The cover basement contact beneath the Rawil axial depression (Western Alps) - True amplitude seismic processing, petrophysical properties, and modeling

Since 1986, several near-vertical seismic reflection profiles have been recorded in Switzerland in order to map the deep geologic structure of the Alps. One objective of this endeavour has been to determine the geometries of the autochthonous basement and of the external crystalline massifs, important elements for understanding the geodynamics of the Alpine orogeny. The PNR-20 seismic line W1, located in the Rawil depression of the western Swiss Alps, provides important information on this subject. It extends northward from the `'Penninic front'' across the Helvetic nappes to the Prealps. The crystalline massifs do not outcrop along this profile. Thus, the interpretation of `'near-basement'' reflections has to be constrained by down-dip projections of surface geology, `'true amplitude'' processing, rock physical property studies and modelling. 3-D seismic modelling has been used to evaluate the seismic response of two alternative down-dip projection models. To constrain the interpretation in the southern part of the profile, `'true amplitude'' processing has provided information on the strength of the reflections. Density and velocity measurements on core samples collected up-dip from the region of the seismic line have been used to evaluate reflection coefficients of typical lithologic boundaries in the region. The cover-basement contact itself is not a source of strong reflections, but strong reflections arise from within the overlaying metasedimentary cover sequence, allowing the geometry of the top of the basement to be determined on the basis of `'near-basement'' reflections. The front of the external crystalline massifs is shown to extend beneath the Prealps, about 6 km north of the expected position. A 2-D model whose seismic response shows reflection patterns very similar to the observed is proposed.

Lifelong dynamics of human CD4+CD25+ regulatory T cells: insights from in vivo data and mathematical modeling.

Despite their limited proliferation capacity, regulatory T cells (T(regs)) constitute a population maintained over the entire lifetime of a human organism. The means by which T(regs) sustain a stable pool in vivo are controversial. Using a mathematical model, we address this issue by evaluating several biological scenarios of the origins and the proliferation capacity of two subsets of T(regs): precursor CD4(+)CD25(+)CD45RO(-) and mature CD4(+)CD25(+)CD45RO(+) cells. The lifelong dynamics of T(regs) are described by a set of ordinary differential equations, driven by a stochastic process representing the major immune reactions involving these cells. The model dynamics are validated using data from human donors of different ages. Analysis of the data led to the identification of two properties of the dynamics: (1) the equilibrium in the CD4(+)CD25(+)FoxP3(+)T(regs) population is maintained over both precursor and mature T(regs) pools together, and (2) the ratio between precursor and mature T(regs) is inverted in the early years of adulthood. Then, using the model, we identified three biologically relevant scenarios that have the above properties: (1) the unique source of mature T(regs) is the antigen-driven differentiation of precursors that acquire the mature profile in the periphery and the proliferation of T(regs) is essential for the development and the maintenance of the pool; there exist other sources of mature T(regs), such as (2) a homeostatic density-dependent regulation or (3) thymus- or effector-derived T(regs), and in both cases, antigen-induced proliferation is not necessary for the development of a stable pool of T(regs). This is the first time that a mathematical model built to describe the in vivo dynamics of regulatory T cells is validated using human data. The application of this model provides an invaluable tool in estimating the amount of regulatory T cells as a function of time in the blood of patients that received a solid organ transplant or are suffering from an autoimmune disease.

Mathematical modeling and analysis of the interaction of populations of bacteria and bacteriophages within chicken intestine

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Estimation de la fonction rénale par l'equation MDRD: intérêt et limites pour l'adaptation des doses de médicaments [Renal function estimation by MDRD equation: interest and limitations for drug dosing].

