Networks from gene expression time series: characterization of correlation patterns

This paper describes characteristic features of networks reconstructed from gene expression time series data. Several null models are considered in order to discriminate between informations embedded in the network that are related to real data, and features that are due to the method used for network reconstruction (time correlation).Comment: 10 pages, 3 BMP figures, 1 Table. To appear in Int. J. Bif. Chaos, July 2007, Volume 17, Issue

Conditions chimiques contrôlant l'atténuation naturelle des BTEX et solvants chlorés : un état des connaissances

L'atténuation naturelle des BTEX (Benzène, Toluène, Ethyl-benzène, Xylène) et des solvants chlorés est de plus en plus étudiée en raison des potentialités offertes par cette technique de gestion. Cet article, après avoir présenté les aspects abiotiques de l'atténuation détaille les conditions chimiques nécessaires à la réalisation des réactions de biodégradation des polluants organiques. Les aspects thermodynamiques sont abordés afin de décliner les réactions possibles et celles qui ne le sont pas selon les environnements chimiques. La dégradation des BTEX est focalisée sur le benzène, produit le plus toxique et le moins dégradable sur la plupart des sites. Les détails de la dégradation du benzène sur le terrain sont analysés dans la littérature et leur comparaison permet de décrire les mécanismes responsables de celle-ci. Dans le cas des solvants chlorés, l'attention est portée sur le TCE (Trichloréthylène), produit le plus couramment rencontré sur les sites pollués. Une mise en parallèle des évolutions de teneurs observées et des conditions chimiques locales permet de mettre en évidence les conditions nécessaires à la dégradation du TCE, et de ses congénères, ainsi que les cinétiques de dégradation dans différentes conditions. La mise en évidence du rôle prépondérant des conditions chimiques conduit à remettre en cause l'utilisation répandue des constantes de dégradation du premier ordre et donne des pistes pour les modèles nécessaires à une prédiction plus fine de l'atténuation naturelle.The increasing reliance on natural attenuation in dealing with contaminated sites in North America is the consequence of:1. the extremely long duration and high cost of aquifer rehabilitation by classical methods, and 2. the discovery of natural biodegradation in many different situations. However, the use of this management technique is questionable, as intrinsic biodegradation is highly dependent on chemical conditions and particularly on redox equilibria. This paper describes the role of these chemical conditions on BTEX and chlorinated solvent attenuation and, by analyzing the current research, we try to define current limits of the predictability of natural attenuation in field conditions.Natural attenuation is defined as the sum of processes able to decrease the pollutant concentration at a sampling point in an aquifer. Several physical processes such as dispersion, retardation and solubility play a role in natural attenuation. However, only biodegradation can significantly reduce the overall amount of pollutants in an aquifer, thereby allowing the pollutant concentration to reach the low levels that are required by regulations. The physical processes cited above can be modelled at a site to account for their effect, but the main focus is on biodegradation.A detailed analysis of the basic thermodynamics of redox reactions involved in biodegradation is necessary to describe the reactions that can potentially occur. A rough analysis shows that BTEX is mainly degraded by oxidation and therefore is degraded more efficiently in aerobic media. However, toluene (and sometime ethylbenzene and xylene) can be degraded by fermentation and thus degradation occurs even in methanogenic conditions. In contrast, chlorinated solvents are degraded mainly by reduction, with the exception of c-DCE (cis-dichloroethylene) and VC (vinyl chloride), which are degraded by reduction and oxidation, thus having two degradative pathways. An overall comparison of reaction rates obtained from laboratory and field experiments clearly demonstrates that under field conditions the supply of redox reactants is a limiting factor in the reaction kinetics.Degradation of BTEX under field conditions has been widely documented, and toluene ethylbenzene and xylene degradation occurred in almost all chemical environments. The most persistent product observed in almost all the studies was benzene. Due to its persistence, and also its carcinogenic and toxic properties, we focussed on the results obtained for benzene. The kinetic constant for degradation of benzene under most field conditions ranged from almost no degradation in the reduced parts of the plume to fast degradation at the oxygenated border. Degradation under nitrate, methane or iron reducing conditions was almost insignificant, but degradation did occur under sulphate reducing conditions. A detailed analysis of the data on benzene degradation under sulphate reducing conditions showed that there is a competition between bacterial populations for electron acceptors. Benzene is degraded only if electron acceptors are in excess and if no other easily degradable carbon source is present.The analysis of experimental data on chlorinated solvents is more difficult because fewer studies exist and the degradation processes are slower and more complex. Significant intrinsic biodegradation occurs mainly by reductive dechlorination, with co-metabolism being important only under modified conditions. In the field, PCE (perchloroethylene) and TCE degradation occurred only under methanogenic and sulphate reducing conditions, while c-DCE was degraded in oxygenated media and finally VC degradation occurred under almost all redox potentials. The kinetics of degradation were slow, with half-lives in the order of 1 to several years. It was shown that the variability of such constants was quite high within the same site. This variability could be explained by the availability of reducing species, particularly hydrogen. By comparing the estimated and real length of solvent plumes it was shown that biodegradation was more important than transport for the sites with the most reducing conditions. At other sites, the necessity of both methanogenic conditions and a sufficient pool of electron donors in the aquifer was demonstrated. The high toxicity of VC, when compared to TCE, was of lower concern since it was shown that the plume size was equal to or smaller than that of TCE. This was due to a fast degradation kinetics for VC observed under aerobic conditions.In conclusion, the controversy surrounding the use of models based on first-order degradation constants arose because of the strong dependence of this constant on prevailing chemical conditions. If the target at risk is far away, use of the statistics on plume length existing for BTEX seems to be sufficient. However, when the benzene content is high and the target at risk is close, there is a need to predict the size of the reduced plume. The approach is the same for more substituted chlorinated solvents. The most important data, which are often missing, are the amount of total 'easily' degradable carbon (i.e. BTEX, short chain acids or alcohols) delivered by the source that will generate the reduced plume. In order to achieve a more precise prediction, models incorporating the whole redox chain need to be developed and tested against existing field data

