Tandem LTR-retrotransposon structures are common and highly polymorphic in plant genomes

Background: LTR-retrotransposons (LTR-RT) are a major component of plant genomes and important drivers of genome evolution. Most LTR-RT copies in plant genomes are defective elements found as truncated copies, nested insertions or as part of more complex structures. The recent availability of highly contiguous plant genome assemblies based on long-read sequences now allows to perform detailed characterization of these complex structures and to evaluate their importance for plant genome evolution.Results: The detailed analysis of two rice loci containing complex LTR-RT structures showed that they consist of tandem arrays of LTR copies sharing internal LTRs. Our analyses suggests that these LTR-RT tandems are the result of a single insertion and not of the recombination of two independent LTR-RT elements. Our results also suggest that gypsy elements may be more prone to form these structures. We show that these structures are highly polymorphic in rice and therefore have the potential to generate genetic variability. We have developed a computational pipeline (IDENTAM) that scans genome sequences and identifies tandem LTR-RT candidates. Using this tool, we have detected 266 tandems in a pangenome built from the genomes of 76 accessions of cultivated and wild rice, showing that tandem LTR-RT structures are frequent and highly polymorphic in rice. Running IDENTAM in the Arabidopsis, almond and cotton genomes showed that LTR-RT tandems are frequent in plant genomes of different size, complexity and ploidy level. The complexity of differentiating intra-element variations at the nucleotide level among haplotypes is very high, and we found that graph-based pangenomic methodologies are appropriate to resolve these structures.Conclusions: Our results show that LTR-RT elements can form tandem arrays. These structures are relatively abundant and highly polymorphic in rice and are widespread in the plant kingdom. Future studies will contribute to understanding how these structures originate and whether the variability that they generate has a functional impact

Origin of the anomalous Hall effect in Cr-doped RuO₂

RuO2 is one of the most highlighted candidates for altermagnetism. However, the most recent muon spin spectroscopy and neutron studies demonstrated the absence of magnetic order in this system. The electronic structure of RuO2 hints at a possibility of realizing a magnetically ordered state upon hole doping, and such a possibility was explored experimentally in Cr-doped RuO2, where it was suggested that this system exhibits the anomalous Hall effect (AHE) due to altermagnetism. In this paper, based on our density functional calculations, we revise the results obtained for this system and propose a different interpretation of experimental results. Our calculations suggest that extra holes are bound to Cr impurity and do not dope Ru bands, which remain nonmagnetic. Thus, the observed AHE is not due to the altermagnetism but stems entirely from magnetic Cr ions. © 2025 authors

Delicate curvature bounces in the no-boundary wave function and in the late universe

Theoretical considerations motivate us to consider vacuum energy to be ableto decay and to assume that the spatial geometry of the universe is closed.Combining both aspects leads to the possibility that the universe, or certainregions thereof, can collapse and subsequently undergo a curvature bounce. Thismay have occurred in the very early universe, in a pre-inflationary phase. Wediscuss the construction of the corresponding no-boundary instantons and showthat they indeed reproduce a bouncing history of the universe, interestinglywith a small and potentially observable departure from classicality during thecontracting phase. Such an early bouncing history receives a large weightingand provides competition for a more standard inflationary branch of the wavefunction. Curvature bounces may also occur in the future. We discuss theconditions under which they may take place, allowing for density fluctuationsin the matter distribution in the universe. Overall, we find that curvaturebounces require a delicate combination of matter content and initial conditionsto occur, though with significant consequences if these conditions are met.<br

Contributions of short- and long-range white matter tracts in dynamic compensation with aging

Optimal brain function is shaped by a combination of global information integration, facilitated by long-range connections, and local processing, which relies on short-range connections and underlying biological factors. With aging, anatomical connectivity undergoes significant deterioration, which affects the brain's overall function. Despite the structural loss, previous research has shown that normative patterns of functions remain intact across the lifespan, defined as the compensatory mechanism of the aging brain. However, the crucial components in guiding the compensatory preservation of the dynamical complexity and the underlying mechanisms remain uncovered. Moreover, it remains largely unknown how the brain readjusts its biological parameters to maintain optimal brain dynamics with age; in this work, we provide a parsimonious mechanism using a whole-brain generative model to uncover the role of sub-communities comprised of short-range and long-range connectivity in driving the dynamic compensation process in the aging brain. We utilize two neuroimaging datasets to demonstrate how short- and long-range white matter tracts affect compensatory mechanisms. We unveil their modulation of intrinsic global scaling parameters, such as global coupling strength and conduction delay, via a personalized large-scale brain model. Our key finding suggests that short-range tracts predominantly amplify global coupling strength with age, potentially representing an epiphenomenon of the compensatory mechanism. This mechanistically explains the significance of short-range connections in compensating for the major loss of long-range connections during aging. This insight could help identify alternative avenues to address aging-related diseases where long-range connections are significantly deteriorated

A Parameter Study of the Electromagnetic Signatures of an Analytical Mini-Disk Model for Supermassive Binary Black Hole Systems

Supermassive black holes (SMBHs) are thought to be located at the centers ofmost galactic nuclei. When galaxies merge they form supermassive black holebinary (SMBHB) systems and these central SMBHs will also merge at later times,producing gravitational waves (GWs). Because galaxy mergers are likely gas-richenvironments, SMBHBs are also potential sources of electromagnetic (EM)radiation. The EM signatures depend on gas dynamics, orbital dynamics, andradiation processes. The gas dynamics are governed by general relativisticmagnetohydrodynamics (MHD) in a time-dependent spacetime. Numerically solvingthe MHD equations for a time-dependent binary spacetime is computationallyexpensive. Therefore, it is challenging to conduct a full exploration of theparameter space of these systems and the resulting EM signatures. We havedeveloped an analytical accretion disk model for the mini-disks of an SMBHBsystem and produced images and light curves using a general relativisticray-tracing code and a superimposed harmonic binary black hole metric. Thisanalytical model greatly reduces the time and computational resources needed toexplore these systems, while incorporating some key information fromsimulations. We present a parameter space exploration of the SMBHB system inwhich we have studied the dependence of the EM signatures on the spins of theblack holes (BHs), the mass ratio, the accretion rate, the viewing angle, andthe initial binary separation. Additionally, we study how the commonly usedfast-light approximation affects the EM signatures and evaluate its validity inGRMHD simulations.<br

Observation of the Open-Charm Tetraquark Candidate T_cs0^* ⁢(2870)⁰ in the B⁻→D⁻D⁰K_S⁰ Decay

An amplitude analysis of B−→D−⁢D0⁢KS0 decays is performed using proton-proton collision data, corresponding to an integrated luminosity of 9  fb−1, collected with the LHCb detector at center-of-mass energies of 7, 8, and 13 TeV. A resonant structure of spin-parity 0+ is observed in the D0⁢KS0 invariant-mass spectrum with a significance of 5.3σ. The mass and width of the state, modeled with a Breit-Wigner line shape, are determined to be 2883±11±8  MeV/c2 and 87−47+22 ±17  MeV, respectively, where the first uncertainties are statistical and the second systematic. These properties and the quark content are consistent with those of the open-charm tetraquark candidate Tcs⁢0*⁢(2870)0 observed previously in the D+⁢K− final state of the B−→D−⁢D+⁢K− decay. This result confirms the existence of the Tcs⁢0* ⁢(2870)0 state in a new decay mode. The Tcs⁢1* ⁢(2900)0 state, reported in the B−→D−⁢D+⁢K− decay, is also searched for in the D0⁢KS0 invariant-mass spectrum of the B− →D−⁢D0⁢KS0 decay, without finding evidence for it