The MDRD (Modification of diet in renal disease) equation enables glomerular filtration rate (GFR) estimation from serum creatinine only. Thus, the laboratory can report an estimated GFR (eGFR) with each serum creatinine assessment, increasing therefore the recognition of renal failure. Predictive performance of MDRD equation is better for GFR < 60 ml/min/1,73 m2. A normal or near-normal renal function is often underestimated by this equation. Overall, MDRD provides more reliable estimations of renal function than the Cockcroft-Gault (C-G) formula, but both lack precision. MDRD is not superior to C-G for drug dosing. Being adjusted to 1,73 m2, MDRD eGFR has to be back adjusted to the patient's body surface area for drug dosing. Besides, C-G has the advantage of a greater simplicity and a longer use.

Protocol for the modeling the epidemiologic transition study: a longitudinal observational study of energy balance and change in body weight, diabetes and cardiovascular disease risk.

ABSTRACT: BACKGROUND: The prevalence of obesity has increased in societies of all socio-cultural backgrounds. To date, guidelines set forward to prevent obesity have universally emphasized optimal levels of physical activity. However there are few empirical data to support the assertion that low levels of energy expenditure in activity is a causal factor in the current obesity epidemic are very limited. METHODS: The Modeling the Epidemiologic Transition Study (METS) is a cohort study designed to assess the association between physical activity levels and relative weight, weight gain and diabetes and cardiovascular disease risk in five population-based samples at different stages of economic development. Twenty-five hundred young adults, ages 25-45, were enrolled in the study; 500 from sites in Ghana, South Africa, Seychelles, Jamaica and the United States. At baseline, physical activity levels were assessed using accelerometry and a questionnaire in all participants and by doubly labeled water in a subsample of 75 per site. We assessed dietary intake using two separate 24-h recalls, body composition using bioelectrical impedance analysis, and health history, social and economic indicators by questionnaire. Blood pressure was measured and blood samples collected for measurement of lipids, glucose, insulin and adipokines. Full examination including physical activity using accelerometry, anthropometric data and fasting glucose will take place at 12 and 24 months. The distribution of the main variables and the associations between physical activity, independent of energy intake, glucose metabolism and anthropometric measures will be assessed using cross-section and longitudinal analysis within and between sites. DISCUSSION: METS will provide insight on the relative contribution of physical activity and diet to excess weight, age-related weight gain and incident glucose impairment in five populations' samples of young adults at different stages of economic development. These data should be useful for the development of empirically-based public health policy aimed at the prevention of obesity and associated chronic diseases.

Modeling of hybrid systems by piecewise decomposition

Piecewise linear models systems arise as mathematical models of systems in many practical applications, often from linearization for nonlinear systems. There are two main approaches of dealing with these systems according to their continuous or discrete-time aspects. We propose an approach which is based on the state transformation, more particularly the partition of the phase portrait in different regions where each subregion is modeled as a two-dimensional linear time invariant system. Then the Takagi-Sugeno model, which is a combination of local model is calculated. The simulation results show that the Alpha partition is well-suited for dealing with such a system

Influence of structural heterogeneities and of large scale topography on imbricate gravitational rock slope failures: New insights from 3-D physical modeling and geomorphological analysis

Initial topography and inherited structural discontinuities are known to play a dominant role in rock slope stability. Previous 2-D physical modeling results demonstrated that even if few preexisting fractures are activated/propagated during gravitational failure all of those heterogeneities had a great influence on mobilized volume and its kinematics. The question we address in the present study is to determine if such a result is also observed in 3-D. As in 2-D previous models we examine geologically stable model configuration, based upon the well documented landslide at Randa, Switzerland. The 3-D models consisted of a homogeneous material in which several fracture zones were introduced in order to study simplified but realistic configurations of discontinuities (e.g. based on natural example rather than a parametric study). Results showed that the type of gravitational failure (deep-seated landslide or sequential failure) and resulting slope morphology evolution are the result of the interplay of initial topography and inherited preexisting fractures (orientation and density). The three main results are i) the initial topography exerts a strong control on gravitational slope failure. Indeed in each tested configuration (even in the isotropic one without fractures) the model is affected by a rock slide, ii) the number of simulated fracture sets greatly influences the volume mobilized and its kinematics, and iii) the failure zone involved in the 1991 event is smaller than the results produced by the analog modeling. This failure may indicate that the zone mobilized in 1991 is potentially only a part of a larger deep-seated landslide and/or wider deep seated gravitational slope deformation.

