bluuebunny/crossref_metadata_2025_split huggingface dataset:
Magnetically driven coupling in relativistic radiation-mediated shocks
Authors: Mahlmann J F , Vanthieghem A , Philippov A A , Levinson A , Nakar E , Fiuza F 
Published: January 2023

ABSTRACT
The radiation drag in photon-rich environments of cosmic explosions can seed kinetic instabilities by inducing velocity spreads between relativistically streaming plasma components. Such microturbulence is likely imprinted on the breakout signals of radiation-mediated shocks. However, large-scale, transverse magnetic fields in the deceleration region of the shock transition can suppress the dominant kinetic instabilities by preventing the development of velocity separations between electron–positron pairs and a heavy ion species. We use a 1D five-fluid radiative transfer code to generate self-consistent profiles of the radiation drag force and plasma composition in the deceleration region. For increasing magnetization, our models predict rapidly growing pair multiplicities and a substantial radiative drag developing self-similarly throughout the deceleration region. We extract the critical magnetization parameter σc, determining the limiting magnetic field strength at which a three-species plasma can develop kinetic instabilities before reaching the isotropized downstream. For a relativistic, single ion plasma drifting with γu = 10 in the upstream of a relativistic radiation-mediated shock, we find the threshold σc ≈ 10−7 for the onset of microturbulence. Suppression of plasma instabilities in the case of multi-ion composition would likely require much higher values of σc. Identifying high-energy signatures of microturbulence in shock breakout signals and combining them with the magnetization limits provided in this work will allow a deeper understanding of the magnetic environment of cosmic explosions like supernovae, gamma-ray bursts, and neutron star binary mergers.
Jet power, intrinsic γ-ray luminosity, and accretion in jetted AGNs
Authors: Chen Yongyun , Gu Qiusheng , Fan Junhui , Yu Xiaoling , Ding Nan , Guo Xiaotong , Xiong Dingrong 
Published: January 2023

ABSTRACT
The correlation between the kinetic jet power Pjet, intrinsic γ-ray luminosity (Lint), and accretion (Ldisc) may reveal the underlying jet physics in various black hole systems. We study the relation between kinetic jet power, intrinsic γ-ray luminosity, and accretion by using a large sample of jetted active galactic nuclei (AGNs), including flat-spectrum radio quasars (FSRQs), BL Lacertae objects (BL Lacs), γ-ray narrow-line Seyfert 1 galaxies (γNLS1s), and radio galaxies. Our main results are as follows: (1) The slope indices of the relation between Pjet and Lint are 0.85 ± 0.01 for the whole sample, 0.70 ± 0.02 for the FSRQs, 0.83 ± 0.03 for the BL Lacs, 0.68 ± 0.11 for the γNLS1s, and 0.93 ± 0.09 for the radio galaxies, respectively. The jets in γNLS1s and radio galaxies almost follow the same Pjet–Lint correlation that was obtained for Fermi blazars. (2) The slope indices of the relation between Lint and Ldisc are 1.05 ± 0.02 for the whole sample, 0.94 ± 0.05 for the FSRQs, 1.14 ± 0.05 for the BL Lacs, and 0.92 ± 0.18 for the γNLS1s, respectively. The γNLS1s and radio galaxies almost also follow the Lint–Ldisc correlation derived for Fermi blazars. (3) The jet power is larger than the luminosity of accretion discs for almost all jetted AGNs. Jet power depends on both the Eddington ratio and black hole mass. We obtain log Pjet ∼ (1.00 ± 0.02)log Ldisc for the whole sample, which is consistent with the theoretically predicted coefficient. These results may imply that the jets of jetted AGNs are powered by the Blandford–Znajek mechanism.
HLC2: a highly efficient cross-matching framework for large astronomical catalogues on heterogeneous computing environments
Authors: Zhang Yajie , Yu Ce , Sun Chao , Xiao Jian , Li Kun , Mu Yifei , Cui Chenzhou 
Published: January 2023

