bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deciphering the origins and growth of supermassive black holes
Authors: Aggarwal Yash 
Published: December 2024

ABSTRACT
We present a well-tested, theoretically supported empirical relation that helps decipher the origins, growth, and properties of supermassive black holes (SMBHs). Based on theoretical considerations and analysis of mass (MBH) versus age (t) distribution of high-redshift (&gt;5.6) SMBHs, we get MBH = Ms exp [14.6(t – 100)/t(Myr)], which gives the SMBH's seed mass Ms, and its derivative gives the instantaneous mass-accretion rate. It yields seeds of ∼20–420 M☉ (solar masses) for the recently discovered SMBHs GNz11, CEERS_1019, and UHZ1, and ∼3 × 104 M☉ for the largest (1.24 × 1010 M☉) high-z SMBH. It is applied to 132446 SMBHs at z &lt; 2.4. The resultant seeds are classified based on size and likely formation mechanism: ∼54 per cent are classified as light (&lt;350 M☉) deemed to be Pop III remnants; ∼40 per cent as intermediate (350–2 × 103 M☉) and ∼6 per cent as heavier seeds (2 × 103–3 × 104 M☉), both of which formed possibly by mergers of Pop III remnants. The direct collapse black hole (DCBH) mechanism is not required but not excluded. Furthermore, the results show the following. The mass-accretion rate increases exponentially from the seed's inception (z ∼ 30), reaches a broad plateau at z ∼ 8.5–6 coincident with the epoch of reionization, and decreases monotonically thereafter. Sub-Eddington accretion is the norm, except during the first ∼150 Myr SMBHs either experienced super-Eddington accretion or the radiative efficiency was much &lt; 0.1. The largest seed can potentially grow via luminous accretion to (6.6 ± 2.2) × 1010 M☉, consistent with a theoretical limit of ∼5 × 1010 M☉. The Eddington ratio decreases and radiative efficiency increases as z decreases, consistent with recent findings.
A spectrophotometric analysis and dust properties of classical nova V5584 Sgr
Authors: Bisht Mohit Singh , Raj A , Walter F M , Bisht D , Shaw Gargi , Belwal K , Biswas S 
Published: December 2024

ABSTRACT
In this work, optical observations of the nova V5584 Sgr are presented. These observations cover different phases including pre-maximum, early decline, and nebular. The spectra are dominated by hydrogen Balmer, Fe ii, and O i lines with P-Cygni profiles in the early phase, which are subsequently observed in complete emission. The presence of numerous Fe ii lines and low ejecta velocity aligns with the Fe ii type nova classification. From optical and NIR colours, it is clear that this nova manifests dust formation in the ejecta. The dust temperature and mass were estimated from a spectral energy distribution (SED) fit to the JHK band magnitudes and the Wide field Infrared Survey Explorer data. Light-curve analysis shows t$_2$ and t$_3$ values of $\sim$ 26 and $\sim$ 48 d, classifying the nova as moderately fast. The physical and chemical properties during early decline and later phases were evaluated using the photoionization code CLOUDY. The best-fitting model parameters from two epochs of multiwavelength spectra are compatible with a hot white dwarf source with a roughly constant luminosity of $\sim$(2.08 $\pm$ 0.10) $\times$ 10$^{36}$ erg s$^{-1}$. We find an ejected mass of $\sim$(1.59 $\pm$ 0.04) $\times$ 10$^{-4}$ M$_{\odot }$. Abundance analysis indicates that the ejecta is significantly enriched relative to solar values, with O/H = 30.2, C/H = 10.8, He/H = 1.8, Mg/H = 1.68, Na/H = 1.55, and N/H = 45.5 in the early decline phase, and O/H = 4.5, Ne/H = 1.5, and N/H = 24.5 in the nebular phase.
Modelling biases from constant stellar mass-to-light ratio assumption in galaxy dynamics and strong lensing
Authors: Liang Yan , Xu Dandan , Sluse Dominique , Sonnenfeld Alessandro , Shu Yiping 
Published: December 2024

