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Search Results: 1 - 10 of 7754 matches for " Philippe Lamy "
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A review of software for microarray genotyping
Philippe Lamy, Jakob Grove, Carsten Wiuf
Human Genomics , 2011, DOI: 10.1186/1479-7364-5-4-304
Abstract: The use of microarrays and microarray technology in research is now more than 15 years old and has had a tremendous impact on many aspects of research. Suddenly, it became possible to profile and survey whole genomes and to compare genomes across individuals and species to an extent that was hardly possible before. The perception of the genome changed as genome-wide data became available to everyone.This review focuses narrowly on software used for genotyping of single nucleotide polymorphisms (SNPs) in connection with SNP microarrays (or 'arrays' for short). There are an estimated ten million or more SNPs in the human genome [1]. For each of these, there are three possible genotypes (assuming diploidy), AA, BB (homozygous) and AB (heterozygous), where A and B denote the two possible alleles. The first commercial SNP array was released in 1996 by Affymetrix (Santa Clara, CA) and targeted about 1,500 human SNPs,[2] a tiny fraction of all SNPs. Since then, many different manufacturers have developed microarrays for genome-wide genotyping, including Affymetrix, Agilent (Santa Clara, CA), Illumina (San Diego, CA) and Nimblegen (Madison, WI), with arrays designed for many different organisms.SNP arrays have found uses in many research areas and contexts -- for example, association mapping,[3] linkage disequilibrium mapping,[4] phasing,[5] inference on demography and ancestry,[6] evolution [7] and loss-of-heterozygosity analysis in cancer [8]. Early usage of SNP arrays sought to estimate loss of heterozygosity in cancer by comparing DNA from germline and tumour cells [9]. In addition, SNP arrays have been used to estimate copy numbers in cancers [10] (similar to the use of comparative genomic hybridisation [CGH] arrays) and copy number variants (CNVs) in populations [11]. The newest arrays from Affymetrix and Illumina both contain probes for CNVs and copy number polymorphisms (CNPs).Today, SNP microarrays are able to genotype more than a million SNPs simultaneously (Table
Normal subgroup generated by a plane polynomial automorphism
Jean-Philippe Furter,Stéphane Lamy
Mathematics , 2009,
Abstract: We study the normal subgroup generated by a non trivial element f in the group G of complex plane polynomial automorphisms having Jacobian determinant 1. On one hand if f has length at most 8 relatively to the classical amalgamated product structure of G, we prove that = G. On the other hand if f is a sufficiently generic element of even length at least 14, we prove that is a proper subgroup of G.
The evolution of plasma parameters on a coronal source surface at 2.3 Rs during solar minimum
Leonard Strachan,Alexander V. Panasyuk,John L. Kohl,Philippe Lamy
Physics , 2011, DOI: 10.1088/0004-637X/745/1/51
Abstract: We analyze data from the Solar and Heliospheric Observatory to produce global maps of coronal outflow velocities and densities in the regions where the solar wind is undergoing acceleration. The maps use UV and white light coronal data obtained from the Ultraviolet Coronagraph Spectrometer and the Large Angle Spectroscopic Coronagraph, respectively, and a Doppler dimming analysis to determine the mean outflow velocities. The outflow velocities are defined on a sphere at 2.3 Rs from Sun-center and are organized by Carrington Rotations during the solar minimum period at the start of solar cycle 23. We use the outflow velocity and density maps to show that while the solar minimum corona is relatively stable during its early stages, the shrinkage of the north polar hole in the later stages leads to changes in both the global areal expansion of the coronal hole and the derived internal flux tube expansion factors of the solar wind. The polar hole areal expansion factor and the flux tube expansion factors (between the coronal base and 2.3 Rs) start out as super-radial but then they become more nearly radial as the corona progresses away from solar minimum. The results also support the idea that the largest flux tube expansion factors are located near the coronal hole/streamer interface, at least during the deepest part of the solar minimum period.
The tame automorphism group of an affine quadric threefold acting on a square complex
Cinzia Bisi,Jean-Philippe Furter,Stéphane Lamy
Mathematics , 2013,
Abstract: We study the group Tame(SL$_2$) of tame automorphisms of a smooth affine 3-dimensional quadric, which we can view as the underlying variety of SL(2,$\mathbb{C}$). We construct a square complex on which the group admits a natural cocompact action, and we prove that the complex is CAT(0) and hyperbolic. We propose two applications of this construction: We show that any finite subgroup in Tame(SL$_2$) is linearizable, and that Tame(SL$_2$) satisfies the Tits alternative.
A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays
Philippe Lamy, Claus L Andersen, Lars Dyrskjot, Niels Torring, Carsten Wiuf
BMC Bioinformatics , 2007, DOI: 10.1186/1471-2105-8-434
Abstract: We show that our method is able to recover the underlying copy-number changes in simulated data sets with high accuracy (above 97.71%). Moreover, although the known copy-numbers could be well recovered in simulated cancer samples with more than 70% cancer cells (and less than 30% normal cells), we demonstrate that including the mixture proportion in the HMM increases the accuracy of the method. Finally, the method is tested on HapMap samples and on bladder and prostate cancer samples.The HMM method developed here uses the genotype calls of germline DNA and the allelic SNP intensities from the tumour DNA to estimate allelic copy-numbers (including changes) in the tumour. It differentiates between different events like uniparental disomy and allelic imbalances. Moreover, the HMM can estimate the mixture proportion, and thus inform about the purity of the tumour sample.Chromosomal abnormalities such as loss-of-heterozygosity (LOH) or genomic copy-number changes are frequent in tumour cells. LOH occurs when a heterozygous marker in germline DNA of an individual becomes homozygous in cancer DNA of the same individual. This event is the result of losing one allele of a chromosomal region while the other allele is retained, duplicated (uniparental disonomy), or multiplicated (uniparental polysomy). In the same way, chromosomal amplifications can be unbalanced (if only one allele of a chromosomal region is multiplicated) or balanced (if both alleles are multiplicated). Detecting chromosomal abnormalities is important in cancer research as it allows the discovery of chromosomal regions possibly harbouring cancer-related genes such as tumour suppressor genes or oncogenes. It may also be used to identify genomic markers (i.e. chromosomal abnormalities) that may distinguish between clinically important stages in the disease course, e.g. markers of metastasis or markers of treatment response.Single nucleotide polymorphisms (SNPs) account for most of the genetic variation in the
Using data mining techniques to explore physicians' therapeutic decisions when clinical guidelines do not provide recommendations: methods and example for type 2 diabetes
Massoud Toussi, Jean-Baptiste Lamy, Philippe Le Toumelin, Alain Venot
BMC Medical Informatics and Decision Making , 2009, DOI: 10.1186/1472-6947-9-28
Abstract: We analyzed the French national guidelines for the management of type 2 diabetes to identify clinical conditions that are not covered or those for which the guidelines do not provide recommendations. We extracted patient records corresponding to each clinical condition from a database of type 2 diabetic patients treated at Avicenne University Hospital of Bobigny, France. We explored physicians' prescriptions for each of these profiles using C5.0 decision-tree learning algorithm. We developed decision-trees for different levels of detail of the therapeutic decision, namely the type of treatment, the pharmaco-therapeutic class, the international non proprietary name, and the dose of each medication. We compared the rules generated with those added to the guidelines in a newer version, to examine their similarity.We extracted 27 rules from the analysis of a database of 463 patient records. Eleven rules were about the choice of the type of treatment and thirteen rules about the choice of the pharmaco-therapeutic class of each drug. For the choice of the international non proprietary name and the dose, we could extract only a few rules because the number of patient records was too low for these factors. The extracted rules showed similarities with those added to the newer version of the guidelines.Our method showed its usefulness for completing guidelines recommendations with rules learnt automatically from physicians' prescriptions. It could be used during the development of guidelines as a complementary source from practice-based knowledge. It can also be used as an evaluation tool for comparing a physician's therapeutic decisions with those recommended by a given set of clinical guidelines. The example we described showed that physician practice was in some ways ahead of the guideline.Clinical guidelines are useful decision support tools for physicians. Their purpose is to bring medical evidence to the point of practice. Physicians need to make clinical decisions base
The solar wind as seen by SOHO/SWAN since 1996: comparison with SOHO/LASCO C2 coronal densities
Rosine Lallement,Eric Quemerais,Philippe Lamy,Jean-Loup Bertaux,Stephane Ferron,Walter Schmidt
Physics , 2010,
Abstract: We update the SOHO/SWAN H Lyman-alpha brightness analysis to cover the 1996-2008 time interval. A forward model applied to the intensity maps provides the latitude and time dependence of the interstellar Hydrogen ionisation rate over more than a full solar cycle. The hydrogen ionisation, being almost entirely due to charge-exchange with solar wind ions, reflects closely the solar wind flux. Our results show that the solar wind latitudinal structure during the present solar minimum is strikingly different from the previous minimum, with a much wider slow solar wind equatorial belt which persists until at least the end of 2008. We compute absolute values of the in-ecliptic H ionisation rates using OMNI solar wind data and use them to calibrate our ionisation rates at all heliographic latitudes. We then compare the resulting fluxes with the synoptic LASCO/C2 electron densities at 6 solar radii. The two time-latitude patterns are strikingly similar over all the cycle. This comparison shows that densities at 6 solar radii can be used to infer the solar wind type close to its source, with high (resp. low) densities tracing the slow (resp. fast) solar wind, simply because the density reflects at which altitude occurs the acceleration. The comparison between the two minima suggests that the fast polar wind acceleration occurs at larger distance during the current minimum compared to the previous one. This difference, potentially linked to the magnetic field decrease or(and) the coronal temperature decrease should be reproduced by solar wind expansion models.
