Miracle-dz/UniFAR-FTUs huggingface dataset:
The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA

The raw material for viral evolution is provided by intra-host mutations occurring during replication, transcription or post-transcription. Replication and transcription of Coronaviridae proceed through the synthesis of negative-sense ‘antigenomes’ acting as templates for positive-sense genomic and subgenomic RNA. Hence, mutations in the genomes of SARS-CoV-2 and other coronaviruses can occur during (and after) the synthesis of either negative-sense or positive-sense RNA, with potentially distinct patterns and consequences. We explored for the first time the mutational spectrum of SARS-CoV-2 (sub)genomic and anti(sub)genomic RNA. We use a high-quality deep sequencing dataset produced using a quantitative strand-aware sequencing method, controlled for artefacts and sequencing errors, and scrutinized for accurate detection of within-host diversity. The nucleotide differences between negative- and positive-sense strand consensus vary between patients and do not show dependence on age or sex. Similarities and differences in mutational patterns between within-host minor variants on the two RNA strands suggested strand-specific mutations or editing by host deaminases and oxidative damage. We observe generally neutral and slight negative selection on the negative strand, contrasting with purifying selection in ORF1a, ORF1b and S genes of the positive strand of the genome.
Cryptic diversity impacts model selection and macroevolutionary inferences in diversification analyses

Species persist in landscapes through ecological dynamics but proliferate at wider spatial scales through evolutionary mechanisms. Disentangling the contribution of each dynamic is challenging, but the increasing use of dated molecular phylogenies opened new perspectives. First, the increasing use of DNA sequences in biodiversity inventory shed light on a substantial amount of cryptic diversity in species-rich ecosystems. Second, explicit diversification models accounting for various eco-evolutionary models are now available. Integrating both advances, we explored diversification trajectories among 10 lineages of freshwater fishes in Sundaland, for which time-calibrated and taxonomically rich phylogenies are available. By fitting diversification models to dated phylogenies and incorporating DNA-based species delimitation methods, the impact of cryptic diversity on diversification model selection and related inferences is explored. Eight clades display constant speciation rate model as the most likely if cryptic diversity is accounted, but nine display a signature of diversification slowdowns when cryptic diversity is ignored. Cryptic diversification occurs during the last 5 Myr for most groups, and palaeoecological models received little support. Most cryptic lineages display restricted range distribution, supporting geographical isolation across homogeneous landscapes as the main driver of diversification. These patterns question the persistence of cryptic diversity and its role during species proliferation.
The banded colour patterns of sea snakes discourage attack by predatory fishes, enabling Batesian mimicry by harmless species

The evolution of bright ‘warning’ colours in nontoxic animals often is attributed to mimicry of toxic species, but empirical tests of that hypothesis must overcome the logistical challenge of quantifying differential rates of predation in nature. Populations of a harmless sea snake species (Emydocephalus annulatus) in New Caledonia exhibit colour polymorphism, with around 20% of individuals banded rather than melanic. Stability in that proportion over 20 years has been attributed to Batesian mimicry of deadly snake species by banded morphs of the harmless taxon. This hypothesis requires that banded colours reduce a snake's vulnerability to predation. We tested that idea by pulling flexible snake-shaped models through the water and recording responses by predatory fish. Black and banded lures attracted similar numbers of following fish, but attacks were directed almost exclusively to black lures. Our methods overcome several ambiguities associated with experimental studies on mimicry in terrestrial snakes and support the hypothesis that banded colour patterns reduce a non-venomous marine snake's vulnerability to predation.
Simulated ΛCDM analogues of the thin plane of satellites around the Andromeda galaxy are not kinematically coherent structures