The Kondo Effect in the Unitary Limit

We observe a strong Kondo effect in a semiconductor quantum dot when a small magnetic field is applied. The Coulomb blockade for electron tunneling is overcome completely by the Kondo effect and the conductance reaches the unitary-limit value. We compare the experimental Kondo temperature with the theoretical predictions for the spin-1/2 Anderson impurity model. Excellent agreement is found throughout the Kondo regime. Phase coherence is preserved when a Kondo quantum dot is included in one of the arms of an Aharonov-Bohm ring structure and the phase behavior differs from previous results on a non-Kondo dot.Comment: 10 page

Nongalvanic thermometry for ultracold two-dimensional electron domains

Measuring the temperature of a two-dimensional electron gas at temperatures of a few mK is a challenging issue, which standard thermometry schemes may fail to tackle. We propose and analyze a nongalvanic thermometer, based on a quantum point contact and quantum dot, which delivers virtually no power to the electron system to be measured.Comment: 5 pages, 3 figure

Single-electron tunneling in InP nanowires

We report on the fabrication and electrical characterization of field-effect devices based on wire-shaped InP crystals grown from Au catalyst particles by a vapor-liquid-solid process. Our InP wires are n-type doped with diameters in the 40-55 nm range and lengths of several microns. After being deposited on an oxidized Si substrate, wires are contacted individually via e-beam fabricated Ti/Al electrodes. We obtain contact resistances as low as ~10 kOhm, with minor temperature dependence. The distance between the electrodes varies between 0.2 and 2 micron. The electron density in the wires is changed with a back gate. Low-temperature transport measurements show Coulomb-blockade behavior with single-electron charging energies of ~1 meV. We also demonstrate energy quantization resulting from the confinement in the wire.Comment: 4 pages, 3 figure

Pauli spin blockade in CMOS double quantum dot devices

Silicon quantum dots are attractive candidates for the development of scalable, spin-based qubits. Pauli spin blockade in double quantum dots provides an efficient, temperature independent mechanism for qubit readout. Here we report on transport experiments in double gate nanowire transistors issued from a CMOS process on 300 mm silicon-on-insulator wafers. At low temperature the devices behave as two few-electron quantum dots in series. We observe signatures of Pauli spin blockade with a singlet-triplet splitting ranging from 0.3 to 1.3 meV. Magneto-transport measurements show that transitions which conserve spin are shown to be magnetic-field independent up to B = 6 T.Comment: 5 pages , 4 figure

A speaker adaptive DNN training approach for speaker-independent acoustic inversion

We address the speaker-independent acoustic inversion (AI) problem, also referred to as acoustic-to-articulatory mapping. The scarce availability of multi-speaker articulatory data makes it difficult to learn a mapping which generalizes from a limited number of training speakers and reliably reconstructs the articulatory movements of unseen speakers. In this paper, we propose a Multi-task Learning (MTL)-based approach that explicitly separates the modeling of each training speaker AI peculiarities from the modeling of AI characteristics that are shared by all speakers. Our approach stems from the well known Regularized MTL approach and extends it to feed-forward deep neural networks (DNNs). Given multiple training speakers, we learn for each an acoustic-to-articulatory mapping represented by a DNN. Then, through an iterative procedure, we search for a canonical speaker-independent DNN that is "similar" to all speaker-dependent DNNs. The degree of similarity is controlled by a regularization parameter. We report experiments on the University of Wisconsin X-ray Microbeam Database under different training/testing experimental settings. The results obtained indicate that our MTL-trained canonical DNN largely outperforms a standardly trained (i.e., single task learning-based) speaker independent DNN