Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations.

Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting one to three genomic sites per cell. We engineer an Acidaminococcus Cas12a (AsCas12a) variant, multiplexed transcriptional interference AsCas12a (multiAsCas12a), that incorporates R1226A, a mutation that stabilizes the ribonucleoprotein-DNA complex via DNA nicking. The multiAsCas12a-KRAB fusion improves CRISPRi activity over DNase-dead AsCas12a-KRAB fusions, often rescuing the activities of lentivirally delivered CRISPR RNAs (crRNA) that are inactive when used with the latter. multiAsCas12a-KRAB supports CRISPRi using 6-plex crRNA arrays in high-throughput pooled screens. Using multiAsCas12a-KRAB, we discover enhancer elements and dissect the combinatorial function of cis-regulatory elements in human cells. These results instantiate a group testing framework for efficiently surveying numerous combinations of chromatin perturbations for biological discovery and engineering.

Localisation of vibrational modes in high-entropy oxides.

The recently-discovered high-entropy oxides (HEO's) offer a paradoxical combination of crystalline arrangement and high disorder. They differ qualitatively from established paradigms for disordered solids such as glasses and alloys. In these latter systems, it is well known that disorder induces localised vibrational excitations. In this article, we explore the possibility of disorder-induced localisation in Mg0.2Co0.2Ni0.2Cu0.2Zn0.2O, the prototypical HEO with rock-salt structure. To describe phononic excitations, we model the interatomic potentials for the cation-oxygen interactions by fitting to the physical properties of the parent binary oxides. We validate our model against the experimentally determined crystal structure and optical conductivity. The resulting phonon spectrum shows wave-like propagating modes at low energies and localised modes at high energies. Localisation is reflected in signatures such as participation ratio and correlation amplitude. Finally, we argue that mass disorder can be increased to enhance localisation. We consider a hypothetical material, high-entropy telluride-oxide, where tellurium atoms are admixed into the anion sublattice. This shows a larger localised fraction, with additional localised modes appearing in the middle of the spectrum. Our results demonstrate that HEO's are a promising platform to study Anderson localisation of phonons.

Higher-order combinatorial chromatin perturbations by engineered CRISPR-Cas12a for functional genomics.

Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting 1-3 genomic sites per cell. To develop a tool for higher-order ( > 3) combinatorial targeting of genomic sites with CRISPRi in functional genomics screens, we engineered an Acidaminococcus Cas12a variant -- referred to as mul tiplexed transcriptional interference AsCas12a (multiAsCas12a). multiAsCas12a incorporates a key mutation, R1226A, motivated by the hypothesis of nicking-induced stabilization of the ribonucleoprotein:DNA complex for improving CRISPRi activity. multiAsCas12a significantly outperforms prior state-of-the-art Cas12a variants in combinatorial CRISPRi targeting using high-order multiplexed arrays of lentivirally transduced CRISPR RNAs (crRNA), including in high-throughput pooled screens using 6-plex crRNA array libraries. Using multiAsCas12a CRISPRi, we discover new enhancer elements and dissect the combinatorial function of cis-regulatory elements. These results instantiate a group testing framework for efficiently surveying potentially numerous combinations of chromatin perturbations for biological discovery and engineering.

Dirofilariasis mouse models for heartworm preclinical research.

Introduction: Dirofilariasis, including heartworm disease, is a major emergent veterinary parasitic infection and a human zoonosis. Currently, experimental infections of cats and dogs are used in veterinary heartworm preclinical drug research. Methods: As a refined alternative in vivo heartworm preventative drug screen, we assessed lymphopenic mouse strains with ablation of the interleukin-2/7 common gamma chain (γc) as susceptible to the larval development phase of Dirofilaria immitis. Results: Non-obese diabetic (NOD) severe combined immunodeficiency (SCID)γc-/- (NSG and NXG) and recombination-activating gene (RAG)2-/-γc-/- mouse strains yielded viable D. immitis larvae at 2-4 weeks post-infection, including the use of different batches of D. immitis infectious larvae, different D. immitis isolates, and at different laboratories. Mice did not display any clinical signs associated with infection for up to 4 weeks. Developing larvae were found in subcutaneous and muscle fascia tissues, which is the natural site of this stage of heartworm in dogs. Compared with in vitro-propagated larvae at day 14, in vivo-derived larvae had completed the L4 molt, were significantly larger, and contained expanded Wolbachia endobacteria titres. We established an ex vivo L4 paralytic screening system whereby assays with moxidectin or levamisole highlighted discrepancies in relative drug sensitivities in comparison with in vitro-reared L4 D. immitis. We demonstrated effective depletion of Wolbachia by 70%-90% in D. immitis L4 following 2- to 7-day oral in vivo exposures of NSG- or NXG-infected mice with doxycycline or the rapid-acting investigational drug, AWZ1066S. We validated NSG and NXG D. immitis mouse models as a filaricide screen by in vivo treatments with single injections of moxidectin, which mediated a 60%-88% reduction in L4 larvae at 14-28 days. Discussion: Future adoption of these mouse models will benefit end-user laboratories conducting research and development of novel heartworm preventatives via increased access, rapid turnaround, and reduced costs and may simultaneously decrease the need for experimental cat or dog use.

