bluuebunny/crossref_metadata_2025_split huggingface dataset:
Turbulent heating in a stratified medium
Authors: Wang C , Oh S P , Ruszkowski M 
Published: January 2023

ABSTRACT
There is considerable evidence for widespread subsonic turbulence in galaxy clusters, most notably from Hitomi. Turbulence is often invoked to offset radiative losses in cluster cores, both by direct dissipation and by enabling turbulent heat diffusion. However, in a stratified medium, buoyancy forces oppose radial motions, making turbulence anisotropic. This can be quantified via the Froude number Fr, which decreases inward in clusters as stratification increases. We exploit analogies with MHD turbulence to show that wave–turbulence interactions increase cascade times and reduce dissipation rates ϵ ∝ Fr. Equivalently, for a given energy injection/dissipation rate ϵ, turbulent velocities u must be higher compared to Kolmogorov scalings. High-resolution hydrodynamic simulations show excellent agreement with the ϵ ∝ Fr scaling, which sets in for Fr ≲ 0.1. We also compare previously predicted scalings for the turbulent diffusion coefficient D ∝ Fr2 and find excellent agreement, for Fr ≲ 1. However, we find a different normalization, corresponding to stronger diffusive suppression by more than an order of magnitude. Our results imply that turbulent diffusion is more heavily suppressed by stratification, over a much wider radial range, than turbulent dissipation. Thus, the latter potentially dominates. Furthermore, this shift implies significantly higher turbulent velocities required to offset cooling, compared to previous models. These results are potentially relevant to turbulent metal diffusion in the galaxy groups and clusters (which is likewise suppressed), and to planetary atmospheres.
A new method to determine X-ray luminosity functions of AGN and their evolution with redshift
Authors: Alqasim Ahlam , Page Mat J 
Published: January 2023

ABSTRACTAlmost all massive galaxies today are understood to contain supermassive black holes (SMBH) at their centres. SMBHs grew by accreting material from their surroundings, emitting X-rays as they did so. X-ray luminosity functions (XLFs) of active galactic nuclei (AGN) have been extensively studied in order to understand the AGN population’s cosmological properties and evolution. We present a new fixed rest-frame method to achieve a more accurate study of the AGN XLF evolution over cosmic time. Normally, XLFs are constructed in a fixed observer-frame energy band, which can be problematic because it probes different rest-frame energies at different redshifts. In the new method, we construct XLFs in the fixed rest-frame band instead, by varying the observed energy band with redshift. We target a rest-frame 2–8 keV band using XMM-Newton and HEAO 1 X-ray data, with seven observer-frame energy bands that vary with redshift for 0 &lt; z &lt; 3. We produce the XLFs using two techniques; one to construct a binned XLF, and one using a maximum likelihood (ML) fit, which makes use of the full unbinned source sample. We find that our ML best-fitting pure luminosity evolution results for both methods are consistent with each other, suggesting that performing XLF evolution studies with the high-redshift data limited to high-luminosity AGN is not very sensitive to the choice of fixed observer-frame or rest-frame energy band, which is consistent with our expectation that high-luminosity AGN typically show little absorption. We have demonstrated the viability of the new method in measuring the XLF evolution.
Globular cluster metallicity distributions in the E-MOSAICS simulations
Authors: Pfeffer Joel , Kruijssen J M Diederik , Bastian Nate , Crain Robert A , Trujillo-Gomez Sebastian 
Published: January 2023

