Application of simulated annealing to the biclustering of gene expression data.

In a gene expression data matrix, a bicluster is a submatrix of genes and conditions that exhibits a high correlation of expression activity across both rows and columns. The problem of locating the most significant bicluster has been shown to be NP-complete. Heuristic approaches such as Cheng and Church's greedy node deletion algorithm have been previously employed. It is to be expected that stochastic search techniques such as evolutionary algorithms or simulated annealing might improve upon such greedy techniques. In this paper we show that an approach based on simulated annealing is well suited to this problem, and we present a comparative evaluation of simulated annealing and node deletion on a variety of datasets. We show that simulated annealing discovers more significant biclusters in many cases. Furthermore, we also test the ability of our technique to locate biologically verifiable biclusters within an annotated set of genes.     

Service level negotiation andcops-sls protocol

The Internet is a set of interconnected domains in which different QoS technologies can be deployed. The dynamic provision of end-to-end QoS over heterogeneousip networks assumes the negotiation of mutually acceptablesla. This paper presents the concept of intra-, inter- and multiple-domain service level negotiation using thecops-sls protocol. The negotiation process gives different parties in the negotiation the ability to agree upon the service level that a data stream can obtain, along with the permissible pricing of the service.     

Generalized nonlinear Schrödinger equation for dispersive susceptibility and permeability: application to negative index materials

A new generalized nonlinear Schr?dinger equation describing the propagation of ultrashort pulses in bulk media exhibiting frequency dependent dielectric susceptibility and magnetic permeability is derived and used to characterize wave propagation in a negative index material. The equation has new features that are distinct from ordinary materials (mu=1): the linear and nonlinear coefficients can be tailored through the linear properties of the medium to attain any combination of signs unachievable in ordinary matter, with significant potential to realize a wide class of solitary waves.     

Are the Elements Elementary? Nineteenth-Century Chemical and Spectroscopical Answers

We analyze the role and influence of a tradition of research linked to the concept of primary matter in nineteenth-century studies on the nature of the elements.The suggestion of William Prout (1785-1850) in 1816 that the atomic weights of pure chemical elements are whole numbers and multiples of the atomic weight of hydrogen, taken as unity, was met with serious confutations,which in turn prompted several attempts to save Prouts hypothesis.We discuss these attempts in detail and the objections raised against them, for instance by Dmitry Ivanovich Mendeleev (1834-1907). We pay particular attention to the use of spectroscopy as a method for proving the existence of elementary forms of matter inside atoms. Leaders in this field of research were two English scientists, the astrophysicist Norman Lockyer (1836-1920) and the chemist William Crookes (1832- 1919). Both of their approaches involved the idea of primary matter. However, while Crookess approach proved to be incorrect, Lockyers ideas survived for several years and supported the discovery of the electron by J.J.Thomson (1856-1940).     

Ultrasonic characterization of heavy metal TeO2–WO3–PbO glasses below room temperature

The longitudinal ultrasonic attenuation measurements have been made using pulse echo method at fundamental frequencies of 2, 4, 6 and 8 MHz in 20WO₃–(80−x) TeO₂–xPbO ternary tellurite glasses (x=10, 12.5, 15, 17.5 and 20 mol%) in the temperature range 160–280 K. The results showed the presence of a broad peak which shifts to higher temperature with increasing frequency. The ultrasonic attenuation peaks suggest that the experimental behavior is controlled by thermally activated structural relaxations. The internal friction, acoustic activation energy, deformation potential, relaxation strength, number of loss centers and density of state have been calculated both as a function of temperature and PbO content. The acoustic activation energy was found to decrease from 0.156 to 0.135 eV with the increase of PbO content. The results showed that both the number of loss centers and their activation energy decrease with the atomic ring size. An increase in the density of state is observed with addition of PbO content at the same frequency in the whole range of temperature which is associated with structural units formed when PbO is added.     

