Similarity in targets with REST points to neural and glioblastoma related miRNAs

There are groups of genes that need coordinated repression in multiple contexts, for example if they code for proteins that work together in a pathway or in a protein complex. Redundancy of biological regulatory networks implies that such coordinated repression might occur at both the pre- and post-transcriptional level, though not necessarily simultaneously or under the same conditions. Here, we propose that such redundancy in the global regulatory network can be detected by the overlap between the putative targets of a transcriptional repressor, as identified by a ChIP-seq experiment, and predicted targets of a microRNA (miRNA). To test this hypothesis, we used publicly available ChIP-seq data of the neural transcriptional repressor RE1 silencing transcription factor (REST) from 15 different cell samples. We found 20 miRNAs, each of which shares a significant amount of predicted targets with REST. The set of predicted associations between these 20 miRNAs and the overlapping REST targets is enriched in known miRNA targets. Many of the detected miRNAs have functions related to neural identity and glioblastoma, which could be expected from their overlap in targets with REST. We propose that the integration of experimentally determined transcription factor binding sites with miRNA-target predictions provides functional information on miRNAs

Avoided energy cost of producing minerals: The case of iron ore

There is growing concern about the decline of the ore grade in mines and the increased energy usage for processing and refining metals. In the limit, where no concentrated deposits exist, minerals must be obtained from bare rock. A method for quantitatively assessing the “free bonus” granted by nature in providing concentrated minerals in mines and thus assessing the quality of the different resources is estimating how much energy is needed to concentrate the minerals, as they are already in mines, from bare rock. This bonus granted by nature reduces the costs of human mining and metallurgical processes, as well as the mining effort required of future generations. In this study, the concentration of high-iron-content minerals in common rocks was investigated via a computational model developed using the HSC software. As expected, the range of results for the specific energy for the concentration of iron from common rocks was considerably higher than the energy required by modern processes. This reveals the need to value current iron deposits and the challenge of developing sustainable methods of metal production to satisfy the needs of the present and future generations

Gravity and Geometric Phases

The behavior of a quantum test particle satisfying the Klein-Gordon equation in a certain class of 4 dimensional stationary space-times is examined. In a space-time of a spinning cosmic string, the wave function of a particle in a box is shown to acquire a geometric phase when the box is transported around a closed path surrounding the string. When interpreted as an Aharonov-Anandan geometric phase, the effect is shown to be related to the Aharonov-Bohm effect.Comment: 11 pages, latex fil

Recent developments in the characterization of superconducting films by microwaves

We describe and analyze selected surface impedance data recently obtained by different groups on cuprate, ruthenate and diboride superconducting films on metallic and dielectric substrates for fundamental studies and microwave applications. The discussion includes a first review of microwave data on MgB2, the weak-link behaviour of RABiTS-type YBa2Cu3O7-d tapes, and the observation of a strong anomalous power-dependence of the microwave losses in MgO at low temperatures. We demonstrate how microwave measurements can be used to investigate electronic, magnetic, and dielectric dissipation and relaxation in the films and substrates. The impact of such studies reaches from the extraction of microscopic information to the engineering of materials and further on to applications in power systems and communication technology.Comment: Invited contribution to EUCAS2001, accepted for publication in Physica C in its present for

The self-consistent bounce: an improved nucleation rate

We generalize the standard computation of homogeneous nucleation theory at zero temperature to a scenario in which the bubble shape is determined self-consistently with its quantum fluctuations. Studying two scalar models in 1+1 dimensions, we find the self-consistent bounce by employing a two-particle irreducible (2PI) effective action in imaginary time at the level of the Hartree approximation. We thus obtain an effective single bounce action which determines the rate exponent. We use collective coordinates to account for the translational invariance and the growth instability of the bubble and finally present a new nucleation rate prefactor. We compare the results with those obtained using the standard 1-loop approximation and show that the self-consistent rate can differ by several orders of magnitude.Comment: 28 pages, revtex, 7 eps figure

Do Instantons Like a Colorful Background?

