Observation of out-of-phase bilayer plasmons in YBa_2Cu_3O_7-delta

The temperature dependence of the c-axis optical conductivity \sigma(\omega) of optimally and overdoped YBa_2Cu_3O_x (x=6.93 and 7) is reported in the far- (FIR) and mid-infrared (MIR) range. Below T_c we observe a transfer of spectral weight from the FIR not only to the condensate at \omega = 0, but also to a new peak in the MIR. This peak is naturally explained as a transverse out-of-phase bilayer plasmon by a model for \sigma(\omega) which takes the layered crystal structure into account. With decreasing doping the plasmon shifts to lower frequencies and can be identified with the surprising and so far not understood FIR feature reported in underdoped bilayer cuprates.Comment: 7 pages, 3 eps figures, Revtex, epsfi

Differential proportionality - a normalization-free approach to differential gene expression

AbstractGene expression data, such as those generated by next generation sequencing technologies (RNA-seq), are of an inherently relative nature: the total number of sequenced reads has no biological meaning. This issue is most often addressed with various normalization techniques which all face the same problem: once information about the total mRNA content of the origin cells is lost, it cannot be recovered by mere technical means. Additional knowledge, in the form of an unchanged reference, is necessary; however, this reference can usually only be estimated. Here we propose a novel method where sample normalization is unnecessary, but important insights can be obtained nevertheless. Instead of trying to recover absolute abundances, our method is entirely based on ratios, so normalization factors cancel by default. Although the differential expression of individual genes cannot be recovered this way, the ratios themselves can be differentially expressed (even when their constituents are not). Yet, most current analyses are blind to these cases, while our approach reveals them directly. Specifically, we show how the differential expression of gene ratios can be formalized by decomposing log-ratio variance (LRV) and deriving intuitive statistics from it. Although small LRVs have been used to detect proportional genes in gene expression data before, we focus here on the change in proportionality factors between groups of samples (e.g. tissue-specific proportionality). For this, we propose a statistic that is equivalent to the squared t-statistic of one-way ANOVA, but for gene ratios. In doing so, we show how precision weights can be incorporated to account for the peculiarities of count data, and, moreover, how a moderated statistic can be derived in the same way as the one following from a hierarchical model for individual genes. We also discuss approaches to deal with zero counts, deriving an expression of our statistic that is able to incorporate them. In providing a detailed analysis of the connections between the differential expression of genes and the differential proportionality of pairs, we facilitate a clear interpretation of new concepts. The proposed framework is applied to a data set from GTEx consisting of 98 samples from the cerebellum and cortex, with selected examples shown. A computationally efficient implementation of the approach in R has been released as an addendum to the propr package.1</jats:p

P2Y receptors in the mammalian nervous system: pharmacology, ligands and therapeutic potential

P2Y receptors for extracellular nucleotides are coupled to activation of a variety of G proteins and stimulate diverse intracellular signaling pathways that regulate functions of cell types that comprise the central nervous system (CNS). There are 8 different subtypes of P2Y receptor expressed in cells of the CNS that are activated by a select group of nucleotide agonists. Here, the agonist selectivity of these 8 P2Y receptor subtypes is reviewed with an emphasis on synthetic agonists with high potency and resistance to degradation by extracellular nucleotidases that have potential applications as therapeutic agents. In addition, the recent identification of a wide variety of subtype-selective antagonists is discussed, since these compounds are critical for discerning cellular responses mediated by activation of individual P2Y receptor subtypes. The functional expression of P2Y receptor subtypes in cells that comprise the CNS is also reviewed and the role of each subtype in the regulation of physiological and pathophysiological responses is considered. Other topics include the role of P2Y receptors in the regulation of blood-brain barrier integrity and potential interactions between different P2Y receptor subtypes that likely impact tissue responses to extracellular nucleotides in the CNS. Overall, current research suggests that P2Y receptors in the CNS regulate repair mechanisms that are triggered by tissue damage, inflammation and disease and thus P2Y receptors represent promising targets for the treatment of neurodegenerative diseases

Magnetic Breakdown in the electron-doped cuprate superconductor Nd2−x_{2-x}Cex_xCuO4_4: the reconstructed Fermi surface survives in the strongly overdoped regime

We report on semiclassical angle-dependent magnetoresistance oscillations (AMRO) and the Shubnikov-de Haas effect in the electron-overdoped cuprate superconductor Nd$_{2-x}$Ce$_x$CuO$_4$. Our data provide convincing evidence for magnetic breakdown in the system. This shows that a reconstructed multiply-connected Fermi surface persists, at least at strong magnetic fields, up to the highest doping level of the superconducting regime. Our results suggest an intimate relation between translational symmetry breaking and the superconducting pairing in the electron-doped cuprate superconductors.Comment: 5 pages, 4 figures, submitted to PR

Global Examination of the 12^{12}C+12^{12}C Reaction Data at Low and Intermediate Energies

We examine the $^{12}$C+$^{12}$C elastic scattering over a wide energy range from 32.0 to 70.7 MeV in the laboratory system within the framework of the Optical model and the Coupled-Channels formalism. The $^{12}$C+$^{12}$C system has been extensively studied within and over this energy range in the past. These efforts have been futile in determining the shape of the nuclear potential in the low energy region and in describing the individual angular distributions, single-angle 50$^{0}$ to 90$^{0}$ excitation functions and reaction cross-section data simultaneously. In order to address these problems systematically, we propose a potential that belongs to a family other than the one used to describe higher energy experimental data and show that it is possible to use it over this wide energy range. This potential also predicts the resonances at correct energies with reasonable widths.Comment: 30 pages with 13 eps figues and 3 tables, LaTeX-Revtex

