Showing papers by "University of Rennes published in 2006"

A comparison of classification techniques for the P300 Speller

Abstract: This study assesses the relative performance characteristics of five established classification techniques on data collected using the P300 Speller paradigm, originally described by Farwell and Donchin (1988 Electroenceph. Clin. Neurophysiol. 70 510). Four linear methods: Pearson's correlation method (PCM), Fisher's linear discriminant (FLD), stepwise linear discriminant analysis (SWLDA) and a linear support vector machine (LSVM); and one nonlinear method: Gaussian kernel support vector machine (GSVM), are compared for classifying offline data from eight users. The relative performance of the classifiers is evaluated, along with the practical concerns regarding the implementation of the respective methods. The results indicate that while all methods attained acceptable performance levels, SWLDA and FLD provide the best overall performance and implementation characteristics for practical classification of P300 Speller data.

Expression of cytochromes P450, conjugating enzymes and nuclear receptors in human hepatoma heparg cells

Abstract: Most human hepatocyte cell lines lack a substantial set of liver-specific functions, especially major cytochrome P450 (P450)-related enzyme activities, making them unrepresentative of in vivo hepatocytes. We have used the HepaRG cells, derived from a human hepatocellular carcinoma, which exhibit a high differentiation pattern after 2 weeks at confluency to determine whether they could mimic human hepatocytes for drug metabolism and toxicity studies. We show that when passaged at low density, these cells reversed to an undifferentiated morphology, actively divided, and, after having reached confluency, formed typical hepatocyte-like colonies surrounded by biliary epithelial-like cells. By contrast, when seeded at high density, hepatocyte-like clusters retained their typical differentiated morphology. Transcripts of various nuclear receptors (aryl hydrocarbon receptor, pregnane X receptor, constitutive androstane receptor, peroxisome proliferator-activated receptor alpha), P450s (CYP1A2, 2C9, 2D6, 2E1, 3A4), phase 2 enzymes (UGT1A1, GSTA1, GSTA4, GSTM1), and other liver-specific functions were estimated by reverse transcriptase-quantitative polymerase chain reaction and were found to be expressed, for most of them, at comparable levels in both confluent differentiated and high-density differentiated HepaRG cells and in cultured primary human hepatocytes. For several transcripts, the levels were strongly increased in the presence of 2% dimethyl sulfoxide. Measurement of basal activities of several P450s and their response to prototypical inducers as well as analysis of metabolic profiles and cytotoxicity of several compounds confirmed the functional resemblance of HepaRG cells to primary cultured human hepatocytes. In conclusion, HepaRG cells constitute the first human hepatoma cell line expressing high levels of the major P450s involved in xenobiotic metabolism and represent a reliable surrogate to human hepatocytes for drug metabolism and toxicity studies.

Eukaryotic control on bacterial cell cycle and differentiation in the Rhizobium-legume symbiosis

Abstract: Symbiosis between legumes and Rhizobium bacteria leads to the formation of root nodules where bacteria in the infected plant cells are converted into nitrogen-fixing bacteroids. Nodules with a persistent meristem are indeterminate, whereas nodules without meristem are determinate. The symbiotic plant cells in both nodule types are polyploid because of several cycles of endoreduplication (genome replication without mitosis and cytokinesis) and grow consequently to extreme sizes. Here we demonstrate that differentiation of bacteroids in indeterminate nodules of Medicago and related legumes from the galegoid clade shows remarkable similarity to host cell differentiation. During bacteroid maturation, repeated DNA replication without cytokinesis results in extensive amplification of the entire bacterial genome and elongation of bacteria. This finding reveals a positive correlation in prokaryotes between DNA content and cell size, similar to that in eukaryotes. These polyploid bacteroids are metabolically functional but display increased membrane permeability and are nonviable, because they lose their ability to resume growth. In contrast, bacteroids in determinate nodules of the nongalegoid legumes lotus and bean are comparable to free-living bacteria in their genomic DNA content, cell size, and viability. Using recombinant Rhizobium strains nodulating both legume types, we show that bacteroid differentiation is controlled by the host plant. Plant factors present in nodules of galegoid legumes but absent from nodules of nongalegoid legumes block bacterial cell division and trigger endoreduplication cycles, thereby forcing the endosymbionts toward a terminally differentiated state. Hence, Medicago and related legumes have evolved a mechanism to dominate the symbiosis.

