Statistical data mining for symbol associations in genomic databases

A methodology is proposed to automatically detect significant symbol associations in genomic databases. A new statistical test is proposed to assess the significance of a group of symbols when found in several genesets of a given database. Applied to symbol pairs, the thresholded p-values of the test define a graph structure on the set of symbols. The cliques of that graph are significant symbol associations, linked to a set of genesets where they can be found. The method can be applied to any database, and is illustrated MSigDB C2 database. Many of the symbol associations detected in C2 or in non-specific selections did correspond to already known interactions. On more specific selections of C2, many previously unkown symbol associations have been detected. These associations unveal new candidates for gene or protein interactions, needing further investigation for biological evidence

Craponne – Allée Henri-Matisse

À l’issue du projet de construction de deux maisons mitoyennes sur une parcelle située allée Henri-Matisse à Craponne, trois sondages ont été réalisés dans le cadre d’un diagnostic prescrit par le Service régional de l’archéologie. La présence présumée de l’aqueduc de l’Yzeron dans ce secteur, ainsi que celle de la voie d’Aquitaine, n’a pas été reconnue dans l’emprise de cette intervention. Une seule structure a été trouvée. Il s’agit d’un drain daté de la période contemporaine

Saint-Genis-Laval – Zac Vallon des Hôpitaux (tranche 1)

Le projet d’aménagement de la Zac du Vallon des Hôpitaux se situe à environ 1 km au nord-est du bourg médiéval de Saint-Genis-Laval et à 10 km au sud-ouest de Lyon. 114 sondages ont été réalisés lors du diagnostic, sur un terrain morcelé couvrant une surface de 4,6 ha, à des altitudes comprises entre 198 et 217 m NGF. Au sud du projet, 65 structures archéologiques datées de la Préhistoire à l’époque contemporaine ont été trouvées. Un dépôt de deux vases partiellement conservés (une coupe et u..

Saint-Pierre-d’Albigny – Chemin du Pré de la Cure

Le diagnostic réalisé sur les parcelles 303 et 304 à Saint-Pierre-d’Albigny n’a donné lieu à aucune découverte de vestige ancien. Les neuf sondages pratiqués ont atteint le dépôt tardiglaciaire du cône de déjection en place dans tout le secteur. Trois structures, d’époque contemporaine, ont été trouvées. Un fossé, orienté est-ouest, a été repéré dans trois sondages. Son comblement est daté du début du xxe s. Il se situe en limite nord d’une parcelle signalée sur le cadastre napoléonien. ..

On the potential of transit surveys in star clusters: impact of correlated noise and radial velocity follow-up

We present an extension of the formalism recently proposed by Pepper and Gaudi to evaluate the yield of transit surveys in homogeneous stellar systems, incorporating the impact of correlated noise on transit time-scales on the detectability of transits, and simultaneously incorporating the magnitude limits imposed by the need for radial velocity (RV) follow-up of transit candidates. New expressions are derived for the different contributions to the noise budget on transit time-scales and the least-squares detection statistic for box-shaped transits, and their behaviour as a function of stellar mass is re-examined. Correlated noise that is constant with apparent stellar magnitude implies a steep decrease in detection probability at the high-mass end which, when considered jointly with the RV requirements, can severely limit the potential of otherwise promising surveys in star clusters. However, we find that small-aperture, wide-field surveys may detect hot Neptunes whose RV signal can be measured with present-day instrumentation in very nearby (<100 pc) cluster

Isochrone ages for field dwarfs: method and application to the age-metallicity relation