Water-Assisted Concerted Proton-Electron Transfer at Co(II)-Aquo Sites in Polyoxotungstates With Photogenerated RuIII(bpy)33+ Oxidant

The cobalt substituted polyoxotungstate [Co₆(H₂O)₂(α-B-PW₉O₃₄)₂(PW₆O₂₆)]¹⁷⁻ ( Co6 ) displays fast electron transfer (ET) kinetics to photogenerated Ru^III(bpy)₃³⁺, 4 to 5 orders of magnitude faster than the corresponding ET observed for cobalt oxide nanoparticles. Mechanistic evidence has been acquired indicating that: (i) the one-electron oxidation of Co6 involves Co(II) aquo or Co(II) hydroxo groups (abbreviated as Co6(II) −OH ₂ and Co6(II) −OH, respectively, whose speciation in aqueous solution is associated to a pK_a of 7.6), and generates a Co(III)−OH moiety ( Co6(III) −OH), as proven by transient absorption spectroscopy; (ii) at pH>pK_a, the Co6(II) −OH→Ru^III(bpy)₃³⁺ ET occurs via bimolecular kinetics, with a rate constant k close to the diffusion limit and dependent on the ionic strength of the medium, consistent with reaction between charged species; (iii) at pH <pK_a, the process involves Co6(II) − OH₂ → Co6(III)−OH transformation and proceeds via a multiple-site, concerted proton electron transfer (CPET) where water assists the transfer of the proton, as proven by the absence of effect of buffer base concentrations on the rate of the ET and by a H/D kinetic isotope in a range of 1.2–1.4. The reactivity of water is ascribed to its organization on the surface of the polyanionic scaffold through hydrogen bond networking involving the Co(II)−OH₂ group.     

Effects of Spiro-Cyclohexane Substitution of Nitroxyl Biradicals on Dynamic Nuclear Polarization

Spiro-substituted nitroxyl biradicals are widely used as reagents for dynamic nuclear polarization (DNP), which is especially important for biopolymer research. The main criterion for their applicability as polarizing agents is the value of the spin–spin exchange interaction parameter (J), which can vary considerably when different couplers are employed that link the radical moieties. This paper describes a study on biradicals, with a ferrocene-1,1′-diyl-substituted 1,3-diazetidine-2,4-diimine coupler, that have never been used before as DNP agents. We observed a substantial difference in the temperature dependence between Electron Paramagnetic Resonance (EPR) spectra of biradicals carrying either methyl or spirocyclohexane substituents and explain the difference using Density Functional Theory (DFT) calculation results. It was shown that the replacement of methyl groups by spirocycles near the N-O group leads to an increase in the contribution of conformers having J ≈ 0. The DNP gain observed for the biradicals with methyl substituents is three times higher than that for the spiro-substituted nitroxyl biradicals and is inversely proportional to the contribution of biradicals manifesting the negligible exchange interaction. The effects of nucleophiles and substituents in the nitroxide biradicals on the ring-opening reaction of 1,3-diazetidine and the influence of the ring opening on the exchange interaction were also investigated. It was found that in contrast to the methyl-substituted nitroxide biradical (where we observed the ring-opening reaction upon the addition of amines), the ring opening does not occur in the spiro-substituted biradical owing to a steric barrier created by the bulky cyclohexyl substituents.     

