bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing E-MOSAICS predictions of high-redshift proto-globular clusters with JWST observations in lensed galaxies
Authors: Pfeffer Joel , Forbes Duncan A , Romanowsky Aaron J , Bastian Nate , Crain Robert A , Kruijssen J M Diederik , Bekki Kenji , Brodie Jean P , Chevance Mélanie , Couch Warrick J , Gannon Jonah S 
Published: December 2024

ABSTRACT
High-resolution imaging and strong gravitational lensing of high-redshift galaxies have enabled the detection of compact sources with properties similar to nearby massive star clusters. Often found to be very young, these sources may be globular clusters detected in their earliest stages. In this work, we compare predictions of high-redshift ($z \sim 1$–10) star cluster properties from the E-MOSAICS simulation of galaxy and star cluster formation with those of the star cluster candidates in strongly lensed galaxies from JWST and Hubble Space Telescope (HST) imaging. We select galaxies in the simulation that match the luminosities of the majority of lensed galaxies with star cluster candidates observed with JWST. We find that the luminosities, ages, and masses of the brightest star cluster candidates in the high-redshift galaxies are consistent with the E-MOSAICS model. In particular, the brightest cluster ages are in excellent agreement. The results suggest that star clusters in both low- and high-redshift galaxies may form via common mechanisms. However, the brightest clusters in the lensed galaxies tend to be $\approx 1$–$1.5 \, \rm {mag}$ brighter and $\approx 0.5$ dex more massive than the median E-MOSAICS predictions. We discuss the large number of effects that could explain the discrepancy, including simulation and observational limitations, stellar population models, cluster detection biases, and nuclear star clusters. Understanding these limitations would enable stronger tests of globular cluster formation models.
Stage IV baryonic feedback correction for non-Gaussianity inference
Authors: Grandón Daniela , Sellentin Elena 
Published: December 2024

ABSTRACT
Non-Gaussian statistics of the projected weak lensing field are powerful estimators that can outperform the constraining power of the two-point functions in inferring cosmological parameters. This is because these estimators extract the non-Gaussian information contained in the small scales. However, fully leveraging the statistical precision of such estimators is hampered by theoretical uncertainties, such as those arising from baryonic physics. Moreover, as non-Gaussian estimators mix different scales, there exists no natural cut-off scale below which baryonic feedback can be completely removed. We therefore present a Bayesian solution for accounting for baryonic feedback uncertainty in weak lensing non-Gaussianity inference. Our solution implements Bayesian model averaging (BMA), a statistical framework that accounts for model uncertainty and combines the strengths of different models to produce more robust and reliable parameter inferences. We demonstrate the effectiveness of this approach in a Stage IV convergence peak count analysis, including three baryonic feedback models. We find that the resulting BMA posterior distribution safeguards parameter inference against biases due to baryonic feedback, and therefore provides a robust framework for obtaining accurate cosmological constraints at Stage IV precision under model uncertainty scenarios.
JADES: measuring reionization properties using Lyman-alpha emission
Authors: Jones Gareth C , Bunker Andrew J , Saxena Aayush , Arribas Santiago , Bhatawdekar Rachana , Boyett Kristan , Cameron Alex J , Carniani Stefano , Charlot Stephane , Curtis-Lake Emma , Hainline Kevin , Johnson Benjamin D , Kumari Nimisha , Maseda Michael V , Rix Hans-Walter , Robertson Brant E , Tacchella Sandro , Übler Hannah , Williams Christina C , Willott Chris , Witstok Joris , Zhu Yongda 
Published: December 2024

