bluuebunny/crossref_metadata_2025_split huggingface dataset:
GHOST commissioning science results – II: a very metal-poor star witnessing the early galactic assembly
Authors: Sestito Federico , Hayes Christian R , Venn Kim A , Jensen Jaclyn , McConnachie Alan W , Pazder John , Waller Fletcher , Ardern-Arentsen Anke , Jablonka Pascale , Martin Nicolas F , Matsuno Tadafumi , Navarro Julio F , Starkenburg Else , Vitali Sara , Bassett John , Berg Trystyn A M , Diaz Ruben , Edgar Michael L , Firpo Veronica , Gomez-Jimenez Manuel , Kalari Venu , Lambert Sam , Lawrence Jon , Robertson Gordon , Ruiz-Carmona Roque , Salinas Ricardo , Sebo Kim M , Venkatesan Sudharshan 
Published: February 2024

ABSTRACT
This study focuses on Pristine$\_180956.78$−294759.8 (hereafter P180956, [Fe/H] = −1.95 ± 0.02), a star selected from the Pristine Inner Galaxy Survey (PIGS), and followed-up with the recently commissioned Gemini High-resolution Optical SpecTrograph (GHOST) at the Gemini South telescope. The GHOST spectrograph’s high efficiency in the blue spectral region (3700−4800 Å) enables the detection of elemental tracers of early supernovae (e.g. Al, Mn, Sr, and Eu). The star exhibits chemical signatures resembling those found in ultrafaint dwarf (UFD) systems, characterized by very low abundances of neutron-capture elements (Sr, Ba, and Eu), which are uncommon among stars in the Milky Way halo. Our analysis suggests that P180956 bears the chemical imprints of a small number (2 or 4) of low-mass hypernovae ($\sim 10{-}15{\rm \, M_\odot }$), which are needed to mostly reproduce the abundance pattern of the light-elements (e.g. [Si, Ti/Mg, Ca] ∼0.6), and one fast-rotating intermediate-mass supernova ($\sim 300{\rm \, km \ s^{-1}}$, $\sim 80{-}120{\rm \, M_\odot }$), which is the main channel contributing to the high [Sr/Ba] (∼+1.2). The small pericentric ($\sim 0.7{\rm \, kpc}$) and apocentric ($\sim 13{\rm \, kpc}$) distances and its orbit confined to the plane ($\lesssim 2{\rm \, kpc}$) indicate that this star was likely accreted during the early Galactic assembly phase. Its chemo-dynamical properties suggest that P180956 formed in a system similar to a UFD galaxy accreted either alone, as one of the low-mass building blocks of the proto-Galaxy, or as a satellite of Gaia–Sausage–Enceladus. The combination of Gemini’s large aperture with GHOST’s high efficiency and broad spectral coverage makes this new spectrograph one of the leading instruments for near-field cosmology investigations.
Image-based automatic wind velocity profiler for adaptive optics
Authors: Diaz Sebastian J , Tejos Cristian , Guesalaga Andres 
Published: February 2024

ABSTRACT
Adaptive optics (AO) systems correct optical phase aberrations of the incoming light generated by the atmosphere. To do so simultaneous estimators of the atmospheric turbulence parameters are required. For the family of wide-field AO (WFAO) systems, this information must be stratified in altitude. Among these vectorized estimations, wind profiling in altitude is needed for the reduction of temporal errors in AO loops or for the estimation of turbulence coherence time. This paper proposes a turbulence wind profiler called image processing based peak tracking algorithm (ipta). ipta is an image-processing based approach that automatically and reliably estimates wind velocity for several turbulent layers along the line of sight. The estimation of each wind layer is achieved by tracking peaks produced in cross-correlation maps from pairs of wavefront sensors (WFSs) slopes using the technique known as SLODAR (slope detection and ranging). Results for simulated and on-sky WFS data sets demonstrate that ipta outperforms one of the state of the art wind profiler methods [the profiler covariance parametrization of wind velocity (CAW)] in terms of accuracy and speed. Results also show that, in terms of execution time, our method scales better when the number of WFS lenslets is increased. Being an open source and reliable tool, we believe ipta can be a useful wind profiler for the AO community.
Prospects for detecting proto-neutron star rotation and spin-down using supernova neutrinos
Authors: Prasanna Tejas , Thompson Todd A , Hirata Christopher 
Published: February 2024

