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Search Results: 1 - 10 of 470 matches for " Hugues Sicotte "
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Angular Momemtum and Large-Scale Magnetic Field in Textures Seeded Models
Hugues Sicotte
Physics , 1994,
Abstract: We start by pedagigically reviewing the problem of large scale magnetic fields. We explain the acquisition of angular momentum in the general context of Dark Matter models and we use this result to derive a dynamical mechanism for magnetic field generation. This mechanism does not produce any magnetic field for standard CDM, but it does for a large class of other models. We apply this mechanism in the context of the texture scenario of large-scale structure formation. Resulting constraints on the texture scenario and other models are discussed.
SNPPicker: High quality tag SNP selection across multiple populations
Hugues Sicotte, David N Rider, Gregory A Poland, Neelam Dhiman, Jean-Pierre A Kocher
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-129
Abstract: SNPPicker optimizes the selection of tag SNPs from common bin-tagging programs to design custom genotyping panels. The application uses a multi-step search strategy in combination with a statistical model to maximize the genotyping success of the selected tag SNPs. User preference toward functional SNPs can also be taken into account as secondary criteria. SNPPicker can also optimize tag SNP selection for a panel tagging multiple populations. SNPPicker can optimize custom genotyping panels including all the assay-specific constraints of Illumina's GoldenGate and Infinium assays.A new application has been developed to maximize the success of custom multi-population genotyping panels. SNPPicker also takes into account user constraints including options for controlling runtime. Perl Scripts, Java source code and executables are available under an open source license for download at http://mayoresearch.mayo.edu/mayo/research/biostat/software.cfm webciteDespite the commercial availability of affordable genome wide genotyping panels, custom-designed SNPs panels are frequently used for high resolution genotyping studies focusing on specific genes or chromosomal regions. The design of custom SNP panels for genotyping studies aims to minimize the number of SNPs to genotype while maximizing the information content of the panel.The number of SNPs to genotype can be minimized by taking advantage of linkage disequilibrium (LD) between SNP alleles in the same population. A number of algorithms are available to assess LD between SNPs and select tag SNPs representative of groups of correlated SNPs called bins [1-5]. These bin-tagging algorithms use population specific sets of reference genotypes to compute bins and tag SNPs and report all possible tag SNP candidates for each bin. Note that Tagger, which reports the best tag SNP, also provides an exportable table of r2 values between SNPs that can be used to compute all tag SNPs candidates. Since these tag SNPs candidates are theore
IP-FCM Measures Physiologic Protein-Protein Interactions Modulated by Signal Transduction and Small-Molecule Drug Inhibition
Stephen E. P. Smith, Anya T. Bida, Tessa R. Davis, Hugues Sicotte, Steven E. Patterson, Diana Gil, Adam G. Schrum
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0045722
Abstract: Protein-protein interactions (PPI) mediate the formation of intermolecular networks that control biological signaling. For this reason, PPIs are of outstanding interest in pharmacology, as they display high specificity and may represent a vast pool of potentially druggable targets. However, the study of physiologic PPIs can be limited by conventional assays that often have large sample requirements and relatively low sensitivity. Here, we build on a novel method, immunoprecipitation detected by flow cytometry (IP-FCM), to assess PPI modulation during either signal transduction or pharmacologic inhibition by two different classes of small-molecule compounds. First, we showed that IP-FCM can detect statistically significant differences in samples possessing a defined PPI change as low as 10%. This sensitivity allowed IP-FCM to detect a PPI that increases transiently during T cell signaling, the antigen-inducible interaction between ZAP70 and the T cell antigen receptor (TCR)/CD3 complex. In contrast, IP-FCM detected no ZAP70 recruitment when T cells were stimulated with antigen in the presence of the src-family kinase inhibitor, PP2. Further, we tested whether IP-FCM possessed sufficient sensitivity to detect the effect of a second, rare class of compounds called SMIPPI (small-molecule inhibitor of PPI). We found that the first-generation non-optimized SMIPPI, Ro-26-4550, inhibited the IL-2:CD25 interaction detected by IP-FCM. This inhibition was detectable using either a recombinant CD25-Fc chimera or physiologic full-length CD25 captured from T cell lysates. Thus, we demonstrate that IP-FCM is a sensitive tool for measuring physiologic PPIs that are modulated by signal transduction and pharmacologic inhibition.
