Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi.

Fungi that decay wood have characteristic associations with certain tree species, but the mechanistic bases for these associations are poorly understood. We studied substrate-specific gene expression and RNA editing in six species of wood-decaying fungi from the 'Antrodia clade' (Polyporales, Agaricomycetes) on three different wood substrates (pine, spruce, and aspen) in submerged cultures. We identified dozens to hundreds of substrate-biased genes (i.e., genes that are significantly upregulated in one substrate relative to the other two substrates) in each species, and these biased genes are correlated with their host ranges. Evolution of substrate-biased genes is associated with gene family expansion, gain and loss of genes, and variation in cis- and trans- regulatory elements, rather than changes in protein coding sequences. We also demonstrated widespread RNA editing events in the Antrodia clade, which differ from those observed in the Ascomycota in their distribution, substitution types, and the genomic environment. Moreover, we found that substrates could affect editing positions and frequency, including editing events occurring in mRNA transcribed from wood-decay-related genes. This work shows the extent to which gene expression and RNA editing differ among species and substrates, and provides clues into mechanisms by which wood-decaying fungi may adapt to different hosts

Collapse of the vortex-lattice inductance and shear modulus at the melting transition in untwinned YBa2Cu3O7\rm YBa_2Cu_3O_7

The complex resistivity $\hat{\rho}(\omega)$ of the vortex lattice in an untwinned crystal of 93-K $\rm YBa_2Cu_3O_7$ has been measured at frequencies $\omega/2\pi$ from 100 kHz to 20 MHz in a 2-Tesla field $\bf H\parallel c$, using a 4-probe RF transmission technique that enables continuous measurements versus $\omega$ and temperature $T$. As $T$ is increased, the inductance ${\cal L}_s(\omega) ={\rm Im} \hat{\rho}(\omega)/ \omega$ increases steeply to a cusp at the melting temperature $T_m$, and then undergoes a steep collapse consistent with vanishing of the shear modulus $c_{66}$. We discuss in detail the separation of the vortex-lattice inductance from the `volume' inductance, and other skin-depth effects. To analyze the spectra, we consider a weakly disordered lattice with a low pin density. Close fits are obtained to $\rho_1(\omega)$ over 2 decades in $\omega$. Values of the pinning parameter $\kappa$ and shear modulus $c_{66}$ obtained show that $c_{66}$ collapses by over 4 decades at $T_m$, whereas $\kappa$ remains finite.Comment: 11 pages, 8 figures, Phys. Rev. B, in pres

Intimate partner violence and substance abuse among minority women receiving care from an inner-city emergency department

Objective. The study describes the rates of lifetime and current IPV among women awaiting care in an emergency department and explores the association between IPV and having a drug abuse problem, and IPV and having an alcohol abuse problem, after controlling for demographic factors and history of childhood victimization. Methods. Face-to-face interviews were conducted with 143 low-level triaged women recruited from an inner-city emergency department. Results. Nearly one-half reported ever experiencing IPV, and over 18% reported IPV during the year before the interview. A higher proportion of abused women reported a history of regular crack, cocaine, or heroin use and visiting shooting galleries or crack houses. Participants who were physically abused by their partner during the past year (15%, n = 21) were more likely than nonabused women (85%, n = 122) to report higher scores on the Alcohol Use Disorders Identification Test (AUDIT) (4.9 vs. 2.4), a measure of alcohol-related problems, and the Drug Abuse Severity Test (DAST) (3.0 vs. 1.3), a measure of drug-related problems. Sexually abused women (6%, n = 9) were more likely than their counterparts (94%, n = 134) to have significantly higher AUDIT scores (6.4 vs. 2.5). The findings have implications for how the intersecting public health problems of IPV and substance abuse should be taken into consideration in research and patient care protocols in emergency departments

Chaotic Repellers in Antiferromagnetic Ising Model

For the first time we present the consideration of the antiferromagnetic Ising model in case of fully developed chaos and obtain the exact connection between this model and chaotic repellers. We describe the chaotic properties of this statistical mechanical system via the invariants characterizing a fractal set and show that in chaotic region it displays phase transition at {\it positive} "temperature" $\beta_c = 0.89$. We obtain the density of the invariant measure on the chaotic repeller.Comment: LaTeX file, 10 pages, 4 PS figurs upon reques