Metal vinylidenes and allenylidenes in catalysis: applications in anti-Markovnikov additions to terminal alkynes and alkene metathesis.

Abstract: The involvement of a catalytic metal vinylidene species was proposed for the first time in 1986 to explain the regioselective formation of vinyl carbamates directly from terminal alkynes, carbon dioxide, and amines. Since this initial report, various metal vinylidenes and allenylidenes, which are key activation intermediates, have proved extremely useful for many alkyne transformations. They have contributed to the rational design of new catalytic reactions. This 20th anniversary is a suitable occasion to present the advancement of organometallic vinylidenes and allenylidenes in catalysis.

Ring-opening polymerization of lactide with group 3 metal complexes supported by dianionic alkoxy-amino-bisphenolate ligands: combining high activity, productivity, and selectivity.

Abstract: A series of new alkoxy-amino-bis(phenols) (H2L 1-6) has been synthesized by Mannich condensations of substituted phenols, formaldehyde, and amino ethers or diamines. The coordination properties of these dianionic ligands towards yttrium, lanthanum, and neodymium have been studied. The resulting Group 3 metal complexes have been used as initiators for the ring-opening polymerization of rac-lactide to provide poly(lactic acid)s (PLAs). The polymerizations are living, as evidenced by the narrow polydispersities of the isolated polymers, together with the linear natures of number average molecular weight versus conversion plots and monomer-to-catalyst ratios. Complex [Y(L6){N(SiHMe2)2}(THF)] (17) polymerized rac-lactide to heterotactic PLA (Pr = 0.90 at 20 degrees C) and meso-lactide to syndiotactic PLA (Pr = 0.75 at 20 degrees C). The in situ formation of [Y(L6)(OiPr)(THF)] (18) from 17 and 2-propanol resulted in narrower molecular weight distributions (PDI = 1.06). With complex 18, highly heterotactic PLAs with narrow molecular weight distributions were obtained with high activities and productivities at room temperature. The natures of the ligand substituents were shown to have a significant influence on the degree of control of the polymerizations, and in particular on the tacticity of the polymer.

Charge instability in quadrupolar chromophores: symmetry breaking and solvatochromism.

Abstract: We present a joint theoretical and experimental work aimed to understand the spectroscopic behavior of multipolar dyes of interest for nonlinear optics (NLO) applications. In particular, we focus on the occurrence of broken-symmetry states in quadrupolar organic dyes and their spectroscopic consequences. To gain a unified description, we have developed a model based on a few-state description of the charge-transfer processes characterizing the low-energy physics of these systems. The model takes into account the coupling between electrons and slow degrees of freedom, namely, molecular vibrations and polar solvation coordinates. We predict the occurrence of symmetry breaking in either the ground or first excited state. In this respect, quadrupolar chromophores are classified in three different classes, with distinctively different spectroscopic behavior. Cases of true and false symmetry breaking are discriminated and discussed by making resort to nonadiabatic calculations. The theoretical model is applied to three representative quadrupolar chromophores: their qualitatively different solvatochromic properties are connected to the presence or absence of broken-symmetry states and related to two-photon absorption (TPA) cross-sections. The proposed approach provides useful guidelines for the synthesis of dyes for TPA application and represents a general and unifying reference frame to understand energy-transfer processes in multipolar molecular systems, offering important clues to understand basic properties of materials of interest for NLO and energy-harvesting applications.

BSDE with quadratic growth and unbounded terminal value

Abstract: In this paper, we study the existence of solution to BSDE with quadratic growth and unbounded terminal value. The main idea consists in using a localization procedure together with a priori bounds.

