No planet for HD 166435

The G0V star HD166435 has been observed by the fiber-fed spectrograph ELODIE as one of the targets in the large extra-solar planet survey that we are conducting at the Observatory of Haute-Provence. We detected coherent, low-amplitude, radial-velocity variations with a period of 3.7987days, suggesting a possible close-in planetary companion. Subsequently, we initiated a series of high-precision photometric observations to search for possible planetary transits and an additional series of CaII H and K observations to measure the level of surface magnetic activity and to look for possible rotational modulation. Surprisingly, we found the star to be photometrically variable and magnetically active. A detailed study of the phase stability of the radial-velocity signal revealed that the radial-velocity variability remains coherent only for durations of about 30days. Analysis of the time variation of the spectroscopic line profiles using line bisectors revealed a correlation between radial velocity and line-bisector orientation. All of these observations, along with a one-quarter cycle phase shift between the photometric and the radial-velocity variationss, are well explained by the presence of dark photospheric spots on HD166435. We conclude that the radial-velocity variations are not due to gravitational interaction with an orbiting planet but, instead, originate from line-profile changes stemming from star spots on the surface of the star. The quasi-coherence of the radial-velocity signal over more than two years, which allowed a fair fit with a binary model, makes the stability of this star unusual among other active stars. It suggests a stable magnetic field orientation where spots are always generated at about the same location on the surface of the star.Comment: 9 pages, 8 figures, Accepted for publication in A&

Reactive Hall response

The zero temperature Hall constant R_H, described by reactive (nondissipative) conductivities, is analyzed within linear response theory. It is found that in a certain limit, R_H is directly related to the density dependence of the Drude weight implying a simple picture for the change of sign of charge carriers in the vicinity of a Mott-Hubbard transition. This novel formulation is applied to the calculation of R_H in quasi-one dimensional and ladder prototype interacting electron systems.Comment: 4 pages, 3 Postscript figure

The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters

Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called nearest-neighbor model, which estimates the hybridization free energy of a given sequence as a sum of dinucleotide terms. Compared with its solution counterparts, hybridization in DNA microarrays may be hindered due to the presence of a solid surface and of a high density of DNA strands. We present here a study aimed at the determination of hybridization free energies in DNA microarrays. Experiments are performed on custom Agilent slides. The solution contains a single oligonucleotide. The microarray contains spots with a perfect matching complementary sequence and other spots with one or two mismatches: in total 1006 different probe spots, each replicated 15 times per microarray. The free energy parameters are directly fitted from microarray data. The experiments demonstrate a clear correlation between hybridization free energies in the microarray and in solution. The experiments are fully consistent with the Langmuir model at low intensities, but show a clear deviation at intermediate (non-saturating) intensities. These results provide new interesting insights for the quantification of molecular interactions in DNA microarrays.Comment: 31 pages, 5 figure

The ELODIE survey for northern extra--solar planets I. 6 new extra--solar planet candidates

Precise radial-velocity observations at Haute-Provence Observatory (OHP, France) with the ELODIE echelle spectrograph have been undertaken since 1994. In addition to several discoveries described elsewhere, including and following that of 51 Peg b, they reveal new sub-stellar companions with essentially moderate to long periods. We report here about such companions orbiting five solar-type stars (HD 8574, HD 23596, HD 33636, HD 50554, HD 106252) and one sub-giant star (HD 190228). The companion of HD 8574 has an intermediate period of 227.55 days and a semi--major axis of 0.77 AU. All other companions have long periods, exceeding 3 years, and consequently their semi-major axes are around or above 2 AU. The detected companions have minimum masses m2sini ranging from slightly more than 2 M_Jup to 10.6 M_Jup. These additional objects reinforce the conclusion that most planetary companions have masses lower than 5 M_Jup but with a tail of the mass distribution going up above 15 M_Jup. The orbits are all eccentric and 4 out of 6 have an eccentricity of the order of 0.5. Four stars exhibit solar metallicity, one is metal-rich and one metal-poor. With 6 new extra-solar planet candidates discovered, increasing their total known to-date number to 115, the ELODIE Planet Search Survey yield is currently 18. We emphasize that 3 out of the 6 companions could in principle be resolved by diffraction-limited imaging on 8m-class telescopes depending on the achievable contrast, and therefore be primary targets for first attempts of extra-solar planet direct imaging.Comment: 13 pages, 10 figures, 3 tables, accepted for publication in A&A, appendix A will only appear in the electronic versio

