocorrelation interacted with disturbance rate and survival rate to shape the mean dispersal ability observed in the metacommunity. Our results also revealed that many species with various degrees of specialization (i.e. different niche breadths) can coexist together. However specialist species were favoured in the absence of disturbance, and when dispersal was unlimited. In contrast, high disturbance rate selected for more generalist species, associated with low competitive ability.The spatial structure of the environment, together with disturbance and species traits, thus strongly impacts species diversity and, more importantly, species composition. Species composition is known to affect several important metacommunity properties such as ecosystem functioning, resistance and reaction to invasion, to habitat fragmentation and to climate changes. This work allowed a better understanding of the mechanisms responsible for species composition, which is of crucial importance to predict the fate of natural metacommunities in changing environments

Population genomics of eusocial insects: the costs of a vertebrate-like effective population size

The evolution of reproductive division of labour and social life in social insects has lead to the emergence of several life-history traits and adaptations typical of larger organisms: social insect colonies can reach masses of several kilograms, they start reproducing only when they are several years old, and can live for decades. These features and the monopolization of reproduction by only one or few individuals in a colony should affect molecular evolution by reducing the effective population size. We tested this prediction by analysing genome-wide patterns of coding sequence polymorphism and divergence in eusocial vs. noneusocial insects based on newly generated RNA-seq data. We report very low amounts of genetic polymorphism and an elevated ratio of nonsynonymous to synonymous changes - a marker of the effective population size - in four distinct species of eusocial insects, which were more similar to vertebrates than to solitary insects regarding molecular evolutionary processes. Moreover, the ratio of nonsynonymous to synonymous substitutions was positively correlated with the level of social complexity across ant species. These results are fully consistent with the hypothesis of a reduced effective population size and an increased genetic load in eusocial insects, indicating that the evolution of social life has important consequences at both the genomic and population levels.

Cefuroxime prophylaxis is effective in noninstrumented spine surgery : a double-blind, placebo-controlled study

Rapport de synthèse : Plusieurs investigateurs ont démontré que l'utilisation d'une antibiothérapie prophylactique lors d'interventions neurochirurgicales en terrain non infecté (chirurgie propre) réduisait le taux d'infection. Toutefois, ces taux d'infections sont très variables en fonction des types de chirurgie et de la durée des interventions. Les craniotomies, la mise en place ou le remplacement de shunt ventriculo-cardiaque, l'extirpation de méningiomes intracrâniens et les interventions d'une durée de plus de quatre heures sont grevées d'un taux d'infections post-opératoires plus élevé. Si une prophylaxie antibiotique est maintenant reconnue et utilisée dans ce type de chirurgie, il n'a jamais été démontré que cette pratique amène un bénéfice dans les cas de chirurgie pour hernie discale. Des études ont montré que de nombreux organismes potentiellement pathogènes pouvaient être collectés et cultivés à proximité voire dans le champ opératoire. Malgré ces observations, le taux d'infections post-opératoires reste peu important (entre 1-4% selon les centres). Il n'est actuellement pas possible de distinguer le rôle respectif d'une antibiothérapie prophylactique et des pratiques d'asepsie habituelles (y compris l'usage de solutions de rinçage antiseptiques) dans la faible incidence des infections post-opératoires en ce qui concerne la chirurgie des hernies discales. Lorsque des opérations de chirurgie dite «propre » sont grevées d'un taux de complications aussi bas, une prophylaxie antibiotique n'est généralement pas recommandée, en raison d'un rapport coût-bénéfice défavorable. Le but de cette étude est d'évaluer la nécessité d'une antibiothérapie prophylactique par une céphalosporine de seconde génération (cefuroxime 1,5 g intraveineuse) dans la prévention des infections post-opératoires au cours d'une chirurgie pour hernie discale. Il s'agit d'un essai clinique prospectif, contrôlé contre placebo en insu réciproque, à répartition aléatoire. L'étude a été conduite dans les services de neurochirurgie de l'Hôpital Universitaire de Genève et du Centre Hospitalier Universitaire Vaudois de Lausanne. L'ensemble des patients admis dans ces deux services pour une opération de hernie discale et ayant donné leur consentement ont été inclus dans l'étude qui s'est déroulé sur une période de 6 ans. Mille trois cent soixante-neuf patients opérés pour une hernie discale ont été inclus dans cet essai et 132 patients ont été exclus de l'analyse pour diverses raisons. Au total 1'237 patients ont été analysés, respectivement 613 et 624 patients dans le groupe cefuroxime et le groupe placebo. Les patients des deux groupes présentaient des caractéristiques identiques. Nous n'avons objectivé aucun effet secondaire indésirable attribuable à la cefuroxime ou au placebo. Huit (1.3%) patients du groupe cefuroxime et 18 patients (2.8%) du groupe placebo ont développé une infection du site opératoire (P=0.073). Neuf des patients infectés dans le groupe placebo présentaient une infection profonde du site opératoire (spondylodiscite, abcès épidural) et aucun dans le groupe cefuroxime (P<0.01). Tous les patients avec infection profonde du site opératoire ont été traités par antibiothérapie par voie intraveineuse pour au moins 4 semaines et il a été procédé à une reprise chirurgicale chez deux patients. Ces résultats montrent qu'il faut traiter 69 patients avec une antibiothérapie prophylactique de cefuroxime pour prévenir une infection du site opératoire. En conclusion, l'administration d'une dose de cefuroxime 1.5 g intraveineuse comme prophylaxie lors d'opération de hernie discale, permet de réduire significativement le risque d'infection profonde du site opératoire.

