Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data

Motivation: The development of the omics technologies such as transcriptomics, proteomics and metabolomics has made possible the realization of systems biology studies where biological systems are interrogated at different levels of biochemical activity (gene expression, protein activity and/or metabolite concentration). An effective approach to the analysis of these complex datasets is the joined visualization of the disparate biomolecular data on the framework of known biological pathways

Preprocessing Argumentation Frameworks via Replacement Patterns

A fast-growing research direction in the study of formal argumentation is the development of practical systems for central reasoning problems underlying argumentation. In particular, numerous systems for abstract argumentation frameworks (AF solvers) are available today, covering several argumentation semantics and reasoning tasks. Instead of proposing another algorithmic approach for AF solving, we introduce in this paper distinct AF preprocessing techniques as a solver-independent approach to obtaining performance improvements of AF solvers. We establish a formal framework of replacement patterns to perform local simplifications that are faithful with respect to standard semantics for AFs. Moreover, we provide a collection of concrete replacement patterns. Towards potential applicability, we employ the patterns in a preliminary empirical evaluation of their influence on AF solver performance.Peer reviewe

Kondo Resonance in a Mesoscopic Ring Coupled to a Quantum Dot: Exact Results for the Aharonov-Bohm/Casher Effects

We study the persistent currents induced by both the Aharonov-Bohm and Aharonov-Casher effects in a one-dimensional mesoscopic ring coupled to a side-branch quantum dot at Kondo resonance. For privileged values of the Aharonov-Bohm-Casher fluxes, the problem can be mapped onto an integrable model, exactly solvable by a Bethe ansatz. In the case of a pure magnetic Aharonov-Bohm flux, we find that the presence of the quantum dot has no effect on the persistent current. In contrast, the Kondo resonance interferes with the spin-dependent Aharonov-Casher effect to induce a current which, in the strong-coupling limit, is independent of the number of electrons in the ring.Comment: Replaced with published version; 5 page

The Kondo Box: A Magnetic Impurity in an Ultrasmall Metallic Grain

We study the Kondo effect generated by a single magnetic impurity embedded in an ultrasmall metallic grain, to be called a ``Kondo box''. We find that the Kondo resonance is strongly affected when the mean level spacing in the grain becomes larger than the Kondo temperature, in a way that depends on the parity of the number of electrons on the grain. We show that the single-electron tunneling conductance through such a grain features Kondo-induced Fano-type resonances of measurable size, with an anomalous dependence on temperature and level spacing.Comment: 4 Latex pages, 4 figures, submitted to Phys. Rev. Let

Mesoscopic Kondo Effect in an Aharonov-Bohm Ring

An interacting quantum dot inserted in a mesoscopic ring is investigated. A variational ansatz is employed to describe the ground state of the system in the presence of the Aharonov-Bohm flux. It is shown that, for even number of electrons with the energy level spacing smaller than the Kondo temperature, the persistent current has a value similar to that of a perfect ring with the same radius. On the other hand, for a ring with odd number electrons, the persistent current is found to be strongly suppressed compared to that of an ideal ring, which implies the suppression of the Kondo-resonant transmission. Various aspects of the Kondo-assisted persistent current are discussed.Comment: 4 pages Revtex, 4 Postscript figures, final version to appear in Phys. Rev. Lett. 85, No.26 (Dec. 25, 2000

Chandra study of an overdensity of X-ray sources around two distant (z~0.5) clusters