ABSTRACT
A constant stellar mass-to-light ratio $M_\star /L$ has been widely used in studies of galaxy dynamics and strong lensing, which aim at disentangling the mass distributions of dark matter and baryons. However, systematic biases arising from constant $M_\star /L$ assumption have not been fully quantified. In this work, we take massive early-type galaxies from the TNG100 simulation to investigate possible systematic biases in the inferences due to a constant $M_\star /L$ assumption. We construct two-component matter density models, where one component describes the dark matter, the other for the stars, which is made to follow the light profile by assuming a constant $M_\star /L$. We fit the two-component model directly to the total matter density distributions of simulated galaxies to eliminate systematics coming from other model assumptions. We find that galaxies generally have more centrally concentrated stellar mass profile than their light distribution. Given the light profiles adopted (i.e. single- and double-Sérsic profiles), the assumption of a constant $M_\star /L$ would artificially break the model degeneracy between baryons and dark matter for non-constant$M_\star /L$ systems. For such systems, without knowing the true $M_{\star }/L$ but assuming a constant ratio, the two-component modelling procedure tend to generally overestimate $M_{\star }/L$ by $30{\small --}50~{{\ \rm per\ cent}}$, and underestimate the central dark matter fraction $f_{\rm DM}$ by $\sim 20~{{\ \rm per\ cent}}$ on average.
Evolutionary growth of molecular clouds as traced by their infrared bright fraction
Authors: Watkins E J , Peretto N , Rigby A J , Smith R J , Kreckel K , Fuller G A 
Published: December 2024

ABSTRACT
Understanding how stars form, evolve, and impact molecular clouds is key to understanding why star formation is such an inefficient process globally. In this paper, we use the infrared bright fraction, $f_\text{IRB}$ (the fraction of a given molecular cloud that appears bright against the 8 $\mu$m Milky Way background) as a proxy for time evolution to test how cloud properties change as star formation evolves. We apply this metric to 12 000 high-mass star-forming molecular clouds we identify using the Herschel–Hi-GAL survey between $|\ell |{\lt }70^{\circ }$ on the Milky Way plane. We find clouds are not static while forming stars. Instead, molecular clouds continuously gain mass while star formation progresses. By performing principal component analysis on the cloud properties, we find that they evolve down two paths distinguished by their mass gain. Most clouds (80 per cent) gain four times more mass as a function of $f_\text{IRB}$. The remaining 20 per cent experience an extreme period of growth, growing in mass by a factor of 150 on average and during this period, they initially gain mass fast enough to outpace their star formation. For all clouds, it is only after half their area becomes star forming that mass-loss occurs. We expect stellar feedback and potentially galactic shear is responsible. By analysing cloud positions, we suggest that the rate of mass growth may be linked to the larger galactic environment. Altogether, these results have strong implications on how we assess star-forming ability on cloud scales when assuming molecular cloud masses are fixed in time.
Spectroscopic observations of flares and superflares on AU Mic
Authors: Odert P , Leitzinger M , Greimel R , Kabáth P , Lipták J , Heinzel P , Karjalainen R , Wollmann J , Guenther E W , Skarka M , Srba J , Škoda P , Frýda J , Brahm R , Vanzi L , Janík J 
Published: December 2024

ABSTRACT
The young active flare star AU Mic is the planet host star with the highest flare rate from Transiting Exoplanet Survey Satellite data. Therefore, it represents an ideal target for dedicated ground-based monitoring campaigns with the aim to characterize its numerous flares spectroscopically. We performed such spectroscopic monitoring with the ESO1.52-m telescope of the PLATOSpec consortium. In more than 190 h of observations, we find 24 flares suitable for detailed analysis. We compute their parameters (duration, peak flux, and energy) in eight chromospheric lines (H $\alpha$, H $\beta$, H $\gamma$, H $\delta$, Na i D1&D2, He i D3, He i 6678) and investigate their relationships. Furthermore, we obtained simultaneous photometric observations and low-resolution spectroscopy for part of the spectroscopic runs. We detect one flare in the g$^{\prime }$-band photometry, which is associated with a spectroscopic flare. Additionally, an extreme flare event occurred on 2023-09-16 of which only a time around its possible peak was observed, during which chromospheric line fluxes were raised by up to a factor of three compared to the following night. The estimated energy of this event is around $10^{33}$ erg in H $\alpha$ alone, i.e. a rare chromospheric line superflare.
BUFFALO wild wings: a high-precision free-form lens model of MACSJ0416 with constraints on dark matter from substructure and highly magnified arcs
Authors: Perera Derek , Williams Liliya L R , Liesenborgs Jori , Kelly Patrick L , Taft Sarah H , Li Sung Kei , Jauzac Mathilde , Diego Jose M , Natarajan Priyamvada , Steinhardt Charles L , Faisst Andreas L , Rich R Michael , Limousin Marceau 
Published: December 2024