A large fraction of the dwarf satellites orbiting the Andromeda galaxy are surprisingly aligned in a thin, extended and apparently kinematically coherent planar structure. Such a structure is not easily found in simulations based on the Cold Dark Matter model ({\Lambda}CDM). Using 21 high resolution cosmological simulations we analyse the kinematics of planes of satellites similar to the one around Andromeda. We find good agreement when co-rotation is characterized by the line-of-sight velocity. At the same time, when co-rotation is inferred by the angular momenta of the satellites, the planes are in agreement with the plane around our Galaxy. We find such planes to be common in our high concentration haloes. The number of co-rotating satellites obtained from the sign of the line-of-sight velocity shows large variations depending on the viewing angle and is consistent with that obtained from a sample with random velocities. We find that the clustering of angular momentum vectors of the satellites in the plane is a better measure of the kinematic coherence. Thus we conclude that the line-of- sight velocity is not well suited as a proxy for the kinematical coherence of the plane. Analysis of the kinematics of our planes shows a fraction of $\sim$30% chance aligned satellites. Tracking the satellites in the plane back in time reveals that these planes are a transient feature and not kinematically coherent as would appear at first sight. Thus we expect some of the satellites in the plane around Andromeda to have high velocities perpendicular to the plane.
Twisted Brauer monoids

We investigate the structure of the twisted Brauer monoid , comparing and contrasting it with the structure of the (untwisted) Brauer monoid . We characterize Green's relations and pre-orders on , describe the lattice of ideals and give necessary and sufficient conditions for an ideal to be idempotent generated. We obtain formulae for the rank (smallest size of a generating set) and (where applicable) the idempotent rank (smallest size of an idempotent generating set) of each principal ideal; in particular, when an ideal is idempotent generated, its rank and idempotent rank are equal. As an application of our results, we describe the idempotent generated subsemigroup of (which is not an ideal), as well as the singular ideal of (which is neither principal nor idempotent generated), and we deduce that the singular part of the Brauer monoid is idempotent generated, a result previously proved by Maltcev and Mazorchuk.
Subfactors and quantum information theory

Author(s): Naaijkens, Pieter | Abstract: We consider quantum information tasks in an operator algebraic setting, where we consider normal states on von Neumann algebras. In particular, we consider subfactors N⊂M, that is, unital inclusions of von Neumann algebras with trivial center. One can ask the following question: given a normal state ω on M, how much can one learn by only doing measurements from N? We argue how the Jones index [M:N] can be used to give a quantitative answer to this, showing how the rich theory of subfactors can be used in a quantum information context. As an example we discuss how the Jones index can be used in the context of wiretap channels. Subfactors also occur naturally in physics. Here we discuss two examples: rational conformal field theories and Kitaev's toric code on the plane, a prototypical example of a topologically ordered model. There we can directly relate aspects of the general setting to physical properties such as the quantum dimension of the excitations. In the example of the toric code we also show how we can calculate the index via an approximation with finite dimensional systems. This explicit construction sheds more light on the connection between topological order and the Jones index.
BULLET CLUSTERS IN THE MareNostrum UNIVERSE

We estimate the expected distribution of displacements between the dark matter (DM) and gas cores in simulated clusters. We use the MareNostrum Universe, one of the largest non-radiative, SPH ΛCDM cosmological simulations. We find that projected two-dimensional (2D) displacements between DM and gas, equal or larger than the observed in the Bullet Cluster, are expected in 1%–2% of the clusters with masses larger than 1014 h−1 M☉. The 2D displacement distribution is roughly the same between redshifts 0 < z < 0.5 when multiplied by a factor of (1 + z)−1/2. We conclude that the separations between DM and gas as observed in the Bullet Cluster can easily be found in a ΛCDM universe. Furthermore, we find that the displacement distribution is not very sensitive to the normalization of the power spectrum. Upcoming surveys could extend the measurements of these displacements between DM and gas into large samples of hundreds of clusters, providing a potential test for ΛCDM.
Radial velocity measurements of the pulsating zirconium star: LS IV−14 ◦ 116 ⋆

The helium-rich hot subdwarf LSIV−14 ◦ 116 shows remarkably high surface abundances of zirconium, yttrium, strontium, and germanium, indicative of strong chemical stratification in the photosphere. It also shows photometric behaviour indicative of non-radial g-mode pulsations, despite having surface properties inconsistent with any known pulsational instability zone. We have conducted a search for radial velocity variability. This has demonstrated that at least one photometric period is observable in several absorption lines as a radial velocity variation with a semi-amplitude in excess of 5kms −1 . A correlation between line strength and pulsation amplitude provides evidence that the photosphere pulsates differentially. The ratio of light to velocity amplitude is too small to permit the largest amplitude oscillation to be radial.
Matrix product solutions to the reflection equation from three dimensional integrability

