Multimodel inference and multimodel averaging in empirical modeling of occupational exposure levels.

Empirical modeling of exposure levels has been popular for identifying exposure determinants in occupational hygiene. Traditional data-driven methods used to choose a model on which to base inferences have typically not accounted for the uncertainty linked to the process of selecting the final model. Several new approaches propose making statistical inferences from a set of plausible models rather than from a single model regarded as 'best'. This paper introduces the multimodel averaging approach described in the monograph by Burnham and Anderson. In their approach, a set of plausible models are defined a priori by taking into account the sample size and previous knowledge of variables influent on exposure levels. The Akaike information criterion is then calculated to evaluate the relative support of the data for each model, expressed as Akaike weight, to be interpreted as the probability of the model being the best approximating model given the model set. The model weights can then be used to rank models, quantify the evidence favoring one over another, perform multimodel prediction, estimate the relative influence of the potential predictors and estimate multimodel-averaged effects of determinants. The whole approach is illustrated with the analysis of a data set of 1500 volatile organic compound exposure levels collected by the Institute for work and health (Lausanne, Switzerland) over 20 years, each concentration having been divided by the relevant Swiss occupational exposure limit and log-transformed before analysis. Multimodel inference represents a promising procedure for modeling exposure levels that incorporates the notion that several models can be supported by the data and permits to evaluate to a certain extent model selection uncertainty, which is seldom mentioned in current practice.

Complementarities between mathematical and computational modeling: the case of the repeated Prisoners' Dilemma

We study the properties of the well known Replicator Dynamics when applied to a finitely repeated version of the Prisoners' Dilemma game. We characterize the behavior of such dynamics under strongly simplifying assumptions (i.e. only 3 strategies are available) and show that the basin of attraction of defection shrinks as the number of repetitions increases. After discussing the difficulties involved in trying to relax the 'strongly simplifying assumptions' above, we approach the same model by means of simulations based on genetic algorithms. The resulting simulations describe a behavior of the system very close to the one predicted by the replicator dynamics without imposing any of the assumptions of the mathematical model. Our main conclusion is that mathematical and computational models are good complements for research in social sciences. Indeed, while computational models are extremely useful to extend the scope of the analysis to complex scenarios hard to analyze mathematically, formal models can be useful to verify and to explain the outcomes of computational models.

Structured output SVM for remote sensing image classification

In the recent years, kernel methods have revealed very powerful tools in many application domains in general and in remote sensing image classification in particular. The special characteristics of remote sensing images (high dimension, few labeled samples and different noise sources) are efficiently dealt with kernel machines. In this paper, we propose the use of structured output learning to improve remote sensing image classification based on kernels. Structured output learning is concerned with the design of machine learning algorithms that not only implement input-output mapping, but also take into account the relations between output labels, thus generalizing unstructured kernel methods. We analyze the framework and introduce it to the remote sensing community. Output similarity is here encoded into SVM classifiers by modifying the model loss function and the kernel function either independently or jointly. Experiments on a very high resolution (VHR) image classification problem shows promising results and opens a wide field of research with structured output kernel methods.

Inexperienced sonographers can successfully visualize and assess a three-dimensional image of the fetal face using a standardized ultrasound protocol

Introduction: A standardized three-dimensional ultrasonographic (3DUS) protocol is described that allows fetal face reconstruction. Ability to identify cleft lip with 3DUS using this protocol was assessed by operators with minimal 3DUS experience. Material and Methods: 260 stored volumes of fetal face were analyzed using a standardized protocol by operators with different levels of competence in 3DUS. The outcomes studied were: (1) the performance of post-processing 3D face volumes for the detection of facial clefts; (2) the ability of a resident with minimal 3DUS experience to reconstruct the acquired facial volumes, and (3) the time needed to reconstruct each plane to allow proper diagnosis of a cleft. Results: The three orthogonal planes of the fetal face (axial, sagittal and coronal) were adequately reconstructed with similar performance when acquired by a maternal-fetal medicine specialist or by residents with minimal experience (72 vs. 76%, p = 0.629). The learning curve for manipulation of 3DUS volumes of the fetal face corresponds to 30 cases and is independent of the operator's level of experience. Discussion: The learning curve for the standardized protocol we describe is short, even for inexperienced sonographers. This technique might decrease the length of anatomy ultrasounds and improve the ability to visualize fetal face anomalies.