Prediction of fat-free mass using bioelectrical impedance analysis in young adults from five populations of African origin.

Background/objectives:Bioelectrical impedance analysis (BIA) is used in population and clinical studies as a technique for estimating body composition. Because of significant under-representation in existing literature, we sought to develop and validate predictive equation(s) for BIA for studies in populations of African origin.Subjects/methods:Among five cohorts of the Modeling the Epidemiologic Transition Study, height, weight, waist circumference and body composition, using isotope dilution, were measured in 362 adults, ages 25-45 with mean body mass indexes ranging from 24 to 32. BIA measures of resistance and reactance were measured using tetrapolar placement of electrodes and the same model of analyzer across sites (BIA 101Q, RJL Systems). Multiple linear regression analysis was used to develop equations for predicting fat-free mass (FFM), as measured by isotope dilution; covariates included sex, age, waist, reactance and height(2)/resistance, along with dummy variables for each site. Developed equations were then tested in a validation sample; FFM predicted by previously published equations were tested in the total sample.Results:A site-combined equation and site-specific equations were developed. The mean differences between FFM (reference) and FFM predicted by the study-derived equations were between 0.4 and 0.6âeuro0/00kg (that is, 1% difference between the actual and predicted FFM), and the measured and predicted values were highly correlated. The site-combined equation performed slightly better than the site-specific equations and the previously published equations.Conclusions:Relatively small differences exist between BIA equations to estimate FFM, whether study-derived or published equations, although the site-combined equation performed slightly better than others. The study-derived equations provide an important tool for research in these understudied populations.

Application of the european customer satisfaction index to postal services. Structural equation models versus partial least squars

Customer satisfaction and retention are key issues for organizations in today’s competitive market place. As such, much research and revenue has been invested in developing accurate ways of assessing consumer satisfaction at both the macro (national) and micro (organizational) level, facilitating comparisons in performance both within and between industries. Since the instigation of the national customer satisfaction indices (CSI), partial least squares (PLS) has been used to estimate the CSI models in preference to structural equation models (SEM) because they do not rely on strict assumptions about the data. However, this choice was based upon some misconceptions about the use of SEM’s and does not take into consideration more recent advances in SEM, including estimation methods that are robust to non-normality and missing data. In this paper, both SEM and PLS approaches were compared by evaluating perceptions of the Isle of Man Post Office Products and Customer service using a CSI format. The new robust SEM procedures were found to be advantageous over PLS. Product quality was found to be the only driver of customer satisfaction, while image and satisfaction were the only predictors of loyalty, thus arguing for the specificity of postal services

Using environmental niche modeling to understand biological invasions in a changing world