We formulate a quantized reflection equation in which q-boson valued L and K matrices satisfy the reflection equation up to conjugation by a solution to the Isaev–Kulish 3D reflection equation. By forming its n-concatenation along the q-boson Fock space followed by suitable reductions, we construct families of solutions to the reflection equation in a matrix product form connected to the 3D integrability. They involve the quantum R matrices of the antisymmetric tensor representations of and the spin representations of , and .
Continuity of discrete homomorphisms of diffeomorphism groups

Let $M$ and $N$ be two closed $C^{\infty}$ manifolds and let $\text{Diff}_c(M)$ denote the group of $C^{\infty}$ diffeomorphisms isotopic to the identity. We prove that any (discrete) group homomorphism between $\text{Diff}_c(M)$ and $\text{Diff}_c(N)$ is continuous. We also show that a non-trivial group homomorphism $\Phi: \text{Diff}_c(M) \to \text{Diff}_c(N)$ implies that $\dim(M) \leq \dim(N)$ and give a classification of such homomorphisms when $\dim(M) = \dim(N)$.
Using multipoles of the correlation function to measure H(z), DA(z) and β(z) from Sloan Digital Sky Survey luminous red galaxies

Galaxy clustering data can be used to measure the cosmic expansion history H(z), the angular-diameter distance D_A(z), and the linear redshift-space distortion parameter beta(z). Here we present a method for using effective multipoles of the galaxy two-point correlation function (\xi_0(s), \xi_2(s), \xi}_4(s), and \xi_6(s), with s denoting the comoving separation) to measure H(z), D_A(z)$, and beta(z), and validate it using LasDamas mock galaxy catalogs. Our definition of effective multipoles explicitly incorporates the discreteness of measurements, and treats the measured correlation function and its theoretical model on the same footing. We find that for the mock data, \xi_0+\xi_2+\xi_4 captures nearly all the information, and gives significantly stronger constraints on H(z), D_A(z), and beta(z), compared to using only \xi_0+\xi_2. We apply our method to the sample of luminous red galaxies (LRGs) from the Sloan Digital Sky Survey (SDSS) Data Release 7 (DR7) without assuming a dark energy model or a flat Universe. We find that \xi}_4(s) deviates on scales of s<60Mpc/h from the measurement from mock data (in contrast to \xi_0(s), \xi_2(s), and \xi_6(s)), thus we only use \xi_0+\xi_2 for our fiducial constraints. We obtain {H(0.35), D_A(0.35), Omega_mh^2, beta(z)} = {79. 6_{-8.7}^{+8.3} km/s/Mpc, 1057_{-87}^{+88}Mpc, 0.103\pm0.015, 0.44\pm0.15} using \xi_0+\xi_2. We find that H(0.35)r_s(z_d)/c and D_A(0.35)/r_s(z_d) (where r_s(z_d) is the sound horizon at the drag epoch) are more tightly constrained: {H(0.35)r_s(z_d)/c, D_A(0.35)/r_s(z_d)} = {0. 0437_{-0.0043}^{+0.0041}, 6. 48_{-0.43}^{+0.44}\} using \xi_0+\xi_2.
Gravitational Effects of Rotating Braneworld Black Holes

We study the light deflection effect and the relativistic periastron and frame-dragging precessions for a rotating black hole localized on the brane in the Randall-Sundrum braneworld scenario. Focusing on a light ray, which passes through the field of the black hole in its equatorial plane, we first calculate the deflection angle in the weak field limit. We obtain an analytical formula, involving the related perturbative parameters of the field up to the second order. We then proceed with the numerical calculation of the deflection angle in the strong field limit when the light ray passes at the closest distance of approach to the limiting photon orbit. We show that the deflection angles for the light ray, winding maximally rotating Kerr and braneworld black holes in the same direction as their rotation, become essentially indistinguishable from each other for a specific value of the negative tidal charge. The same feature occurs in the relativistic precession frequencies at characteristic radii, for which the radial epicyclic frequency of the test particle motion attains its highest value. These results show that to distinguish between these two types of black holes one also needs to know the precise value of the angular momentum from independent observations, which for a maximally rotating braneworld black hole must exceed the Kerr bound in general relativity.
Recent Results of Solid-State Spectroscopy

