Midgap states and charge inhomogeneities in corrugated graphene

We study the changes induced by the effective gauge field due to ripples on the low energy electronic structure of graphene. We show that zero energy Landau levels will form, associated to the smooth deformation of the graphene layer, when the height corrugation, $h$, and the length of the ripple, $l$, are such that $h^2 / (l a) \gtrsim 1$, where $a$ is the lattice constant. The existence of localized levels gives rise to a large compressibility at zero energy, and to the enhancement of instabilities arising from electron-electron interactions including electronic phase separation. The combined effect of the ripples and an external magnetic field breaks the valley symmetry of graphene leading to the possibility of valley selection

On the ab initio calculation of CVV Auger spectra in closed-shell systems

We propose an ab initio method to evaluate the core-valence-valence (CVV) Auger spectrum of systems with filled valence bands. The method is based on the Cini-Sawatzky theory, and aims at estimating the parameters by first-principles calculations in the framework of density-functional theory (DFT). Photoemission energies and the interaction energy for the two holes in the final state are evaluated by performing DFT simulations for the system with varied population of electronic levels. Transition matrix elements are taken from atomic results. The approach takes into account the non-sphericity of the density of states of the emitting atom, spin-orbit interaction in core and valence, and non quadratic terms in the total energy expansion with respect to fractional occupation numbers. It is tested on two benchmark systems, Zn and Cu metals, leading in both cases to L23M45M45 Auger peaks within 2 eV from the experimental ones. Detailed analysis is presented on the relative weight of the various contributions considered in our method, providing the basis for future development. Especially problematic is the evaluation of the hole-hole interaction for systems with broad valence bands: our method underestimates its value in Cu, while we obtain excellent results for this quantity in Zn.Comment: 20 pages, 5 figures, 4 table

Equilibrium and time-dependent Josephson current in one-dimensional superconducting junctions

We investigate the transport properties of a one-dimensional superconductor-normal metal-superconductor (S-N-S) system described within the tight-binding approximation. We compute the equilibrium dc Josephson current and the time-dependent oscillating current generated after the switch-on of a constant bias. In the first case an exact embedding procedure to calculate the Nambu-Gorkov Keldysh Green's function is employed and used to derive the continuum and bound states contributions to the dc current. A general formalism to obtain the Andreev bound states (ABS) of a normal chain connected to superconducting leads is also presented. We identify a regime in which all Josephson current is carried by the ABS and obtain an analytic formula for the current-phase relation in the limit of long chains. In the latter case the condition for perfect Andreev reflections is expressed in terms of the microscopic parameters of the model, showing a limitation of the so called wide-band-limit (WBL) approximation. When a finite bias is applied to the S-N-S junction we compute the exact time-evolution of the system by solving numerically the time-dependent Bogoliubov-deGennes equations. We provide a microscopic description of the electron dynamics not only inside the normal region but also in the superconductors, thus gaining more information with respect to WBL-based approaches. Our scheme allows us to study the ac regime as well as the transient dynamics whose characteristic time-scale is dictated by the velocity of multiple Andreev reflections

The kinetics of ER fusion protein activation in vivo.

Reversibly switchable proteins are powerful tools with which to explore protein function in vitro and in vivo. For example, the activity of many proteins fused to the hormone-binding domain of the modified oestrogen receptor (ER(TAM)) can be regulated by provision or removal of 4-hydroxytamoxifen (4-OHT). Despite the widespread use of ER(TAM) fusions in vivo, inadequate data are available as to the most efficacious routes for systemic tamoxifen delivery. In this study, we have used two well-characterized ER(TAM) fusion proteins, both reversibly activated by 4-OHT, to compare the effectiveness and kinetics of 4-OHT delivery in mice in vivo by either tamoxifen in food or by intraperitoneal injection. Our data indicate that dietary tamoxifen offers an effective, facile and ethically preferable means for long-term activation of ER(TAM) fusion proteins in vivo.This is the final published version. It's also available from the publishers at: http://www.nature.com/onc/journal/vaop/ncurrent/full/onc201478a.html

Nine years of comparative effectiveness research education and training: initiative supported by the PhRMA Foundation

The term comparative effectiveness research (CER) took center stage with passage of the American Recovery and Reinvestment Act (2009). The companion US$1.1 billion in funding prompted the launch of initiatives to train the scientific workforce capable of conducting and using CER. Passage of the Patient Protection and Affordable Care Act (2010) focused these initiatives on patients, coining the term ‘patient-centered outcomes research’ (PCOR). Educational and training initiatives were soon launched. This report describes the initiative of the Pharmaceutical Research and Manufacturers Association of America (PhRMA) Foundation. Through provision of grant funding to six academic Centers of Excellence, to spearheading and sponsoring three national conferences, the PhRMA Foundation has made significant contributions to creation of the scientific workforce that conducts and uses CER/PCOR

