bluuebunny/crossref_metadata_2025_split huggingface dataset:
A CMB lensing analysis of the extended mass distribution of clusters
Authors: Toscano Facundo , Luparello Heliana , Gonzalez Elizabeth Johana , Lambas Diego Garcia 
Published: October 2023

ABSTRACT
The aim of this work is to study the anisotropic weak lensing signal associated with the mass distribution of massive clusters of galaxies using the cosmic microwave background (CMB) data. For this purpose, we stack patches of the Planck Collaboration (2018) CMB lensing convergence map centred on SDSS DR8 redMaPPer clusters within the redshift range [0.4, 0.5]. We obtain mean radial profiles of the convergence parameter κ finding strong signals at scales as large as 40 Mpch−1. By orienting the clusters along their major axis defined through the galaxy member distribution, we find a significant difference between the parallel and perpendicular-oriented convergence profiles. The amplitude of the profile along the parallel direction is about 50 per cent larger than that along the perpendicular direction, indicating that the clusters are well aligned with the surrounding mass distribution. From a model with an anisotropic surface mass density, we obtain a suitable agreement for both mass and ellipticities of clusters compared to results derived from weak lensing shear estimates, finding strong evidence of the correlation between the galaxy cluster member distribution and the large-scale mass distribution.
X-ray polarization properties of partially ionized equatorial obscurers around accreting compact objects
Authors: Podgorný J , Marin F , Dovčiak M 
Published: October 2023

ABSTRACT
We present the expected X-ray polarization signal resulting from distant reprocessing material around black holes. Using a central isotropic power-law emission at the centre of the simulated model, we add distant equatorial and axially symmetric media that are covering the central accreting sources. We include partial ionization and partial transparency effects, and the impact of various polarization and steepness of the primary radiation spectrum. The results are obtained with the Monte Carlo code STOKES that considers both line and continuum processes and computes the effects of scattering and absorption inside static homogenous wedge-shaped and elliptical toroidal structures, varying in relative size, composition and distance to the source. We provide first order estimates for parsec-scale reprocessing in Compton-thin and Compton-thick active galactic nuclei, as well as winds around accreting stellar-mass compact objects, for observer’s inclinations above and below the grazing angle. The resulting reprocessed polarization can reach tens of per cent with either parallel or perpendicular orientation with respect to the axis of symmetry, depending on subtle details of the geometry, density, and ionization structure. We also show how principal parameters constrained from X-ray spectroscopy or polarimetry in other wavelengths can lift the shown degeneracies in X-ray polarization. We provide an application example of the broad modelling discussion by revisiting the recent IXPE 2–8 keV X-ray polarimetric observation of the accreting stellar-mass black hole in Cygnus X-3 from the perspective of partial transparency and ionization of the obscuring outflows.
Anisotropic strong lensing as a probe of dark matter self-interactions
Authors: Dhanasingham Birendra , Cyr-Racine Francis-Yan , Mace Charlie , Peter Annika H G , Benson Andrew 
Published: October 2023

