Automatic formal derivation of the oscillation condition

International audienceThe behavior of a quartz crystal oscillator can be described by a nonlinear characteristic polynomial whose coefficients are function of the circuit parameters. Solving the polynomial in the frequency domain leads to the steady state oscillation amplitude and frequency. In the time domain, it gives the oscillator signal transient. Deriving the characteristic polynomial from the circuit description involves lengthy and tedious algebraic calculations if they are performed by hand. They may be now performed by using the symbolic manipulation capabilities of commercially available softwares. However, symbolic analysis using brute force method inevitably leads to an explosion of terms in equations. The paper will present a fully automatic method for generating the coding of an oscillator characteristic polynomial directly from the SPICE description netlist. The code thus generated is eventually compiled and takes place in an oscillator library. Then it is linked with the numerical main program that solves the polynomials. Solutions to overcome problems related to automatic symbolic calculations are presented and discussed. It is shown that the method used leads to concise and efficient code

Am and pm noise analysis in quartz crystal oscillators: symbolic calculus approach

International audienceIncreasing performance of quartz crystal oscillators as well as predictability requirements when developing the devices need accurate analysis of noise sources. Our work is devoted to understand how an oscillator reacts to additive noise of an element in the electronic circuit. Up to now, oscillator designers often refer to the well-known Leeson's model to explain the shape of phase noise spectral density. This physical model only allows one to obtain the global phase noise spectrum. By considering each noise source individually, we can obtain the comparative contribution of the sources. Then AM and PM noise source spectra can be related to the circuit architecture. The influence of an individual noise source can be obtained from the differential equation describing the oscillator behavior. Nevertheless, setup of the differential equation from the inspection of the circuit involves lengthy and tedious algebraic calculations almost impossible to achieve by hand. By using symbolic calculation capability of formal calculus programs, it is possible to automatically derive the differential equation of the oscillator including noise sources from a SPICE netlist description of the circuit. The resulting expressions can be edited under the form of high level language code (Fortran, C, ...) which is eventually compiled and linked with the numerical programs calculating the noise spectra. This paper presents the method to construct the differential equations in a fully automatic way regardless of the studied oscillator circuit

Histone Deacetylase Inhibitors Up-Regulate the Expression of Tight Junction Proteins

Abstract Histone deacetylase (HDAC) inhibitors promote cell maturation, differentiation, and apoptosis through changes in gene expression. Differentiated epithelial cells are characterized by apical tight junctions (TJ), which play a role in cell-cell adhesion, polarity, and the permeability barrier function of epithelia. The relationship between cellular differentiation and expression of TJ-associated proteins is not known. Here, we investigated whether HDAC inhibitors affect the expression of TJ proteins in cultured cells by immunoblotting, immunofluorescence, and quantitative real-time, reverse transcription-PCR. We find that the HDAC inhibitor sodium butyrate significantly up-regulates the protein levels of cingulin, ZO-1, and ZO-2 in Rat-1 fibroblasts, cingulin in COS-7 cells, and cingulin and occludin in HeLa cells. Levels of mRNA for cingulin, ZO-1, and ZO-2 are also increased in sodium butyrate–treated Rat-1 fibroblasts. Up-regulation of cingulin is reversible and dose dependent and requires de novo protein synthesis and protein kinase activity, because it is inhibited by cycloheximide and by the protein kinase inhibitor H-7. Up-regulation of TJ proteins by sodium butyrate is linked to the ability of sodium butyrate to inhibit HDAC activity, because suberoylanilide hydroxamic acid, a HDAC inhibitor of a different structural class, also up-regulates cingulin, ZO-1, and ZO-2 expression in Rat-1 fibroblasts. These results indicate that cellular differentiation correlates with kinase-dependent up-regulation of the expression of specific TJ proteins

Analyse différentielle de puces à ADN. Comparaison entre méthodes wrapper et filter.

13Dans le cadre de données d'expression génétique, nous nous intéressons aux méthodes qui permettent d'identifier les gènes significativement différentiellement exprimés entre deux situations biologiques. Nous allons comparer une méthode classique d'analyse par tests d'hypothèses à des méthodes d'analyse différentielle par régression régularisée. La difficulté de ce genre de jeu de données est la profusion de variables (les gènes) pour assez peu d'individus (les profils d'expression). La stratégie usuelle consiste à mettre en oeuvre autant de tests qu'il y a de variables et de considérer que les variables principales sont celles qui ont la « meilleure »p-value. Une stratégie alternative pourrait consister à choisir de classer les variables non plus en fonction de leur significativité (pour un test), mais plutôt de le classer suivant leur poids dans le modèle régularisé obtenu. Dans la bibliographie, les premières méthodes sont dites filter1, les deuxièmes sont plutôt dites wrapper2. Un bon aperçu de ce que sont les méthodes wrapper et filter est donné dans [9]. Le cadre ressemble à celui de l'apprentissage supervisé, car on dispose de profils d'expression géniques pour si possible l'ensemble du génome d'un organisme, chaque puce appartenant à une classe- situation biologique particulière (par exemple malade vs sain). L'implémentation des méthodes évoquées dans ce rapport a été effectuée sous R [16]

