Mutations in the Arabidopsis Peroxisomal ABC Transporter COMATOSE Allow Differentiation between Multiple Functions In Planta: Insights from an Allelic Series

COMATOSE (CTS), the Arabidopsis homologue of human Adrenoleukodystrophy protein (ALDP), is required for import of substrates for peroxisomal β-oxidation. A new allelic series and a homology model based on the bacterial ABC transporter, Sav1866, provide novel insights into structure-function relations of ABC subfamily D proteins. In contrast to ALDP, where the majority of mutations result in protein absence from the peroxisomal membrane, all CTS mutants produced stable protein. Mutation of conserved residues in the Walker A and B motifs in CTS nucleotide-binding domain (NBD) 1 resulted in a null phenotype but had little effect in NBD2, indicating that the NBDs are functionally distinct in vivo. Two alleles containing mutations in NBD1 outside the Walker motifs (E617K and C631Y) exhibited resistance to auxin precursors 2,4-dichlorophenoxybutyric acid (2,4-DB) and indole butyric acid (IBA) but were wild type in all other tests. The homology model predicted that the transmission interfaces are domain-swapped in CTS, and the differential effects of mutations in the conserved "EAA motif" of coupling helix 2 supported this prediction, consistent with distinct roles for each NBD. Our findings demonstrate that CTS functions can be separated by mutagenesis and the structural model provides a framework for interpretation of phenotypic data

The Role of Booster Vaccination and Ongoing Viral Evolution In Seasonal Circulation of SARS-CoV-2

Periodic resurgences of COVID-19 in the coming years can be expected, while public health interventions may be able to reduce their intensity. We used a transmission model to assess how the use of booster doses and non-pharmaceutical interventions (NPIs) amid ongoing pathogen evolution might influence future transmission waves. We find that incidence is likely to increase as NPIs relax, with a second seasonally driven surge expected in autumn 2022. However, booster doses can greatly reduce the intensity of both waves and reduce cumulative deaths by 20% between 7 January 2022 and 7 January 2023. Reintroducing NPIs during the autumn as incidence begins to increase again could also be impactful. Combining boosters and NPIs results in a 30% decrease in cumulative deaths, with potential for greater impacts if variant-adapted boosters are used. Reintroducing these NPIs in autumn 2022 as transmission rates increase provides similar benefits to sustaining NPIs indefinitely (307 000 deaths with indefinite NPIs and boosters compared with 304 000 deaths with transient NPIs and boosters). If novel variants with increased transmissibility or immune escape emerge, deaths will be higher, but vaccination and NPIs are expected to remain effective tools to decrease both cumulative and peak health system burden, providing proportionally similar relative impacts

Comparing initial-data sets for binary black holes

We compare the results of constructing binary black hole initial data with three different decompositions of the constraint equations of general relativity. For each decomposition we compute the initial data using a superposition of two Kerr-Schild black holes to fix the freely specifiable data. We find that these initial-data sets differ significantly, with the ADM energy varying by as much as 5% of the total mass. We find that all initial-data sets currently used for evolutions might contain unphysical gravitational radiation of the order of several percent of the total mass. This is comparable to the amount of gravitational-wave energy observed during the evolved collision. More astrophysically realistic initial data will require more careful choices of the freely specifiable data and boundary conditions for both the metric and extrinsic curvature. However, we find that the choice of extrinsic curvature affects the resulting data sets more strongly than the choice of conformal metric.Comment: 18 pages, 12 figures, accepted for publication in Phys. Rev.

Black Hole Interaction Energy

The interaction energy between two black holes at large separation distance is calculated. The first term in the expansion corresponds to the Newtonian interaction between the masses. The second term corresponds to the spin-spin interaction. The calculation is based on the interaction energy defined on the two black holes initial data. No test particle approximation is used. The relation between this formula and cosmic censorship is discussed.Comment: 18 pages, 2 figures, LaTeX2

Hard Instances of the Constrained Discrete Logarithm Problem

The discrete logarithm problem (DLP) generalizes to the constrained DLP, where the secret exponent $x$ belongs to a set known to the attacker. The complexity of generic algorithms for solving the constrained DLP depends on the choice of the set. Motivated by cryptographic applications, we study sets with succinct representation for which the constrained DLP is hard. We draw on earlier results due to Erd\"os et al. and Schnorr, develop geometric tools such as generalized Menelaus' theorem for proving lower bounds on the complexity of the constrained DLP, and construct sets with succinct representation with provable non-trivial lower bounds