ABSTRACT
Ly$\alpha$ is the transition to the ground state from the first excited state of hydrogen (the most common element). Resonant scattering of this line by neutral hydrogen greatly impedes its emergence from galaxies, so the fraction of galaxies emitting Ly$\alpha$ is a tracer of the neutral fraction of the intergalactic medium (IGM), and thus the history of reionization. In previous works, we used early JWST/NIRSpec data from the JWST Advanced Deep Extragalactic Survey (JADES) to classify and characterize Ly$\alpha$ emitting galaxies (LAEs). This survey is approaching completion, and the current sample is nearly an order of magnitude larger. From a sample of 795  galaxies in JADES at $4.0\lt z\lt 14.3$, we find evidence for Ly$\alpha$ emission in 150 sources. We reproduce the previously found correlation between Ly$\alpha$ escape fraction ($f\rm _{esc}^{Ly\alpha }$) – Ly$\alpha$ rest-frame equivalent width (${\rm REW}_{\rm Ly\alpha }$) and the negative correlation between Ly$\alpha$ velocity offset – $f\rm _{esc}^{Ly\alpha }$. Both $f\rm _{esc}^{Ly\alpha }$ and ${\rm REW}_{\rm Ly\alpha }$ decrease with redshift ($z\gtrsim 5.5$), indicating the progression of reionization on a population scale. Our data are used to demonstrate an increasing IGM transmission of Ly$\alpha$ from $z\sim 14-6$. We measure the completeness-corrected fraction of LAEs ($X\rm _{Ly\alpha }$) from $z=4-9.5$. An application of these $X\rm _{Ly\alpha }$ values to the results of previously utilized semi-analytical models suggests a high neutral fraction at $z=7$ (${X_{\rm HI}}\sim 0.8-0.9$). Using an updated fit to the intrinsic distribution of ${\rm REW}_{\rm Ly\alpha }$ results in a lower value in agreement with current works (${X_{\rm HI}}= 0.64_{-0.21}^{+0.13}$). This sample of LAEs will be paramount for unbiased population studies of galaxies in the EoR.
Investigating the correlation between the magnetic field orientation and molecular outflow direction in some molecular clouds
Authors: Nath Mazumdar S , Das H S , Wolf S 
Published: December 2024

ABSTRACT
This study examines the relationship between the magnetic field orientation of a molecular cloud and its outflow axis, using data from 22 molecular clouds. We find that the position angles of the outflow axis ($\theta _{\text{out}}$) and the cloud-scale magnetic field in the core, measured in the submillimetre region ($\theta _B^{\text{sub}}$), are correlated to each other irrespective of the alignment or misalignment between the two axes. However, it is important to note that these observed position angles are projections on to the plane of the sky. To assess the statistical significance of our findings, we conduct a statistical test to account for the projection effect and find minimal impact. Moreover, we identify a possible role of the Galactic magnetic field orientation ($\theta _{\text{GP}}$) in determining the outflow direction by assessing the offset ($\theta _{\text{off}} = \theta _B - \theta _{\text{GP}}$) in both the core and envelope regions. Furthermore, we explore the influence of parameters such as magnetic field strength (B), the position angle of the minor axis of the cloud cores ($\theta _{\text{min}}$), the inclination angle of the outflow ($i_{\text{out}}$), and other factors on the alignment between the outflow and cloud-scale magnetic field axes ($|\theta _{\text{OB}}| = |\theta _{\text{out}} - \theta _B^{\text{sub}}|$). Our analysis suggests that the orientation of the outflow axis is determined by the combined influence of the magnetic field orientation, the minor axis, the inclination angle of the outflow, and the associated magnetic field strength.
Broad-band study of the Be X-ray binary RX J0520.5–6932 during its outburst in 2024
Authors: Yang H N , Maitra C , Vasilopoulos G , Haberl F , Jenke P A , Karaferias A S , Sharma R , Beri A , Ji L , Jin C , Yuan W , Zhang Y J , Wang C Y , Xu X P , Liu Y , Zhang W D , Zhang C , Ling Z X , Liu H Y , Cheng H Q , Pan H W 
Published: December 2024

ABSTRACT
A new giant outburst of the Be X-ray binary RX J0520.5–6932 was detected and subsequently observed with several space-borne and ground-based instruments. This study presents a comprehensive analysis of the optical and X-ray data, focusing on the spectral and timing characteristics of selected X-ray observations. A joint fit of spectra from simultaneous observations performed by the X-ray telescope (XRT) on the Neil Gehrels Swift Observatory (Swift) and Nuclear Spectroscopic Telescope ARray (NuSTAR) provides broad-band parameter constraints, including a cyclotron resonant scattering feature (CRSF) at $32.2_{-0.7}^{+0.8}$ keV with no significant energy change since 2014, and a weaker Fe line. Independent spectral analyses of observations by the Lobster Eye Imager for Astronomy, Einstein Probe (EP), Swift–XRT, and NuSTAR demonstrate the consistency of parameters across different bands. Luminosity variations during the current outburst were tracked. The light curve of the Optical Gravitational Lensing Experiment (OGLE) aligns with the X-ray data in both 2014 and 2024. Spin evolution over 10 yr is studied after adding Fermi Gamma-ray Burst Monitor data, improving the orbital parameters, with an estimated orbital period of 24.39 d, slightly differing from OGLE data. Despite intrinsic spin-up during outbursts, a spin-down of $\sim$0.04 s over 10.3 yr is suggested. For the new outburst, the pulse profiles indicate a complicated energy-dependent shape, with decreases around 15 and 25 keV in the pulsed fraction, a first for an extragalactic source. Phase-resolved NuSTAR data indicate variations in parameters such as flux, photon index, and CRSF energy with rotation phase.
Ejecta width and magnetization reflected in gamma-ray burst early afterglows: implication for reverse shock component and shallow decay phase
Authors: Kusafuka Yo , Asano Katsuaki 
Published: December 2024

