Approximation of event probabilities in noisy cellular processes

Molecular noise, which arises from the randomness of the discrete events in the cell, significantly influences fundamental biological processes. Discrete-state continuous-time stochastic models (CTMC) can be used to describe such effects, but the calculation of the probabilities of certain events is computationally expensive. We present a comparison of two analysis approaches for CTMC. On one hand, we estimate the probabilities of interest using repeated Gillespie simulation and determine the statistical accuracy that we obtain. On the other hand, we apply a numerical reachability analysis that approximates the probability distributions of the system at several time instances. We use examples of cellular processes to demonstrate the superiority of the reachability analysis if accurate results are required

Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution

<p>Abstract</p> <p>Background</p> <p>The Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) comprise an apparently monophyletic class of viruses that infect a broad variety of eukaryotic hosts. Recent progress in isolation of new viruses and genome sequencing resulted in a substantial expansion of the NCLDV diversity, resulting in additional opportunities for comparative genomic analysis, and a demand for a comprehensive classification of viral genes.</p> <p>Results</p> <p>A comprehensive comparison of the protein sequences encoded in the genomes of 45 NCLDV belonging to 6 families was performed in order to delineate cluster of orthologous viral genes. Using previously developed computational methods for orthology identification, 1445 Nucleo-Cytoplasmic Virus Orthologous Groups (NCVOGs) were identified of which 177 are represented in more than one NCLDV family. The NCVOGs were manually curated and annotated and can be used as a computational platform for functional annotation and evolutionary analysis of new NCLDV genomes. A maximum-likelihood reconstruction of the NCLDV evolution yielded a set of 47 conserved genes that were probably present in the genome of the common ancestor of this class of eukaryotic viruses. This reconstructed ancestral gene set is robust to the parameters of the reconstruction procedure and so is likely to accurately reflect the gene core of the ancestral NCLDV, indicating that this virus encoded a complex machinery of replication, expression and morphogenesis that made it relatively independent from host cell functions.</p> <p>Conclusions</p> <p>The NCVOGs are a flexible and expandable platform for genome analysis and functional annotation of newly characterized NCLDV. Evolutionary reconstructions employing NCVOGs point to complex ancestral viruses.</p

3D surface reconstruction using dense optical flow combined to feature matching: Application to endoscopy

International audienceIn structure from motion (SfM) algorithms, the surface reconstruction performance strongly depends on the quality of the determination of homologous points between images. Classical feature matching-based methods as integrated in the state-of the-art SfM-algorithms are often inoperative for scenes including weak structures and textures (e.g., as those in medical endoscopic videos). This contribution introduces an effective solution based on the combination of dense optical flow and feature matching. The accuracy and robustness of the proposed method were validated using results obtained for a phantom with known dimensions and with patient data, respectively. Apart from the high performance obtained for cystoscopy and gastroscopy, the proposed solution has a high potential in other medical and non-medical scenes.Dans les algorithmes de structures à partir du mouvement (SfM), la performance de la reconstruction des surfaces dépend fortement de la qualité de la détermination des points homologues entre images. Les méthodes SfM de référence sont souvent inopérantes pour les scènes avec peu de structures et textures faiblement contrastées car elles reposent uniquement sur l'appariement de caractéristiques. Cette contribution présente une solution associant un flot optique dense à la mise en correspondance de caractéristiques. La précision et la robustesse de la reconstruction ont été validées via des résultats obtenus pour un fantôme avec des dimensions connues et avec des données patient en cystoscopie et en gastroscopie, respectivement. Plus généralement, cette approche a un fort potentiel pour toute scène peu constrastée, médicales ou non

Look-Ahead Benchmark Bias in Portfolio Performance Evaluation

Performance of investment managers are evaluated in comparison with benchmarks, such as financial indices. Due to the operational constraint that most professional databases do not track the change of constitution of benchmark portfolios, standard tests of performance suffer from the "look-ahead benchmark bias," when they use the assets constituting the benchmarks of reference at the end of the testing period, rather than at the beginning of the period. Here, we report that the "look-ahead benchmark bias" can exhibit a surprisingly large amplitude for portfolios of common stocks (up to 8% annum for the S&P500 taken as the benchmark) -- while most studies have emphasized related survival biases in performance of mutual and hedge funds for which the biases can be expected to be even larger. We use the CRSP database from 1926 to 2006 and analyze the running top 500 US capitalizations to demonstrate that this bias can account for a gross overestimation of performance metrics such as the Sharpe ratio as well as an underestimation of risk, as measured for instance by peak-to-valley drawdowns. We demonstrate the presence of a significant bias in the estimation of the survival and look-ahead biases studied in the literature. A general methodology to test the properties of investment strategies is advanced in terms of random strategies with similar investment constraints.Comment: 16 pages, 1 table, 4 figure

Model Checking Contest @ Petri Nets, Report on the 2013 edition

This document presents the results of the Model Checking Contest held at Petri Nets 2013 in Milano. This contest aimed at a fair and experimental evaluation of the performances of model checking techniques applied to Petri nets. This is the third edition after two successful editions in 2011 and 2012. The participating tools were compared on several examinations (state space generation and evaluation of several types of formul{\ae} -- reachability, LTL, CTL for various classes of atomic propositions) run on a set of common models (Place/Transition and Symmetric Petri nets). After a short overview of the contest, this paper provides the raw results from the contest, model per model and examination per examination. An HTML version of this report is also provided (http://mcc.lip6.fr).Comment: one main report (422 pages) and two annexes (1386 and 1740 pages

Cell cycle features of primate embryonic stem cells.

International audienceUsing flow cytometry measurements combined with quantitative analysis of cell cycle kinetics, we show that rhesus monkey embryonic stem cells (ESCs) are characterized by an extremely rapid transit through the G1 phase, which accounts for 15% of the total cell cycle duration. Monkey ESCs exhibit a non-phasic expression of cyclin E, which is detected during all phases of the cell cycle, and do not growth-arrest in G1 after gamma-irradiation, reflecting the absence of a G1 checkpoint. Serum deprivation or pharmacological inhibition of mitogen-activated protein kinase kinase (MEK) did not result in any alteration in the cell cycle distribution, indicating that ESC growth does not rely on mitogenic signals transduced by the Ras/Raf/MEK pathway. Taken together, these data indicate that rhesus monkey ESCs, like their murine counterparts, exhibit unusual cell cycle features in which cell cycle control mechanisms operating during the G1 phase are reduced or absent

Numerical scheme for a stratigraphic model with erosion constraint and nonlinear gravity flux

International audienceIn this work, we study an extension of the model introduced by Eymard et al. [Int. J. Numer. Methods Engrg. 60, 527–248 (2004)] for the simulation of large scale transport processes of sediments, subject to an erosion constraint. The novelty we consider lies in the diffusion law relating the flux of sediments and the slope of the topography, that now involves a p-Laplacian with p > 2 in order to get more realistic landscape evolutions. This physical sophistication entails the construction of an entirely new numerical scheme, the details of which shall be supplied