ABSTRACT
Galaxy-scale strongly lensed systems have been shown to provide a unique technique for exploring the underlying physics of dark matter at sub-galactic scales. In the past, much attention was given to detecting and studying individual haloes in a strong lens system. In addition to the subhaloes, line-of-sight haloes contribute significantly to the small perturbations in lensed images. In prior work, we demonstrated that these line-of-sight haloes imprint a distinctive anisotropic signature and hence give rise to a detectable non-zero parity-even quadrupole moment in the effective convergence field’s two-point correlation function. In this study, we show that these line-of-sight haloes also produce a non-zero curl component of the effective deflection field with a parity-odd quadrupole moment of the two-point function. These multipole moments have the ability to statistically separate line-of-sight haloes from dark matter substructure. In this paper, we examine how these multipole moments evolve in the presence of warm dark matter and self-interacting dark matter in terms of central density evolution and dark matter halo abundance. Importantly, we show that these different multipole moments display exquisite sensitivity to both the amplitude and the velocity dependence of the dark matter self-interaction cross-section. Our approach opens the door for strong lensing observations to probe dark matter self-interaction over a broad range of relative velocities.
The first X-ray polarimetric observation of the black hole binary LMC X-1
Authors: Podgorný J , Marra L , Muleri F , Rodriguez Cavero N , Ratheesh A , Dovčiak M , Mikušincová R , Brigitte M , Steiner J F , Veledina A , Bianchi S , Krawczynski H , Svoboda J , Kaaret P , Matt G , García J A , Petrucci P-O , Lutovinov A , Semena A , Di Marco A , Negro M , Weisskopf M C , Ingram A , Poutanen J , Beheshtipour B , Chun S , Hu K , Mizuno T , Sixuan Z , Tombesi F , Zane S , Agudo I , Antonelli L A , Bachetti M , Baldini L , Baumgartner W H , Bellazzini R , Bongiorno S D , Bonino R , Brez A , Bucciantini N , Capitanio F , Castellano S , Cavazzuti E , Chen C , Ciprini S , Costa E , De Rosa A , Del Monte E , Di Gesu L , Di Lalla N , Donnarumma I , Doroshenko V , Ehlert S R , Enoto T , Evangelista Y , Fabiani S , Ferrazzoli R , Gunji S , Hayashida K , Heyl J , Iwakiri W , Jorstad S G , Karas V , Kislat F , Kitaguchi T , Kolodziejczak J J , La Monaca F , Latronico L , Liodakis I , Maldera S , Manfreda A , Marin F , Marinucci A , Marscher A P , Marshall H L , Massaro F , Mitsuishi I , Ng C-Y , O’Dell S L , Omodei N , Oppedisano C , Papitto A , Pavlov G G , Peirson A L , Perri M , Pesce-Rollins M , Pilia M , Possenti A , Puccetti S , Ramsey B D , Rankin J , Roberts O J , Romani R W , Sgrò C , Slane P , Soffitta P , Spandre G , Swartz D A , Tamagawa T , Tavecchio F , Taverna R , Tawara Y , Tennant A F , Thomas N E , Trois A , Tsygankov S S , Turolla R , Vink J , Wu K , Xie F 
Published: October 2023

ABSTRACT
We report on an X-ray polarimetric observation of the high-mass X-ray binary LMC X-1 in the high/soft state, obtained by the Imaging X-ray Polarimetry Explorer (IXPE) in 2022 October. The measured polarization is below the minimum detectable polarization of 1.1 per cent (at the 99 per cent confidence level). Simultaneously, the source was observed with the Neutron Star Interior Composition Explorer (NICER), Nuclear Spectroscopic Telescope Array (NuSTAR), and Spectrum-Rontgen-Gamma (SRG)/Astronomical Roentgen Telescope – X-ray Concentrator (ART-XC) instruments, which enabled spectral decomposition into a dominant thermal component and a Comptonized one. The low 2–8 keV polarization of the source did not allow for strong constraints on the black hole spin and inclination of the accretion disc. However, if the orbital inclination of about 36° is assumed, then the upper limit is consistent with predictions for pure thermal emission from geometrically thin and optically thick discs. Assuming the polarization degree of the Comptonization component to be 0, 4, or 10 per cent, and oriented perpendicular to the polarization of the disc emission (in turn assumed to be perpendicular to the large-scale ionization cone orientation detected in the optical band), an upper limit to the polarization of the disc emission of 1.0, 0.9, or 0.9 per cent, respectively, is found (at the 99 per cent confidence level).
Gaia uncovers difference in B and Be star binarity at small scales: evidence for mass transfer causing the Be phenomenon
Authors: Dodd Jonathan M , Oudmaijer René D , Radley Isaac C , Vioque Miguel , Frost Abigail J 
Published: October 2023