Similar origin for low- and high-albedo Jovian Trojans and Hilda asteroids ?
Micha?l Marsset,Pierre Vernazza,Florian Gourgeot,Christophe Dumas,Mirel Birlan,Philippe Lamy,Richard P. Binzel
Physics , 2014, DOI: 10.1051/0004-6361/201424105
Abstract: Hilda asteroids and Jupiter Trojans are two low-albedo (p$_{\rm v}$ ~ 0.07) populations for which the Nice model predicts an origin in the primordial Kuiper Belt region. However, recent surveys by WISE and the Spitzer Space Telescope (SST) have revealed that ~2% of these objects possess high albedos (p$_{\rm v}$ > 0.15), which might indicate interlopers - that is, objects not formed in the Kuiper Belt - among these two populations. Here, we report spectroscopic observations in the visible and/or near-infrared spectral ranges of twelve high-albedo (p$_{\rm v}$ > 0.15) Hilda asteroids and Jupiter Trojans. These twelve objects have spectral properties similar to those of the low- albedo population, which suggests a similar composition and hence a similar origin for low- and high-albedo Hilda asteroids and Jupiter Trojans. We therefore propose that most high albedos probably result from statistical bias or uncertainties that affect the WISE and SST measurements. However, some of the high albedos may be true and the outcome of some collision-induced resurfacing by a brighter material that could include water ice. Future work should attempt to investigate the nature of this supposedly bright material. The lack of interlopers in our sample allows us to set an upper limit of 0.4% at a confidence level of 99.7% on the abundance of interlopers with unexpected taxonomic classes (e.g., A-, S-, V-type asteroids) among these two populations.
Probing the Solar Wind Acceleration Region with the Sun--Grazing Comet C/2002 S2
Silvio Giordano,John C. Raymond,Philippe Lamy,Michael Uzzo,Danuta Dobrzycka
Physics , 2014, DOI: 10.1088/0004-637X/798/1/47
Abstract: Comet C/2002 S2, a member of the Kreutz family of Sungrazing comets, was discovered in white light images of the SOHO/LASCO coronagraph on 2002 September 18 and observed in \hi\, \lya\, emission by the SOHO/UVCS instrument at four different heights as it approached the Sun. The \hi\, \lya\, line profiles detected by UVCS are analyzed to determine the spectral parameters: line intensity, width and Doppler shift with respect to the coronal background. Two dimensional comet images of these parameters are reconstructed at the different heights. A novel aspect of the observations of this sungrazing comet data is that, whereas the emission from the most of the tail is blue--shifted, that along one edge of the tail is red--shifted. We attribute these shifts to a combination of solar wind speed and interaction with the magnetic field. In order to use the comet to probe the density, temperature and speed of the corona and solar wind through which it passes, as well as to determine the outgassing rate of the comet, we develop a Monte Carlo simulation of the \hi\, \lya\, emission of a comet moving through a coronal plasma. From the outgassing rate, we estimate a nucleus diameter of about 9 meters. This rate steadily increases as the comet approaches the Sun while the optical brightness decreases by more than a factor of ten and suddenly recovers. This indicates that the optical brightness is determined by the lifetimes of the grains, sodium atoms and molecules produced by the comet.
The variation of the solar diameter and irradiance : eclipse observation of July, 11, 2010
Koutchmy Serge,Bazin Cyril,Prado Jean-Yves,Lamy Philippe,Rocher Patrick
Physics , 2012,
Abstract: The variation of the solar diameter is the subject of hot debates due to the possible effect on Earth climate and also due to different interpretations of long period solar variabilities, including the total solar irradiance. We shortly review the topic and show that rather long term variations, corresponding to a length well over a a solar magnetic cycle, are interesting to consider. The very recently launched mission "Picard" is entirely devoted to the topic but will just permit a short term evaluation. At the time of the last total solar eclipse of 11/07/2010, several experiments were prepared to precisely measure the transit time of the Moon related to the precise value of the solar diameter. Preliminary results coming from the use of a specially designed CNES photometer, put on different atolls of the French Polynesia, are presented. In addition the results of new experiments devoted to fast observations of flash spectra, including their precise chronodating, are illustrated and discussed. A new definition of the edge of the Sun, free of spurious scattered light effects strongly affecting all out of eclipse observations, is emerging from these observations, in agreement with the most advanced attempts of modelling the outer layers of the photosphere. We also argue for a definite answer concerning the solar diameter measurement from eclipses based on a better precision of lunar profiles coming from lunar altimetry space experiments which will be possible in the following decades.
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