Quantum Simulation of the Bosonic Creutz Ladder with a Parametric Cavity.

There has been a growing interest in realizing quantum simulators for physical systems where perturbative methods are ineffective. The scalability and flexibility of circuit quantum electrodynamics make it a promising platform for implementing various types of simulators, including lattice models of strongly coupled field theories. Here, we use a multimode superconducting parametric cavity as a hardware-efficient analog quantum simulator, realizing a lattice in synthetic dimensions with complex hopping interactions. The coupling graph, i.e., the realized model, can be programmed in situ. The complex-valued hopping interaction further allows us to simulate, for instance, gauge potentials and topological models. As a demonstration, we simulate a plaquette of the bosonic Creutz ladder. We characterize the lattice with scattering measurements, reconstructing the experimental Hamiltonian and observing important precursors of topological features including nonreciprocal transport and Aharonov-Bohm caging. This platform can be easily extended to larger lattices and different models involving other interactions.

Tripartite Genuine Non-Gaussian Entanglement in Three-Mode Spontaneous Parametric Down-Conversion.

We show that the states generated by a three-mode spontaneous parametric down-conversion (SPDC) interaction Hamiltonian possess tripartite entanglement of a different nature to other paradigmatic three-mode entangled states generated by the combination of two-mode SPDC interactions. While two-mode SPDC generates Gaussian states whose entanglement can be characterized by standard criteria based on two-mode quantum correlations, these criteria fail to capture the entanglement generated by three-mode SPDC. We use criteria built from three-mode correlation functions to show that the class of states recently generated in a superconducting-circuit implementation of three-mode SPDC ideally have tripartite entanglement, contrary to recent claims in the literature. These criteria are suitable for triple SPDC but we show that they fail to detect tripartite entanglement in other states which are known to possess it, which illustrates the existence of two fundamentally different notions of tripartite entanglement in three-mode continuous-variable systems.

Publisher Correction: Probing the strongly driven spin-boson model in a superconducting quantum circuit.

The original PDF and HTML versions of this Article omitted the ORCID ID of the authors L. Magazzù and P. Forn-Díaz. (L. Magazzù: 0000-0002-4377-8387; P. Forn-Diaz: 0000-0003-4365-5157).The original PDF version of this Article contained errors in Eqs. (2), (6), (13), (14), (25), (26). These equations were missing all instances of 'Γ' and 'Δ', which are correctly displayed in the HTML version.Similarly, the inline equation in the third sentence of the caption of Fig. 2 was missing the left hand term 'Ω'.The original HTML version of this Article contained errors in Table 1. The correct version of the sixth row of the first column states 'Figure 2' instead of the original, incorrect 'Figure'. And the correction version of the ninth row of the first column states 'Figure 3' instead of the original, incorrect 'Figure'.This has been corrected in both the PDF and HTML versions of the Article.

Probing the strongly driven spin-boson model in a superconducting quantum circuit.

Quantum two-level systems interacting with the surroundings are ubiquitous in nature. The interaction suppresses quantum coherence and forces the system towards a steady state. Such dissipative processes are captured by the paradigmatic spin-boson model, describing a two-state particle, the "spin", interacting with an environment formed by harmonic oscillators. A fundamental question to date is to what extent intense coherent driving impacts a strongly dissipative system. Here we investigate experimentally and theoretically a superconducting qubit strongly coupled to an electromagnetic environment and subjected to a coherent drive. This setup realizes the driven Ohmic spin-boson model. We show that the drive reinforces environmental suppression of quantum coherence, and that a coherent-to-incoherent transition can be achieved by tuning the drive amplitude. An out-of-equilibrium detailed balance relation is demonstrated. These results advance fundamental understanding of open quantum systems and bear potential for the design of entangled light-matter states.

Antiferromagnetic vs. non-magnetic ε phase of solid oxygen. Periodic density functional theory studies using a localized atomic basis set and the role of exact exchange.