ABSTRACT
We present new free-form and hybrid mass reconstructions of the galaxy cluster lens MACS J0416.1$-$2403 at $z=0.396$ using the lens inversion method GRALE. The reconstructions use 237 spectroscopically confirmed multiple images from Bergamini et al. (2023) as the main input. Our primary model reconstructs images to a positional accuracy of 0.191 arcsec, thus representing one of the most precise reconstructions of this lens to date. Our models find broad agreement with previous reconstructions, and identify two $\sim 10^{12}\, {\rm M}_{\odot }$ light-unaffiliated substructures. We focus on two highly magnified arcs: Spock and Mothra. Our model features a unique critical curve structure around the Spock arc with 2 crossings. This structure enables sufficient magnification across this arc to potentially explain the large number of transients as microlensing events of supergiant stars. Additionally, we develop a model of the millilens substructure expected to be magnifying Mothra, which may be a binary pair of supergiants with $\mu \sim 6000$. This model accounts for flexibility in the millilens position while preserving the observed flux and minimizing image position displacements along the Mothra arc. We constrain the millilens mass and core radius to $\lesssim 10^6 {\rm M}_{\odot }$ and $\lesssim 17$ pc, respectively, which would render it one of the smallest and most compact substructures constrained by lensing. If the millilens is dominated by wave dark matter, the axion mass is constrained to be $\lesssim 3.0 \times 10^{-21}$ eV. Further monitoring of this lens with JWST will uncover more transients, permitting tighter constraints on the structure surrounding these two arcs.
A first glimpse at the MeerKAT DEEP2 field at S-band
Authors: Ranchod S , Wagenveld J D , Klöckner H -R , Wucknitz O , Deane R P , Sridhar S S , Barr E , Buchner S , Camilo F , Damas-Segovia A , Kasemann C , Kramer M , Legodi L S , Mao S A , Menten K , Rammala I , Rugel M R , Wieching G 
Published: December 2024

ABSTRACT
We present the first wide-field extragalactic continuum catalogue with the MeerKAT S-band (2.5 GHz), of the radio-selected DEEP2 field. The combined image over the S1 (1.96–2.84 GHz) and S4 (2.62–3.50 GHz) sub-bands has an angular resolution of 6.8 arcsec $\times$ 3.6 arcsec (4.0 arcsec $\times$ 2.4 arcsec) at a robust weighting of $R = 0.3$ ($R=-0.5$) and a sensitivity of 4.7 (7.5) µJy beam$^{-1}$ with an on-source integration time of 70 min and a minimum of 52 of the 64 antennas, for respective observations. We present the differential source counts for this field, as well as a morphological comparison of resolved sources between S-band and archival MeerKAT L-band images. We find consistent source counts with the literature and provide spectral indices fitted over a combined frequency range of 1.8 GHz. These observations provide an important first demonstration of the capabilities of MeerKAT S-band imaging with relatively short integration times, as well as a comparison with existing S-band surveys, highlighting the rich scientific potential with future MeerKAT S-band surveys.
Long-term optical variations in Swift J1858.6–0814: evidence for ablation and comparisons to radio properties
Authors: Rhodes L , Russell D M , Saikia P , Alabarta K , van den Eijnden J , Knight A H , Baglio M C , Lewis F 
Published: December 2024

ABSTRACT
We present optical monitoring of the neutron star low-mass X-ray binary Swift J1858.6–0814 during its 2018–2020 outburst and subsequent quiescence. We find that there was strong optical variability present throughout the entire outburst period covered by our monitoring, while the average flux remained steady. The optical spectral energy distribution is blue on most dates, consistent with emission from an accretion disc, interspersed by occasional red flares, likely due to optically thin synchrotron emission. We find that the fractional rms variability has comparable amplitudes in the radio and optical bands. This implies that the long-term variability is likely to be due to accretion changes, seen at optical wavelengths, that propagate into the jet, seen at radio frequencies. We find that the optical flux varies asymmetrically about the orbital period, peaking at phase $\sim$0.7, with a modulation amplitude that is the same across all optical wavebands, suggesting that reprocessing off of the disc, companion star and ablated material is driving the phase dependence. The evidence of ablation found in X-ray binaries is vital in understanding the long-term evolution of neutron star X-ray binaries and how they evolve into (potentially isolated) millisecond pulsars.
A case of polyarteritis nodosa with severe lower limb ulcer that was treated with prednisolone and tocilizumab
Authors: Okubo Naoto , Oba Yuki , Ikuma Daisuke , Mizuno Hiroki , Yamanouchi Masayuki , Suwabe Tatsuya , Ubara Yoshifumi , Sawa Naoki 
Published: December 2024

