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Chinese Annals of Mathematics,Series B 2017年第2期38卷 579-590页

作者： frank MERLE Universitéde Cergy-pontoise MathématiquesCNRSCNRSF-95000 Cergy-PontoiseFrance Institut des HautesEtudes Scientifiques 35 Route de Chartres91440 Bures-sur-YvetteFrance

The author considers mass critical nonlinear Schrdinger and Korteweg-de Vries equations. A review on results related to the blow-up of solution of these equations is given.

关键词： Dispersive nonlinear PDE, Criticality, Asymptotics, Blow-up, Globalsolution, Soliton

Generation of Synthetic Transcriptome Data with Defined Statistical Properties for the Development and Testing of New Analysis Methods

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Genomics, Proteomics & Bioinformatics 2007年第1期5卷 45-52页

作者： Guillaume Brysbaert Sebastian Noth Arndt Benecke Systems Epigenomics Group Institut des Hautes Etudes Scientifiques/Institut de Recherches InterdisciplinairesCNRS/INSERM 91440 Bures sur Yvette France

We have previously developed a combined signal/variance distribution model that accounts for the particular statistical properties of datasets generated on the Applied Biosystems AB1700 transcriptome system. Here we show that this model can be efficiently used to generate synthetic datasets with statistical properties virtually identical to those of the actual data by aid of the JAVA application *** creator 1.0 that we have developed. The fundamentally different structure of AB1700 transcriptome profiles requires re-evaluation, adaptation, or even redevelopment of many of the standard microarray analysis methods in order to avoid misinterpretation of the data on the one hand, and to draw full benefit from their increased specificity and sensitivity on the other hand. Our composite data model and the *** creator 1.0 application thereby not only present proof of the correctness of our parameter estimation, but also provide a tool for the generation of synthetic test data that will be useful for further development and testing of analysis methods.

关键词： transcriptome microarray analysis signal/variance distribution distribution modeling parameter approximation synthetic data generation

High-Sensitivity Transcriptome Data Structure and Implications for Analysis and Biologic Interpretation

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Genomics, Proteomics & Bioinformatics 2006年第4期4卷 212-229页

作者： Sebastian Noth Guillaume Brysbaert franois-Xavier Pellay Arndt Benecke Systems Epigenomics Group Institut des Hautes Etudes Scientifiques/Institut de Recherches InterdisciplinairesCNRS/INSERM91440 Bures sur YvetteFrance.

Novel microarray technologies such as the AB1700 platform from Applied Biosysterns promise significant increases in the signal dynamic range and a higher sensitivity for weakly expressed transcripts. We have compared a representative set of AB1700 data with a similarly representative Affymetrix HG-U133A dataset. The AB1700 design extends the signal dynamic detection range at the lower bound by one order of magnitude. The lognormal signal distribution profiles of these highsensitivity data need to be represented by two independent distributions. The additional second distribution covers those transcripts that would have gone undetected using the Affymetrix technology. The signal-dependent variance distribution in the AB1700 data is a non-trivial function of signal intensity, describable using a composite function. The drastically different structure of these highsensitivity transcriptome profiles requires adaptation or even redevelopment of the standard microarray analysis methods. Based on the statistical properties, we have derived a signal variance distribution model for AB1700 data that is necessary for such development. Interestingly, the dual lognormal distribution observed in the AB1700 data reflects two fundamentally different biologic mechanisms of transcription initiation.

关键词： transcriptome microarray analysis signal/variance distribution distribution modeling parameter approximation stochastic transcription initiation

Normalization Using Weighted Negative Second Order Exponential Error functions(NeONORM) Provides Robustness Against Asym-metries in Comparative Transcriptome Profiles and Avoids false Calls

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Genomics, Proteomics & Bioinformatics 2006年第2期4卷 90-109页

作者： Sebastian Noth Guillaume Brysbaert Arndt Benecke Systems Epigenomics Group Institut des Hautes Etudes Scientifiques/Institut de Recherches InterdisciplinairesCNRS/INSERM 91440 Bures sur Yvette France.

Studies on high-throughput global gene expression using microarray technology have generated ever larger amounts of systematic transcriptome data. A major challenge in exploiting these heterogeneous datasets is how to normalize the expression profiles by inter-assay methods. Different non-linear and linear normalization methods have been developed, which essentially rely on the hypothesis that the true or perceived logarithmic fold-change distributions between two different assays are symmetric in nature. However, asymmetric gene expression changes are frequently observed, leading to suboptimal normalization results and in consequence potentially to thousands of false calls. Therefore, we have specifically investigated asymmetric comparative transcriptome profiles and developed the normalization using weighted negative second order exponential error functions （NeONORM） for robust and global inter-assay normalization. NeONORM efficiently damps true gene regulatory events in order to minimize their misleading impact on the norrealization process. We evaluated NeONORM＇s applicability using artificial and true experimental datasets, both of which demonstrated that NeONORM could be systematically applied to inter-assay and inter-condition comparisons.

关键词： microarray statistical analysis normalization asymmetry robustness

Measuring Policy Performance in Online Pricing with Offline Data:Worst-case Perspective and Bayesian Perspective

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Journal of Systems Science and Systems Engineering 2023年第3期32卷 352-371页

作者： Yue Wang Zeyu Zheng Department of Computational Medicine University of CaliforniaLos AngelesCA 90095USA Institut des Hautes Etudes Scientifiques Bures-sur-YvetteEssonne 91440France Department of Industrial Engineering and Operations Research University of CaliforniaBerkeleyCA 94720USA

The problems of online pricing with offline data,among other similar online decision making with offline data problems,aim at designing and evaluating online pricing policies in presence of a certain amount of existing offline *** evaluate pricing policies when offline data are available,the decision maker can either position herself at the time point when the offline data are already observed and viewed as deterministic,or at the time point when the offline data are not yet generated and viewed as *** write a framework to discuss how and why these two different positions are relevant to online policy evaluations,from a worst-case perspective and from a Bayesian *** then use a simple online pricing setting with offline data to illustrate the constructions of optimal policies for these two approaches and discuss their differences,especially whether we can decompose the searching for the optimal policy into independent subproblems and optimize separately,and whether there exists a deterministic optimal policy.

关键词： Online pricing offline data performance measure worst-case approach Bayesian approach

EXPERIMENTAL TESTS Of GRAVITATIONAL THEORY

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Chinese Physics C 2016年第10期40卷 349-354页

作者： T. Damour IHES Bures-sur-Yvette France

Einstein＇s General Relativity, the current ＂standard＂ theory of gravitation, describes gravity as a universal deformation of the Minkowski metric：

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CDS:A fold-change Based Statistical Test for Concomitant Identification of Distinctness and Similarity in Gene Expression Analysis

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Genomics,Proteomics & Bioinformatics 2012年第3期10卷 127-135页

作者： Nicolas Tchitchek José felipe Golib Dzib Brice Targat Sebastian Noth Arndt Benecke Annick Lesne Institut des Hautes Etudes Scientifiques Bures-sur-Yvette 91440France Centre National de la Recherche Scientifique USR3078Bures-sur-Yvette 91440France Laboratoire de Physique Théorique de la Matière Condensée CNRS UMR7600Université Pierre et Marie Curie-Paris 6Paris 75005France

The problem of identifying differential activity such as in gene expression is a major defeat in biostatistics and *** important,however much less frequently studied,is the question of similar activity from one biological condition to *** foldchange,or ratio,is usually considered a relevant criterion for stating difference and similarity between ***,no statistical method for concomitant evaluation of similarity and distinctness currently exists for biological *** microarray,digital PCR(dPCR),and Next-Generation Sequencing(NGS) technologies frequently provide a means of coefficient of variation estimation for individual *** fold-change,and by making the assumption that measurements are normally distributed with known variances,we designed a novel statistical test that allows us to detect concomitantly,thus using the same formalism,differentially and similarly expressed genes(http://***).Given two sets of gene measurements in different biological conditions,the probabilities of making type I and type II errors in stating that a gene is differentially or similarly expressed from one condition to the other can be ***,a confidence interval for the fold-change can be ***,we demonstrate that the assumption of normality can be relaxed to consider arbitrary distributions *** Concomitant evaluation of Distinctness and Similarity(CDS) statistical test correctly estimates similarities and differences between measurements of gene *** implementation,being time and memory efficient,allows the use of the CDS test in high-throughput data analysis such as microarray,dPCR,and NGS ***,the CDS test can be applied to the comparison of single measurements(N:1) provided the variance(or coefficient of variation) of the signals is known,making CDS a valuable tool also in biomedical analysis where typically a single measurement per

关键词： Statistical test fold-change Distinctness Similarity Gene expression Single measurement Patient study

Quality Assessment of Transcriptome Data Using Intrinsic Statistical Properties

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Genomics, Proteomics & Bioinformatics 2010年第1期8卷 57-71页