ABSTRACT
After a successful supernova, a proto-neutron star (PNS) cools by emitting neutrinos on ∼1–100 s time-scales. Provided that there are neutrino emission ‘hotspots’ or ‘cold-spots’ on the surface of the rotating PNS, we can expect a periodic modulation in the number of neutrinos observable by detectors. We show that Fourier transform techniques can be used to determine the PNS rotation rate from the neutrino arrival times. Provided there is no spin-down, a 1-parameter Discrete Fourier Transform (DFT) is sufficient to determine the spin period of the PNS. If the PNS is born as a magnetar with polar magnetic field strength B0 ≳ 1015 G and is ‘slowly’ rotating with an initial spin period ≳100 ms, then it can spin-down to periods of the order of seconds during the cooling phase. We propose a modified DFT technique with three frequency parameters to detect spin-down. Due to lack of neutrino data from a nearby supernova except the ∼20 neutrinos detected from SN1987A, we use toy models and one physically motivated modulating function to generate neutrino arrival times. We use the false alarm rate (FAR) to quantify the significance of the Fourier power spectrum peaks. We show that PNS rotation and spin-down are detected with $\rm FAR\,\lt\, 2~{{\ \rm per\ cent}}$ (2σ) for periodic signal content $\rm M\gtrsim 13-15~{{\ \rm per\ cent}}$ if 5 × 103 neutrinos are detected in ∼3 s and with $\rm FAR\,\lt\, 1{{\ \rm per\ cent}}$ for $\rm M\,\ge 5{{\ \rm per\ cent}}$ if 5 × 104 neutrinos are detected in ∼3 s. Since we can expect ∼104−105 neutrino detections from a supernova at 10 kpc, detection of PNS rotation and spin-down is possible using the neutrinos from the next Galactic supernova.
The VLBA CANDELS GOODS-North Survey. II – Wide-field source catalogue comparison between the VLBA, EVN, e-MERLIN, and VLA
Authors: Njeri Ann , Deane Roger P , Radcliffe J F , Beswick R J , Thomson A P , Muxlow T W B , Garrett M A , Harrison C M 
Published: February 2024

ABSTRACT
Deep radio surveys of extragalactic legacy fields trace a large range of spatial and brightness temperature sensitivity scales, and therefore have differing biases to radio-emitting physical components within galaxies. This is particularly true of radio surveys performed at $\lesssim 1 \ \mathrm{arcsec}$ angular resolutions, and so robust comparisons are necessary to better understand the biases present in each survey. We present a multiresolution and multiwavelength analysis of the sources detected in a new Very Long Baseline Array (VLBA) survey of the Cosmic Assembly Near-IR Deep Extragalactic Legacy Survey Great Observatories Origins Deep Survey-North field. For the 24 VLBA-selected sources described in Paper I, we augment the VLBA data with EVN data, and ∼0.1–1 arcsec angular resolution data provided by Very Large Array (VLA) and enhanced-Multi Element Remotely Linked Interferometry Network. This sample includes new active galactic nuclei (AGN) detected in this field, thanks to a new source extraction technique that adopts priors from ancillary multiwavelength data. The high brightness temperatures of these sources (TB ≳ 106 K) confirm AGN cores, that would often be missed or ambiguous in lower-resolution radio data of the same sources. Furthermore, only 15 sources are identified as ‘radiative’ AGN based on available X-ray and infrared constraints. By combining VLA and VLBA measurements, we find evidence that the majority of the extended radio emission is also AGN dominated, with only three sources with evidence for extended potentially star formation-dominated radio emission. We demonstrate the importance of wide-field multiresolution (arcsecond–milliarcsecond) coverage of the faint radio source population, for a complete picture of the multiscale processes within these galaxies.
3D NLTE Lithium abundances for late-type stars in GALAH DR3
Authors: Wang Ella Xi , Nordlander Thomas , Buder Sven , Ciucă Ioana , Soen Alexander , Martell Sarah , Ness Melissa , Lind Karin , McKenzie Madeleine , Stello Dennis 
Published: February 2024