GLOSSI: a method to assess the association of genetic loci-sets with complex diseases
High-Seng Chai, Hugues Sicotte, Kent R Bailey, Stephen T Turner, Yan W Asmann, Jean-Pierre A Kocher
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-102
Abstract: In a simulation study, GLOSSI showed sufficient power to detect loci-sets with less than 10% of SNPs having moderate-to-large effect sizes and intermediate minor allele frequency values. When applied to a biological dataset where no single SNP-association was found in a previous study, GLOSSI was able to identify several loci-sets that are significantly related to blood pressure response to an antihypertensive drug.GLOSSI is valuable for association of SNPs at multiple genetic loci with complex disease phenotypes. In contrast to methods based on the Kolmogorov-Smirnov statistic, the approach is parametric and only utilizes information from within the interrogated loci-set. It properly accounts for dependency among SNPs and allows the testing of loci-sets of any size.The genetic component of complex disorders such as hypertension, Parkinson's disease, cancer, and diabetes is believed to result from the compound effect of multiple DNA variations in different chromosomal regions. In this context, the paradigm of searching across the genome for univariate single nucleotide polymorphism (SNP) associations may not be the most appropriate or realistic strategy. A preferred approach would consider the effects of multiple SNPs jointly. Unstructured enumeration of all possible combinations of SNPs for association is computationally demanding, if not infeasible. Variable selection needs to be performed before testing such multi-locus effects due to the discrepancy between numbers of SNPs and sample size in a typical genome-wide association study. In the current work, we focused the proposed association analyses of SNPs belonging to genes that are biologically related. The criteria for grouping SNPs can be based on biological theory, expert opinion, or localization in genes that control the same functional process or are co-regulated. Such groups of SNPs will be referred to as loci-sets. We have developed a method called GLOSSI (Gene-loci Set Analysis) to score loci-sets as a f
La matérialité décadente et l'économie: entre la fascination et la ruse
Geneviève Sicotte
Nordlit : Tidsskrift i litteratur og kultur , 2012,
Abstract: Decadent literature is characterized by numerous descriptions of material luxury, whether in decoration, clothing and trinkets. This treatment of materiality has generally been interpreted by critics as a literary refusal of the bourgeois world, which was seen to be obsessed with productive work. But the evolution of the bourgeoisie in the last decades of the 19th century leads to new types of consumption precisely based on the useless and the unnecessary. It must then be understood that the literary representation of luxury is in part influenced by the behavior of the rising haute bourgeoisie of the time. Therefore, the decadent materialism could be seen not as a transgressive figure, but as a figure of disengagement, strongly influenced by the social codes of its time. However, in the most interesting literary texts, the representation of beautiful objects is problematized, marked by negativity, the gift and the play on the decorative status of the text. This representation sets up the terms of a real economic counter-discourse.
La matérialité décadente et l'économie: entre la fascination et la ruse
Geneviève Sicotte
Nordlit : Tidsskrift i litteratur og kultur , 2012,
Abstract: Decadent literature is characterized by numerous descriptions of material luxury, whether in decoration, clothing and trinkets. This treatment of materiality has generally been interpreted by critics as a literary refusal of the bourgeois world, which was seen to be obsessed with productive work. But the evolution of the bourgeoisie in the last decades of the 19th century leads to new types of consumption precisely based on the useless and the unnecessary. It must then be understood that the literary representation of luxury is in part influenced by the behavior of the rising haute bourgeoisie of the time. Therefore, the decadent materialism could be seen not as a transgressive figure, but as a figure of disengagement, strongly influenced by the social codes of its time. However, in the most interesting literary texts, the representation of beautiful objects is problematized, marked by negativity, the gift and the play on the decorative status of the text. This representation sets up the terms of a real economic counter-discourse.