Functional Redundancy Patterns Reveal Non-Random Assembly Rules in a Species-Rich Marine Assemblage

The relationship between species and the functional diversity of assemblages is fundamental in ecology because it contains key information on functional redundancy, and functionally redundant ecosystems are thought to be more resilient, resistant and stable. However, this relationship is poorly understood and undocumented for species-rich coastal marine ecosystems. Here, we used underwater visual censuses to examine the patterns of functional redundancy for one of the most diverse vertebrate assemblages, the coral reef fishes of New Caledonia, South Pacific. First, we found that the relationship between functional and species diversity displayed a non-asymptotic power-shaped curve, implying that rare functions and species mainly occur in highly diverse assemblages. Second, we showed that the distribution of species amongst possible functions was significantly different from a random distribution up to a threshold of ∼90 species/transect. Redundancy patterns for each function further revealed that some functions displayed fast rates of increase in redundancy at low species diversity, whereas others were only becoming redundant past a certain threshold. This suggested non-random assembly rules and the existence of some primordial functions that would need to be fulfilled in priority so that coral reef fish assemblages can gain a basic ecological structure. Last, we found little effect of habitat on the shape of the functional-species diversity relationship and on the redundancy of functions, although habitat is known to largely determine assemblage characteristics such as species composition, biomass, and abundance. Our study shows that low functional redundancy is characteristic of this highly diverse fish assemblage, and, therefore, that even species-rich ecosystems such as coral reefs may be vulnerable to the removal of a few keystone species

3D-CE5.h: Merge candidate list for disparity compensated prediction

HEVC implements a candidate vector list for merge and skip modes. The construction of this list has been extensively studied in the JCT-VC group (see for instance JCTVC-G039). It has been shown in JCTVC-I0293 that it is possible to improve the HEVC coding performance by adding in the merge list copies of the first candidate shifted by an arbitrary offset. The same basis is considered in this document and applied to disparity compensation. A gain of 0.3 % is obtained on average on side views

CE5.h related: Merge candidate list extension for disparity compensated prediction

HEVC implements a candidate vector list for merge and skip modes. The construction of this list has been extensively studied in the JCT-VC group (see for instance JCTVC-G039). It has been shown in JCTVC-I0293 that it is possible to improve the HEVC coding performance by adding in the merge list copies of the first candidate shifted by an arbitrary offset. The same basis is considered in this document and applied to disparity compensation. A gain of 0.4 % is obtained on average on side views

Neurogenin2 Directs Granule Neuroblast Production and Amplification while NeuroD1 Specifies Neuronal Fate during Hippocampal Neurogenesis

The specification and differentiation of dentate gyrus granule neurons in the hippocampus require temporally and spatially coordinated actions of both intrinsic and extrinsic molecules. The basic helix-loop-helix transcription factor Neurogenin2 (Ngn2) and NeuroD1 are key regulators in these processes. Based on existing classification, we analyzed the molecular events occurring during hippocampal neurogenesis, primarily focusing on juvenile animals. We found that Ngn2 is transiently expressed by late type-2a amplifying progenitors. The Ngn2 progenies mature into hippocampal granule neurons. Interestingly, the loss of Ngn2 at early stages of development leads to a robust reduction in neurogenesis, but does not disturb granule neuron maturation per se. We found that the role of Ngn2 is to maintain progenitors in an undifferentiated state, allowing them to amplify prior to their maturation into granule neurons upon NeuroD1 induction. When we overexpressed Ngn2 and NeuroD1 in vivo, we found NeuroD1 to exhibit a more pronounced neuron-inductive effect, leading to granule neuron commitment, than that displayed by Ngn2. Finally, we observed that all markers expressed during the transcriptional control of hippocampal neurogenesis in rodents are also present in the human hippocampus. Taken together, we demonstrate a critical role of for Ngn2 and NeuroD1 in controlling neuronal commitment and hippocampal granule neuroblast formation, both during embryonic development and in post-natal hippocampal granule neurogenesis

Livrable D3.3 of the PERSEE project : 2D coding tools

49Livrable D3.3 du projet ANR PERSEECe rapport a été réalisé dans le cadre du projet ANR PERSEE (n° ANR-09-BLAN-0170). Exactement il correspond au livrable D3.3 du projet. Son titre : 2D coding tool