K-matrices for 2D conformal field theories

In this paper we examine fermionic type characters (Universal Chiral Partition Functions) for general 2D conformal field theories with a bilinear form given by a matrix of the form K \oplus K^{-1}. We provide various techniques for determining these K-matrices, and apply these to a variety of examples including (higher level) WZW and coset conformal field theories. Applications of our results to fractional quantum Hall systems and (level restricted) Kostka polynomials are discussed.Comment: 59 pages, 2 figures, v2: note added, minor changes, references added, v3: typos correcte

Exclusion statistics in conformal field theory and the UCPF for WZW models

In this paper we further elaborate on the notion of fractional exclusion statistics, as introduced by Haldane, in two-dimensional conformal field theory, and its connection to the Universal Chiral Partition Function as defined by McCoy and collaborators. We will argue that in general, besides the pseudo-particles introduced recently by Guruswamy and Schoutens, one needs additional `null quasi-particles' to account for the null-states in the quasi-particle Fock space. We illustrate this in several examples of WZW-models.Comment: plain TeX, 31 pages; ref adde

Quantum Nonlinear Switching Model

We present a method, the dynamical cumulant expansion, that allows to calculate quantum corrections for time-dependent quantities of interacting spin systems or single spins with anisotropy. This method is applied to the quantum-spin model \hat{H} = -H_z(t)S_z + V(\bf{S}) with H_z(\pm\infty) = \pm\infty and \Psi (-\infty)=|-S> we study the quantity P(t)=(1-_t/S)/2. The case V(\bf{S})=-H_x S_x corresponds to the standard Landau-Zener-Stueckelberg model of tunneling at avoided-level crossing for N=2S independent particles mapped onto a single-spin-S problem, P(t) being the staying probability. Here the solution does not depend on S and follows, e.g., from the classical Landau-Lifshitz equation. A term -DS_z^2 accounts for particles' interaction and it makes the model nonlinear and essentially quantum mechanical. The 1/S corrections obtained with our method are in a good accord with a full quantum-mechanical solution if the classical motion is regular, as for D>0.Comment: 4 Phys. Rev. pages 2 Fig

Dichloroacetate and PX-478 exhibit strong synergistic effects in a various number of cancer cell lines

Background: One key approach for anticancer therapy is drug combination. Drug combinations can help reduce doses and thereby decrease side effects. Furthermore, the likelihood of drug resistance is reduced. Distinct alterations in tumor metabolism have been described in past decades, but metabolism has yet to be targeted in clinical cancer therapy. Recently, we found evidence for synergism between dichloroacetate (DCA), a pyruvate dehydrogenase kinase inhibitor, and the HIF-1 alpha inhibitor PX-478. In this study, we aimed to analyse this synergism in cell lines of different cancer types and to identify the underlying biochemical mechanisms. Methods: The dose-dependent antiproliferative effects of the single drugs and their combination were assessed using SRB assays. FACS, Western blot and HPLC analyses were performed to investigate changes in reactive oxygen species levels, apoptosis and the cell cycle. Additionally, real-time metabolic analyses (Seahorse) were performed with DCA-treated MCF-7 cells. Results: The combination of DCA and PX-478 produced synergistic effects in all eight cancer cell lines tested, including colorectal, lung, breast, cervical, liver and brain cancer. Reactive oxygen species generation and apoptosis played important roles in this synergism. Furthermore, cell proliferation was inhibited by the combination treatment. Conclusions: Here, we found that these tumor metabolism-targeting compounds exhibited a potent synergism across all tested cancer cell lines. Thus, we highly recommend the combination of these two compounds for progression to in vivo translational and clinical trials

Exclusion Statistics in Conformal Field Theory -- generalized fermions and spinons for level-1 WZW theories

We systematically study the exclusion statistics for quasi-particles for Conformal Field Theory spectra by employing a method based on recursion relations for truncated spectra. Our examples include generalized fermions in c<1 unitary minimal models, Z_k parafermions, and spinons for the su(n)_1, so(n)_1 and sp(2n)_1 Wess-Zumino-Witten models. For some of the latter examples we present explicit expressions for finitized affine characters and for the N-spinon decomposition of affine characters.Comment: LaTeX, 49 pages, some further clarifications added, refs added and updated. Nucl. Phys. B, to be publishe