The role of corticothalamic coupling in human temporal lobe epilepsy.

Abstract: The EEG activity of the thalamus and temporal lobe structures (hippocampus, entorhinal cortex and neocortex) was obtained using intracerebral recordings (stereoelectroencephalography, SEEG) performed in patients with TLE seizures undergoing pre-surgical evaluation. Synchrony was studied using a statistical measure of SEEG signal interdependencies (non-linear correlation). The results demonstrated an overall increase of synchrony between the thalamus and temporal lobe structures during seizures. Moreover, although there was great inter-individual variability, we found that values from seizure onset period were significantly higher than values from the background period (P = 0.001). Values at the end of seizure were significantly higher than values from the seizure onset (P < 0.0001). Several indices were also defined in order to correlate some clinical features to the degree of coupling between cortical structures and the thalamus. In patients with mesial TLE seizures, a correlation was found between the degree of thalamocortical synchrony and the presence of an early loss of consciousness but not with other clinical parameters. In addition, surgical prognosis seemed better in patients with low values of thalamocortical couplings at the seizure onset. This report demonstrates that the thalamus and remote cortical structures synchronize their activity during TLE seizures and suggest that the extension of the epileptogenic network to the thalamus is a potential important factor determining surgical prognosis.

Improved Signal-to-Noise Ratio Estimation for Speech Enhancement

Abstract: This paper addresses the problem of single-microphone speech enhancement in noisy environments. State-of-the-art short-time noise reduction techniques are most often expressed as a spectral gain depending on the signal-to-noise ratio (SNR). The well-known decision-directed (DD) approach drastically limits the level of musical noise, but the estimated a priori SNR is biased since it depends on the speech spectrum estimation in the previous frame. Therefore, the gain function matches the previous frame rather than the current one which degrades the noise reduction performance. The consequence of this bias is an annoying reverberation effect. We propose a method called two-step noise reduction (TSNR) technique which solves this problem while maintaining the benefits of the decision-directed approach. The estimation of the a priori SNR is refined by a second step to remove the bias of the DD approach, thus removing the reverberation effect. However, classic short-time noise reduction techniques, including TSNR, introduce harmonic distortion in enhanced speech because of the unreliability of estimators for small signal-to-noise ratios. This is mainly due to the difficult task of noise power spectrum density (PSD) estimation in single-microphone schemes. To overcome this problem, we propose a method called harmonic regeneration noise reduction (HRNR). A nonlinearity is used to regenerate the degraded harmonics of the distorted signal in an efficient way. The resulting artificial signal is produced in order to refine the a priori SNR used to compute a spectral gain able to preserve the speech harmonics. These methods are analyzed and objective and formal subjective test results between HRNR and TSNR techniques are provided. A significant improvement is brought by HRNR compared to TSNR thanks to the preservation of harmonics

Toward Functional π-Conjugated Organophosphorus Materials: Design of Phosphole-Based Oligomers for Electroluminescent Devices

Abstract: The photophysical, electrochemical, and optoelectronic properties of conjugated systems incorporating dibenzophosphole or phosphole moieties are described. Dibenzophosphole derivatives are not suitable materials for OLEDs due to their weak photoluminescence (PL) in the solid state and the instability of the devices. Variation of the substitution pattern of phospholes and chemical modification of their P atoms afford thermally stable derivatives, which are photo- and electroluminescent. Comparison of the optical properties of solution and thin film of thioxophospholes shows that these compounds do not form aggregates in the solid state. This property, which is also supported by an X-ray diffraction study of three novel derivatives, results in an enhancement of the fluorescence quantum yields in the solid state. In contrast, (phosphole)gold(I) complexes exhibit a broad emission in thin film, which is due to the formation of aggregates. Single- and multilayer OLEDs using these P derivatives as the emissive layer have been fabricated. The emission color of these devices and their performances vary with the nature of the P material. Interestingly, di(2-thienyl)thiooxophosphole is an efficient host for the red dopant DCJTB, and devices using the gold complexes have broad emission spectra.

Colloidal ZnO nanostructures and functional coatings: A survey

Abstract: The past research work devoted to ZnO nanocolloidal sol-gel route is reviewed. It highlights the cluster chemistry of alcoholic ZnAc2 solutions and the results of ZnO colloid growth investigations performed worldwide. Moreover, the role of doping and co-doping in the processing of functional ZnO coatings is discussed. The possibilities of tuning the optical properties are also reported with a particular attention to luminescence. The last part of this paper deals with electrical and photoelectrochemical properties of ZnO nanocrystals and their aggregates.

Linear and nonlinear causality between signals: methods, examples and neurophysiological applications

Abstract: In this paper, we will present and review the most usual methods to detect linear and nonlinear causality between signals: linear Granger causality test (Geweke in J Am Stat Assoc 77:304–313, 1982) extended to direct causality in multivariate case (LGC), directed coherence (DCOH, Saito and Harashima in Recent advances in EEG and EMG data processing, Elsevier, Amsterdam, 1981), partial directed coherence (PDC, Sameshima and Baccala 1999) and nonlinear Granger causality test of Baek and Brock (in Working Paper University of Iowa, 1992) extended to direct causality in multivariate case (partial nonlinear Granger causality, PNGC). All these methods are tested and compared on several ARX, Poisson and nonlinear models, and on neurophysiological data (depth EEG). The results show that LGC, DCOH and PDC are not very robust in relation to nonlinear linkages but they seem to correctly find linear linkages if only the autoregressive parts are nonlinear. PNGC is extremely dependent on the choice of parameters. Moreover, LGC and PNGC may give misleading results in the case of causality on a spectral band, which is illustrated by our neurophysiological database.

Synthesis, Crystal Structures, Linear and Nonlinear Optical Properties, and Theoretical Studies of (p‐R‐Phenyl)‐, (p‐R‐Phenylethynyl)‐, and (E)‐[2‐(p‐R‐Phenyl)ethenyl]dimesitylboranes and Related Compounds

Abstract: The (p-R-phenyl)dimesitylboranes (R=Me(2)N, MeO, MeS, Br, I), (p-R-phenylethynyl)dimesitylboranes (R=Me(2)N, MeO, MeS, H), (E)-[2-(p-R-phenyl)ethenyl]dimesitylboranes (R=Me(2)N, H(2)N, MeO, MeS, H, CN, NO(2)), (E)-[2-(2-thienyl)ethenyl]dimesitylborane, and (E)-[2-(o-carboranyl)ethenyl]dimesitylborane have been prepared through the reaction of the appropriate p-R-phenyl- and p-R-phenylethynyllithium reagents with dimesitylboron fluoride and by hydroboration of the appropriate p-R-phenylacetylene, 2-ethynylthiophene, and o-ethynylcarborane with dimesitylborane. Their UV/Vis absorption and emission spectra have been recorded in a range of solvents with the fluorescence maxima of the donor-substituted compounds in particular exhibiting large bathochromic shifts in highly polar solvents, indicative of charge transfer leading to large dipole moments in the excited state. The molecular structures of the (p-R-phenyl)dimesitylboranes (R=Me(2)N, MeO, MeS, Br, I), the (E)-[2-(p-R-phenyl)ethenyl]dimesitylboranes (R=Me(2)N, H(2)N MeO, MeS, H), (p-R-phenylethynyl)dimesitylborane (R=Me(2)N), and (E)-[2-(2-thienyl)ethenyl]dimesitylborane, which have been determined from single-crystal X-ray diffraction measurements, offer evidence of increased conjugation in the ground state with increased donor strength of the R substituent. Their first- and second-order molecular hyperpolarizabilities have been obtained from EFISH and THG measurements, the first-order hyperpolarizabilities being largest for the strongest R-substituent donors. AM1 calculations have been performed on these compounds, showing reasonable agreement with the experimentally obtained bond lengths and hyperpolarizabilities, as well as on several related hypothetical compounds containing multiple C==C bonds, most of which are proposed to have even larger hyperpolarizabilities.