ABSTRACT
Polyarteritis nodosa (PAN) is a rare systemic necrotising vasculitis that can lead to the formation of refractory lower limb ulcers requiring amputation. The standard treatment for severe PAN involves combination therapy with steroids and cyclophosphamide; however, some cases prove to be challenging. Recently, case reports have described the use of biological agents for PAN treatment. We present the case of a 61-year-old Japanese man with cutaneous PAN and refractory recurrent lower limb ulcers. In 2017, the patient was admitted to the hospital because of exacerbation of a right lower limb ulcer. Despite combination therapy with corticosteroids, cyclophosphamide, and endovascular therapy, the gangrene in the right lower leg progressed, and amputation was performed. The patient was temporarily stabilised with prednisolone monotherapy. In 2019, new ulcers were observed on the left lower limb. Owing to steroid resistance, subcutaneous tocilizumab (162 mg/week) was initiated. Over a few months, the ulcer healed completely, and left lower limb amputation was avoided. Therefore, tocilizumab could potentially be one of the treatment options for severe cases in the future.
Optimization of ACE-tRNAs function in translation for suppression of nonsense mutations
Authors: Porter Joseph J , Ko Wooree , Sorensen Emily G , Lueck John D 
Published: December 2024

Abstract
Nonsense suppressor transfer RNAs (tRNAs) or AntiCodon-Edited tRNAs (ACE-tRNAs) have long been envisioned as a therapeutic approach to overcome genetic diseases resulting from the introduction of premature termination codons (PTCs). The ACE-tRNA approach for the rescue of PTCs has been hampered by ineffective delivery through available modalities for gene therapy. Here we have screened a series of ACE-tRNA expression cassette sequence libraries containing &gt;1800 members in an effort to optimize ACE-tRNA function and provide a roadmap for optimization in the future. By optimizing PTC suppression efficiency of ACE-tRNAs, we have decreased the amount of ACE-tRNA required by ∼16-fold for the most common cystic fibrosis-causing PTCs.
CRISPR-based dissection of miRNA binding sites using isogenic cell lines is hampered by pervasive noise
Authors: Prajapat Mahendra K , Maria Andrea G , Vidigal Joana A 
Published: December 2024

Abstract
Non-coding regulatory sequences play essential roles in adjusting gene output to cellular needs and are thus critical to animal development and health. Numerous such sequences have been identified in mammalian genomes ranging from transcription factors binding motifs to recognition sites for RNA-binding proteins and non-coding RNAs. The advent of CRISPR has raised the possibility of assigning functionality to individual endogenous regulatory sites by facilitating the generation of isogenic cell lines that differ by a defined set of genetic modifications. Here we investigate the usefulness of this approach to assign function to individual miRNA binding sites. We find that the process of generating isogenic pairs of mammalian cell lines with CRISPR-mediated mutations introduces extensive molecular and phenotypic variability between biological replicates confounding attempts at assigning function to the binding site. Our work highlights an important consideration when employing CRISPR editing to characterize non-coding regulatory sequences in cell lines and calls for the development and adoption of alternative strategies to address this question in the future.
Point mutations in functionally diverse genes are associated with increased natural DNA transformation in multidrug resistant Streptococcus pneumoniae
Authors: Peillard-Fiorente Flora , Pham Nguyen Phuong , Gingras Hélène , Godin Chantal , Feng Jie , Leprohon Philippe , Ouellette Marc 
Published: December 2024

Abstract
DNA transformation is key for phenotypic diversity and adaptation of Streptococcus pneumoniae including in the emergence of multidrug resistance (MDR). Under laboratory conditions, DNA transformation is facilitated by the artificial triggering of competence by the competence stimulating peptide (CSP). In ongoing DNA transformation work, we observed that exogenous CSP was dispensable depending on the combination of strains and culture media. Here, we carried out a chemogenomic screen to select for S. pneumoniae mutants capable of natural transformation in medium that normally would not sustain natural transformation. Our chemogenomic screen relied on chemical mutagenesis followed by selection of mutants with increased DNA transformation capacities. Sequencing the genome of these mutants revealed an abundance and diversity of mutated genes proven experimentally to increase natural transformation. A genome wide association study between MDR and sensitive clinical isolates revealed gene mutations associated with MDR, many of which intersected with those pinpointed by our chemogenomic screens and that were proven to increase natural transformation. S. pneumoniae has adopted DNA transformation as its lifestyle and can select for mutations facilitating DNA transformation.
KRBP72 facilitates ATPase-dependent editing progression through a structural roadblock in mitochondrial A6 mRNA
Authors: Dubey Ashutosh P , Tylec Brianna L , Yi Soon , Tedeschi Frank A , Smith Joseph T , Read Laurie K 
Published: December 2024