Effective notch method assessment of misalignment for fatigue loaded welds

 The objective of this thesis work was to assess axial misalignment in fatigue loaded welds using the effective notch method. As a result, the fatigue behaviour of non-load carrying cruciform fillet welded joint under cyclic tensile loading has been studied. Various degrees of axial misalignment have been found in one series of non-load carrying cruciform fillet welded joints used in a laboratory investigation. As a result, it was important to carry out a comprehensive investigation since axial misalignment forms part of thequality of fatigue loaded structure and can reduce the fatigue strength. To extend the study, the correlation between fatigue strength and stress ratio, as well as stress concentration factor, were also studied. Moreover, a closer investigation of place of crack initiation and its dependence on weld sequence and imperfections of test specimen (angular distortion) was studied. For the fatigue class calculations, FEM (finite element method) and the effectivenotch approach are used. The addressed variable is the axial misalignment whichis introduce by modeling the entire joint. Fracture mechanics based calculations are also used and quantitatively compared with effective notch and experimental results.

Demogenetics in metapopulations

SUMMARY : Human-induced habitat fragmentation constitutes a major threat to biodiversity. Small and isolated populations suffer from increased stochasticity and from limited rescue effects. These two factors may be sufficient to cause local extinctions but fragmentation induces some genetic consequences that can also contribute significantly to extinction risks. Increased genetic drift reduces the effectiveness of selection against deleterious mutations, leading to their progressive accumulation. Drift also decreases both the standing genetic variation and the rate of fixation of beneficial mutations, limiting the evolutionary potential of isolated populations. Demography and genetics further interact and feed back on each other, progressively driving fragmented populations into "extinction vortices". The aim of the thesis was to better understand the processes occurring in fragmented populations. For this, I combined simulation studies and empirical data from three species that live in structured habitats. Chapter 1 and 2 investigate the demography of two shrew species in fragmented habitats. I showed that connectivity and habitat quality strongly affect the demography of the greater white-tooted shrew, although demographic stochasticity was extremely high. I also demonstrated that habitat fragmentation is one of the leading factors allowing the local coexistence of two competing shrew species. Chapter 3 and 4 focus on measuring connectivity in fragmented populations based on genetic data. In particular, I showed that genetic data can be used to detect the landscape elements impeding dispersal. In Chapter 5 that deals with the accumulation of deleterious mutations in fragmented populations, I demonstrated that mutation accumulation, as well a time to extinction, can be predicted from simple demographic and genetic measures. In the last two chapters, I monitored individual reproductive success in an isolated tree frogs population. These data allowed quantifying the effective population size, a measure closely linked to population evolutionary potential. To conclude, this thesis brings some new insights into the processes occurring in fragmented populations, and I hope it will contribute to the improvement of the management and conservation of fragmented populations.