ABSTRACT
Lithium’s susceptibility to burning in stellar interiors makes it an invaluable tracer for delineating the evolutionary pathways of stars, offering insights into the processes governing their development. Observationally, the complex Li production and depletion mechanisms in stars manifest themselves as Li plateaus, and as Li-enhanced and Li-depleted regions of the HR diagram. The Li-dip represents a narrow range in effective temperature close to the main-sequence turn-off, where stars have slightly super-solar masses and strongly depleted Li. To study the modification of Li through stellar evolution, we measure 3D non-local thermodynamic equilibrium (NLTE) Li abundance for 581 149 stars released in GALAH DR3. We describe a novel method that fits the observed spectra using a combination of 3D NLTE Li line profiles with blending metal-line strength that are optimized on a star-by-star basis. Furthermore, realistic errors are determined by a Monte Carlo nested sampling algorithm which samples the posterior distribution of the fitted spectral parameters. The method is validated by recovering parameters from a synthetic spectrum and comparing to 26 stars in the Hypatia catalogue. We find 228 613 Li detections, and 352 536 Li upper limits. Our abundance measurements are generally lower than GALAH DR3, with a mean difference of 0.23 dex. For the first time, we trace the evolution of Li-dip stars beyond the main sequence turn-off and up the subgiant branch. This is the first 3D NLTE analysis of Li applied to a large spectroscopic survey, and opens up a new era of precision analysis of abundances for large surveys.
Periodically modulated FRB as extreme mass ratio binaries
Authors: Katz J I 
Published: February 2024

ABSTRACT
The activity of at least one repeating fast radio burst (FRB) source is periodically modulated. If this modulation is the result of precession of the rotation axis and throat of an accretion disc around a black hole, driven by a companion that is also the source of accreted mass, then it may be possible to constrain the mass of the black hole. The dynamics is analogous to that of superorbital periods in ordinary mass-transfer binaries in which the accreting object may be a stellar-mass black hole, a neutron star or a white dwarf, but in the FRB source it may be an intermediate-mass black hole. In a semidetached (mass-transferring) binary, the orbital period is nearly proportional to the −1/2 power of the mean density of the mass-losing star and nearly independent of the mass of the primary, but the ratio of precessional to orbital periods scales approximately as the −2/3 power of the mass ratio for small mass ratios (massive accretors). Assuming a value for the secondary’s density and identifying the observed modulation period as a disc precession period would determine the mass ratio and the mass of the black hole. This model and magnetar-SNR (supernova remnant) models make distinguishable predictions of the evolution of the rotation measure that may soon be tested in FRB 121102.
Mapping Geological Events and Nitrogen Fixation Evolution Onto the Timetree of the Evolution of Nitrogen-Fixation Genes
Authors: Pi Hong-Wei , Chiang Yin-Ru , Li Wen-Hsiung 
Published: February 2024