ABSTRACT
To study the ejecta property dependence of the gamma-ray burst (GRB) afterglow, we carry out spherically symmetrical one-dimensional special relativistic magnetohydrodynamic simulations of magnetized outflows with an adaptive mesh refinement method. The Lorentz factor evolutions of forward and reverse shocks induced by the interaction between magnetized ejecta and an ambient medium are investigated for a wide range of magnetization and width of the ejecta. The forward shock evolution is described by the magnetic acceleration, coasting, transition, and self-similar deceleration phases. According to our simulation results, we numerically calculate the corresponding radiation. Based on our numerical results, to model afterglow light curves in general cases, we construct semi-analytical formulae for the Lorentz factor evolutions. The magnetization and ejecta width dependence are clearly seen in the reverse shock light curves. The transition phase with a reasonable ejecta width can reproduce the shallow decay phase in the observed GRB afterglow. The inverse Compton emission in the magnetic acceleration phase can be responsible for the very steep rise of the early TeV emission in GRB 221009A.
Building a Semi-analytic Black Hole Seeding Model using IllustrisTNG Host Galaxies
Authors: Evans Analis Eolyn , Blecha Laura , Bhowmick Aklant Kumar 
Published: December 2024

ABSTRACT
A major open question in astrophysics is the mechanisms by which massive black holes (BHs) form in the early Universe, which pose constraints on seeding models. We study BH formation and evolution in a flexible model combining the cosmological IllustrisTNG (TNG) simulations with semi-analytic modelling in post-processing. We identify our TNG model hosts based on various criteria including a minimum gas mass of $10^7$–$10^9$${\rm M}_{\odot }$, total host mass of $10^{8.5}$–$10^{10.5}$${\rm M}_{\odot }$, and a maximum gas metallicity of 0.01–0.1 $\mathrm{Z}_{\odot }$. Each potential host is assigned a BH seed with a probability of 0.01–1. The populations follow the TNG galaxy merger tree. This approach improves upon the predictive power of the simple TNG BH seeding prescription, narrowing down plausible seeding parameter spaces, and it is readily adaptable to other cosmological simulations. Several model realizations predict $z\lesssim 4$ BH mass densities that are consistent with empirical data as well as the TNG BHs. However, high-redshift BH number densities can differ by factors of $\sim$ 10 to $\gtrsim$ 100 between seeding parameters. In most model realizations, $\lesssim 10^5$${\rm M}_{\odot }$ BHs substantially outnumber heavier BHs at high redshifts. Mergers between such BHs are prime targets for gravitational-wave detection with Laser Interferometer Space Antenna. The $z=0$ BH mass densities in most realizations of the model agree well with observations, but our strictest seeding criteria fail at high redshift. Our findings strongly motivate the need for better empirical constraints on high-z BHs, and they underscore the significance of recent active galactic nucleus discoveries with JWST.
First investigation of void statistics in numerical relativity simulations
Authors: Williams Michael J , Macpherson Hayley J , Wiltshire David L , Stevens Chris 
Published: December 2024

ABSTRACT
We apply and extend standard tools for void statistics to cosmological simulations that solve Einstein’s equations with numerical relativity (NR). We obtain a simulated void catalogue without Newtonian approximations, using a new watershed void finder that operates on fluid-based NR simulations produced with the Einstein Toolkit. We compare and contrast measures of void size and void fraction, and compare radial stacked density profiles to empirically-derived Hamaus–Sutter–Wandelt (HSW) density profiles and profiles based on distance to void boundaries. We recover statistics roughly consistent with Newtonian N-body simulations where such a comparison is meaningful. We study the variation of dynamical spatial curvature and local expansion explicitly demonstrating the spatial fluctuations of these quantities in void regions. We find that voids in our simulations expand ∼10–30 per cent faster than the global average, and the spatial curvature density parameter in the centre of voids reaches ∼60–80 per cent.
Neural network emulator to constrain the high-z IGM thermal state from Lyman-α forest flux autocorrelation function
Authors: Jin Zhenyu , Wolfson Molly , Hennawi Joseph F , González-Hernández Diego 
Published: December 2024