ABSTRACT
Cross-matching operation, which is to find corresponding data for the same celestial object or region from multiple catalogues, is indispensable to astronomical data analysis and research. Due to the large amount of astronomical catalogues generated by the ongoing and next-generation large-scale sky surveys, the time complexity of the cross-matching is increasing dramatically. Heterogeneous computing environments provide a theoretical possibility to accelerate the cross-matching, but the performance advantages of heterogeneous computing resources have not been fully utilized. To meet the challenge of cross-matching for substantial increasing amount of astronomical observation data, this paper proposes Heterogeneous-computing-enabled Large Catalogue Cross-matcher (HLC2), a high-performance cross-matching framework based on spherical position deviation on CPU-GPU heterogeneous computing platforms. It supports scalable and flexible cross-matching and can be directly applied to the fusion of large astronomical catalogues from survey missions and astronomical data centres. A performance estimation model is proposed to locate the performance bottlenecks and guide the optimizations. A two-level partitioning strategy is designed to generate an optimized data placement according to the positions of celestial objects to increase throughput. To make HLC2 a more adaptive solution, the architecture-aware task splitting, thread parallelization, and concurrent scheduling strategies are designed and integrated. Moreover, a novel quad-direction strategy is proposed for the boundary problem to effectively balance performance and completeness. We have experimentally evaluated HLC2 using public released catalogue data. Experiments demonstrate that HLC2 scales well on different sizes of catalogues and the cross-matching speed is significantly improved compared to the state-of-the-art cross-matchers.
Debiasing standard siren inference of the Hubble constant with marginal neural ratio estimation
Authors: Gagnon-Hartman Samuel , Ruan John , Haggard Daryl 
Published: January 2023

ABSTRACT
Gravitational wave (GW) standard sirens may resolve the Hubble tension, provided that standard siren inference of H0 is free from systematic biases. However, standard sirens from binary neutron star (BNS) mergers suffer from two sources of systematic bias, one arising from the anisotropy of GW emission, and the other from the anisotropy of electromagnetic (EM) emission from the kilonova. For an observed sample of BNS mergers, the traditional Bayesian approach to debiasing involves the direct computation of the detection likelihood. This is infeasible for large samples of detected BNS merger due to the high dimensionality of the parameter space governing merger detection. In this study, we bypass this computation by fitting the Hubble constant to forward simulations of the observed GW and EM data under a simulation-based inference (SBI) framework using marginal neural ratio estimation. A key innovation of our method is the inclusion of BNS mergers that were only detected in GW, which allows for estimation of the bias introduced by EM anisotropy. Our method corrects for $\sim 90{{\ \rm per\ cent}}$ of the bias in the inferred value of H0 when telescope follow-up observations of BNS mergers have extensive tiling of the merger localization region, using known telescope sensitivities and assuming a model of kilonova emission. Our SBI-based method thus enables a debiased inference of the Hubble constant of BNS mergers, including both mergers with detected EM counterparts and those without.
The origin of buckling instability in galactic bars: Searching for the scapegoat
Authors: Li Xingchen , Shlosman Isaac , Pfenniger Daniel , Heller Clayton 
Published: January 2023

ABSTRACT
We analyse the origin of the buckling instability in stellar bars using high-resolution N-body simulations. Previous studies have promoted the non-resonant firehose instability to be responsible for the vertical buckling. We have analysed the buckling process following the resonant excitation of stellar orbits in the bar. We find that (1) the buckling is associated with an abrupt increase in the central mass concentration and triggers velocities within the bar. The velocity field forms circulation cells, increasing vorticity, which is absent in classical firehose instability; (2) The bending amplitude is non-linear when measured by isodensity contours or curvature of the Laplace plane, which has a substantial effect on the stellar motions; (3) The planar and vertical 2:1 resonances appear only with the buckling and quickly reach the overlapping phase, thus supporting the energy transfer from horizontal to vertical motions; (4) Using non-linear orbit analysis, we analyse the stellar oscillations and find that stars cross the vertical 2:1 resonance simultaneously with the buckling. The overlapping planar and vertical 2:1 resonances trapping more than 25 per cent of the bar particles provide the ‘smoking gun’ pointing to a close relationship between the bending of stellar orbits and the resonant action – these particles are assuring the cohesive response in the growing vertical asymmetry. We conclude that resonant excitation is important in triggering the buckling instability, and the contribution from the non-resonant firehose instability should be re-evaluated. Finally, we discuss some observational implications of buckling on the kinematics in face-on and inclined galactic discs.
X-ray polarimetry as a tool to measure the black hole spin in microquasars: simulations of IXPE capabilities
Authors: Mikusincova Romana , Dovciak Michal , Bursa Michal , Lalla Niccolo Di , Matt Giorgio , Svoboda Jiri , Taverna Roberto , Zhang Wenda 
Published: January 2023

ABSTRACT
Measurements of the angular momentum (spin) of astrophysical black holes are extremely important, as they provide information on the black hole formation and evolution. We present simulated observations of an X-ray binary system with the Imaging X-ray Polarimetry Explorer (IXPE), with the aim to study the robustness of black hole spin and geometry measurements using X-ray polarimetry. As a representative example, we used the parameters of GRS 1915+105 in its former unobscured, soft state. In order to simulate the polarization properties, we modelled the source emission with a multicolour blackbody accounting for thermal radiation from the accretion disc, including returning radiation. Our analysis shows that the polarimetric observations in the X-ray waveband will be able to estimate both spin and inclination of the system with a good precision [without returning radiation we obtained for the lowest spin Δa ≤ 0.4 (0.4/0.998 ∼ 40 per cent) for spin and Δi ≤ 30° (30°/70$^\circ \, \sim$ 43 per cent) for inclination, while for the higher spin values we obtained Δa ≤ 0.12 (∼12 per cent) for spin and Δi ≤ 20° (∼29 per cent) for inclination, within 1σ errors]. When focusing on the case of returning radiation and treating inclination as a known parameter, we were able to successfully reconstruct spin and disc albedo in Δa ≤ 0.15 (∼15 per cent) interval and Δ albedo ≤0.45 (45 per cent) intervals within 1σ errors. We conclude that X-ray polarimetry will be a useful tool to constrain black hole spins, in addition to timing and spectral-fitting methods.
MOND as a peculiar case of the SIV theory
Authors: Maeder Andre 
Published: January 2023

ABSTRACTThe scale invariant theory is preserving the fundamental physical properties of General Relativity, while enlarging the group of invariances subtending gravitation theory (Dirac 1973; Canuto et al. 1977). The scale-invariant vacuum (SIV) theory assumes as gauging condition that ‘The macroscopic empty space is scale invariant, homogeneous, and isotropic’. Some basic properties in Weyl’s Integrable Geometry and cotensor calculus are examined in relation with scalar–tensor theories. Possible scale invariant effects are strongly reduced by matter density, both at the cosmological and local levels. The weak field limit of SIV tends to MOND when the scale factor is taken as constant, an approximation valid (&lt;1 per cent) over the last 400 Myr. A better understanding of the a0-parameter is obtained: it corresponds to the equilibrium point of the Newtonian and SIV dynamical acceleration. Parameter a0 is not a universal constant, it depends on the density and age of the Universe. As MOND is doing, SIV theory avoids the call to dark matter, moreover the cosmological models predict accelerated expansion.
Impact of newly measured 26Al(n, p)26Mg and 26Al(n, α)23Na reaction rates on the nucleosynthesis of 26Al in stars
Authors: Battino Umberto , Lederer-Woods Claudia , Pignatari Marco , Soós Benjámin , Lugaro Maria , Vescovi Diego , Cristallo Sergio , Woods Philip J , Karakas Amanda 
Published: January 2023

ABSTRACT
The cosmic production of the short-lived radioactive nuclide 26Al is crucial for our understanding of the evolution of stars and galaxies. However, simulations of the stellar sites producing 26Al are still weakened by significant nuclear uncertainties. We re-evaluate the 26Al(n, p)26Mg, and 26Al(n, α)23Na ground state reactivities from 0.01 GK to 10 GK, based on the recent n_TOF measurement combined with theoretical predictions and a previous measurement at higher energies, and test their impact on stellar nucleosynthesis. We computed the nucleosynthesis of low- and high-mass stars using the Monash nucleosynthesis code, the NuGrid mppnp code, and the FUNS stellar evolutionary code. Our low-mass stellar models cover the 2–3 M⊙ mass range with metallicities between Z = 0.01 and 0.02, their predicted 26Al/27Al ratios are compared to 62 meteoritic SiC grains. For high-mass stars, we test our reactivities on two 15 M⊙ models with Z = 0.006 and 0.02. The new reactivities allow low-mass AGB stars to reproduce the full range of 26Al/27Al ratios measured in SiC grains. The final 26Al abundance in high-mass stars, at the point of highest production, varies by a factor of 2.4 when adopting the upper, or lower limit of our rates. However, stellar uncertainties still play an important role in both mass regimes. The new reactivities visibly impact both low- and high-mass stars nucleosynthesis and allow a general improvement in the comparison between stardust SiC grains and low-mass star models. Concerning explosive nucleosynthesis, an improvement of the current uncertainties between T9∼0.3 and 2.5 is needed for future studies.
A standalone editing protein deacylates mischarged canavanyl-tRNAArg to prevent canavanine incorporation into proteins
Authors: Hauth Franziskus , Funck Dietmar , Hartig Jörg S 
Published: January 2023