Abstract
Nitrogen is essential for all organisms, but biological nitrogen fixation (BNF) occurs only in a small fraction of prokaryotes. Previous studies divided nitrogenase-gene-carrying prokaryotes into Groups I to IV and provided evidence that BNF first evolved in bacteria. This study constructed a timetree of the evolution of nitrogen-fixation genes and estimated that archaea evolved BNF much later than bacteria and that nitrogen-fixing cyanobacteria evolved later than 1,900 MYA, considerably younger than the previous estimate of 2,200 MYA. Moreover, Groups III and II/I diverged ∼2,280 MYA, after the Kenorland supercontinent breakup (∼2,500–2,100 MYA) and the Great Oxidation Event (∼2,400–2,100 MYA); Groups III and Vnf/Anf diverged ∼2,086 MYA, after the Yarrabubba impact (∼2,229 MYA); and Groups II and I diverged ∼1,920 MYA, after the Vredefort impact (∼2,023 MYA). In summary, this study provided a timescale of BNF events and discussed the possible effects of geological events on BNF evolution.
DNA hypomethylation activates Cdk4/6 and Atr to induce DNA replication and cell cycle arrest to constrain liver outgrowth in zebrafish
Authors: Madakashira Bhavani P , Magnani Elena , Ranjan Shashi , Sadler Kirsten C 
Published: February 2024

AbstractCoordinating epigenomic inheritance and cell cycle progression is essential for organogenesis. UHRF1 connects these functions during development by facilitating maintenance of DNA methylation and cell cycle progression. Here, we provide evidence resolving the paradoxical phenotype of uhrf1 mutant zebrafish embryos which have activation of pro-proliferative genes and increased number of hepatocytes in S-phase, but the liver fails to grow. We uncover decreased Cdkn2a/b and persistent Cdk4/6 activation as the mechanism driving uhrf1 mutant hepatocytes into S-phase. This induces replication stress, DNA damage and Atr activation. Palbociclib treatment of uhrf1 mutants prevented aberrant S-phase entry, reduced DNA damage, and rescued most cellular and developmental phenotypes, but it did not rescue DNA hypomethylation, transposon expression or the interferon response. Inhibiting Atr reduced DNA replication and increased liver size in uhrf1 mutants, suggesting that Atr activation leads to dormant origin firing and prevents hepatocyte proliferation. Cdkn2a/b was downregulated pro-proliferative genes were also induced in a Cdk4/6 dependent fashion in the liver of dnmt1 mutants, suggesting DNA hypomethylation as a mechanism of Cdk4/6 activation during development. This shows that the developmental defects caused by DNA hypomethylation are attributed to persistent Cdk4/6 activation, DNA replication stress, dormant origin firing and cell cycle inhibition.
Ccq1 restrains Mre11-mediated degradation to distinguish short telomeres from double-strand breaks
Authors: Audry Julien , Zhang Haitao , Kerr Carly , Berkner Kathleen L , Runge Kurt W 
Published: February 2024

Abstract
Telomeres protect chromosome ends and are distinguished from DNA double-strand breaks (DSBs) by means of a specialized chromatin composed of DNA repeats bound by a multiprotein complex called shelterin. We investigated the role of telomere-associated proteins in establishing end-protection by studying viable mutants lacking these proteins. Mutants were studied using a Schizosaccharomyces pombe model system that induces cutting of a ‘proto-telomere’ bearing telomere repeats to rapidly form a new stable chromosomal end, in contrast to the rapid degradation of a control DSB. Cells lacking the telomere-associated proteins Taz1, Rap1, Poz1 or Rif1 formed a chromosome end that was stable. Surprisingly, cells lacking Ccq1, or impaired for recruiting Ccq1 to the telomere, converted the cleaved proto-telomere to a rapidly degraded DSB. Ccq1 recruits telomerase, establishes heterochromatin and affects DNA damage checkpoint activation; however, these functions were separable from protection of the new telomere by Ccq1. In cells lacking Ccq1, telomere degradation was greatly reduced by eliminating the nuclease activity of Mre11 (part of the Mre11–Rad50–Nbs1/Xrs2 DSB processing complex), and higher amounts of nuclease-deficient Mre11 associated with the new telomere. These results demonstrate a novel function for S. pombe Ccq1 to effect end-protection by restraining Mre11-dependent degradation of the DNA end.
Global identification of mRNA-interacting circular RNAs by CLiPPR-Seq
Authors: Singh Suman , Shyamal Sharmishtha , Das Arundhati , Panda Amaresh C 
Published: February 2024