Expanded Vandermonde powers and sum rules for the two-dimensional one-component plasma

The two-dimensional one-component plasma (2dOCP) is a system of $N$ mobile particles of the same charge $q$ on a surface with a neutralising background. The Boltzmann factor of the 2dOCP at temperature $T$ can be expressed as a Vandermonde determinant to the power $\Gamma=q^{2}/(k_B T)$. Recent advances in the theory of symmetric and anti-symmetric Jack polymonials provide an efficient way to expand this power of the Vandermonde in their monomial basis, allowing the computation of several thermodynamic and structural properties of the 2dOCP for $N$ values up to 14 and $\Gamma$ equal to 4, 6 and 8. In this work, we explore two applications of this formalism to study the moments of the pair correlation function of the 2dOCP on a sphere, and the distribution of radial linear statistics of the 2dOCP in the plane

Holography, Pade Approximants and Deconstruction

We investigate the relation between holographic calculations in 5D and the Migdal approach to correlation functions in large N theories. The latter employs Pade approximation to extrapolate short distance correlation functions to large distances. We make the Migdal/5D relation more precise by quantifying the correspondence between Pade approximation and the background and boundary conditions in 5D. We also establish a connection between the Migdal approach and the models of deconstructed dimensions.Comment: 28 page

Second order gauge invariant gravitational perturbations of a Kerr black hole

We investigate higher than the first order gravitational perturbations in the Newman-Penrose formalism. Equations for the Weyl scalar $\psi_4,$ representing outgoing gravitational radiation, can be uncoupled into a single wave equation to any perturbative order. For second order perturbations about a Kerr black hole, we prove the existence of a first and second order gauge (coordinates) and tetrad invariant waveform, $\psi_I$, by explicit construction. This waveform is formed by the second order piece of $\psi_4$ plus a term, quadratic in first order perturbations, chosen to make $\psi_I$ totally invariant and to have the appropriate behavior in an asymptotically flat gauge. $\psi_I$ fulfills a single wave equation of the form ${\cal T}\psi_I=S,$ where ${\cal T}$ is the same wave operator as for first order perturbations and $S$ is a source term build up out of (known to this level) first order perturbations. We discuss the issues of imposition of initial data to this equation, computation of the energy and momentum radiated and wave extraction for direct comparison with full numerical approaches to solve Einstein equations.Comment: 19 pages, REVTEX. Some misprints corrected and changes to improve presentation. Version to appear in PR

On the nature of the finite-temperature transition in QCD

We discuss the nature of the finite-temperature transition in QCD with N_f massless flavors. Universality arguments show that a continuous (second-order) transition must be related to a 3-D universality class characterized by a complex N_f X N_f matrix order parameter and by the symmetry-breaking pattern [SU(N_f)_L X SU(N_f)_R]/Z(N_f)_V -> SU(N_f)_V/Z(N_f)_V, or [U(N_f)_L X U(N_f)_R]/U(1)_V -> U(N_f)_V/U(1)_V if the U(1)_A symmetry is effectively restored at T_c. The existence of any of these universality classes requires the presence of a stable fixed point in the corresponding 3-D Phi^4 theory with the expected symmetry-breaking pattern. Otherwise, the transition is of first order. In order to search for stable fixed points in these Phi^4 theories, we exploit a 3-D perturbative approach in which physical quantities are expanded in powers of appropriate renormalized quartic couplings. We compute the corresponding Callan-Symanzik beta-functions to six loops. We also determine the large-order behavior to further constrain the analysis. No stable fixed point is found, except for N_f=2, corresponding to the symmetry-breaking pattern [SU(2)_L X SU(2)_R]/Z(2)_V -> SU(2)_V/Z(2)_V equivalent to O(4) -> O(3). Our results confirm and put on a firmer ground earlier analyses performed close to four dimensions, based on first-order calculations in the framework of the epsilon=4-d expansion. These results indicate that the finite-temperature phase transition in QCD is of first order for N_f>2. A continuous transition is allowed only for N_f=2. But, since the theory with symmetry-breaking pattern [U(2)_L X U(2)_R]/U(1)_V -> U(2)_V/U(1)_V does not have stable fixed points, the transition can be continuous only if the effective breaking of the U(1)_A symmetry is sufficiently large.Comment: 30 pages, 3 figs, minor correction