We present results from a Chandra X-ray Observatory study of the field X-ray source populations in 4 different observations: two high-redshift (z~0.5) clusters of galaxies 3C295 and RXJ003033.2+261819; and two non-cluster fields with similar exposure time. Surprisingly, the 0.5-2 keV source surface densities (~900-1200 sources deg**-2 at a flux limit of 1.5x10**-15 erg cm**-2s**-1) measured in an ~8'x8' area surrounding each cluster exceed by a factor of ~2 the value expected on the basis of the ROSAT and Chandra logN-logS, with a significance of ~2 sigma each, or ~3.5 sigma when the 2 fields are combined (i.e. a probability to be a statistical fluctuation of <1% and <0.04%, respectively). The same analysis performed on the non-cluster fields and on the outer chips of the cluster fields does NOT show evidence of such an excess. In both cluster fields, the summed 0.5-10 keV spectrum of the detected objects is well fitted by a power-law with Gamma~1.7 similar to AGNs and shows no sign of intrinsic absorption. The few (~10 out of 35) optical identifications available to date confirm that most of them are, as expected, AGNs but the number of redshifts available is too small to allow conclusions on their nature. We discuss possible interpretations of the overdensity in terms of: a statistical variation of Cosmic Background sources; a concentration of AGNs and/or powerful starburst galaxies associated with the clusters; and g ravitational lensing of background QSO's by the galaxy clusters. All explanations are however difficult to reconcile with the large number of excess sources detected. Deeper X-ray observations and more redshifts measurements are clearly required to settle the issue.Comment: 22 LateX pages (including Tables and Figures), uses psfig.sty and emulateapj.sty. Accepted for publication in Astrophysical Journa

Spectroscopic analysis of finite size effects around a Kondo quantum dot

We consider a simple setup in which a small quantum dot is strongly connected to a finite size box. This box can be either a metallic box or a finite size quantum wire.The formation of the Kondo screening cloud in the box strongly depends on the ratio between the Kondo temperature and the box level spacing. By weakly connecting two metallic reservoirs to the quantum dot, a detailed spectroscopic analysis can be performed. Since the transport channels and the screening channels are almost decoupled, such a setup allows an easier access to the measure of finite-size effects associated with the finite extension of the Kondo cloud.Comment: contribution to Les Houches proceeding, ``Quantum magnetism'' 200

Kondo screening cloud effects in mesoscopic devices

We study how finite size effects may appear when a quantum dot in the Kondo Coulomb blockade regime is embedded into a mesoscopic device with finite wires. These finite size effects appear when the size of the mesoscopic device containing the quantum dot is of the order of the size of Kondo cloud and affect all thermodynamic and transport properties of the Kondo quantum dot. We also generalize our results to the experimentally relevant case where the wires contain several transverse modes/channels. Our results are based on perturbation theory, Fermi liquid theory and slave boson mean field theory.Comment: 19 pages, 9 figure

NO synthase-generated NO acts downstream of auxin in regulating Fe-deficiency-induced root branching that enhances Fe-deficiency tolerance in tomato plants

In response to Fe-deficiency, various dicots increase their root branching which contributes to the enhancement of ferric-chelate reductase activity. Whether this Fe-deficiency-induced response eventually enhances the ability of the plant to tolerate Fe-deficiency or not is still unclear and evidence is also scarce about the signals triggering it. In this study, it was found that the SPAD-chlorophyll meter values of newly developed leaves of four tomato (Solanum lycocarpum) lines, namely line227/1 and Roza and their two reciprocal F1 hybrid lines, were positively correlated with their root branching under Fe-deficient conditions. It indicates that Fe-deficiency-induced root branching is critical for plant tolerance to Fe-deficiency. In another tomato line, Micro-Tom, the increased root branching in Fe-deficient plants was accompanied by the elevation of endogenous auxin and nitric oxide (NO) levels, and was suppressed either by the auxin transport inhibitors NPA and TIBA or the NO scavenger cPTIO. On the other hand, root branching in Fe-sufficient plants was induced either by the auxin analogues NAA and 2,4-D or the NO donors NONOate or SNP. Further, in Fe-deficient plants, NONOate restored the NPA-terminated root branching, but NAA did not affect the cPTIO-terminated root branching. Fe-deficiency-induced root branching was inhibited by the NO-synthase (NOS) inhibitor L-NAME, but was not affected by the nitrate reductase (NR) inhibitor NH4+, tungstate or glycine. Taking all of these findings together, a novel function and signalling pathway of Fe-deficiency-induced root branching is presented where NOS-generated rather than NR-generated NO acts downstream of auxin in regulating this Fe-deficiency-induced response, which enhances the plant tolerance to Fe-deficiency