Pedagogic model for Deeply Virtual Compton Scattering with quark-hadron duality

We show how quark-hadron duality can emerge for valence spin averaged structure functions, and for the non-forward distributions of Deeply Virtual Compton Scattering. Novel factorisations of the non-forward amplitudes are proposed. Some implications for large angle scattering and deviations from the quark counting rules are illustrated.Comment: Version accepted by Phys. Rev.

Doping-Dependent Raman Resonance in the Model High-Temperature Superconductor HgBa2CuO4+d

We study the model high-temperature superconductor HgBa2CuO4+d with electronic Raman scattering and optical ellipsometry over a wide doping range. The resonant Raman condition which enhances the scattering cross section of "two-magnon" excitations is found to change strongly with doping, and it corresponds to a rearrangement of inter-band optical transitions in the 1-3 eV range seen by ellipsometry. This unexpected change of the resonance condition allows us to reconcile the apparent discrepancy between Raman and x-ray detection of magnetic fluctuations in superconducting cuprates. Intriguingly, the strongest variation occurs across the doping level where the antinodal superconducting gap reaches its maximum.Comment: 4 pages, 4 figures, contact authors for Supplemental Materia

Hall, Seebeck, and Nernst Coefficients of Underdoped HgBa2CuO4+d: Fermi-Surface Reconstruction in an Archetypal Cuprate Superconductor

Charge density-wave order has been observed in cuprate superconductors whose crystal structure breaks the square symmetry of the CuO2 planes, such as orthorhombic YBa2Cu3Oy (YBCO), but not so far in cuprates that preserve that symmetry, such as tetragonal HgBa2CuO4+d (Hg1201). We have measured the Hall (R_H), Seebeck (S), and Nernst coefficients of underdoped Hg1201 in magnetic fields large enough to suppress superconductivity. The high-field R_H(T) and S(T) are found to drop with decreasing temperature and become negative, as also observed in YBCO at comparable doping. In YBCO, the negative R_H and S are signatures of a small electron pocket caused by Fermi-surface reconstruction, attributed to charge density-wave modulations observed in the same range of doping and temperature. We deduce that a similar Fermi-surface reconstruction takes place in Hg1201, evidence that density-wave order exists in this material. A striking similarity is also found in the normal-state Nernst coefficient, further supporting this interpretation. Given the model nature of Hg1201, Fermi-surface reconstruction appears to be common to all hole-doped cuprates, suggesting that density-wave order is a fundamental property of these materials

Efficient Vertical Transport of Black Carbon in the Planetary Boundary Layer

Vertical distribution of black carbon (BC) determines the layer where its heating impacts exert. This study presents continuous and simultaneous measurements at surface and on a mountain site above the wintertime planetary boundary layer influenced by uplifted surface anthropogenic emissions. BC was observed efficiently transported upwards by daytime convective mixing. However, this vertical transport was less for other particulate masses. An about twofold higher BC mass fraction was thus present at mountain than surface, hereby a lowered single-scattering albedo (SSA) by 0.06. This may be caused by the evaporative loss of condensed semivolatile materials, prevailing the secondary particulate formation, in a cleaner environment containing less precursors. The elevated BC mass corresponded with the most intensive solar radiation at midday, wielding more heating impacts over the planetary boundary layer (PBL). This phenomenon may apply to other remote regions where a reduced SSA will introduce more positive radiative effects. © 2020. American Geophysical Union. All Rights Reserved

Epigenetic memory in induced pluripotent stem cells.

Somatic cell nuclear transfer and transcription-factor-based reprogramming revert adult cells to an embryonic state, and yield pluripotent stem cells that can generate all tissues. Through different mechanisms and kinetics, these two reprogramming methods reset genomic methylation, an epigenetic modification of DNA that influences gene expression, leading us to hypothesize that the resulting pluripotent stem cells might have different properties. Here we observe that low-passage induced pluripotent stem cells (iPSCs) derived by factor-based reprogramming of adult murine tissues harbour residual DNA methylation signatures characteristic of their somatic tissue of origin, which favours their differentiation along lineages related to the donor cell, while restricting alternative cell fates. Such an 'epigenetic memory' of the donor tissue could be reset by differentiation and serial reprogramming, or by treatment of iPSCs with chromatin-modifying drugs. In contrast, the differentiation and methylation of nuclear-transfer-derived pluripotent stem cells were more similar to classical embryonic stem cells than were iPSCs. Our data indicate that nuclear transfer is more effective at establishing the ground state of pluripotency than factor-based reprogramming, which can leave an epigenetic memory of the tissue of origin that may influence efforts at directed differentiation for applications in disease modelling or treatment

Relationship among superconductivity, pseudogap, and high-energy magnetic fluctuations in a model high-Tc superconductor from electronic Raman scattering

We use electronic Raman scattering to study the model single-layer cuprate superconductor HgBa2CuO4+d. In an overdoped sample, we observe a pronounced amplitude enhancement of a high-energy peak related to two-magnon excitations in insulating cuprates upon cooling below the critical temperature Tc. This effect is accompanied by the appearance of the superconducting gap and a pairing peak above the gap in the Raman spectrum, and it can be understood as a consequence of feedback of the Cooper pairing interaction on the high-energy magnetic fluctuations. All of these effects occur already above Tc in two underdoped samples, demonstrating a related feedback mechanism associated with the pseudogap.Comment: 4 pages, 4 figure

Modulation of enhancer looping and differential gene targeting by Epstein-Barr virus transcription factors directs cellular reprogramming

Epstein-Barr virus (EBV) epigenetically reprogrammes B-lymphocytes to drive immortalization and facilitate viral persistence. Host-cell transcription is perturbed principally through the actions of EBV EBNA 2, 3A, 3B and 3C, with cellular genes deregulated by specific combinations of these EBNAs through unknown mechanisms. Comparing human genome binding by these viral transcription factors, we discovered that 25% of binding sites were shared by EBNA 2 and the EBNA 3s and were located predominantly in enhancers. Moreover, 80% of potential EBNA 3A, 3B or 3C target genes were also targeted by EBNA 2, implicating extensive interplay between EBNA 2 and 3 proteins in cellular reprogramming. Investigating shared enhancer sites neighbouring two new targets (WEE1 and CTBP2) we discovered that EBNA 3 proteins repress transcription by modulating enhancer-promoter loop formation to establish repressive chromatin hubs or prevent assembly of active hubs. Re-ChIP analysis revealed that EBNA 2 and 3 proteins do not bind simultaneously at shared sites but compete for binding thereby modulating enhancer-promoter interactions. At an EBNA 3-only intergenic enhancer site between ADAM28 and ADAMDEC1 EBNA 3C was also able to independently direct epigenetic repression of both genes through enhancer-promoter looping. Significantly, studying shared or unique EBNA 3 binding sites at WEE1, CTBP2, ITGAL (LFA-1 alpha chain), BCL2L11 (Bim) and the ADAMs, we also discovered that different sets of EBNA 3 proteins bind regulatory elements in a gene and cell-type specific manner. Binding profiles correlated with the effects of individual EBNA 3 proteins on the expression of these genes, providing a molecular basis for the targeting of different sets of cellular genes by the EBNA 3s. Our results therefore highlight the influence of the genomic and cellular context in determining the specificity of gene deregulation by EBV and provide a paradigm for host-cell reprogramming through modulation of enhancer-promoter interactions by viral transcription factors

Composite structural motifs of binding sites for delineating biological functions of proteins

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs which represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.Comment: 34 pages, 7 figure