ABSTRACT
The metallicity distributions of globular cluster (GC) systems in galaxies are a critical test of any GC formation scenario. In this work, we investigate the predicted GC metallicity distributions of galaxies in the MOdelling Star cluster population Assembly In Cosmological Simulations within EAGLE (E-MOSAICS) simulation of a representative cosmological volume (L = 34.4 comoving Mpc). We find that the predicted GC metallicity distributions and median metallicities from the fiducial E-MOSAICS GC formation model agree well the observed distributions, except for galaxies with masses $M_\ast \sim 2 \times 10^{10} \, \rm {M}_{\odot }$, which contain an overabundance of metal-rich GCs. The predicted fraction of galaxies with bimodal GC metallicity distributions (37 ± 2 per cent in total; 45 ± 7 per cent for $M_\ast \gt 10^{10.5} \, \rm {M}_{\odot }$) is in good agreement with observed fractions ($44^{+10}_{-9}$ per cent), as are the mean metallicities of the metal-poor and metal-rich peaks. We show that, for massive galaxies ($M_\ast \gt 10^{10} \, \rm {M}_{\odot }$), bimodal GC distributions primarily occur as a result of cluster disruption from initially-unimodal distributions, rather than as a result of cluster formation processes. Based on the distribution of field stars with GC-like abundances in the Milky Way, we suggest that the bimodal GC metallicity distribution of Milky Way GCs also occurred as a result of cluster disruption, rather than formation processes. We conclude that separate formation processes are not required to explain metal-poor and metal-rich GCs, and that GCs can be considered as the surviving analogues of young massive star clusters that are readily observed to form in the local Universe today.
Classifying the satellite plane membership of Centaurus A’s dwarf galaxies using orbital alignment constraints
Authors: Kanehisa Kosuke Jamie , Pawlowski Marcel S , Müller Oliver , Sohn Sangmo Tony 
Published: January 2023

ABSTRACT
The flattened, possibly co-rotating plane of satellite galaxies around Centaurus A, if more than a fortuitous alignment, adds to the pre-existing tension between the well-studied Milky Way and M31 planes and the Lambda cold dark matter model of structure formation. It was recently reported that the Centaurus A satellite plane (CASP) may be rotationally supported, but a further understanding of the system’s kinematics is elusive in the absence of full 3D velocities. We constrain the transverse velocities of 27 satellites that would rotationally stabilize the Centaurus A plane, and classify the satellites by whether their possible orbits are consistent with the CASP. Five satellites are identified to be unlikely to participate in the plane, two of which are clearly non-members. Despite their previously reported line-of-sight velocity trend suggestive of a common co-rotating motion, 17 out of 22 potential CASP members are consistent with either orbital direction within both the full range of possible kinematics as well as when limiting orbits to those within the plane. On the other hand, disregarding the 5 off-plane satellites found to be inconsistent with CASP membership enhances the significance of the CASP’s line-of-sight velocity trend fivefold. Our results are robust with different mass estimates of the Centaurus A halo, and the adoption of either spherical or triaxial NFW potentials.
A search for dark matter among Fermi-LAT unidentified sources with systematic features in machine learning
Authors: Gammaldi V , Zaldívar B , Sánchez-Conde M A , Coronado-Blázquez J 
Published: January 2023

ABSTRACT
Around one-third of the point-like sources in the Fermi-LAT catalogues remain as unidentified sources (unIDs) today. Indeed, these unIDs lack a clear, univocal association with a known astrophysical source. If dark matter (DM) is composed of weakly interacting massive particles (WIMPs), there is the exciting possibility that some of these unIDs may actually be DM sources, emitting gamma-rays from WIMPs annihilation. We propose a new approach to solve the standard, machine learning (ML) binary classification problem of disentangling prospective DM sources (simulated data) from astrophysical sources (observed data) among the unIDs of the 4FGL Fermi-LAT catalogue. We artificially build two systematic features for the DM data which are originally inherent to observed data: the detection significance and the uncertainty on the spectral curvature. We do it by sampling from the observed population of unIDs, assuming that the DM distributions would, if any, follow the latter. We consider different ML models: Logistic Regression, Neural Network (NN), Naive Bayes, and Gaussian Process, out of which the best, in terms of classification accuracy, is the NN, achieving around $93.3{{\ \rm per\ cent}} \pm 0.7{{\ \rm per\ cent}}$ performance. Other ML evaluation parameters, such as the True Negative and True Positive rates, are discussed in our work. Applying the NN to the unIDs sample, we find that the degeneracy between some astrophysical and DM sources can be partially solved within this methodology. None the less, we conclude that there are no DM source candidates among the pool of 4FGL Fermi-LAT unIDs.
Discovery and description of two young open clusters in the primordial group of NGC 6871
Authors: Casado Juan , Hendy Yasser 
Published: January 2023

