Boost-HiC: computational enhancement of long-range contacts in chromosomal contact maps

International audienceGenome-wide chromosomal contact maps are widely used to uncover the 3D organisation of genomes. They rely on the collection of millions of contacting pairs of genomic loci. Contact frequencies at short range are usually well measured in experiments, while there is a lot of missing information about long-range contacts. We propose to use the sparse information contained in raw contact maps to determine high-confidence contact frequency between all pairs of loci. Our algorithmic procedure, Boost-HiC, enables the detection of Hi-C patterns such as chromosomal compartments at a resolution that would be otherwise only attainable by sequencing a hundred times deeper the experimental Hi-C library

Field-effect control of superconductivity and Rashba spin-orbit coupling in top-gated LaAlO3/SrTiO3 devices

The recent development in the fabrication of artificial oxide heterostructures opens new avenues in the field of quantum materials by enabling the manipulation of the charge, spin and orbital degrees of freedom. In this context, the discovery of two-dimensional electron gases (2-DEGs) at LAlO3/SrTiO3 interfaces, which exhibit both superconductivity and strong Rashba spin-orbit coupling (SOC), represents a major breakthrough. Here, we report on the realisation of a field-effect LaAlO3/SrTiO3 device, whose physical properties, including superconductivity and SOC, can be tuned over a wide range by a top-gate voltage. We derive a phase diagram, which emphasises a field-effect-induced superconductor-to-insulator quantum phase transition. Magneto-transport measurements indicate that the Rashba coupling constant increases linearly with electrostatic doping. Our results pave the way for the realisation of mesoscopic devices, where these two properties can be manipulated on a local scale by means of top-gates

Critical Opalescence in Baryonic QCD Matter

We show that critical opalescence, a clear signature of second-order phase transition in conventional matter, manifests itself as critical intermittency in QCD matter produced in experiments with nuclei. This behaviour is revealed in transverse momentum spectra as a pattern of power laws in factorial moments, to all orders, associated with baryon production. This phenomenon together with a similar effect in the isoscalar sector of pions (sigma mode) provide us with a set of observables associated with the search for the QCD critical point in experiments with nuclei at high energies.Comment: 7 pages, 1 figur

beta-amyloid modulation of synaptic transmission and plasticity

The sequencing of β amyloid protein (Aβ) in 1984 led to the formulation of the “amyloid hypothesis” of Alzheimer's disease (AD) (Glenner and Wong, 1984). The hypothesis proposed that accumulation of Aβ is responsible for AD-related pathology, including Aβ deposits, neurofibrillary tangles, and eventual neuronal cell death (Tanzi and Bertram, 2005). Within a few years, four groups cloned the amyloid precursor protein (APP) gene from which Aβ is processed (Goldgaber et al., 1987; Kang et al., 1987; Robakis et al., 1987; Tanzi et al., 1987). Linkage analysis mapped the gene to chromosome 21, and mutations in APP were found that led to the inappropriate processing of APP into the Aβ1–42 peptide (Goate et al., 1991; Mullan et al., 1992) (for review, see Tanzi and Bertram, 2005). However, these mutations are responsible for only a small fraction of the early-onset familial AD, and the search began for other genes that might also influence the processing of Aβ. Several novel mutations were identified in the presenilins (Levy-Lahad et al., 1995; Rogaev et al., 1995; Sherrington et al., 1995), and apolipoprotein E4 was identified as a major risk factor for the most frequent form of AD (Strittmatter et al., 1993; Mahley et al., 2006)