The question of the non-magnetic (NM) vs. antiferromagnetic (AF) nature of the ε phase of solid oxygen is a matter of great interest and continuing debate. In particular, it has been proposed that the ε phase is actually composed of two phases, a low-pressure AF ε1 phase and a higher pressure NM ε0 phase [Crespo et al., Proc. Natl. Acad. Sci. U. S. A., 2014, 111, 10427]. We address this problem through periodic spin-restricted and spin-polarized Kohn-Sham density functional theory calculations at pressures from 10 to 50 GPa using calibrated GGA and hybrid exchange-correlation functionals with Gaussian atomic basis sets. The two possible configurations for the antiferromagnetic (AF1 and AF2) coupling of the 0 ≤ S ≤ 1 O2 molecules in the (O2)4 unit cell were studied. Full enthalpy-driven geometry optimizations of the (O2)4 unit cells were done to study the pressure evolution of the enthalpy difference between the non-magnetic and both antiferromagnetic structures. We also address the evolution of structural parameters and the spin-per-molecule vs. pressure. We find that the spin-less solution becomes more stable than both AF structures above 50 GPa and, crucially, the spin-less solution yields lattice parameters in much better agreement with experimental data at all pressures than the AF structures. The optimized AF2 broken-symmetry structures lead to large errors of the a and b lattice parameters when compared with experiments. The results for the NM model are in much better agreement with the experimental data than those found for both AF models and are consistent with a completely non-magnetic (O2)4 unit cell for the low-pressure regime of the ε phase.

Quantum heat engine with coupled superconducting resonators.

We propose a quantum heat engine composed of two superconducting transmission line resonators interacting with each other via an optomechanical-like coupling. One resonator is periodically excited by a thermal pump. The incoherently driven resonator induces coherent oscillations in the other one due to the coupling. A limit cycle, indicating finite power output, emerges in the thermodynamical phase space. The system implements an all-electrical analog of a photonic piston. Instead of mechanical motion, the power output is obtained as a coherent electrical charging in our case. We explore the differences between the quantum and classical descriptions of our system by solving the quantum master equation and classical Langevin equations. Specifically, we calculate the mean number of excitations, second-order coherence, as well as the entropy, temperature, power, and mean energy to reveal the signatures of quantum behavior in the statistical and thermodynamic properties of the system. We find evidence of a quantum enhancement in the power output of the engine at low temperatures.

The V + I defects in diamond: An ab initio investigation of the electronic structure, of the Raman and IR spectra, and of their possible recombination.

The double defect in diamond, vacancy (V) plus 〈100〉 self-split-interstitial (V+I), is investigated at the ab initio quantum mechanical level, by considering the vicinal case VI1 (V is one of the first neighbors of one of the two C atoms constituting the I defect) and the two possible "second neighbors" cases, VI2D, VI2S, in which a carbon atom is a first neighbor of both V and I. The case in which the two defects are at a larger distance is simulated by considering the two isolated defects separately (VI∞). A 6-21G local Gaussian-type basis set and the B3LYP hybrid functional are used for most of the calculations; richer basis sets and other functionals (a global hybrid as PBE0, a range-separated hybrid as HSE06, LDA, PBE, and Hartree-Fock) have also been used for comparison. With this computational approach we evaluate the energy difference between the various spin states, the location of the corresponding bands in the energy gap of pristine diamond, as well as the defect formation energy of the four defects. The path for the recombination of V and I is explored for the vicinal case, by using the distinguished reaction coordinate strategy. A barrier as high as 0.75 eV is found with B3LYP between VI1 and the perfect diamond recombined structure; when other hybrids are used, as PBE0 or HSE06, the barrier increases up to 1.01 eV (pure density functional theory produces lower barriers: 0.62 and 0.67 for PBE and LDA, respectively). Such a barrier is lower than the one estimated in a very indirect way through experimental data, ranging from 1.3 to 1.7 eV. It confirms however the evidence of the extremely low recombination rate also at high temperature. The Raman (and IR) spectra of the various defects are generated, which permit one to unambiguously attribute to these defects (thanks also to the graphical animation of the modes) many of the peaks observed in damaged diamond above the dominant peak of perfect bulk. For the residual non-attributed peaks, more complicated aggregations of defects should be explored.

Single-shot read-out of a superconducting qubit using a Josephson parametric oscillator.

We propose and demonstrate a read-out technique for a superconducting qubit by dispersively coupling it with a Josephson parametric oscillator. We employ a tunable quarter wavelength superconducting resonator and modulate its resonant frequency at twice its value with an amplitude surpassing the threshold for parametric instability. We map the qubit states onto two distinct states of classical parametric oscillation: one oscillating state, with 185±15 photons in the resonator, and one with zero oscillation amplitude. This high contrast obviates a following quantum-limited amplifier. We demonstrate proof-of-principle, single-shot read-out performance, and present an error budget indicating that this method can surpass the fidelity threshold required for quantum computing.