L'activité humaine affecte particulièrement la biodiversité, qui décline à une vitesse préoccupante. Parmi les facteurs réduisant la biodiversité, on trouve les espèces envahissantes. Symptomatiques d'un monde globalisé où l'échange se fait à l'échelle de la planète, certaines espèces, animales ou végétales, sont introduites, volontairement ou accidentellement par l'activité humaine (par exemple lors des échanges commerciaux ou par les voyageurs). Ainsi, ces espèces atteignent des régions qu'elles n'auraient jamais pu coloniser naturellement. Une fois introduites, l'absence de compétiteur peut les rendre particulièrement nuisibles. Ces nuisances sont plus ou moins directes, allant de problèmes sanitaires (p. ex. les piqûres très aigües des fourmis de feu, originaires d'Amérique du Sud et colonisant à une vitesse fulgurante les USA, l'Australie ou la Chine) à des nuisances sur la biodiversité (p. ex. les ravages de la perche du Nil sur la diversité unique des poissons Cichlidés du Lac Victoria). Il est donc important de pouvoir prévenir de telles introductions. De plus, pour le biologiste, ces espèces représentent une rare occasion de pouvoir comprendre les mécanismes évolutifs et écologiques qui expliquent le succès des envahissantes dans un monde où les équilibres sont bouleversés. Les modèles de niche environnementale sont un outil particulièrement utile dans le cadre de cette problématique. En reliant des observations d'espèces aux conditions environnementales où elles se trouvent, ils peuvent prédire la distribution potentielle des envahissantes, permettant d'anticiper et de mieux limiter leur impact. Toutefois, ils reposent sur des hypothèses pas évidentes à démontrer. L'une d'entre elle étant que la niche d'une espèce reste constante dans le temps, et dans l'espace. Le premier objectif de mon travail est de comparer si la niche d'une espèce envahissante diffère entre sa distribution d'origine native et celle d'origine introduite. En étudiant 50 espèces de plantes et 168 espèces de Mammifères, je démontre que c'est le cas et que par corolaire, il est possible de prédire leurs distributions. La deuxième partie de mon travail consiste à comprendre quelles seront les interactions entre le changement climatiques et les envahissantes, afin d'estimer leur impact sous un climat réchauffé. En étudiant la distribution de 49 espèces de plantes envahissantes, je démontre que les montagnes, régions relativement préservée par ce problème, deviendront bien plus exposées aux risques d'invasions biologiques. J'expose aussi comment les interactions entre l'activité humaine, le réchauffement climatique et les espèces envahissantes menacent la vigne sauvage en Europe et propose des zones géographiques particulièrement adaptée pour sa conservation. Enfin, à une échelle beaucoup plus locale, je montre qu'il est possible d'utiliser ces modèles de niches le long d'une rivière à une échelle extrêmement fine (1 mètre), potentiellement utile pour rationnaliser des mesures de conservations sur le terrain. - Biodiversity is significantly negatively affected by human activity. Invasive species are one of the most important factors causing biodiversity's decline. Intimately linked to the era of global trade, some plant or animal species can be accidentally or casually introduced with human activity (e.g. trade or travel). In this way, these species reach areas they could never reach through natural dispersal. Once naturalized, the lack of competitors can make these species highly noxious. Their effect is more or less direct, from sanitary problems (e.g. the harmful sting of Fire Ants, originating from South America and now spreading throughout USA, China and Australia) or can affect biodiversity (e.g. the Nile perch, devastating the one of the richest hotspot of Cichlid fishes diversity in Lake Victoria). It is thus important to prevent such harmful introductions. Moreover, invasive species represent for biologists one of the rare occasions to understand the evolutionary and ecological mechanisms behind the success of invaders in a world where natural equilibrium is already disturbed. Environmental niche models are particularly useful to tackle this problematic. By relating species observation to the environmental conditions where they occur, they can predict the potential distribution of invasive species, allowing a better anticipation and thus limiting their impact. However, they rely on strong assumption, one of the most important being that the modeled niche remains constant through space and time. The first aim of my thesis is to quantify the difference between the native and the invaded niche. By investigating 50 plant and 168 mammal species, I show that the niche is at least partially conserved, supporting for reliable predictions of invasive' s potential distributions. The second aim of my thesis is to understand the possible interactions between climate change and invasive species, such as to assess their impact under a warmer climate. By studying 49 invasive plant species, I show that mountain areas, which were relatively preserved, will become more suitable for biological invasions. Additionally, I show how interactions between human activity, global warming and invasive species are threatening the wild grapevine in Europe and propose geographical areas particularly adapted for conservation measures. Finally, at a much finer scale where conservation plannings ultimately take place, I show that it is possible to model the niche at very high resolution (1 meter) in an alluvial area allowing better prioritizations for conservation.