ABSTRACT
Be stars make up almost 20 per cent of the B star population, and are rapidly rotating stars surrounded by a disc; however the origin of this rotation remains unclear. Mass transfer within close binaries provides the leading hypothesis, with previous detections of stripped companions to Be stars supporting this. Here, we exploit the exquisite astrometric precision of Gaia to carry out the largest to date comparative study into the binarity of matched samples of nearby B and Be stars from the Bright Star Catalogue. By utilizing new ‘proper motion anomaly’ values, derived from Gaia DR2 and DR3 astrometric data alongside previous values calculated using Hipparcos and Gaia data, and the Gaia-provided RUWE, we demonstrate that we can identify unresolved binaries down to separations of 0.02 arcsec. Using these measures, we find that the binary fractions of B and Be stars are similar between 0.04 and 10 arcsec, but the Be binary fraction is significantly lower than that of the B stars for separations below 0.04 arcsec. As the separation range of these ‘missing’ binaries is too large for mass transfer, and stripped companions are not retrieved by these measures, we suggest the companions migrate inwards via binary hardening within a triple system. This confirms statistically for the first time the hypothesis that binary interaction causes the Be phenomenon, with migration causing the dearth of Be binaries between 0.02 and 0.04 arcsec. Furthermore, we suggest that triplicity plays a vital role in this migration, and thus in the formation of Be stars as a whole.
QUIJOTE scientific results – XIII. Intensity and polarization study of the microwave spectra of supernova remnants in the QUIJOTE-MFI wide survey: CTB 80, Cygnus Loop, HB 21, CTA 1, Tycho, and HB 9
Authors: López-Caraballo C H , Ruiz-Granados B , Génova-Santos R T , Fernández-Torreiro M , Rubiño-Martín J A , Peel M W , Poidevin F , Artal E , Ashdown M , Barreiro R B , Casas F J , de la Hoz E , González-González R , Guidi F , Herranz D , Hoyland R , Lasenby A , Martínez-González E , Piccirillo L , Rebolo R , Tramonte D , Vansyngel F , Vielva P , Watson R A 
Published: October 2023

ABSTRACT
We use the new QUIJOTE-MFI wide survey (11, 13, 17, and 19 GHz) to produce spectral energy distributions (SEDs), on an angular scale of 1°, of the supernova remnants (SNRs) CTB 80, Cygnus Loop, HB 21, CTA 1, Tycho, and HB 9. We provide new measurements of the polarized synchrotron radiation in the microwave range. The intensity and polarization SEDs are obtained and modelled by combining QUIJOTE-MFI maps with ancillary data. In intensity, we confirm the curved spectra of CTB 80 and HB 21 with a break frequency νb at 2.0$^{+1.2}_{-0.5}$ and 5.0$^{+1.2}_{-1.0}$ GHz, respectively; and spectral indices above the break of $-0.6^{+0.04}_{-0.05}$ and $-0.86^{+0.04}_{-0.05}$. We provide constraints on the Anomalous Microwave Emission, suggesting that it is negligible towards these SNRs. From a simultaneous intensity and polarization fit, we recover synchrotron spectral indices as flat as −0.24, and the whole sample has a mean and scatter of −0.44 ± 0.12. The polarization fractions have a mean and scatter of 6.1 ± 1.9 per cent. When combining our results with the measurements from other QUIJOTE (Q-U-I JOint TEnerife CMB experiment) studies of SNRs, we find that radio spectral indices are flatter for mature SNRs, and particularly flatter for CTB 80 ($-0.24^{+0.07}_{-0.06}$) and HB 21 ($-0.34^{+0.04}_{-0.03}$). In addition, the evolution of the spectral indices against the SNRs age is modelled with a power-law function, providing an exponent −0.07 ± 0.03 and amplitude −0.49 ± 0.02 (at 10 kyr), which are conservative with respect to previous studies of our Galaxy and the Large Magellanic Cloud.
Sky subtraction of LAMOST at bright night
Authors: Han Bochong , Song Yihan , Zhao Yongheng 
Published: October 2023

ABSTRACT
Sky subtraction is a crucial step in the data reduction process for LAMOST, including dark, bright, and grey nights. During the pilot survey, on bright nights, atmospheric scattering of moonlight can introduce gradients in the sky background. In observations during bright moonlit nights, the sky component is significant, and sometimes, variations in colour can be observed in the sky spectra. This phenomenon is not universally present during observations on bright moonlit nights. Taking this into consideration, this paper proposes a weighted trend-surface method to reconstruct the sky component within the science target fibre, aiming to achieve the subtraction of the sky component. We constructed a sky model using a trend surface, utilizing data from all sky fibre spectra on the same spectrograph to predict the sky component for each fibre spectrum. Subsequently, the reconstructed sky spectrum data were compared with the actually observed sky spectrum data and the ‘super sky’ from LAMOST’s pipeline. The results indicate that our method is closer to the observed real sky spectrum than the ‘super sky’, showing smaller residuals and variance, with an average closer to zero. This method serves as a viable solution, particularly when dealing with colour variations observed during bright moonlit nights.
The Calar Alto Legacy Integral Field Area survey: extended and remastered data release
Authors: Sánchez S F , Galbany L , Walcher C J , García-Benito R , Barrera-Ballesteros J K 
Published: October 2023

ABSTRACT
This paper describes the extended data release (eDR) of the Calar Alto Legacy Integral Field Area (CALIFA) survey. It comprises science-grade quality data for 895 galaxies obtained with the Potsdam Multi Aperture Spectograph/PPak instrument at the 3.5-m telescope at the Calar Alto Observatory along the last 12 yr, using the V500 setup [3700–7500 Å, 6 Å/full-width at half-maximum (FWHM)] and the CALIFA observing strategy. It includes galaxies of any morphological type, star formation stage, a wide range of stellar masses (∼107–1012 M⊙), at an average redshift of ∼0.015 (90 per cent within 0.005 &lt; z &lt; 0.05). Primarily selected based on the projected size and apparent magnitude, we demonstrate that it can be volume corrected resulting in a statistically limited but representative sample of the population of galaxies in the nearby Universe. All the data were homogeneous re-reduced, introducing a set of modifications to the previous reduction. The most relevant is the development and implementation of a new cube-reconstruction algorithm that provides with an (almost) seeing-limited spatial resolution (FWHMPSF ∼ 1.0 arcsec). To illustrate the usability and quality of the data, we extracted two aperture spectra for each galaxy (central 1.5 arcsec and fully integrated), and analyse them using pyFIT3D. We obtain a set of observational and physical properties of both the stellar populations and the ionized gas, that have been compared for the two apertures, exploring their distributions as a function of the stellar masses and morphologies of the galaxies, comparing with recent results in the literature.
TCP J18224935-2408280: a symbiotic star identified during outburst
Authors: Sonith L S , Kamath U S 
Published: October 2023

ABSTRACT
TCP J18224935-2408280 was reported to be in outburst on 2021 May 19. Follow-up spectroscopic observations confirmed that the system was a symbiotic star. We present optical spectra obtained from the Himalayan Chandra Telescope during 2021–22. The early spectra were dominated by Balmer lines, He i lines and high ionization lines such as He ii. In the later observations, Raman scattered O vi was also identified. Outburst in the system started as a disc instability, and later the signature of enhanced shell burning and expansion of photospheric radius of the white dwarf was identified. Hence we suggest this outburst is of combination nova type. The post-outburst temperature of the hot component remains above 1.5 × 105 K indicating a stable shell burning in the system for a prolonged time after the outburst. Based on our analysis of archival multiband photometric data, we find that the system contains a cool giant of M1-2 III spectral type with a temperature of ∼3600 K and a radius of ∼69 R⊙. The pre- and post-outburst light curve shows a periodicity of 631.25 ± 2.93 d; we consider this as the orbital period.
HIV-PULSE: a long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization
Authors: Lambrechts Laurens , Bonine Noah , Verstraeten Rita , Pardons Marion , Noppe Ytse , Rutsaert Sofie , Van Nieuwerburgh Filip , Van Criekinge Wim , Cole Basiel , Vandekerckhove Linos 
Published: October 2023

Abstract
A deep understanding of the composition of the HIV-1 reservoir is necessary for the development of targeted therapies and the evaluation of curative efforts. However, current near full-length (NFL) HIV-1 proviral genome sequencing assays are based on labor-intensive and costly principles of repeated PCRs at limiting dilution, restricting their scalability. To address this, we developed a high-throughput, long-read sequencing assay called HIV-PULSE (HIV Proviral UMI-mediated Long-read Sequencing). This assay uses unique molecular identifiers (UMIs) to tag individual HIV-1 genomes, allowing for the omission of the limiting dilution step and enabling long-range PCR amplification of many NFL genomes in a single PCR reaction, while simultaneously overcoming poor single-read accuracy. We optimized the assay using HIV-infected cell lines and then applied it to blood samples from 18 individuals living with HIV on antiretroviral therapy, yielding a total of 1308 distinct HIV-1 genomes. Benchmarking against the widely applied Full-Length Individual Proviral Sequencing assay revealed similar sensitivity (11 vs 18%) and overall good concordance, although at a significantly higher throughput. In conclusion, HIV-PULSE is a cost-efficient and scalable assay that allows for the characterization of the HIV-1 proviral landscape, making it an attractive method to study the HIV-1 reservoir composition and dynamics.
Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics
Authors: He Weiwei , San Emeterio Josue , Woodside Michael T , Kirmizialtin Serdal , Pollack Lois 
Published: October 2023