Abstract Solid state spectroscopy continues to be an important source of information on the mineralogical composition and physical properties of dust grains both in space and on planetary surfaces. With only a few exceptions, artificially produced or natural terrestrial analog materials, rather than ‘real’ cosmic dust grains, are the subject of solid state astrophysics. The Jena laboratory has provided a large number of data sets characterizing the UV, optical and infrared properties of such cosmic dust analogs. The present paper highlights recent developments and results achieved in this context, focussing on ‘non-standard conditions’ such as very low temperatures, very high temperatures and very long wavelengths.
Interplay between intermittency and dissipation in collisionless plasma turbulence

We study the damping of collisionless Alfvénic turbulence in a strongly magnetised plasma by two mechanisms: stochastic heating (whose efficiency depends on the local turbulence amplitude $\unicode[STIX]{x1D6FF}z_{\unicode[STIX]{x1D706}}$ ) and linear Landau damping (whose efficiency is independent of $\unicode[STIX]{x1D6FF}z_{\unicode[STIX]{x1D706}}$ ), describing in detail how they affect and are affected by intermittency. The overall efficiency of linear Landau damping is not affected by intermittency in critically balanced turbulence, while stochastic heating is much more efficient in the presence of intermittent turbulence. Moreover, stochastic heating leads to a drop in the scale-dependent kurtosis over a narrow range of scales around the ion gyroscale.
Period–luminosity relations for Small Magellanic Cloud Cepheid based on AKARI archival data

In this work we matched the AKARI archival data to the Optical Gravitational Lensing Experiment III (OGLE-III) catalogue to derive the mid-infrared period–luminosity (PL) relations for Small Magellanic Cloud (SMC) Cepheids. Mismatched AKARI sources were eliminated using random-phase colours obtained from the full I-band light curves from OGLE-III. It was possible to derive PL relations in the N3 and N4 bands only, although the S7-, S11-, L15- and L24-band data were also tested. Random-phase correction was included when deriving the PL relation in the N3 and N4 bands using the available time of observations from AKARI data. The final adopted PL relations were N3 =−3.370 log P + 16.527 and N4 =−3.402 log P + 16.556. However, these PL relations may be biased due to the small number of Cepheids in the sample.
Effective field theory interpretation of searches for dark matter annihilation in the Sun with the IceCube Neutrino Observatory

We present a model-independent interpretation of searches for dark matter annihilation in the Sun using an effective field theory approach. We identify a set of effective operators contributing to spin-dependent scattering of dark matter with protons in the nonrelativistic limit and explore simple new physics models which would give rise to such operators. Using the limits on the spin-dependent scattering cross-section set by the IceCube collaboration in their search for dark matter annihilation in the Sun, we derive limits on effective couplings and corresponding masses of mediating particles. We show that the effective field theory interpretation of the IceCube searches provides constraints on dark matter complementary to those from relic density observations and searches at the LHC. Finally, we discuss the impact of astrophysical uncertainties on our results.
The canonical measure on a reductive p-adic group is motivic

Let $G$ be a connected reductive group over a non-Archimedean local field. We prove that its parahoric subgroups are definable in the Denef-Pas language, which is a first-order language of logic used in the theory of motivic integration developed by Cluckers and Loeser. The main technical result is the definability of the connected component of the N\'eron model of a tamely ramified algebraic torus. As a corollary, we prove that the canonical Haar measure on $G$, which assigns volume $1$ to the particular \emph{canonical} maximal parahoric defined by Gross, is motivic. This result resolves a technical difficulty that arose in Cluckers-Gordon-Halupczok and Shin-Templier and permits a simplification of some of the proofs in those articles. It also allows us to show that formal degree of a compactly induced representation is a motivic function of the parameters defining the representation.
Intensity and persistence of water repellency at different soil moisture contents and depths after a forest wildfire