Abstract
Although the functional role of circular RNA (circRNA) interaction with microRNAs and proteins has been studied extensively, circRNA interactions with the protein-coding mRNAs in intact cells remain largely unknown. Here, by employing AMT-mediated proximity ligation of RNA-RNA duplexes followed by circRNA enrichment and deep sequencing, we report a novel Cross-Linking Poly(A) Pulldown RNase R Sequencing (CLiPPR-seq) technology which identified hundreds of mRNA-interacting circRNAs in three different cell types, including βTC6, C2C12 and HeLa cells. Furthermore, CLiPP-seq without RNase R treatment was also performed to identify the mRNA expression in these cells. BLAST analysis of circRNAs in CLiPPR-seq sample with the mRNAs in CLiPP-seq samples determined their potential complementary sequences for circRNA-mRNA interaction. Pulldown of circRNAs and poly(A) RNAs confirmed the direct interaction of circRNAs with target mRNAs. Silencing of mRNA-interacting circRNAs led to the altered expression of target mRNAs in βTC6 cells, suggesting the role of direct interaction of circRNAs with mRNAs in gene expression regulation. CLiPPR-seq thus represents a novel method for illuminating the myriad of uncharacterized circRNA–mRNA hybrids that may regulate gene expression.
Tankyrase-1 regulates RBP-mediated mRNA turnover to promote muscle fiber formation
Authors: Mubaid Souad , Sanchez Brenda Janice , Algehani Rinad A , Skopenkova Viktoriia , Adjibade Pauline , Hall Derek T , Busque Sandrine , Lian Xian Jin , Ashour Kholoud , Tremblay Anne-Marie K , Carlile Graeme , Gagné Jean-Philippe , Diaz-Gaxiola Andrea , Khattak Shahryar , Di Marco Sergio , Thomas David Y , Poirier Guy G , Gallouzi Imed-Eddine 
Published: February 2024

Abstract
Poly(ADP-ribosylation) (PARylation) is a post-translational modification mediated by a subset of ADP-ribosyl transferases (ARTs). Although PARylation-inhibition based therapies are considered as an avenue to combat debilitating diseases such as cancer and myopathies, the role of this modification in physiological processes such as cell differentiation remains unclear. Here, we show that Tankyrase1 (TNKS1), a PARylating ART, plays a major role in myogenesis, a vital process known to drive muscle fiber formation and regeneration. Although all bona fide PARPs are expressed in muscle cells, experiments using siRNA-mediated knockdown or pharmacological inhibition show that TNKS1 is the enzyme responsible of catalyzing PARylation during myogenesis. Via this activity, TNKS1 controls the turnover of mRNAs encoding myogenic regulatory factors such as nucleophosmin (NPM) and myogenin. TNKS1 mediates these effects by targeting RNA-binding proteins such as Human Antigen R (HuR). HuR harbors a conserved TNKS-binding motif (TBM), the mutation of which not only prevents the association of HuR with TNKS1 and its PARylation, but also precludes HuR from regulating the turnover of NPM and myogenin mRNAs as well as from promoting myogenesis. Therefore, our data uncover a new role for TNKS1 as a key modulator of RBP-mediated post-transcriptional events required for vital processes such as myogenesis.
The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations
Authors: Dong Hai-Long , Zhang Chen , Dai Liang , Zhang Yan , Zhang Xing-Hua , Tan Zhi-Jie 
Published: February 2024