We investigate chiral symmetry breaking and color symmetry breaking in QCD. The effective potential of the corresponding scalar condensates is discussed in the presence of non-perturbative contributions from the semiclassical one-instanton sector. We concentrate on a color singlet scalar background which can describe chiral condensation, as well as a color octet scalar background which can generate mass for the gluons. Whereas a non-vanishing singlet chiral field is favored by the instantons, we have found no indication for a preference of color octet backgrounds.Comment: 25 pages, 7 figure

Off-Diagonal Elements of the DeWitt Expansion from the Quantum Mechanical Path Integral

The DeWitt expansion of the matrix element M_{xy} = \left\langle x \right| \exp -[\case{1}{2} (p-A)^2 + V]t \left| y \right\rangle, $(p=-i\partial)$ in powers of $t$ can be made in a number of ways. For $x=y$ (the case of interest when doing one-loop calculations) numerous approaches have been employed to determine this expansion to very high order; when $x \neq y$ (relevant for doing calculations beyond one-loop) there appear to be but two examples of performing the DeWitt expansion. In this paper we compute the off-diagonal elements of the DeWitt expansion coefficients using the Fock-Schwinger gauge. Our technique is based on representing $M_{xy}$ by a quantum mechanical path integral. We also generalize our method to the case of curved space, allowing us to determine the DeWitt expansion of \tilde M_{xy} = \langle x| \exp \case{1}{2} [\case{1}{\sqrt {g}} (\partial_\mu - i A_\mu)g^{\mu\nu}{\sqrt{g}}(\partial_\nu - i A_\nu) ] t| y \rangle by use of normal coordinates. By comparison with results for the DeWitt expansion of this matrix element obtained by the iterative solution of the diffusion equation, the relative merit of different approaches to the representation of $\tilde M_{xy}$ as a quantum mechanical path integral can be assessed. Furthermore, the exact dependence of $\tilde M_{xy}$ on some geometric scalars can be determined. In two appendices, we discuss boundary effects in the one-dimensional quantum mechanical path integral, and the curved space generalization of the Fock-Schwinger gauge.Comment: 16pp, REVTeX. One additional appendix concerning end-point effects for finite proper-time intervals; inclusion of these effects seem to make our results consistent with those from explicit heat-kernel method

Categorizing Different Approaches to the Cosmological Constant Problem

We have found that proposals addressing the old cosmological constant problem come in various categories. The aim of this paper is to identify as many different, credible mechanisms as possible and to provide them with a code for future reference. We find that they all can be classified into five different schemes of which we indicate the advantages and drawbacks. Besides, we add a new approach based on a symmetry principle mapping real to imaginary spacetime.Comment: updated version, accepted for publicatio

Heavy Quarks and Heavy Quarkonia as Tests of Thermalization

We present here a brief summary of new results on heavy quarks and heavy quarkonia from the PHENIX experiment as presented at the "Quark Gluon Plasma Thermalization" Workshop in Vienna, Austria in August 2005, directly following the International Quark Matter Conference in Hungary.Comment: 8 pages, 5 figures, Quark Gluon Plasma Thermalization Workshop (Vienna August 2005) Proceeding

Single Electrons from Heavy Flavor Decays in p+p Collisions at sqrt(s) = 200 GeV

The invariant differential cross section for inclusive electron production in p+p collisions at sqrt(s) = 200 GeV has been measured by the PHENIX experiment at the Relativistic Heavy Ion Collider over the transverse momentum range $0.4 <= p_T <= 5.0 GeV/c at midrapidity (eta <= 0.35). The contribution to the inclusive electron spectrum from semileptonic decays of hadrons carrying heavy flavor, i.e. charm quarks or, at high p_T, bottom quarks, is determined via three independent methods. The resulting electron spectrum from heavy flavor decays is compared to recent leading and next-to-leading order perturbative QCD calculations. The total cross section of charm quark-antiquark pair production is determined as sigma_(c c^bar) = 0.92 +/- 0.15 (stat.) +- 0.54 (sys.) mb.Comment: 329 authors, 6 pages text, 3 figures. Submitted to Phys. Rev. Lett. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm