Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues.

The use of Assay for Transposase-Accessible Chromatin (ATAC-seq) to profile chromatin accessibility has surged over the past years, but its applicability to tissues has been very limited. With the intent of preserving nuclear architecture during long-term storage, cryopreserved nuclei preparations from chicken lung were used to optimize ATAC-seq. Sequencing data were compared with existing DNase-seq, ChIP-seq, and RNA-seq data to evaluate library quality, ultimately resulting in a modified ATAC-seq method capable of generating high quality chromatin accessibility data from cryopreserved nuclei preparations. Using this method, nucleosome-free regions (NFR) identified in chicken lung overlapped half of DNase-I hypersensitive sites, coincided with active histone modifications, and specifically marked actively expressed genes. Notably, sequencing only the subnucleosomal fraction dramatically improved signal, while separation of subnucleosomal reads post-sequencing did not improve signal or peak calling. The broader applicability of this modified ATAC-seq technique was tested using cryopreserved nuclei preparations from pig tissues, resulting in NFR that were highly consistent among biological replicates. Furthermore, tissue-specific NFR were enriched for binding motifs of transcription factors related to tissue-specific functions, and marked genes functionally enriched for tissue-specific processes. Overall, these results provide insights into the optimization of ATAC-seq and a platform for profiling open chromatin in animal tissues

Role of pseudospin in quasiparticle interferences in epitaxial graphene probed by high-resolution scanning tunneling microscopy

Pseudospin, an additional degree of freedom related to the honeycomb structure of graphene, is responsible of many of the outstanding electronic properties found in this material. This article provides a clear understanding of how such pseudospin impacts the quasiparticle interferences of monolayer (ML) and bilayer (BL) graphene measured by low temperature scanning tunneling microscopy and spectroscopy. We have used this technique to map, with very high energy and space resolution, the spatial modulations of the local density of states of ML and BL graphene epitaxialy grown on SiC(0001), in presence of native disorder. We perform a Fourier transform analysis of such modulations including wavevectors up to unit-vectors of the reciprocal lattice. Our data demonstrate that the quasiparticle interferences associated to some particular scattering processes are suppressed in ML graphene, but not in BL graphene. Most importantly, interferences with 2qF wavevector associated to intravalley backscattering are not measured in ML graphene, even on the images with highest resolution. In order to clarify the role of the pseudospin on the quasiparticle interferences, we use a simple model which nicely captures the main features observed on our data. The model unambiguously shows that graphene's pseudospin is responsible for such suppression of quasiparticle interferences features in ML graphene, in particular for those with 2qF wavevector. It also confirms scanning tunneling microscopy as a unique technique to probe the pseudospin in graphene samples in real space with nanometer precision. Finally, we show that such observations are robust with energy and obtain with great accuracy the dispersion of the \pi-bands for both ML and BL graphene in the vicinity of the Fermi level, extracting their main tight binding parameters

Quasiparticle Chirality in Epitaxial Graphene Probed at the Nanometer Scale

Graphene exhibits unconventional two-dimensional electronic properties resulting from the symmetry of its quasiparticles, which leads to the concepts of pseudospin and electronic chirality. Here we report that scanning tunneling microscopy can be used to probe these unique symmetry properties at the nanometer scale. They are reflected in the quantum interference pattern resulting from elastic scattering off impurities, and they can be directly read from its fast Fourier transform. Our data, complemented by theoretical calculations, demonstrate that the pseudospin and the electronic chirality in epitaxial graphene on SiC(0001) correspond to the ones predicted for ideal graphene.Comment: 4 pages, 3 figures, minor change

Characterization of integrated optics components for the second generation of VLTI instruments

Two of the three instruments proposed to ESO for the second generation instrumentation of the VLTI would use integrated optics for beam combination. Several design are studied, including co-axial and multi-axial recombination. An extensive quantity of combiners are therefore under test in our laboratories. We will present the various components, and the method used to validate and compare the different combiners. Finally, we will discuss the performances and their implication for both VSI and Gravity VLTI instruments.Comment: SPIE Astronomical Instrumentation 2008 in Marseille, France -- Equation (7) update

Single 3dd transition metal atoms on multi-layer graphene systems: electronic configurations, bonding mechanisms and role of the substrate

The electronic configurations of Fe, Co, Ni, and Cu adatoms on graphene and graphite have been studied by x-ray magnetic circular dichroism and charge transfer multiplet theory. A delicate interplay between long-range interactions and local chemical bonding is found to influence the adatom equilibrium distance and magnetic moment. The results for Fe and Co are consistent with purely physisorbed species having, however, different 3$d$-shell occupancies on graphene and graphite ($d^{n+1}$ and $d^n$, respectively). On the other hand, for the late 3$d$ metals Ni and Cu a trend towards chemisorption is found, which strongly quenches the magnetic moment on both substrates.Comment: 7 pages, 4 figure