ABSTRACT
A primordial group of open clusters containing NGC 6871 is confirmed and described through Gaia DR3 data and the previous literature. It is a star-forming complex containing at least six young open clusters (OCs), including Teutsch 8, FSR 198, and Biurakan 2. Two nearby OCs (Casado 82 and Casado-Hendy 1) are newly identified and studied in detail and found to be also members of the cited group. The parameters of the components are sufficiently similar to postulate the case of at least six clusters born from a single giant molecular cloud. None of the cluster pairs of the group seems to be an authentic binary cluster, with the possible exception of the candidate pair Teutsch 8/FSR 198. Instead, NGC 6871 seems to be disintegrating, and the primordial group members appear to be dispersing out rapidly. Searching for new open clusters in the vicinity of young or grouped OCs using Gaia data is an efficient strategy to find new associated OCs forming primordial groups.
Exoplanet atmosphere evolution: emulation with neural networks
Authors: Rogers James G , Janó Muñoz Clàudia , Owen James E , Makinen T Lucas 
Published: January 2023

ABSTRACT
Atmospheric mass-loss is known to play a leading role in sculpting the demographics of small, close-in exoplanets. Knowledge of how such planets evolve allows one to ‘rewind the clock’ to infer the conditions in which they formed. Here, we explore the relationship between a planet’s core mass and its atmospheric mass after protoplanetary disc dispersal by exploiting XUV photoevaporation as an evolutionary process. Historically, this inference problem would be computationally infeasible due to the large number of planet models required; however, we use a novel atmospheric evolution emulator which utilizes neural networks to provide three orders of magnitude in speedup. First, we provide a proof of concept for this emulator on a real problem by inferring the initial atmospheric conditions of the TOI-270 multi-planet system. Using the emulator, we find near-indistinguishable results when compared to the original model. We then apply the emulator to the more complex inference problem, which aims to find the initial conditions for a sample of Kepler, K2, and TESS planets with well-constrained masses and radii. We demonstrate that there is a relationship between core masses and the atmospheric mass they retain after disc dispersal. This trend is consistent with the ‘boil-off’ scenario, in which close-in planets undergo dramatic atmospheric escape during disc dispersal. Thus, it appears that the exoplanet population is consistent with the idea that close-in exoplanets initially acquired large massive atmospheres, the majority of which is lost during disc dispersal, before the final population is sculpted by atmospheric loss over 100 Myr to Gyr time-scales.
The multizone chemical evolution of the Galactic bulge: predicting abundances for different radial zones
Authors: Cavichia O , Mollá M , Bazán J J 
Published: January 2023

ABSTRACT
Due to its proximity, the stellar populations of the Galactic bulge (GB) can be resolved and can be studied in detail. This allows tracing the bulge metallicity distribution function (MDF) for different spatial regions within the bulge, which may give us clues about the bulge formation and evolution scenarios. In this work, we developed a chemical evolution model (CEM), taking into account the mass distribution in the bulge and disc, to derive the radial dependence of this time-scale in the Galaxy. Since the infall rate depends on that time-scale in the CEM, the results of the model were used to test a scenario where the bulge is formed inside-out. The obtained results for the [α/Fe] versus [Fe/H] relationship, the MDF and the [Fe/H] radial gradient in the bulge have been compared to available data in the literature. The model is able to reproduce most of the observational data: the spread in the relation [α/Fe] versus [Fe/H], the MDF shape in different regions of the bulge, the [Fe/H] radial gradient inside it, and the age–metallicity relation, as well as the [α/Fe] evolution with age. The results of the model point to a scenario where the bulk of the bulge stars pre-existed the boxy/peanut X-shape bar formation. As a result, the classical origin of the GB is not ruled out, and this scenario may be invoked to explain the chemical properties of the GB.
The radio detection and accretion properties of the peculiar nuclear transient AT 2019avd
Authors: Wang Yanan , Baldi Ranieri D , del Palacio Santiago , Guolo Muryel , Yang Xiaolong , Zhang Yangkang , Done Chris , Castro Segura Noel , Pasham Dheeraj R , Middleton Matthew , Altamirano Diego , Gandhi Poshak , Qiao Erlin , Jiang Ning , Yan Hongliang , Giroletti Marcello , Migliori Giulia , McHardy Ian , Panessa Francesca , Jin Chichuan , Shen Rongfeng , Dai Lixin 
Published: January 2023