Does subthalamic nucleus stimulation induce apathy in Parkinson's disease?

Abstract: Background Subthalamic Nucleus Deep Brain Stimulation (STN-DBS) has been shown to significantly improve motor symptoms in advanced Parkinson’s disease (PD). Only few studies, however, have focused on the non-motor effects of DBS.

Scattering-model-based speckle filtering of polarimetric SAR data

Abstract: A new concept in polarimetric synthetic aperture radar (POLSAR) speckle filtering that preserves the dominant scattering mechanism of each pixel is proposed in this paper. The basic principle is to select pixels of the same scattering characteristics to be included in the filtering process. To achieve this, the algorithm first applies the Freeman and Durden decomposition to separate pixels into three dominant scattering categories: surface, double bounce, and volume, and then unsupervised classification is applied. Speckle filtering is performed using the classification map as a mask. A single-look or multilook pixel centered in a 9 /spl times/ 9 window is filtered by including only pixels in the same and two neighboring classes from the same scattering category. This filter is effective in speckle reduction, while perfectly preserving strong point target signatures, and retains edges, linear, and curved features in the POLSAR data. The effect of speckle filtering on scattering characteristics, such as entropy, anisotropy, and alpha angle, will be discussed.

Climatic forcing of erosion, landscape, and tectonics in the Bhutan Himalayas

Abstract: A fundamental objective in studies of climate-erosion-tectonics coupling is to document convincing correlation between observable indicators of these processes on the scale of a mountain range. The eastern Himalayas are a unique range to quantify the contribution of tectonics and climate to long-term erosion rates, because uniform and steady tectonics have persisted for several million years, while monsoonal precipitation patterns have varied in space and time. Specifically, the rise of the Shillong plateau, the only orographic barrier in the Himalayan foreland, has reduced the mean annual precipitation downwind in the eastern Bhutan Himalaya at the Miocene-Pliocene transition. Apatite fission-track (AFT) analyses of 45 bedrock samples from an E-W transect along Bhutan indicate faster long-term erosion rates outside of the rain shadow in the west (1.0‐1.8 mm/yr) than inside of it in the east (0.55‐0.85 mm/yr). Furthermore, an AFT vertical profile in the latter segment reveals a deceleration in erosion rates sometime after 5.9 Ma. In this drier segment of Bhutan, there are remnants of a relict landscape formed under a wetter climate that has not yet equilibrated to the present climatic conditions. Uplift and preservation of the paleolandscape are a result of a climate-induced decrease in erosion rates, rather than of an increase in rock uplift rate. This study documents not only a compelling spatial correlation between long-term erosion and precipitation rates, but also a climatically driven erosion-rate change on the scale of the eastern Himalayas, a change that, in turn, likely influences that region’s recent tectonic evolution.

Time-Resolved in Situ Studies of Oxygen Intercalation into SrCoO2.5, Performed by Neutron Diffraction and X-ray Absorption Spectroscopy

Abstract: Electrochemical oxidation of the antiferromagnetically ordered SrCoO2.5, with brownmillerite-type structure, to the cubic ferromagnet SrCoO3, with perovskite structure, has been investigated in situ by neutron diffraction as well as by X-ray absorption fine structure (XAFS) spectroscopy in specially designed electrochemical cells. The neutron diffraction experiments were performed twice, using two different wavelengths (λ = 1.2921(2) and 4.74 A) in order to better discriminate structural and magnetic changes as functions of the charge transfer. From the neutron diffraction experiments, two intermediate phases, SrCoO2.75 and SrCoO2.82±0.07, were characterized. No superstructure reflections were observed for the corresponding SrCoO2.75 phase. Instead we observed here, for the first time, 3D oxygen ordering during an oxygen intercalation reaction, as established for SrCoO2.82±0.07, which can be described as a tetragonal unit cell, related to the perovskite cell by a ≈ 2(a√2) and c ≈ 2a. The structure of this...