Multipole Ordering and Fluctuations in f-Electron Systems

We investigate effects of multipole moments in f-electron systems both from phenomenological and microscopic viewpoints. First, we discuss significant effects of octupole moment on the magnetic susceptibility in a paramagnetic phase. It is found that even within mean-field approximation, the magnetic susceptibility deviates from the Curie-Weiss law due to interactions between dipole and octupole moments. Next, we proceed to a microscopic theory for multipole ordering on the basis of a j-j coupling scheme. After brief explanation of a method to derive multipole interactions from the $f$-electron model, we discuss several multipole ordered phases depending on lattice structure. Finally, we show our new development of the microscopic approach to the evaluation of multipole response functions. We apply fluctuation exchange approximation to the f-electron model, and evaluate multipole response functions.Comment: 7 pages, 4 figures, Proceedings of ASR-WYP-200

ExTrA: Exoplanets in Transit and their Atmospheres

The ExTrA facility, located at La Silla observatory, will consist of a near-infrared multi-object spectrograph fed by three 60-cm telescopes. ExTrA will add the spectroscopic resolution to the traditional differential photometry method. This shall enable the fine correction of color-dependent systematics that would otherwise hinder ground-based observations. With both this novel method and an infrared-enabled efficiency, ExTrA aims to find transiting telluric planets orbiting in the habitable zone of bright nearby M dwarfs. It shall have the versatility to do so by running its own independent survey and also by concurrently following-up on the space candidates unveiled by K2 and TESS. The exoplanets detected by ExTrA will be amenable to atmospheric characterisation with VLTs, JWST, and ELTs and could give our first peek into an exo-life laboratory.Comment: 15 pages, 11 figures, SPIE 201

Clinical Outcomes of a Hospital-Based Teleophthalmology Service: What Happens to Patients in a Virtual Clinic?

PURPOSE: Demographic changes as well as increasing referral rates from national screening services put pressure on available ophthalmologic resources in the United Kingdom. To improve resource allocation, virtual medical retina clinics were introduced in 2016 in Moorfields Eye Hospital, South Division. The scope of this work was to assess clinical outcomes of patients followed up in a virtual clinic setting. DESIGN: Retrospective database study. PARTICIPANTS: Patients booked for a consecutive appointment in our virtual medical retina clinic. METHODS: Seven hundred twenty-eight patients booked for their second virtual clinic appointment in a tertiary eye care referral center between November 2016 and July 2018 were identified retrospectively from our electronic health records and patient administration systems. Information about disease grade and clinical and visual outcomes was assessed. MAIN OUTCOME MEASURES: Clinical outcome of the virtual clinic visit, including virtual follow-up, urgent referral to face-to-face clinic, or discharge. RESULTS: Seven hundred twelve of 728 patients received a clinical outcome. Four hundred ninety-seven patients (70%) were eligible for further virtual follow-up after the second virtual clinic visit, whereas 15% each (107 and 108 patients) were either discharged or referred to a face-to-face clinic. In total, 661 patients attended their appointments in person and were reviewed by trained staff. Seventeen patients were referred for urgent treatment and 8 patients were not suitable for virtual follow-up. In 542 (82%) of all patients, diabetic retinopathy was the most common diagnosis. CONCLUSIONS: This study reports clinical outcomes of a virtual model of care for medical retina clinics that imply safety of patient care in this clinic setting. This clinic format optimizes the use of already available resources and increases the skills of our existing workforce while maintaining high-quality clinical standards

Growing smooth interfaces with inhomogeneous, moving external fields: dynamical transitions, devil's staircases and self-assembled ripples

We study the steady state structure and dynamics of an interface in a pure Ising system on a square lattice placed in an inhomogeneous external field. The field has a profile with a fixed shape designed to stabilize a flat interface, and is translated with velocity v_e. For small v_e, the interface is stuck to the profile, is macroscopically smooth, and is rippled with a periodicity in general incommensurate with the lattice parameter. For arbitrary orientations of the profile, the local slope of the interface locks in to one of infinitely many rational values (devil's staircase) which most closely approximates the profile. These ``lock-in'' structures and ripples dissappear as v_e increases. For still larger v_e the profile detaches from the interface which is now characterized by standard Kardar-Parisi-Zhang (KPZ) exponents.Comment: 4 pages, 4 figures, published version, minor change

Magnetic Susceptibility of Multiorbital Systems

Effects of orbital degeneracy on magnetic susceptibility in paramagnetic phases are investigated within a mean-field theory. Under certain crystalline electric fields, the magnetic moment consists of two independent moments, e.g., spin and orbital moments. In such a case, the magnetic susceptibility is given by the sum of two different Curie-Weiss relations, leading to deviation from the Curie-Weiss law. Such behavior may be observed in d- and f-electron systems with t_{2g} and Gamma_8 ground states, respectively. As a potential application of our theory, we attempt to explain the difference in the temperature dependence of magnetic susceptibilities of UO_2 and NpO_2.Comment: 4 pages, 3 figure