ABSTRACT
AT 2019avd is a nuclear transient detected from infrared to soft X-rays, though its nature is yet unclear. The source has shown two consecutive flaring episodes in the optical and the infrared bands, and its second flare was covered by X-ray monitoring programs. During this flare, the UVOT/Swift photometries revealed two plateaus: one observed after the peak and the other one appeared ∼240 d later. Meanwhile, our NICER and XRT/Swift campaigns show two declines in the X-ray emission, one during the first optical plateau and one 70–90 d after the optical/UV decline. The evidence suggests that the optical/UV could not have been primarily originated from X-ray reprocessing. Furthermore, we detected a timelag of ∼16–34 d between the optical and UV emission, which indicates the optical likely comes from UV reprocessing by a gas at a distance of 0.01–0.03 pc. We also report the first VLA and VLBA detection of this source at different frequencies and different stages of the second flare. The information obtained in the radio band – namely a steep and a late-time inverted radio spectrum, a high brightness temperature and a radio-loud state at late times – together with the multiwavelength properties of AT 2019avd suggests the launching and evolution of outflows such as disc winds or jets. In conclusion, we propose that after the ignition of black hole activity in the first flare, a super-Eddington flaring accretion disc formed and settled to a sub-Eddington state by the end of the second flare, associated with a compact radio outflow.
Binary neutron star merger simulations with neutrino transport and turbulent viscosity: impact of different schemes and grid resolution
Authors: Zappa Francesco , Bernuzzi Sebastiano , Radice David , Perego Albino 
Published: January 2023

ABSTRACT
We present a systematic numerical relativity study of the impact of different physics input and grid resolution in binary neutron star mergers. We compare simulations employing a neutrino leakage scheme, leakage plus M0 scheme, the M1 transport scheme, and pure hydrodynamics. Additionally, we examine the effect of a sub-grid scheme for turbulent viscosity. We find that the overall dynamics and thermodynamics of the remnant core are robust, implying that the maximum remnant density could be inferred from gravitational wave observations. Black hole collapse instead depends significantly on viscosity and grid resolution. Differently from recent work, we identify possible signatures of neutrino effects in the gravitational waves only at the highest resolutions considered; new high-resolution simulations will be thus required to build accurate gravitational wave templates to observe these effects. Different neutrino transport schemes impact significantly mass, geometry, and composition of the remnant’s disc and ejecta; M1 simulations show systematically larger proton fractions, reaching maximum values larger than 0.4. r-process nucleosynthesis yields reflect the different ejecta compositions; they are in agreement and reproduce residual solar abundances only if M0 or M1 neutrino transport schemes are adopted. We compute kilonova light curves using spherically-symmetric radiation-hydrodynamics evolutions up to 15 d post-merger, finding that they are mostly sensitive to the ejecta mass and electron fraction; accounting for multiple ejecta components appears necessary for reliable light curve predictions. We conclude that advanced neutrino schemes and resolutions higher than current standards are essential for robust long-term evolutions and detailed astrophysical predictions.
Dr.Nod: computational framework for discovery of regulatory non-coding drivers in tissue-matched distal regulatory elements
Authors: Tomkova Marketa , Tomek Jakub , Chow Julie , McPherson John D , Segal David J , Hormozdiari Fereydoun 
Published: January 2023