équilibres problématiques et utopies optimistes. Le marché et le don de Vigny à Baudelaire
Geneviève Sicotte
COnTEXTES : Revue de Sociologie de la Littérature , 2009, DOI: 10.4000/contextes.4265
Abstract: L’univers des arts a ceci de particulier au point de vue des échanges qu’il est un système mixte fondé sur la coexistence du marché et du don. La relative mixité des échanges est en fait une donnée de base de tous les secteurs des sociétés modernes, mais en ce qui concerne le domaine esthétique, elle para t particulièrement forte, occupant de manière inextricablement liée tous les termes de la relation. En effet, dans la production des uvres surviennent tout à la fois et simultanément de...
Genome-Wide Transcriptional Profiling Reveals MicroRNA-Correlated Genes and Biological Processes in Human Lymphoblastoid Cell Lines
Liang Wang, Ann L. Oberg, Yan W. Asmann, Hugues Sicotte, Shannon K. McDonnell, Shaun M. Riska, Wanguo Liu, Clifford J. Steer, Subbaya Subramanian, Julie M. Cunningham, James R. Cerhan, Stephen N. Thibodeau
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0005878
Abstract: Background Expression level of many genes shows abundant natural variation in human populations. The variations in gene expression are believed to contribute to phenotypic differences. Emerging evidence has shown that microRNAs (miRNAs) are one of the key regulators of gene expression. However, past studies have focused on the miRNA target genes and used loss- or gain-of-function approach that may not reflect natural association between miRNA and mRNAs. Methodology/Principal Findings To examine miRNA regulatory effect on global gene expression under endogenous condition, we performed pair-wise correlation coefficient analysis on expression levels of 366 miRNAs and 14,174 messenger RNAs (mRNAs) in 90 immortalized lymphoblastoid cell lines, and observed significant correlations between the two species of RNA transcripts. We identified a total of 7,207 significantly correlated miRNA-mRNA pairs (false discovery rate q<0.01). Of those, 4,085 pairs showed positive correlations while 3,122 pairs showed negative correlations. Gene ontology analyses on the miRNA-correlated genes revealed significant enrichments in several biological processes related to cell cycle, cell communication and signal transduction. Individually, each of three miRNAs (miR-331, -98 and -33b) demonstrated significant correlation with the genes in cell cycle-related biological processes, which is consistent with important role of miRNAs in cell cycle regulation. Conclusions/Significance This study demonstrates feasibility of using naturally expressed transcript profiles to identify endogenous correlation between miRNA and miRNA. By applying this genome-wide approach, we have identified thousands of miRNA-correlated genes and revealed potential role of miRNAs in several important cellular functions. The study results along with accompanying data sets will provide a wealth of high-throughput data to further evaluate the miRNA-regulated genes and eventually in phenotypic variations of human populations.
Anomalous diffusion due to hindering by mobile obstacles undergoing Brownian motion or Orstein-Ulhenbeck processes
Hugues Berry,Hugues Chaté
Quantitative Biology , 2011,
Abstract: In vivo measurements of the passive movements of biomolecules or vesicles in cells consistently report ''anomalous diffusion'', where mean-squared displacements scale as a power law of time with exponent $\alpha< 1$ (subdiffusion). While the detailed mechanisms causing such behaviors are not always elucidated, movement hindrance by obstacles is often invoked. However, our understanding of how hindered diffusion leads to subdiffusion is based on diffusion amidst randomly-located \textit{immobile} obstacles. Here, we have used Monte-Carlo simulations to investigate transient subdiffusion due to \textit{mobile} obstacles with various modes of mobility. Our simulations confirm that the anomalous regimes rapidly disappear when the obstacles move by Brownian motion. By contrast, mobile obstacles with more confined displacements, e.g. Orstein-Ulhenbeck motion, are shown to preserve subdiffusive regimes. The mean-squared displacement of tracked protein displays convincing power-laws with anomalous exponent $\alpha$ that varies with the density of OU obstacles or the relaxation time-scale of the OU process. In particular, some of the values we observed are significantly below the universal value predicted for immobile obstacles in 2d. Therefore, our results show that subdiffusion due to mobile obstacles with OU-type of motion may account for the large variation range exhibited by experimental measurements in living cells and may explain that some experimental estimates are below the universal value predicted for immobile obstacles.
Enseignement précoce : Sept constats pour répondre aux besoins des enfants
Hugues Denisot
Synergies Pologne , 2005,
Abstract:
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