Abstract The Mediterranean mixed coniferous and broad-leaved forest of Moarda (Palermo) was affected by a large wildfire in summer 2020. In spring 2021, burned and unburned loam soil sites were sampled and the water drop penetration time (WDPT) and ethanol percentage (EP) tests applied to assess the influence of wetting-drying processes and soil water content on post-fire soil water repellency (SWR) as well as its vertical distribution. According to the WDPT test, the surface layer of the natural unburned soils was severely hydrophobic at intermediate soil water contents roughly corresponding to wilting point and SWR reduced either for very dry conditions (air- or oven-dried conditions) or wetter conditions close to field capacity. For these soils, EP test yielded results in agreement with WDPT. An influence of the wetting/drying cycle was detected as, for a given soil water content, WDPT was generally higher for the drying than the wetting process. The surface of burned soils was always wettable independently of the soil water content. The vertical distribution of SWR was modified by wildfire and the maximum hydrophobicity layer, that was located at the surface of the unburned soils, moved to a depth of 2–4 cm in the soils of burned sites. The results confirmed that wildfire can induce destruction of soil water repellency (SWR) naturally occurring at the surface of forest soils and create a shallow hydrophobic layer that may increase overland flow and erosion risk.
Candidate type II quasars at 2 < z < 4.3 in the Sloan Digital Sky Survey III

At low redshifts, dust-obscured quasars often have strong yet narrow permitted lines in the rest-frame optical and ultraviolet, excited by the central active nucleus, earning the designation Type II quasars. We present a sample of 145 candidate Type II quasars at redshifts between 2 and 4.3, encompassing the epoch at which quasar activity peaked in the universe. These objects, selected from the quasar sample of the Baryon Oscillation Spectroscopic Survey of the Sloan Digital Sky Survey III, are characterized by weak continuum in the rest-frame ultraviolet (typical continuum magnitude of i \approx 22) and strong lines of CIV and Ly \alpha, with Full Width at Half Maximum less than 2000 kms-1. The continuum magnitudes correspond to an absolute magnitude of -23 or brighter at redshift 3, too bright to be due exclusively to the host galaxies of these objects. Roughly one third of the objects are detected in the shorter-wavelength bands of the WISE survey; the spectral energy distributions (SEDs) of these objects appear to be intermediate between classic Type I and Type II quasars seen at lower redshift. Five objects are detected at rest frame 6\mu m by Spitzer, implying bolometric luminosities of several times 10^46 erg s-1. We have obtained polarization measurements for two objects; they are roughly 3% polarized. We suggest that these objects are luminous quasars, with modest dust extinction (A_V ~ 0.5 mag), whose ultraviolet continuum also includes a substantial scattering contribution. Alternatively, the line of sight to the central engines of these objects may be partially obscured by optically thick material.
Nematicidal Effect of Raphasatin from Raphanus Sativus Against Meloidogyne Incognita

Abstract The nematicidal activity of radish bulb (Raphanus sativus) methanol (RME) and aqueous extracts (RAE) was tested against the second stage (J2) root knot nematode Meloidogyne incognita model. The EC50 of RME after 3 d of J2 immersion in test solutions was 312 ± 65 μg/ml. However, no activity was noted for RAE (EC50 > 1,000 μg/ml). The chemical composition analysis of the methanol extract carried out by the GC–MS technique showed that 4-methylthio-3-butenyl isothiocyanate (raphasatin) was the most abundant compound at 20%. This pure compound strongly induced J2 paralysis with an EC50 of 1.3 ± 0.2 μg/ml after 24 hr. Comparison with other 11 selected isothiocyanates with structure similarity showed that the double bond at position 3 of the alkyl side chain is important for nematicidal activity, followed by the sulfur group at position 5 and the benzyl group at position 2. In addition, raphasatin showed the highest nematicidal activity with the corresponding lowest antioxidant activity of about 92 ± 18 μg/ml. In conclusion, the results of this investigation reveal that R. sativus and its major compound raphasatin can be integrated into the pest management system.