A Versatile Long‐Wavelength‐Absorbing Scaffold for Eu‐Based Responsive Probes

Coumarin‐sensitized, long‐wavelength‐absorbing luminescent Eu^III‐complexes have been synthesized and characterized. The lanthanide binding site consists of a cyclen‐based chelating framework that is attached through a short linker to a 7‐hydroxycoumarin, a 7‐B(OH)₂‐coumarin, a 7‐O‐(4‐pinacolatoboronbenzyl)‐coumarin or a 7‐O‐(4‐methoxybenzyl)‐coumarin. The syntheses are straightforward, use readily available building blocks, and proceed through a small number of high‐yielding steps. The sensitivity of coumarin photophysics to the 7‐substituent enables modulation of the antenna‐absorption properties, and thus the lanthanide excitation spectrum. Reactions of the boronate‐based functionalities (cages) with H₂O₂ yielded the corresponding 7‐hydroxycoumarin species. The same species was produced with peroxynitrite in a ×10⁶–10⁷‐fold faster reaction. Both reactions resulted in the emergence of a strong ≈407 nm excitation band, with concomitant decrease of the 366 nm band of the caged probe. In aqueous solution the methoxybenzyl caged Eu‐complex was quenched by ONOO^?. We have shown that preliminary screening of simple coumarin‐based antennae through UV/Vis absorption spectroscopy is possible as the changes in absorption profile translate with good fidelity to changes in Eu^III‐excitation profile in the fully elaborated complex. Taken together, our results show that the 7‐hydroxycoumarin antenna is a viable scaffold for the construction of turn‐on and ratiometric luminescent probes.     

Rationalization of the behavior of M2(CH3CS2)4I (M = Ni,Pt) chains at room temperature from periodic density functional theory and ab initio cluster calculations

The electrical conductivities and plausible charge‐ordering states in the room temperature (r.t.) phase for MMX chains [Ni₂(dta)₄I]_∞ and [Pt₂(dta)₄I]_∞ (dta = CH₃CS) have been analyzed with periodic density functional theory (DFT) and correlated ab initio calculations combined with the effective Hamiltonian theory. Periodic DFT calculations show a more delocalized nature of the ground state in [Pt₂(dta)₄I]_∞ compared to [Ni₂(dta)₄I]_∞, which features a rather large energy gap between the occupied and empty bands, and charge polarized dimer units. A larger electrical conductivity for the Pt chain can be expected, especially because the Fermi level lies within a band with contributions from Pt and I orbitals. Electronic structure parameters extracted from ab initio cluster calculations show that the large difference between the observed conductivities at 300 K for Ni and Pt compounds, of 3 orders of magnitude, cannot be explained from the parameters extracted from an embedded M₂(dta)₄I₂ dimer fragment alone. When tetramer fragments are considered, we observe that the interdimer transfer integral (t) between neighboring M₂ units connected by an iodine atom at correlated level is comparable in both chains. On the other hand, the energy to transfer an electron from a dimer to the neighboring one (Coulomb repulsion U) is three times larger in the Ni compound with respect to the Pt chain, in line with the poor conductivity of the former. The electronic structure of the M₄(dta)₈I₃ fragment points to an alternate charge‐polarization state for Ni and an average valence state for Pt when the r.t. X‐ray structure is considered. © 2012 Wiley Periodicals, Inc.     

Insights into the Intraspecific Variability of the above and Belowground Emissions of Volatile Organic Compounds in Tomato

The in-vivo monitoring of volatile organic compound (VOC) emissions is a potential non-invasive tool in plant protection, especially in greenhouse cultivation. We studied VOC production from above and belowground organs of the eight parents of the Multi-Parent Advanced Generation Intercross population (MAGIC) tomato population, which exhibits a high genetic variability, in order to obtain more insight into the variability of constitutive VOC emissions from tomato plants under stress-free conditions. Foliage emissions were composed of terpenes, the majority of which were also stored in the leaves. Foliage emissions were very low, partly light-dependent, and differed significantly among genotypes, both in quantity and quality. Soil with roots emitted VOCs at similar, though more variable, rates than foliage. Soil emissions were characterized by terpenes, oxygenated alkanes, and alkenes and phenolic compounds, only a few of which were found in root extracts at low concentrations. Correlation analyses revealed that several VOCs emitted from foliage or soil are jointly regulated and that above and belowground sources are partially interconnected. With respect to VOC monitoring in tomato crops, our results underline that genetic variability, light-dependent de-novo synthesis, and belowground sources are factors to be considered for successful use in crop monitoring.