Ionic liquid droplet as e-microreactor.

Abstract: A powerful approach combining a droplet-based, open digital microfluidic lab-on-a-chip using task-specific ionic liquids as soluble supports to perform solution-phase synthesis is reported as a new tool for chemical applications The negligible volatility of ionic liquids enables their use as stable droplet reactors on a chip surface under air The concept was validated with different ionic liquids and with a multicomponent reaction Indeed, we showed that different ionic liquids can be moved by electrowetting on dielectric (EWOD), and their displacement was compared with aqueous solutions Furthermore, we showed that mixing ionic liquids droplets, each containing a different reagent, in "open" systems is an efficient way of carrying supported organic synthesis This was applied to Grieco's tetrahydroquinolines synthesis with different reagents Analysis of the final product was performed off-line and on-line, and the results were compared with those obtained in a conventional reaction flask This technology opens the way to easy synthesis of minute amounts of compounds ad libitum without the use of complex, expensive, and bulky robots and allows complete automation of the process for embedded chemistry in a portable device It offers several advantages, including simplicity of use, flexibility, and scalability, and appears to be complementary to conventional microfluidic lab-on-a-chip devices usually based on continuous-flow in microchannels

Transcription in four dimensions: nuclear receptor-directed initiation of gene expression

Abstract: Regulated gene expression, achieved through the coordinated assembly of transcription factors, co-regulators and the basal transcription machinery on promoters, is an initial step in accomplishing cell specificity and homeostasis. Traditional models of transcriptional regulation tend to be static, although gene expression profiles change with time to adapt to developmental and environmental cues. Furthermore, biochemical and structural studies have determined that initiation of transcription progresses through a series of ordered events. By integrating time into the analysis of transcription, chromatin immunoprecipitation assays and live-cell imaging techniques have revealed the dynamic, cooperative, functionally redundant and cyclical nature of gene expression. In this review, we present a dynamic model of gene transcription that integrates data obtained by these two techniques.

Fast non local means denoising for 3d MR images

Abstract: One critical issue in the context of image restoration is the problem of noise removal while keeping the integrity of relevant image information Denoising is a crucial step to increase image conspicuity and to improve the performances of all the processings needed for quantitative imaging analysis The method proposed in this paper is based on an optimized version of the Non Local (NL) Means algorithm This approach uses the natural redundancy of information in image to remove the noise Tests were carried out on synthetic datasets and on real 3T MR images The results show that the NL-means approach outperforms other classical denoising methods, such as Anisotropic Diffusion Filter and Total Variation

The Mayer-Rokitansky-Küster-Hauser syndrome (congenital absence of uterus and vagina) – phenotypic manifestations and genetic approaches

Abstract: The Mayer-Rokitansky-Kuster-Hauser (MRKH) syndrome affects at least 1 out of 4500 women and has for a long time been considered as a sporadic anomaly. Congenital absence of upper vagina and uterus is the prime feature of the disease which, in addition, is often found associated with unilateral renal agenesis or adysplasia as well as skeletal malformations (MURCS association). The phenotypic manifestations of MRKH overlap various other syndromes or associations and thus require accurate delineation. Since MRKH manifests itself in males, the term GRES syndrome (Genital, Renal, Ear, Skeletal) might be more appropriate when applied to both sexes. The MRKH syndrome, when described in familial aggregates, seems to be transmitted as an autosomal dominant trait with an incomplete degree of penetrance and variable expressivity. This suggests the involvement of either mutations in a major developmental gene or a limited chromosomal deletion. Until recently progress in understanding the genetics of MRKH syndrome has been slow, however, now HOX genes have been shown to play key roles in body patterning and organogenesis, and in particular during genital tract development. Expression and/or function defects of one or several HOX genes may account for this syndrome.