Quantized conductance in a one-dimensional ballistic oxide nanodevice

Electric-field effect control of two-dimensional electron gases (2-DEG) has enabled the exploration of nanoscale electron quantum transport in semiconductors. Beyond these classical materials, transition metal-oxide-based structures have d-electronic states favoring the emergence of novel quantum orders absent in conventional semiconductors. In this context, the LaAlO3/SrTiO3 interface that combines gate-tunable superconductivity and sizeable spin-orbit coupling is emerging as a promising platform to realize topological superconductivity. However, the fabrication of nanodevices in which the electronic properties of this oxide interface can be controlled at the nanoscale by field-effect remains a scientific and technological challenge. Here, we demonstrate the quantization of conductance in a ballistic quantum point contact (QPC), formed by electrostatic confinement of the LaAlO3/SrTiO3 2-DEG with a split-gate. Through finite source-drain voltage, we perform a comprehensive spectroscopic investigation of the 3d energy levels inside the QPC, which can be regarded as a spectrometer able to probe Majorana states in an oxide 2-DEG

Anomalous thickness-dependent electrical conductivity in van der Waals layered transition metal halide, Nb₃Cl₈

Understanding the electronic transport properties of layered, van der Waals transition metal halides (TMHs) and chalcogenides is a highly active research topic today. Of particular interest is the evolution of those properties with changing thickness as the 2D limit is approached. Here, we present the electrical conductivity of exfoliated single crystals of the TMH, cluster magnet, Nb3Cl8, over a wide range of thicknesses both with and without hexagonal boron nitride (hBN) encapsulation. The conductivity is found to increase by more than three orders of magnitude when the thickness is decreased from 280 µm to 5 nm, at 300 K. At low temperatures and below ~50 nm, the conductance becomes thickness independent, implying surface conduction is dominating. Temperature dependent conductivity measurements indicate Nb3Cl8 is an insulator, however, the effective activation energy decreases from a bulk value of 310 meV to 140 meV by 5 nm. X-ray photoelectron spectroscopy (XPS) shows mild surface oxidation in devices without hBN capping, however, no significant difference in transport is observed when compared to the capped devices, implying the thickness dependent transport behavior is intrinsic to the material. A conduction mechanism comprised of a higher conductivity surface channel in parallel with a lower conductivity interlayer channel is discussed

Vibrio cholerae in the Environment: A Simple Method for Reliable Identification of the Species

A simple screening and identification protocol was assessed for the efficient distinction of colonies of Vibrio cholerae species from others obtained on thiosulphate citrate bile salts sucrose agar after isola\uadtion from different environmental specimens. It was demonstrated here that the yellow colonies (su\uadcrose-fermenting), which are able to grow on nutrient agar without added NaCl and which present a positive oxidase reaction, can be confidently considered as presumptive V. cholerae. Confirmation of the identification was carried out using the API 20E microtest and by species-specific ompW-based polymerase chain reaction: 809 of 925 isolates obtained by this screening procedure were identified as V. cholerae by API 20E and confirmed by PCR. The results showed that the direct use of the PCR-based method for the definite identification of the screened colonies gave better results than the API 20E method: of a selection of 100 isolates presumptively identified as V. cholerae according to the proposed screening procedure, all gave a positive result with PCR but only 94 were confirmed by API 20E. This protocol provides reliable identification of V. cholerae species and is adapted to the capabilities of routine clinical, food-testing and environmental microbiology laboratories

Competition between electron pairing and phase coherence in superconducting interfaces

In LaAlO3/SrTiO3 heterostructures, a gate tunable superconducting electron gas is confined in a quantum well at the interface between two insulating oxides. Remarkably, the gas coexists with both magnetism and strong Rashba spin–orbit coupling. However, both the origin of superconductivity and the nature of the transition to the normal state over the whole doping range remain elusive. Here we use resonant microwave transport to extract the superfluid stiffness and the superconducting gap energy of the LaAlO3/SrTiO3 interface as a function of carrier density. We show that the superconducting phase diagram of this system is controlled by the competition between electron pairing and phase coherence. The analysis of the superfluid density reveals that only a very small fraction of the electrons condenses into the superconducting state. We propose that this corresponds to the weak filling of high- energy dxz/dyz bands in the quantum well, more apt to host superconductivity