ABSTRACT
We present a neural network emulator to constrain the thermal parameters of the intergalactic medium (IGM) at $5.4 \le z \le 6.0$ using the Lyman-$\alpha$ (Ly $\alpha$) forest flux autocorrelation function. Our autodifferentiable JAX-based framework accelerates the surrogate model generation process using approximately 100 sparsely sampled Nyx hydrodynamical simulations with varying combinations of thermal parameters, i.e. the temperature at mean density $T_0$, the slope of the temperature–density relation $\gamma$, and the mean transmission flux $\langle F \rangle$. We show that this emulator has a typical accuracy of 1.0 per cent across the specified redshift range. Bayesian inference of the IGM thermal parameters, incorporating emulator uncertainty propagation, is further expedited using NumPyro Hamiltonian Monte Carlo. We compare both the inference results and computational cost of our framework with the traditional nearest-neighbour interpolation approach applied to the same set of mock Ly $\alpha$ flux. By examining the credibility contours of the marginalized posteriors for $T_0, \gamma , \text{and}~\langle F \rangle$ obtained using the emulator, the statistical reliability of measurements is established through inference on 100 realistic mock data sets of the autocorrelation function.
Statistical dependence of ion-scale waves’ spacecraft-frame polarization observed by Parker Solar Probe on local proton and alpha non-Maxwellian features
Authors: Liu Wen , Jia Huan-Yu , Liu Si-Ming 
Published: December 2024

ABSTRACT
This paper statistically investigate the relationship between the polarization of ion-scale waves in the spacecraft frame and the background plasma environment based on parker solar probe observations within 0.3 au. Our statistical results show that the background solar wind environment of left-handed (LH) and right-handed (RH) ion-scale waves in the spacecraft frame is significantly different. The LH waves corresponds to higher ion temperature ($T_\mathrm{ p}\sim 45.16$ eV, $T_{\alpha }\sim 327.63$ eV), larger alpha particle density ratio ($N_{\alpha }/N_\mathrm{ p}\sim 0.016$), larger temperature ratio ($T_{\alpha }/T_\mathrm{ p}\sim 7.20$), and larger differential speed ($(V_{\alpha }-V_\mathrm{ p})/V_\mathrm{ A}\sim 0.395$) than those ($T_\mathrm{ p}\sim 18.38$ eV, $T_{\alpha }\sim 77.25$ eV, $N_{\alpha }/N_\mathrm{ p}\sim 0.007$, $T_{\alpha }/T_\mathrm{ p}\sim 4.22$, $(V_{\alpha }-V_\mathrm{ p})/V_\mathrm{ A}\sim 0.093$) of RH waves. In addition, LH waves mainly corresponds to $V_{\alpha \mathrm{ p}}/V_\mathrm{ A}\gt 0$ (the moment of alpha velocity is larger than the moment of proton velocity) and their occurrence rate of LH ion-scale waves is proportional to $T_{\alpha }$, $T_\mathrm{ p}$, $T_{\alpha }/T_\mathrm{ p}$, $T_{\alpha \parallel }/T_{\mathrm{ p} \parallel }$, and $V_{\alpha \mathrm{ p}}/V_\mathrm{ A}$, while RH waves do the opposite. Moreover, when $T_{\alpha }/T_\mathrm{ p}\gt 10$, only LH ion-scale wave exists and its occurrence rate is high. Besides, our theoretical results suggest that the high occurrence rate regions of spacecraft-frame LH (RH) ion-scale waves seem to prefer generating LH Alfvén/ion cyclotron waves (RH fast magnetosonic/whistler waves).
Asymmetrical Evolution of Promoter Methylation of Mammalian Genes after Duplication
Authors: de la Fuente Mercedes , Mendizabal Isabel , Han Mira V , Yi Soojin V , Alvarez-Ponce David 
Published: December 2024