Abstract
SARS-CoV-2 depends on −1 programmed ribosomal frameshifting (−1 PRF) to express proteins essential for its replication. The RNA pseudoknot stimulating −1 PRF is thus an attractive drug target. However, the structural models of this pseudoknot obtained from cryo-EM and crystallography differ in some important features, leaving the pseudoknot structure unclear. We measured the solution structure of the pseudoknot using small-angle X-ray scattering (SAXS). The measured profile did not agree with profiles computed from the previously solved structures. Beginning with each of these solved structures, we used the SAXS data to direct all atom molecular dynamics (MD) simulations to improve the agreement in profiles. In all cases, this refinement resulted in a bent conformation that more closely resembled the cryo-EM structures than the crystal structure. Applying the same approach to a point mutant abolishing −1 PRF revealed a notably more bent structure with reoriented helices. This work clarifies the dynamic structures of the SARS-CoV-2 pseudoknot in solution.
A sensor complements the steric gate when DNA polymerase ϵ discriminates ribonucleotides
Authors: Parkash Vimal , Kulkarni Yashraj , Bylund Göran O , Osterman Pia , Kamerlin Shina Caroline Lynn , Johansson Erik 
Published: October 2023

Abstract
The cellular imbalance between high concentrations of ribonucleotides (NTPs) and low concentrations of deoxyribonucleotides (dNTPs), is challenging for DNA polymerases when building DNA from dNTPs. It is currently believed that DNA polymerases discriminate against NTPs through a steric gate model involving a clash between a tyrosine and the 2′-hydroxyl of the ribonucleotide in the polymerase active site in B-family DNA polymerases. With the help of crystal structures of a B-family polymerase with a UTP or CTP in the active site, molecular dynamics simulations, biochemical assays and yeast genetics, we have identified a mechanism by which the finger domain of the polymerase sense NTPs in the polymerase active site. In contrast to the previously proposed polar filter, our experiments suggest that the amino acid residue in the finger domain senses ribonucleotides by steric hindrance. Furthermore, our results demonstrate that the steric gate in the palm domain and the sensor in the finger domain are both important when discriminating NTPs. Structural comparisons reveal that the sensor residue is conserved among B-family polymerases and we hypothesize that a sensor in the finger domain should be considered in all types of DNA polymerases.
Different elongation factors distinctly modulate RNA polymerase II transcription in Arabidopsis
Authors: Obermeyer Simon , Schrettenbrunner Lukas , Stöckl Richard , Schwartz Uwe , Grasser Klaus D 
Published: October 2023

Abstract
Various transcript elongation factors (TEFs) including modulators of RNA polymerase II (RNAPII) activity and histone chaperones tune the efficiency of transcription in the chromatin context. TEFs are involved in establishing gene expression patterns during growth and development in Arabidopsis, while little is known about the genomic distribution of the TEFs and the way they facilitate transcription. We have mapped the genome-wide occupancy of the elongation factors SPT4–SPT5, PAF1C and FACT, relative to that of elongating RNAPII phosphorylated at residues S2/S5 within the carboxyterminal domain. The distribution of SPT4–SPT5 along transcribed regions closely resembles that of RNAPII-S2P, while the occupancy of FACT and PAF1C is rather related to that of RNAPII-S5P. Under transcriptionally challenging heat stress conditions, mutant plants lacking the corresponding TEFs are differentially impaired in transcript synthesis. Strikingly, in plants deficient in PAF1C, defects in transcription across intron/exon borders are observed that are cumulative along transcribed regions. Upstream of transcriptional start sites, the presence of FACT correlates with nucleosomal occupancy. Under stress conditions FACT is particularly required for transcriptional upregulation and to promote RNAPII transcription through +1 nucleosomes. Thus, Arabidopsis TEFs are differently distributed along transcribed regions, and are distinctly required during transcript elongation especially upon transcriptional reprogramming.