Abstract
The subtle differences in the chemical structures of double-stranded (ds) RNA and DNA lead to significant variations in their biological roles and medical implications, largely due to their distinct biophysical properties, such as bending stiffness. Although it is well known that A-form dsRNA is stiffer than B-form dsDNA under physiological salt conditions, the underlying cause of this difference remains unclear. In this study, we employ high-precision magnetic-tweezer experiments along with molecular dynamics simulations and reveal that the relative bending stiffness between dsRNA and dsDNA is primarily determined by the structure- and salt-concentration-dependent ion distribution around their helical structures. At near-physiological salt conditions, dsRNA shows a sparser ion distribution surrounding its phosphate groups compared to dsDNA, causing its greater stiffness. However, at very high monovalent salt concentrations, phosphate groups in both dsRNA and dsDNA become fully neutralized by excess ions, resulting in a similar intrinsic bending persistence length of approximately 39 nm. This similarity in intrinsic bending stiffness of dsRNA and dsDNA is coupled to the analogous fluctuations in their total groove widths and further coupled to the similar fluctuation of base-pair inclination, despite their distinct A-form and B-form helical structures.
NUDT16 regulates CtIP PARylation to dictate homologous recombination repair
Authors: Zhang Zhen , Samsa William E , Gong Zihua 
Published: February 2024

Abstract
CtIP initiates DNA end resection and mediates homologous recombination (HR) repair. However, the underlying mechanisms of CtIP regulation and how the control of its regulation affects DNA repair remain incompletely characterized. In this study, NUDT16 loss decreases CtIP protein levels and impairs CtIP recruitment to double-strand breaks (DSBs). Furthermore, overexpression of a catalytically inactive NUDT16 mutant is unable to rescue decreased CtIP protein and impaired CtIP recruitment to DSBs. In addition, we identified a novel posttranslational modification of CtIP by ADP-ribosylation that is targeted by a PAR-binding E3 ubiquitin ligase, RNF146, leading to CtIP ubiquitination and degradation. These data suggest that the hydrolase activity of NUDT16 plays a major role in controlling CtIP protein levels. Notably, ADP-ribosylation of CtIP is required for its interaction with NUDT16, its localization at DSBs, and for HR repair. Interestingly, NUDT16 can also be ADP-ribosylated. The ADP-ribosylated NUDT16 is critical for CtIP protein stability, CtIP recruitment to DSBs, and HR repair in response to DNA damage. In summary, we demonstrate that NUDT16 and its PARylation regulate CtIP stability and CtIP recruitment to DSBs, providing new insights into our understanding of the regulation of CtIP-mediated DNA end resection in the HR repair pathway.
Evolving precision: rRNA expansion segment 7S modulates translation velocity and accuracy in eukaryal ribosomes
Authors: Rauscher Robert , Eggers Cristian , Dimitrova-Paternoga Lyudmila , Shankar Vaishnavi , Rosina Alessia , Cristodero Marina , Paternoga Helge , Wilson Daniel N , Leidel Sebastian A , Polacek Norbert 
Published: February 2024

Abstract
Ribosome-enhanced translational miscoding of the genetic code causes protein dysfunction and loss of cellular fitness. During evolution, open reading frame length increased, necessitating mechanisms for enhanced translation fidelity. Indeed, eukaryal ribosomes are more accurate than bacterial counterparts, despite their virtually identical, conserved active centers. During the evolution of eukaryotic organisms ribosome expansions at the rRNA and protein level occurred, which potentially increases the options for translation regulation and cotranslational events. Here we tested the hypothesis that ribosomal RNA expansions can modulate the core function of the ribosome, faithful protein synthesis. We demonstrate that a short expansion segment present in all eukaryotes’ small subunit, ES7S, is crucial for accurate protein synthesis as its presence adjusts codon-specific velocities and guarantees high levels of cognate tRNA selection. Deletion of ES7S in yeast enhances mistranslation and causes protein destabilization and aggregation, dramatically reducing cellular fitness. Removal of ES7S did not alter ribosome architecture but altered the structural dynamics of inter-subunit bridges thus affecting A-tRNA selection. Exchanging the yeast ES7S sequence with the human ES7S increases accuracy whereas shortening causes the opposite effect. Our study demonstrates that ES7S provided eukaryal ribosomes with higher accuracy without perturbing the structurally conserved decoding center.