Critical currents in graphene Josephson junctions

We study the superconducting correlations induced in graphene when it is placed between two superconductors, focusing in particular on the supercurrents supported by the 2D system. For this purpose we make use of a formalism placing the emphasis on the many-body aspects of the problem, with the aim of investigating the dependence of the critical currents on relevant variables like the distance L between the superconducting contacts, the temperature, and the doping level. Thus we show that, despite the vanishing density of states at the Fermi level in undoped graphene, supercurrents may exist at zero temperature with a natural 1/L^3 dependence at large L. When temperature effects are taken into account, the supercurrents are further suppressed beyond the thermal length L_T (~ v_F / k_B T, in terms of the Fermi velocity v_F of graphene), entering a regime where the decay is given by a 1/L^5 dependence. On the other hand, the supercurrents can be enhanced upon doping, as the Fermi level is shifted by a chemical potential \mu from the charge neutrality point. This introduces a new crossover length L* ~ v_F / \mu, at which the effects of the finite charge density start being felt, marking the transition from the short-distance 1/L^3 behavior to a softer 1/L^2 decay of the supercurrents at large L. It turns out that the decay of the critical currents is given in general by a power-law behavior, which can be seen as a consequence of the perfect scaling of the Dirac theory applied to the low-energy description of graphene.Comment: 11 pages, 6 figures, to appear in J. Phys.: Condens. Matte

EchidnaCSI: engaging the public in research and conservation of the short-beaked echidna

The short-beaked echidna is an iconic Australian animal and the most-widespread native mammal, inhabiting diverse environments. The cryptic nature of echidnas has limited research into their ecology in most areas; however, from the well-researched and endangered Kangaroo Island echidna population, we understand that the threats include habitat loss, roads, and invasive species. To obtain more information about echidnas Australia-wide, we established the Echidna Conservation Science Initiative (EchidnaCSI) citizen science project. EchidnaCSI calls on members of the public to submit photographs of wild echidnas and learn to identify and collect echidna scats for molecular analysis. To facilitate participation, we developed a smartphone application as well as ongoing social and traditional media activities and community events. In 3 y, more than 9,000 members of the public have downloaded the EchidnaCSI app, collecting 400 scats and submitting over 8,000 sightings of echidnas from across Australia. A subset of submitted scat samples were subjected to DNA extraction and PCR, which validated the approach of using citizen science for scat collection and viability for molecular analysis. To assess the impact of the project through public participation, we surveyed our participants (n = 944) to understand their demographics and motivations for engagement. Survey results also revealed that EchidnaCSI served as a gateway into citizen science more generally for many participants. EchidnaCSI demonstrates the potential for using citizen science approaches to collect high-quality data and material from a cryptic species over a very large geographic area and the considerable engagement value of citizen science research.Tahlia Perry, Alan Stenhouse, Isabella Wilson, Imma Perfetto, Michael W. McKelvey, Michelle Coulson, Rachel A. Ankeny, Peggy D. Rismiller, and Frank Grützne

Identification, isolation and in vitro expansion of human and nonhuman primate T stem cell memory cell

The T cell compartment is phenotypically and functionally heterogeneous; subsets of naive and memory cells have different functional properties, and also differ with respect to homeostatic potential and the ability to persist in vivo. Human stem cell memory T (TSCM) cells, which possess superior immune reconstitution and antitumor response capabilities, can be identified by polychromatic flow cytometry on the basis of the simultaneous expression of several naive markers together with the memory marker CD95. We describe here a protocol based on the minimum set of markers required for optimal identification of human and nonhuman primate (NHP) TSCM cells with commonly available flow cytometers. By using flow sorters, TSCM cells can thereby be isolated efficiently at high yield and purity. With the use of the 5.5-h isolation procedure, depending on the number of cells needed, the sorting procedure can last for 2-15 h. We also indicate multiple strategies for their efficient expansion in vitro at consistent numbers for functional characterization or adoptive transfer experiments

The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions

The current coronavirus disease of 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus (SARS-CoV)-2, has spurred a wave of research of nearly unprecedented scale. Among the different strategies that are being used to understand the disease and develop effective treatments, the study of physical molecular interactions can provide fine-grained resolution of the mechanisms behind the virus biology and the human organism response. We present a curated dataset of physical molecular interactions focused on proteins from SARS-CoV-2, SARS-CoV-1 and other members of the Coronaviridae family that has been manually extracted by International Molecular Exchange (IMEx) Consortium curators. Currently, the dataset comprises over 4400 binarized interactions extracted from 151 publications. The dataset can be accessed in the standard formats recommended by the Proteomics Standards Initiative (HUPO-PSI) at the IntAct database website (https://www.ebi.ac.uk/intact) and will be continuously updated as research on COVID-19 progresses