Design of potent inhibitors of human RAD51 recombinase based on BRC motifs of BRCA2 protein: modeling and experimental validation of a chimera peptide.

We have previously shown that a 28-amino acid peptide derived from the BRC4 motif of BRCA2 tumor suppressor inhibits selectively human RAD51 recombinase (HsRad51). With the aim of designing better inhibitors for cancer treatment, we combined an in silico docking approach with in vitro biochemical testing to construct a highly efficient chimera peptide from eight existing human BRC motifs. We built a molecular model of all BRC motifs complexed with HsRad51 based on the crystal structure of the BRC4 motif-HsRad51 complex, computed the interaction energy of each residue in each BRC motif, and selected the best amino acid residue at each binding position. This analysis enabled us to propose four amino acid substitutions in the BRC4 motif. Three of these increased the inhibitory effect in vitro, and this effect was found to be additive. We thus obtained a peptide that is about 10 times more efficient in inhibiting HsRad51-ssDNA complex formation than the original peptide.

A hierarchical approach to model parameter optimization for developmental systems.

In the context of Systems Biology, computer simulations of gene regulatory networks provide a powerful tool to validate hypotheses and to explore possible system behaviors. Nevertheless, modeling a system poses some challenges of its own: especially the step of model calibration is often difficult due to insufficient data. For example when considering developmental systems, mostly qualitative data describing the developmental trajectory is available while common calibration techniques rely on high-resolution quantitative data. Focusing on the calibration of differential equation models for developmental systems, this study investigates different approaches to utilize the available data to overcome these difficulties. More specifically, the fact that developmental processes are hierarchically organized is exploited to increase convergence rates of the calibration process as well as to save computation time. Using a gene regulatory network model for stem cell homeostasis in Arabidopsis thaliana the performance of the different investigated approaches is evaluated, documenting considerable gains provided by the proposed hierarchical approach.

A methodology for the adaptation of a PMP at the determination of a PMF

This paper presents a new type of very fine grid hydrological model based on the spatiotemporal repartition of a PMP (Probable Maximum Precipitation) and on the topography. The goal is to estimate the influence of this rain on a PMF (Probable Maximum Flood) on a catchment area in Switzerland. The spatiotemporal distribution of the PMP was realized using six clouds modeled by the advection-diffusion equation. The equation shows the movement of the clouds over the terrain and also gives the evolution of the rain intensity in time. This hydrological modeling is followed by a hydraulic modeling of the surface and subterranean flow, done considering the factors that contribute to the hydrological cycle, such as the infiltration, the resurgence and the snowmelt. These added factors make the developed model closer to reality and also offer flexibility in the initial condition that is added to the factors concerning the PMP, such as the duration of the rain, the speed and direction of the wind. All these initial conditions taken together offer a complete image of the PMF.

A stratified approach for modeling the distribution of a threatened ant species in the Swiss National Park

We present models predicting the potential distribution of a threatened ant species, Formica exsecta Nyl., in the Swiss National Park ( SNP). Data to fit the models have been collected according to a random-stratified design with an equal number of replicates per stratum. The basic aim of such a sampling strategy is to allow the formal testing of biological hypotheses about those factors most likely to account for the distribution of the modeled species. The stratifying factors used in this study were: vegetation, slope angle and slope aspect, the latter two being used as surrogates of solar radiation, considered one of the basic requirements of F. exsecta. Results show that, although the basic stratifying predictors account for more than 50% of the deviance, the incorporation of additional non-spatially explicit predictors into the model, as measured in the field, allows for an increased model performance (up to nearly 75%). However, this was not corroborated by permutation tests. Implementation on a national scale was made for one model only, due to the difficulty of obtaining similar predictors on this scale. The resulting map on the national scale suggests that the species might once have had a broader distribution in Switzerland. Reasons for its particular abundance within the SNP might possibly be related to habitat fragmentation and vegetation transformation outside the SNP boundaries.