A new method is presented to compute age estimates from theoretical isochrones using temperature, luminosity and metallicity data for individual stars. Based on Bayesian probability theory, this method avoids the systematic biases affecting simpler strategies and provides reliable estimates of the age probability distribution function for late-type dwarfs. Basic assumptions concerning the a priori parameter distribution suitable for the solar neighbourhood are combined with the likelihood assigned to the observed data to yield the complete posterior age probability. This method is especially relevant for G dwarfs in the 3-15 Gyr range of ages, crucial to the study of the chemical and dynamical history of the Galaxy. In many cases, it yields markedly different results from the traditional approach of reading the derived age from the isochrone nearest to the data point. We show that the strongest process affecting the traditional approach is that of strongly favouring computed ages near the end-of-main-sequence lifetime. The Bayesian method compensates for this potential bias and generally assigns much higher probabilities to lower main-sequence ages, compared with short-lived evolved stages. This has a strong influence on any application to galactic studies, especially given the present uncertainties on the absolute temperature scale of the stellar evolution models. In particular, the known mismatch between the model predictions and the observations for moderately metal-poor dwarfs (−1 5 Gyr) and young, metal-poor objects ([Fe/H] < −0.5 dex, age < 6 Gyr) in many observed AMR plots are artefacts caused by too simple a treatment of the age determination. The incompatibility of those AMR plots with a well-mixed interstellar medium may therefore only be apparent. Incidentally, our results tend to restore confidence in the method of age determination from the chromospheric activity for field dwarf

Searching for the secondary eclipse of CoRoT-Exo-2b and its transit timing variations

With more than 80 transits observed in the CoRoT light curve with a cadence of 32 s, CoRoT-Exo-2b provides an excellent case to search for the secondary eclipse of the planet, with an expected signal of less than 10^-4 in relative flux. The activity of the star causes a modulation on the flux that makes the detection of this signal challenging. We describe the technique used to seek for the secondary eclipse, that leads to a tentative 2.5 sigma detection of a 5.5x10^-5 eclipse. If the effect of the spots are not taken into account, the times of transit centers will also be affected. They could lead to an erroneous detection of periodic transit timing variations of ~20 s and with a 7.45 d period. By measuring the transit central times at different depths of the transit (transit bisectors), we show that there are no such periodic variations in the CoRoT-Exo-2b O-C residuals larger than ~10 s.Comment: 6 pages, 5 figures, to appear in the Proceedings of IAU Symposium 253, "Transiting Planets", May 2008, Cambridge, M

Simultaneous growth of two cancer cell lines evidences variability in growth rates

Cancer cells co-cultured in vitro reveal unexpected differential growth rates that classical exponential growth models cannot account for. Two non-interacting cell lines were grown in the same culture, and counts of each species were recorded at periodic times. The relative growth of population ratios was found to depend on the initial proportion, in contradiction with the traditional exponential growth model. The proposed explanation is the variability of growth rates for clones inside the same cell line. This leads to a log-quadratic growth model that provides both a theoretical explanation to the phenomenon that was observed, and a better fit to our growth data

The effect of red noise on planetary transit detection

Since the discovery of short-period exoplanets a decade ago, photometric surveys have been recognized as a feasible method to detect transiting hot Jupiters. Many transit surveys are now underway, with instruments ranging from 10-cm cameras to the Hubble Space Telescope. However, the results of these surveys have been much below the expected capacity, estimated in the dozens of detections per year. One of the reasons is the presence of systematics (‘red noise') in photometric time-series. In general, yield predictions assume uncorrelated noise (‘white noise'). In this paper, we show that the effect of red noise on the detection threshold and the expected yields cannot be neglected in typical ground-based surveys. We develop a simple method to determine the effect of red noise on photometric planetary transit detections. This method can be applied to determine detection thresholds for transit surveys. We show that the detection threshold in the presence of systematics can be much higher than that with the assumption of white noise, and obeys a different dependence on magnitude, orbital period and the parameters of the survey. Our method can also be used to estimate the significance level of a planetary transit candidate (to select promising candidates for spectroscopic follow-up). We apply our method to the OGLE planetary transit search, and show that it provides a reliable description of the actual detection threshold with real correlated noise. We point out in what way the presence of red noise could be at least partly responsible for the dearth of transiting planet detections from existing surveys, and examine some possible adaptations in survey planning and strategy. Finally, we estimate the photometric stability necessary to the detection of transiting ‘hot Neptunes

An intriguing correlation between the masses and periods of the transiting planets

We point out an intriguing relation between the masses of the transiting planets and their orbital periods. For the six currently known transiting planets, the data are consistent with a decreasing linear relation. The other known short-period planets, discovered through radial-velocity techniques, seem to agree with this relation. We briefly speculate about a tentative physical model to explain such a dependenc