Understanding the ε and ζ High-Pressure Solid Phases of Oxygen. Systematic Periodic Density Functional Theory Studies Using Localized Atomic Basis.

The experimentally characterized ε and ζ phases of solid oxygen are studied by periodic Hartree-Fock (HF) and Density Functional Theory calculations at pressures from 10 to 160 GPa using different types of exchange-correlation functionals with Gaussian atomic basis sets. Full geometry optimizations of the monoclinic C2/m (O2)4 unit cell were done to study the evolution of the structural and electronic properties with pressure. Vibrational calculations were performed at each pressure. While periodic HF does not predict the ε-ζ phase transition in the considered range, Local Density approximation and Generalized Gradient approximation methods predict too low transition pressures. The performance of hybrid functional methods is dependent on the amount of non-local HF exchange. PBE0, M06, B3PW91, and B3LYP approaches correctly predict the structural and electronic changes associated with the phase transition. GGA and hybrid functionals predict a pressure range where both phases coexist, but only the latter type of methods yield results in agreement with experiment. Using the optimized (O2)4 unit cell at each pressure we show, through CASSCF(8,8) calculations, that the greater accuracy of the optimized geometrical parameters with increasing pressure is due to a decreasing multireference character of the unit cell wave function. The mechanism of the transition from the non-conducting to the conducting ζ phase is explained through the Electron Pair Localization Function, which clearly reveals chemical bonding between O2 molecules in the ab crystal planes belonging to different unit cells due to much shorter intercell O2-O2 distances.

Quantum nondemolition detection of a propagating microwave photon.

The ability to nondestructively detect the presence of a single, traveling photon has been a long-standing goal in optics, with applications in quantum information and measurement. Realizing such a detector is complicated by the fact that photon-photon interactions are typically very weak. At microwave frequencies, very strong effective photon-photon interactions in a waveguide have recently been demonstrated. Here we show how this type of interaction can be used to realize a quantum nondemolition measurement of a single propagating microwave photon. The scheme we propose uses a chain of solid-state three-level systems (transmons) cascaded through circulators which suppress photon backscattering. Our theoretical analysis shows that microwave-photon detection with fidelity around 90% can be realized with existing technologies.

Giant cross-Kerr effect for propagating microwaves induced by an artificial atom.

We investigate the effective interaction between two microwave fields, mediated by a transmon-type superconducting artificial atom which is strongly coupled to a coplanar transmission line. The interaction between the fields and atom produces an effective cross-Kerr coupling. We demonstrate average cross-Kerr phase shifts of up to 20 degrees per photon with both coherent microwave fields at the single-photon level. Our results provide an important step toward quantum applications with propagating microwave photons.

Incidence of sexually transmitted infections in HIV-infected and HIV-uninfected adolescents in the USA.

Little is known about the incidence of bacterial sexually transmitted infections (STIs) among HIV-infected versus HIV-uninfected adolescents. This secondary analysis of a national, multisite study included adolescents aged 12-18 years who were behaviourally HIV-infected (n = 346) or HIV-uninfected but at-risk (n = 182). Incidence rates of bacterial STIs (gonorrhoea, chlamydia [CT] and trichomonas [TV; women]) were calculated using Poisson modelling. Factors associated with incident STIs were explored using Cox proportional hazards modelling. HIV-infected versus HIV-uninfected women had higher TV incidence (1.3 versus 0.6/100 person-months; P = 0.002). HIV-uninfected versus HIV-infected women had higher CT incidence (1.6 versus 1.1/100 person-months; P = 0.04). Among women, demographic, behavioural and HIV-related factors were associated with incident STIs. Among men, there were no differences in incident STIs. In this first analysis comparing STI incidence between HIV-infected and HIV-uninfected adolescents, bacterial STI incidence among women significantly differed by HIV status, and factors associated with incident STIs varied by STI and HIV status.

Breakdown of the cross-Kerr scheme for photon counting.

We show, in the context of single-photon detection, that an atomic three-level model for a transmon in a transmission line does not support the predictions of the nonlinear polarizability model known as the cross-Kerr effect. We show that the induced displacement of a probe in the presence or absence of a single photon in the signal field, cannot be resolved above the quantum noise in the probe. This strongly suggests that cross-Kerr media are not suitable for photon counting or related single-photon applications. Our results are presented in the context of a transmon in a one-dimensional microwave waveguide, but the conclusions also apply to optical systems.