The stabilizing effects of the acquired immunity on the schistosomiasis transmission modeling - the sensitivity Analysis

A mathematical model is proposed to analyze the effects of acquired immunity on the transmission of schistosomiasis in the human host. From this model the prevalence curve dependent on four parameters can be obtained. These parameters were estimated fitting the data by the maximum likelihood method. The model showed a good retrieving capacity of real data from two endemic areas of schistosomiasis: Touros, Brazil (Schistosoma mansoni) and Misungwi, Tanzania (S. haematobium). Also, the average worm burden per person and the dispersion of parasite per person in the community can be obtained from the model. In this paper, the stabilizing effects of the acquired immunity assumption in the model are assessed in terms of the epidemiological variables as follows. Regarded to the prevalence curve, we calculate the confidence interval, and related to the average worm burden and the worm dispersion in the community, the sensitivity analysis (the range of the variation) of both variables with respect to their parameters is performed.

The borehole-fluid effect in electrical resistivity imaging

Fluid that fills boreholes in crosswell electrical resistivity investigations provides the necessary electrical contact between the electrodes and the rock formation but it is also the source of image artifacts in standard inversions that do not account for the effects of the boreholes. The image distortions can be severe for large resistivity contrasts between the rock formation and borehole fluid and for large borehole diameters. We have carried out 3D finite-element modeling using an unstructured-grid approach to quantify the magnitude of borehole effects for different resistivity contrasts, borehole diameters, and electrode configurations. Relatively common resistivity contrasts of 100:1 and borehole diameters of 10 and 20 cm yielded, for a bipole length of 5 m, apparent resistivity underestimates of approximately 12% and 32% when using AB-MN configurations and apparent resistivity overestimates of approximately 24% and 95% when using AM-BN configurations. Effects are generally more severe at shorter bipole spacings. We report the results obtained by either including or ignoring the boreholes in inversions of 3D field data from a test site in Switzerland, where approximately 10,000 crosswell resistivity-tomography measurements were made across six acquisition planes among four boreholes. Inversions of raw data that ignored the boreholes filled with low-resistivity fluid paradoxically produced high-resistivity artifacts around the boreholes. Including correction factors based on the modeling results fora ID model with and without the boreholes did not markedly improve the images. The only satisfactory approach was to use a 3D inversion code that explicitly incorporated the boreholes in the actual inversion. This new approach yielded an electrical resistivity image that was devoid of artifacts around the boreholes and that correlated well with coincident crosswell radar images.

Le discours comme image : énonciation et récit "mimétique" dans le "Timée-Critias" de Platon

Problématique: Pourquoi la mise en scène complexe du Timée-Critias avec ses contextes spatio-temporels emboîtés et ses narrations enchâssées? Quelle est la fonction (pragmatique et argumentative) du discours cosmogonique et anthropogonique de Timée intercalé entre le résumé du récit de l'Atlantide dans le prologue du Timée et la narration même de ce récit dans le Critias! Quel est le rapport entre les discours des deux protagonistes et celui de Socrate sur la cité idéale dans la République? Voilà les principales questions auxquelles cette thèse essaie de répondre. Grâce à une approche discursive et sémio-narrative, elle cherche à montrer la fonction pragmatique et la cohérence narrative et sémantique du double dialogue tout en tenant compte des visions du monde divergentes et même contradictoires des deux protagonistes. Elle essaie de comprendre comment les deux, l'un d'origine italique, l'autre Athénien, dans un contexte énonciatif donné et sur la base de leurs conceptions culturelles et «scientifiques» - sur l'homme et sur le monde - et de leurs idées «philosophiques» - sur l'être, le devenir et la connaissance - produisent des discours de signification différente mais traitant tous deux de la genèse, que ce soit celle du monde, de l'homme et des cités. Elle propose en outre de lire le Timée-Critias à la fois comme une continuation et une réécriture de la République: non seulement les trois dialogues ont le même sujet (la meilleure cité), mais ils se caractérisent par des parallèles dans la situation dramatique et énonciative et dans la manière dont se développe la narration. Plan: Les deux premiers chapitres examinent comment les performances discursives de Timée et de Critias se mettent en place dans le prologue, en prêtant une attention particulière aux aspects dramatiques et énonciatifs, mais aussi poétiques et narratifs (énonciateurs/narrateurs et leurs destinataires, fonction et genre des discours résumés et annoncés). Les troisième et quatrième chapitres, consacrés respectivement au long discours de Timée et à celui de Critias dans le dialogue homonyme, comparent d'abord les deux discours aux Hymnes homériques, à la Théogonie d'Hésiode et à la poésie généalogique afin de mieux saisir la fonction pragmatique et la composition de l'ensemble du Timée-Critias-, puis, à partir des principes ontologiques et épistémologiques explicités dans les proèmes, ils se proposent de dégager, en suivant de près la narration, les conceptions cosmologiques, anthropologiques et épistémologiques des deux protagonistes et de voir comment elles déterminent la production et l'énonciation de leurs discours. Enfin, le dernier chapitre reprend certains éléments essentiels étudiés précédemment en élargissant la perspective à la République et à son rapport intertextuel avec le Timée- Critias: il met en regard les contextes énonciatifs et dramatiques et la problématique des deux oeuvres (le rôle des personnages, la question de la réalisation de la meilleure cité), le discours de Timée et les livres six et sept (la khóra et Yagathón, le statut du discours vraisemblable et l'analogie de la ligne), ainsi que le Critias et les livres huit et dix (la dégénérescence de l'Atlantide et de la meilleure cité, la poésie «mimétique» de Critias et celle des poètes critiquée par Socrate).