AbstractError-free translation of the genetic code into proteins is vitally important for all organisms. Therefore, it is crucial that the correct amino acids are loaded onto their corresponding tRNAs. This process is highly challenging when aminoacyl-tRNA-synthetases encounter structural analogues to the native substrate like the arginine antimetabolite canavanine. To circumvent deleterious incorporation due to tRNA mischarging, editing mechanisms have evolved. However, only for half of the tRNA synthetases, editing activity is known and only few specific standalone editing proteins have been described. Understanding the diverse mechanisms resulting in error-free protein synthesis is of great importance. Here, we report the discovery of a protein that is upregulated upon canavanine stimulation in bacteria that live associated with canavanine-producing plants. We demonstrate that it acts as standalone editing protein specifically deacylating canavanylated tRNAArg. We therefore propose canavanyl-tRNAArgdeacylase (CtdA) as systematic name. Knockout strains show severe growth defects in canavanine-containing media and incorporate high amounts of canavanine into the proteome. CtdA is frequently found under control of guanidine riboswitches, revealing a functional connection of canavanine and guanidine metabolisms. Our results are the first to show editing activity towards mischarged tRNAArg and add to the puzzle of how faithful translation is ensured in nature.
Translation initiation of leaderless and polycistronic transcripts in mammalian mitochondria
Authors: Remes Cristina , Khawaja Anas , Pearce Sarah F , Dinan Adam M , Gopalakrishna Shreekara , Cipullo Miriam , Kyriakidis Vasileios , Zhang Jingdian , Dopico Xaquin Castro , Yukhnovets Olessya , Atanassov Ilian , Firth Andrew E , Cooperman Barry , Rorbach Joanna 
Published: January 2023

Abstract
The synthesis of mitochondrial OXPHOS complexes is central to cellular metabolism, yet many molecular details of mitochondrial translation remain elusive. It has been commonly held view that translation initiation in human mitochondria proceeded in a manner similar to bacterial systems, with the mitoribosomal small subunit bound to the initiation factors, mtIF2 and mtIF3, along with initiator tRNA and an mRNA. However, unlike in bacteria, most human mitochondrial mRNAs lack 5′ leader sequences that can mediate small subunit binding, raising the question of how leaderless mRNAs are recognized by mitoribosomes. By using novel in vitro mitochondrial translation initiation assays, alongside biochemical and genetic characterization of cellular knockouts of mitochondrial translation factors, we describe unique features of translation initiation in human mitochondria. We show that in vitro, leaderless mRNA transcripts can be loaded directly onto assembled 55S mitoribosomes, but not onto the mitoribosomal small subunit (28S), in a manner that requires initiator fMet-tRNAMet binding. In addition, we demonstrate that in human cells and in vitro, mtIF3 activity is not required for translation of leaderless mitochondrial transcripts but is essential for translation of ATP6 in the case of the bicistronic ATP8/ATP6 transcript. Furthermore, we show that mtIF2 is indispensable for mitochondrial protein synthesis. Our results demonstrate an important evolutionary divergence of the mitochondrial translation system and further our fundamental understanding of a process central to eukaryotic metabolism.
OKseqHMM: a genome-wide replication fork directionality analysis toolkit
Authors: Liu Yaqun , Wu Xia , d’Aubenton-Carafa Yves , Thermes Claude , Chen Chun-Long 
Published: January 2023

Abstract
During each cell division, tens of thousands of DNA replication origins are co-ordinately activated to ensure the complete duplication of the human genome. However, replication fork progression can be challenged by many factors, including co-directional and head-on transcription-replication conflicts (TRC). Head-on TRCs are more dangerous for genome integrity. To study the direction of replication fork movement and TRCs, we developed a bioinformatics toolkit called OKseqHMM (https://github.com/CL-CHEN-Lab/OK-Seq, https://doi.org/10.5281/zenodo.7428883). Then, we used OKseqHMM to analyse a large number of datasets obtained by Okazaki fragment sequencing to directly measure the genome-wide replication fork directionality (RFD) and to accurately predict replication initiation and termination at a fine resolution in organisms including yeast, mouse and human. We also successfully applied our analysis to other genome-wide sequencing techniques that also contain RFD information (e.g. eSPAN, TrAEL-seq). Our toolkit can be used to predict replication initiation and fork progression direction genome-wide in a wide range of cell models and growth conditions. Comparing the replication and transcription directions allows identifying loci at risk of TRCs, particularly head-on TRCs, and investigating their role in genome instability by checking DNA damage data, which is of prime importance for human health.
HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins
Authors: Zhang Fuhao , Li Min , Zhang Jian , Kurgan Lukasz 
Published: January 2023