Up-regulation of the P2Y2 receptor by cytokines in neuronal cells

Abstract only availableAlzheimer's Disease (AD) is characterized by inflammation and neurodegeneration in the brain due to the presence of extracellular amyloid beta (A β) plaques and neurofibrillary tangles. Microglial and astrocyte cells associated with these plaques and tangles have been shown to release cytokines in AD patients, which have a proinflammatory effect on the brain. The P2Y2 receptor (P2Y2R) is a receptor protein that is up-regulated in response to damage or stress in a variety of tissues, including blood vessels and salivary gland epithelium. Recently our laboratory has shown that activation of the P2Y2R enhances α -secretase-dependent amyloid precursor protein (APP) processing. APP is proteolytically processed by β - and γ -secretases to release neurodegenerative A β. Alternatively, APP can be cleaved within the A β domain by α -secretase releasing the non-amyloidogenic product, sAPP α, which has been shown to have neuroprotective properties. Primary neurons have low P2Y2R expression, however, it has been demonstrated that cytokines up-regulate P2Y2R in smooth muscle cells. Therefore, this study will explore if cytokines up-regulate P2Y2R expression in primary rat neurons and in SH-SY5Y human neuroblastoma cells. Primary rat neurons and SH-SY5Y human neuroblastoma cells were plated on glass cover slips 24 or 48 hours with individual treatment, or a combination of, human interleukin-1 β (IL1- β), tumor necrosis factor α (TNF α), and interferon γ (IF γ). P2Y2R activity was measured by increases in intracellular calcium concentration ([Ca2+]i ) in response to the P2Y2R agonist UTP. Results support the hypothesis that P2Y2R is up-regulated by cytokines in neuronal cells. Furthermore, real-time PCR results indicate a two-fold increase in P2Y2R mRNA after cytokine treatment. Therefore, activation of the up-regulated P2Y2R in stressed neurons generates a neuroprotective (sAPP α) rather than neurodegenerative (A β) peptide. These results could have a substantial impact on the understanding and treatment of neurological disorders such as AD.Life Sciences Undergraduate Research Opportunity Progra

Direct Observation and Anisotropy of the Contribution of Gap nodes in the Low Temperature Specific Heat of YBa_2Cu_3O_7

The specific heat due to line nodes in the superconducting gap of YBa2Cu3O7 has been obscured up to now by magnetic terms of extrinsic origin, even for high quality crystals. We report the specific heat of a new single crystal grown in a non-corrosive BaZrO3 crucible, for which paramagnetic terms are reduced to less than one spin-1/2 center for 20'000 Cu atoms. The contribution of line nodes shows up directly in the difference C(B,T) - C(0,T) at fixed temperatures (T < 5 K) as a function of the magnetic field parallel to the c-axis (B<=14 T). These data illustrate the smooth crossover from C propotional to T^2 at low fields to C propotional to TB^1/2 at high fields, and provide new values for gap parameters which are quantitatively consistent with tunneling spectroscopy and thermal conductivity in the framework of dx^2-y^2 pairing symmetry. Data for B along the nodal and antinodal directions in the ab-plane are also provided. The in-plane anisotropy predicted in the clean limit is not observed.Comment: 29 pages(using Revtex style), 14 postscript figures, submitted to Phys. Rev. B Content of the file changed after replacin

Correlation between Fermi surface transformations and superconductivity in the electron-doped high-TcT_c superconductor Nd2−x_{2-x}Cex_xCuO4_4

Two critical points have been revealed in the normal-state phase diagram of the electron-doped cuprate superconductor Nd$_{2-x}$Ce$_x$CuO$_4$ by exploring the Fermi surface properties of high quality single crystals by high-field magnetotransport. First, the quantitative analysis of the Shubnikov-de Haas effect shows that the weak superlattice potential responsible for the Fermi surface reconstruction in the overdoped regime extrapolates to zero at the doping level $x_c = 0.175$ corresponding to the onset of superconductivity. Second, the high-field Hall coefficient exhibits a sharp drop right below optimal doping $x_{\mathrm{opt}} = 0.145$ where the superconducting transition temperature is maximum. This drop is most likely caused by the onset of long-range antiferromagnetic ordering. Thus, the superconducting dome appears to be pinned by two critical points to the normal state phase diagram.Comment: 9 pages; 7 figures; 1 tabl

Explanation and Elaboration Document for the STROBE-Vet Statement: Strengthening the Reporting of Observational Studies in Epidemiology—Veterinary Extension

The STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) statement was first published in 2007 and again in 2014. The purpose of the original STROBE was to provide guidance for authors, reviewers and editors to improve the comprehensiveness of reporting; however, STROBE has a unique focus on observational studies. Although much of the guidance provided by the original STROBE document is directly applicable, it was deemed useful to map those statements to veterinary concepts, provide veterinary examples and highlight unique aspects of reporting in veterinary observational studies. Here, we present the examples and explanations for the checklist items included in the STROBE-Vet Statement. Thus, this is a companion document to the STROBE-Vet Statement Methods and process document, which describes the checklist and how it was developed

Hole depletion and localization due to disorder in insulating PrBa2Cu3O7-d: a Compton scattering study

The (mostly) insulating behaviour of PrBa2Cu3O7-d is still unexplained and even more interesting since the occasional appearance of superconductivity in this material. Since YBa2Cu3O7-d is nominally iso-structural and always superconducting, we have measured the electron momentum density in these materials. We find that they differ in a striking way, the wavefunction coherence length in PrBa2Cu3O7-d being strongly suppressed. We conclude that Pr on Ba-site substitution disorder is responsible for the metal-insulator transition. Preliminary efforts at growth with a method to prevent disorder yield 90K superconducting PrBa2Cu3O7-d crystallites.Comment: 4 pages, 3 figures, revised version submitted to PR