Abstract
Even though gene duplication is a key source of new genes and evolutionary innovation, it is unclear how duplicates survive the period immediately following gene duplication, in which both copies are functionally redundant. In the absence of epigenetic silencing, the abundance of the gene product would double after gene duplication, which would often have deleterious effects. However, recent duplicates exhibit low expression levels, which could be at least partially explained by high levels of promoter methylation. What evolutionary paths lead to duplicate hypermethylation, and does it affect both duplicates or only one? Here, we compare levels of promoter methylation in 10 human and 16 mouse tissues, between singletons and duplicates and among human–mouse orthologs of different kinds (one-to-one, one-to-many, many-to-one, and many-to-many). Our results indicate that: (i) on average, duplicates are more methylated than singletons in mouse, but less methylated than singletons in human, (ii) recently duplicated genes tend to exhibit high levels of promoter methylation, (iii) genes that undergo duplication tend to be highly methylated before duplication, (iv) after gene duplication, one of the copies (the daughter copy, i.e. the one that relocates to a new genomic context) tends to undergo an additional increase in promoter methylation, whereas the other (the parental copy, which remains in the original genomic location) tends to retain preduplication methylation levels, and (v) daughter copies tend to be lowly expressed. These observations support a model in which daughter copies are repressed via promoter hypermethylation and can thus survive the filter of purifying selection until both copies diverge functionally.
A Spectrum of Audiences for Music Theory, and Some Ways to Connect with Them
Authors: Krebs Harald 
Published: December 2024

Abstract
My paper describes the audiences that I have addressed in public-facing situations—a variety of community audiences, and of academic audiences outside of music. I summarize the tools and techniques that I have found to be useful for connecting with these audiences: visual aids in the form of PowerPoint slides; collaborative creative activity; humor; and live performance.
MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models
Authors: Clarke Alexander W , Høye Eirik , Hembrom Anju Angelina , Paynter Vanessa Molin , Vinther Jakob , Wyrożemski Łukasz , Biryukova Inna , Formaggioni Alessandro , Ovchinnikov Vladimir , Herlyn Holger , Pierce Alexandra , Wu Charles , Aslanzadeh Morteza , Cheneby Jeanne , Martinez Pedro , Friedländer Marc R , Hovig Eivind , Hackenberg Michael , Umu Sinan Uğur , Johansen Morten , Peterson Kevin J , Fromm Bastian 
Published: December 2024

Abstract
We present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to a new server and the creation of a computational mirror, we have expanded the database with the addition of 33 invertebrate species, including representatives of 5 previously unsampled phyla, and 6 mammal species. MirGeneDB now contains entries for 21 822 microRNA genes (5160 of these from the new species) belonging to 1743 microRNA families. The inclusion of these new species allowed us to refine both the evolutionary node of appearance of a number of microRNA genes/families, as well as MirGeneDB’s phylogenetically informed nomenclature system. Updated covariance models of all microRNA families, along with all smallRNA read data are now downloadable. These enhanced annotations will allow researchers to analyze microRNA properties such as secondary structure and features of their biogenesis within a robust phylogenetic context and without the database plagued with numerous false positives and false negatives. In light of these improvements, MirGeneDB 3.0 will assume the responsibility for naming conserved novel metazoan microRNAs. MirGeneDB is part of RNAcentral and Elixir Norway and is publicly and freely available at mirgenedb.org.
Distinct interactomes of ADAR1 nuclear and cytoplasmic protein isoforms and their responses to interferon induction
Authors: Vukić Dragana , Cherian Anna , Keskitalo Salla , Bong Yih Tyng , Marônek Martin , Yadav Leena , Keegan Liam P , Varjosalo Markku , O’Connell Mary A 
Published: December 2024

Abstract
The RNA editing enzyme adenosine deaminase acting on RNA 1 (ADAR1) is essential for correct functioning of innate immune responses. The ADAR1p110 isoform is mainly nuclear and ADAR1p150, which is interferon (IFN) inducible, is predominately cytoplasmic. Using three different methods – co-immunoprecipitation (co-IP) of endogenous ADAR1, Strep-tag co-IP and BioID with individual ADAR1 isoforms – a comprehensive interactome was generated during both homeostasis and the IFN response. Both known and novel interactors as well as editing regulators were identified. Nuclear proteins were detected as stable interactors with both ADAR1 isoforms. In contrast, BioID identified distinct protein networks for each ADAR1 isoform, with nuclear components observed with ADAR1p110 and components of cytoplasmic cellular condensates with ADAR1p150. RNase A digestion distinguished between distal and proximal interactors, as did a double-stranded RNA (dsRNA)-binding mutant of ADAR1 which demonstrated the importance of dsRNA binding for ADAR1 interactions. IFN treatment did not affect the core ADAR1 interactomes but resulted in novel interactions, the majority of which are proximal interactions retained after RNase A treatment. Short treatment with high molecular weight poly(I:C) during the IFN response resulted in dsRNA-binding-dependent changes in the proximal protein network of ADAR1p110 and association of the ADAR1p150 proximal protein network with some components of antiviral stress granules.