AbstractThe sequence-based predictors of RNA-binding residues (RBRs) are trained on either structure-annotated or disorder-annotated binding regions. A recent study of predictors of protein-binding residues shows that they are plagued by high levels of cross-predictions (protein binding residues are predicted as nucleic acid binding) and that structure-trained predictors perform poorly for the disorder-annotated regions and vice versa. Consequently, we analyze a representative set of the structure and disorder trained predictors of RBRs to comprehensively assess quality of their predictions. Our empirical analysis that relies on a new and low-similarity benchmark dataset reveals that the structure-trained predictors of RBRs perform well for the structure-annotated proteins while the disorder-trained predictors provide accurate results for the disorder-annotated proteins. However, these methods work only modestly well on the opposite types of annotations, motivating the need for new solutions. Using an empirical approach, we design HybridRNAbind meta-model that generates accurate predictions and low amounts of cross-predictions when tested on data that combines structure and disorder-annotated RBRs. We release this meta-model as a convenient webserver which is available at https://www.csuligroup.com/hybridRNAbind/.
MARVEL: an integrated alternative splicing analysis platform for single-cell RNA sequencing data
Authors: Wen Wei Xiong , Mead Adam J , Thongjuea Supat 
Published: January 2023

AbstractAlternative splicing is an important source of heterogeneity underlying gene expression between individual cells but remains an understudied area due to the paucity of computational tools to analyze splicing dynamics at single-cell resolution. Here, we present MARVEL, a comprehensive R package for single-cell splicing analysis applicable to RNA sequencing generated from the plate- and droplet-based methods. We performed extensive benchmarking of MARVEL against available tools and demonstrated its utility by analyzing multiple publicly available datasets in diverse cell types, including in disease. MARVEL enables systematic and integrated splicing and gene expression analysis of single cells to characterize the splicing landscape and reveal biological insights.
STAT6 suppression prevents bleomycin‐induced dermal fibrosis
Authors: Huang Jingjing , Puente Hydia , Wareing Nancy E. , Wu Minghua , Mayes Maureen D. , Karmouty‐Quintana Harry , Assassi Shervin , Mills Tingting W. 
Published: January 2023

AbstractFibrosis of the skin and internal organs is a hallmark of systemic sclerosis (SSc). Although the pathogenesis of SSc is poorly understood, increasing evidence suggests that interleukins (IL)‐4 and − 13 contribute to the pathogenesis of skin fibrosis by promoting collagen production and myofibroblast differentiation. Signal transducers and activators of transcription 6 (STAT6) is one of the most important downstream transcription factors activated by both IL‐4 and IL‐13. However, it is not completely understood whether STAT6 plays a role during the pathogenesis of skin fibrosis in SSc. In this study, we observed increased STAT6 phosphorylation in fibrotic skin samples collected from SSc patients as well as bleomycin‐injected murine mice. Knockout of Stat6 in mice significantly (1) suppressed the expression of fibrotic cytokines including Il13, Il17, Il22, Ccl2, and the alternatively activated macrophage marker Cd206; (2) reduced the production of collagen and fibronectin, and (3) attenuated late‐stage skin fibrosis and inflammation induced by bleomycin. Consistently, mice treated with STAT6 inhibitor AS1517499 also attenuated skin fibrosis on day 28. In addition, a co‐culture experiment demonstrated that skin epithelial cells with STAT6 knockdown had reduced cytokine expression in response to IL‐4/IL‐13, and subsequently attenuated fibrotic protein expression in skin fibroblasts. On the other side, STAT6 depletion in skin fibroblasts attenuated IL‐4/IL‐13‐induced cytokine and fibrotic marker expression, and reduced CXCL2 expression in co‐cultured keratinocytes. In summary, our study highlighted an important yet not fully understood role of STAT6 in skin fibrosis by driving innate inflammation and differentiation of alternatively activated macrophages in response to injury.