The HARPS search for southern extra-solar planets I. HD330075 b: a new 'hot Jupiter'

We report on the first extra-solar planet discovered with the brand new HARPS instrument. The planet is a typical 'hot Jupiter' with m2sini = 0.62 MJup and an orbital period of 3.39 days, but from the photometric follow-up of its parent star HD330075 we can exclude the presence of a transit. The induced radial-velocity variations exceed 100 m/s in semi-amplitude and are easily detected by state-of-the-art spectro-velocimeters. Nevertheless, the faint magnitude of the parent star (V = 9.36) benefits from the efficient instrument: With HARPS less than 10 observing nights and 3 hours of total integration time were needed to discover the planet and characterize its orbit. The orbital parameters determined from the observations made during the first HARPS run in July 2003 have been confirmed by 7 additional observations carried out in February 2004. The bisector analysis and a photometric follow-up give no hint for activity-induced radial-velocity variations, indicating that the velocity curve is best explained by the presence of a low-mass companion to the star. In this paper we present a set of 21 measurements of excellent quality with weighted rms as low as 2.0 m/s. These measurements lead to a well defined orbit and consequently to the precise orbital parameters determination of the extra-solar planet HD330075b.Comment: 5 pages, 2 figures, accepted for publication by Astronomy and Astrophysics, see also http://obswww.unige.ch/~udry/planet/planet.htm

Detection of a transit by the planetary companion of HD 80606

We report the detection of a transit egress by the ~ 3.9-Jupiter-mass planet HD 80606b, an object in a highly-eccentric orbit (e ~ 0.93) about its parent star of approximately solar type. The astrophysical reality of the signal of variability in HD 80606 is confirmed by observation with two independent telescope systems, and checks against several reference stars in the field. Differential photometry with respect to the nearby comparison star HD 80607 provides a precise light curve. Modelling of the light curve with a full eccentric-orbit model indicates a planet/star-radius ratio of 0.1057 +/- 0.0018, corresponding to a planet radius of 1.029 R_J for a solar-radius parent star; and a precise orbital inclination of 89.285 +/- 0.023 degrees, giving a total transit duration of 12.1 +/- 0.4 hours. The planet hence joins HD 17156b in a class of highly eccentric transiting planets, in which HD 80606b has both the longest period and most eccentric orbit. The recently reported discovery of a secondary eclipse of HD 80606b by the Spitzer Space Observatory permits a combined analysis with the mid-time of primary transit in which the orbital parameters of the system can be tightly constrained. We derive a transit ephemeris of T_tr = HJD (2454876.344 +/- 0.011) + (111.4277 +/- 0.0032) E.Comment: Accepted for publication in MNRAS Letter

Motif effects in Affymetrix GeneChips seriously affect probe intensities

An Affymetrix GeneChip consists of an array of hundreds of thousands of probes (each a sequence of 25 bases) with the probe values being used to infer the extent to which genes are expressed in the biological material under investigation. In this article, we demonstrate that these probe values are also strongly influenced by their precise base sequence. We use data from >28 000 CEL files relating to 10 different Affymetrix GeneChip platforms and involving nearly 1000 experiments. Our results confirm known effects (those due to the T7-primer and the formation of G-quadruplexes) but reveal other effects. We show that there can be huge variations from one experiment to another, and that there may also be sizeable disparities between batches within an experiment and between CEL files within a batch. © 2012 The Author(s)

Normalized Affymetrix expression data are biased by G-quadruplex formation

Probes with runs of four or more guanines (G-stacks) in their sequences can exhibit a level of hybridization that is unrelated to the expression levels of the mRNA that they are intended to measure. This is most likely caused by the formation of G-quadruplexes, where inter-probe guanines form Hoogsteen hydrogen bonds, which probes with G-stacks are capable of forming. We demonstrate that for a specific microarray data set using the Human HG-U133A Affymetrix GeneChip and RMA normalization there is significant bias in the expression levels, the fold change and the correlations between expression levels. These effects grow more pronounced as the number of G-stack probes in a probe set increases. Approximately 14 of the probe sets are directly affected. The analysis was repeated for a number of other normalization pipelines and two, FARMS and PLIER, minimized the bias to some extent. We estimate that ∼15 of the data sets deposited in the GEO database are susceptible to the effect. The inclusion of G-stack probes in the affected data sets can bias key parameters used in the selection and clustering of genes. The elimination of these probes from any analysis in such affected data sets outweighs the increase of noise in the signal. © 2011 The Author(s)