作者： Guillaume Brysbaert franois-Xavier Pellay Sebastian Noth Arndt Benecke Institut des Hautes études Scientifiques & Institut de Recherche Interdisciplinaire(CNRS USR3078 Université de Lille1)91440 Bures-sur-YvetteFrance

In view of potential application to biomedical diagnosis, tight transcriptome data quality control is compulsory. Usually, quality control is achieved using labeling and hybridization controls added at different stages throughout the processing of the biologic RNA samples. These control measures, however, only reflect the performance of the individual technical manipulations during the entire process and have no bearing as to the continued integrity of the RNA sample itself. Here we demonstrate that intrinsic statistical properties of the resulting transcriptome data signal and signal-variance distributions and their invariance can be identified independently of the animal species studied and the labeling protocol used. from these invariant properties we have developed a data model, the pa- rameters of which can be estimatei：l from individual experiments and used to compute relative quality measures based on similarity with large reference datasets. These quality measures add supplementary, non-redundant in- formation to standard quality control estimates based on spike-in and hybridization controls, and are exploitable in data analysis. A software application for analyzing datasets as well as a reference dataset for AB 1700 arrays are provided. They should allow AB 1700 users to easily integrate this method into their analysis pipeline, and might instigate similar developments for other transcriptome platforms.

关键词： transcriptome microarray quality control distribution properties statistics software

Plasmonics of regular shape particles,a simple group theory approach

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Nano Research 2020年第6期13卷 1597-1603页

作者： Sarra Mitiche Sylvie Marguet fabrice Charra Ludovic Douillard Université Paris-Saclay CEACNRSSPECF-91191Gif sur YvetteFrance Université Paris-Saclay CEACNRSNIMBEF-91191Gif sur YvetteFrance

A simple hand calculation method based on group theory is proposed to predict the near field maps of finite metallic nanoparticles(MNP)of canonical geometries:prism,cube,hexagon,disk,sphere,*** to low order localized surface plasmon resonance *** this article,we report the principles of the group theory approach and demonstrate,through several examples,the general character of the group theory method which can be applied to describe the plasmonic response of particles of finite or infinite symmetry point *** validation is achieved by collection of high-resolution subwavelength near-field maps by photoemission electron microscopy(PEEM)on a representative set of Au colloidal particles exhibiting either finite(hexagon)or infinite(disk,sphere)symmetry point groups.

关键词： surface plasmon resonance group theory hexagon disk sphere photoemission electron microscopy(PEEM)

tuning the properties of confined water in standard and lybrid nanotubes： An infrared spectroscopic study

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Nano Research 2018年第9期11卷 4759-4773页

作者： Yuanyuan Liao Pierre Picot Maxime Laine Jean-Blaise Brubach Pascale Roy Antoine Thill Sophie Le Caer LIONS NIMBE UMR 3685 CEA CNRS Universite Paris-Saclay CEA Saclay Bt. 546 F-91191 Gif-sur-Yvette Cedex France Synchrotron SOLEIL AILES Beamline L'Orme des Mefisier Saint-Aubin BP 48 F-91192 Gif-sur-Yvette Cedex France

Imogolite is a natural nanotubular aluminum silicate clay mineral found in volcanic soils. Its well-defined, tunable structure makes it a good candidate for studying water confinement in a one-dimensional （1D） structure. Water confinement in self-sustaining imogolite thin films was studied using infrared spectroscopy. Two types of synthetic imogolites were investigated： pristine imogolite （IMO-OH） with a hydrophilic inner surface covered with Si-OH groups and hybrid imogolite （IMO-CH3） with a hydrophobic inner surface covered with Si-CH3 groups. Both imogolites have an outer surface that is covered with Al-OH groups. Infrared spectra were recorded in the 20-4,000 cm^-1 spectral range as a function of relative humidity. Analysis of the O-H stretching band provides information on the H bonding of confined water molecules inside and outside the IMO-OH tubes. The scenario for water filling as a function of relative humidity is determined for both systems. Adsorption begins in the IMO-OH tubes at the lowest relative humidity （〈 10%）. The inner surface of the tubes is first covered with water molecules; then, the central part of the tubes is filled, leading to very strong H bonds and a structured spectrum. In contrast, the H bonds of water adsorbed on the outer surfaces of these tubes are weaker. A different scenario is observed for water inside IMO-CH3： Weakly H-bonded water molecules are present, similar to that observed in carbon nanotubes. Water confinement in imogolites is governed by the hydrophilicity of the inner walls. At similar partial pressures, the degree of H bonding depends on the interactions between water and the nanotube wall.

关键词： imogolite nanotubes confinement infrared spectroscopy water isotherms hydrophilic hydrophobic