Synchronous versus asynchronous modeling of gene regulatory networks.

MOTIVATION: In silico modeling of gene regulatory networks has gained some momentum recently due to increased interest in analyzing the dynamics of biological systems. This has been further facilitated by the increasing availability of experimental data on gene-gene, protein-protein and gene-protein interactions. The two dynamical properties that are often experimentally testable are perturbations and stable steady states. Although a lot of work has been done on the identification of steady states, not much work has been reported on in silico modeling of cellular differentiation processes. RESULTS: In this manuscript, we provide algorithms based on reduced ordered binary decision diagrams (ROBDDs) for Boolean modeling of gene regulatory networks. Algorithms for synchronous and asynchronous transition models have been proposed and their corresponding computational properties have been analyzed. These algorithms allow users to compute cyclic attractors of large networks that are currently not feasible using existing software. Hereby we provide a framework to analyze the effect of multiple gene perturbation protocols, and their effect on cell differentiation processes. These algorithms were validated on the T-helper model showing the correct steady state identification and Th1-Th2 cellular differentiation process. AVAILABILITY: The software binaries for Windows and Linux platforms can be downloaded from http://si2.epfl.ch/~garg/genysis.html.

Preliminary regional rockfall hazard mapping using LIDAR-based slope frequency distribution and CONEFALL modeling

A factor limiting preliminary rockfall hazard mapping at regional scale is often the lack of knowledge of potential source areas. Nowadays, high resolution topographic data (LiDAR) can account for realistic landscape details even at large scale. With such fine-scale morphological variability, quantitative geomorphometric analyses become a relevant approach for delineating potential rockfall instabilities. Using digital elevation model (DEM)-based ?slope families? concept over areas of similar lithology and cliffs and screes zones available from the 1:25,000 topographic map, a susceptibility rockfall hazard map was drawn up in the canton of Vaud, Switzerland, in order to provide a relevant hazard overview. Slope surfaces over morphometrically-defined thresholds angles were considered as rockfall source zones. 3D modelling (CONEFALL) was then applied on each of the estimated source zones in order to assess the maximum runout length. Comparison with known events and other rockfall hazard assessments are in good agreement, showing that it is possible to assess rockfall activities over large areas from DEM-based parameters and topographical elements.

Functional analysis and structural modeling of human APOBEC3G reveal the role of evolutionarily conserved elements in the inhibition of human immunodeficiency virus type 1 infection and Alu transposition.

Retroelements are important evolutionary forces but can be deleterious if left uncontrolled. Members of the human APOBEC3 family of cytidine deaminases can inhibit a wide range of endogenous, as well as exogenous, retroelements. These enzymes are structurally organized in one or two domains comprising a zinc-coordinating motif. APOBEC3G contains two such domains, only the C terminal of which is endowed with editing activity, while its N-terminal counterpart binds RNA, promotes homo-oligomerization, and is necessary for packaging into human immunodeficiency virus type 1 (HIV-1) virions. Here, we performed a large-scale mutagenesis-based analysis of the APOBEC3G N terminus, testing mutants for (i) inhibition of vif-defective HIV-1 infection and Alu retrotransposition, (ii) RNA binding, and (iii) oligomerization. Furthermore, in the absence of structural information on this domain, we used homology modeling to examine the positions of functionally important residues and of residues found to be under positive selection by phylogenetic analyses of primate APOBEC3G genes. Our results reveal the importance of a predicted RNA binding dimerization interface both for packaging into HIV-1 virions and inhibition of both HIV-1 infection and Alu transposition. We further found that the HIV-1-blocking activity of APOBEC3G N-terminal mutants defective for packaging can be almost entirely rescued if their virion incorporation is forced by fusion with Vpr, indicating that the corresponding region of APOBEC3G plays little role in other aspects of its action against this pathogen. Interestingly, residues forming the APOBEC3G dimer interface are highly conserved, contrasting with the rapid evolution of two neighboring surface-exposed amino acid patches, one targeted by the Vif protein of primate lentiviruses and the other of yet-undefined function.