Abstract
Uridine insertion/deletion editing of mitochondrial messenger RNAs (mRNAs) in kinetoplastids entails the coordinated action of three complexes. RNA Editing Catalytic Complexes (RECCs) catalyze the enzymatic reactions, while the RNA Editing Substrate Binding Complex (RESC) and RNA Editing Helicase 2 Complex (REH2C) coordinate interactions between RECCs, mRNAs and hundreds of guide RNAs that direct edited sequences. Additionally, numerous auxiliary factors are required for productive editing of specific mRNAs. Here, we elucidate the role of KRBP72, an editing auxiliary factor of the ABC adenosine triphosphatase (ATPase) family that exhibits RNA-binding activity. In procyclic form Trypanosoma brucei, KRBP72 knockdown leads to a pause in editing at the base of a predicted stem loop structure in adenosine triphosphate synthase subunit 6 (A6) mRNA. Enhanced cross-linking and affinity purification revealed KRBP72 binding sites both within and upstream of this stem loop. KRBP72 ATPase activity is essential for its A6 mRNA editing function; however, its RNA-binding activity is dispensable. KRBP72 interacts with most RESC proteins in an RNase-sensitive manner. By contrast, RESC12A associates with KRBP72 in an RNase-insensitive fashion, and RESC12A promotes KRBP72’s interaction with RNA. Hence, KRBP72 ATPase activity facilitates progression of editing through a challenging secondary structure, highlighting this protein's crucial role in A6 mRNA editing.
Structural insights into a DNA polymerase reading the xeno nucleic acid HNA
Authors: Gutfreund Cédric , Betz Karin , Abramov Mikhail , Coosemans Frédérick , Holliger Phillipp , Herdewijn Piet , Marx Andreas 
Published: December 2024

Abstract
Xeno nucleic acids (XNAs) are unnatural analogues of the natural nucleic acids in which the canonical ribose or deoxyribose rings are replaced with alternative sugars, congener structures or even open-ring configurations. The expanding repertoire of XNAs holds significant promise for diverse applications in molecular biology as well as diagnostics and therapeutics. Key advantages of XNAs over natural nucleic acids include their enhanced biostability, superior target affinity and (in some cases) catalytic activity. Natural systems generally lack the mechanisms to transcribe, reverse transcribe or replicate XNAs. This limitation has been overcome through the directed evolution of nucleic acid-modifying enzymes, especially polymerases (pols) and reverse transcriptases (RTs). Despite these advances, the mechanisms by which synthetic RT enzymes read these artificial genetic polymers remain largely unexplored, primarily due to a scarcity of structural information. This study unveils first structural insights into an evolved thermostable DNA pol interacting with the XNA 1,5-anhydrohexitol nucleic acid (HNA), revealing unprecedented HNA nucleotide conformations within a ternary complex with the enzyme. These findings not only deepen our understanding of HNA to DNA reverse transcription but also set the stage for future advancements of this and similar enzymes through deliberate design.
Enzymatic bypass of G-quadruplex structures containing oxidative lesions
Authors: Podbevšek Peter , Plavec Janez 
Published: December 2024

Abstract
The function of many DNA processing enzymes involves sliding along the double helix or individual DNA strands. Stable secondary structures in the form of G-quadruplexes are difficult for such enzymes to bypass. We used a polymerase stop assay to determine which structural features of the human telomeric and the BCL2 promoter G-quadruplexes can stall progression of the Klenow fragment. Primer extension profiles revealed that G-quartets are effective roadblocks for the Klenow fragment, while auxiliary base pairs can be easily bypassed. Furthermore, we utilized 8-oxoguanine to simulate oxidative damage in G-rich regions and determine the effects on enzyme bypass. In rare cases, oxidative lesions reduce the level of G-quadruplex bypass. In general, however, oxidative lesions reduce G-quadruplex stability and facilitate bypassing of such G-rich regions, especially if the lesion persists in unfolding intermediates. Our findings using Klenow fragment can be extrapolated to other G-quadruplex forming sequences and enzymes that utilise a clamp-like structure to slide along DNA and are involved in processes such as gene expression regulation and telomere maintenance.