AbstractThe discovery of cancer driver mutations is a fundamental goal in cancer research. While many cancer driver mutations have been discovered in the protein-coding genome, research into potential cancer drivers in the non-coding regions showed limited success so far. Here, we present a novel comprehensive framework Dr.Nod for detection of non-coding cis-regulatory candidate driver mutations that are associated with dysregulated gene expression using tissue-matched enhancer-gene annotations. Applying the framework to data from over 1500 tumours across eight tissues revealed a 4.4-fold enrichment of candidate driver mutations in regulatory regions of known cancer driver genes. An overarching conclusion that emerges is that the non-coding driver mutations contribute to cancer by significantly altering transcription factor binding sites, leading to upregulation of tissue-matched oncogenes and down-regulation of tumour-suppressor genes. Interestingly, more than half of the detected cancer-promoting non-coding regulatory driver mutations are over 20 kb distant from the cancer-associated genes they regulate. Our results show the importance of tissue-matched enhancer-gene maps, functional impact of mutations, and complex background mutagenesis model for the prediction of non-coding regulatory drivers. In conclusion, our study demonstrates that non-coding mutations in enhancers play a previously underappreciated role in cancer and dysregulation of clinically relevant target genes.
Hypothesis-driven probabilistic modelling enables a principled perspective of genomic compartments
Authors: Kariti Hagai , Feld Tal , Kaplan Noam 
Published: January 2023

AbstractThe Hi-C method has revolutionized the study of genome organization, yet interpretation of Hi-C interaction frequency maps remains a major challenge. Genomic compartments are a checkered Hi-C interaction pattern suggested to represent the partitioning of the genome into two self-interacting states associated with active and inactive chromatin. Based on a few elementary mechanistic assumptions, we derive a generative probabilistic model of genomic compartments, called deGeco. Testing our model, we find it can explain observed Hi-C interaction maps in a highly robust manner, allowing accurate inference of interaction probability maps from extremely sparse data without any training of parameters. Taking advantage of the interpretability of the model parameters, we then test hypotheses regarding the nature of genomic compartments. We find clear evidence of multiple states, and that these states self-interact with different affinities. We also find that the interaction rules of chromatin states differ considerably within and between chromosomes. Inspecting the molecular underpinnings of a four-state model, we show that a simple classifier can use histone marks to predict the underlying states with 87% accuracy. Finally, we observe instances of mixed-state loci and analyze these loci in single-cell Hi-C maps, finding that mixing of states occurs mainly at the cell level.
A parametric approach for molecular encodings using multilevel atomic neighborhoods applied to peptide classification
Authors: Hattab Georges , Anžel Aleksandar , Spänig Sebastian , Neumann Nils , Heider Dominik 
Published: January 2023

Abstract
Exploring new ways to represent and discover organic molecules is critical to the development of new therapies. Fingerprinting algorithms are used to encode or machine-read organic molecules. Molecular encodings facilitate the computation of distance and similarity measurements to support tasks such as similarity search or virtual screening. Motivated by the ubiquity of carbon and the emerging structured patterns, we propose a parametric approach for molecular encodings using carbon-based multilevel atomic neighborhoods. It implements a walk along the carbon chain of a molecule to compute different representations of the neighborhoods in the form of a binary or numerical array that can later be exported into an image. Applied to the task of binary peptide classification, the evaluation was performed by using forty-nine encodings of twenty-nine data sets from various biomedical fields, resulting in well over 1421 machine learning models. By design, the parametric approach is domain- and task-agnostic and scopes all organic molecules including unnatural and exotic amino acids as well as cyclic peptides. Applied to peptide classification, our results point to a number of promising applications and extensions. The parametric approach was developed as a Python package (cmangoes), the source code and documentation of which can be found at https://github.com/ghattab/cmangoes and https://doi.org/10.5281/zenodo.7483771.
Convergent evolution of immune receptors underpins distinct elicitin recognition in closely related Solanaceous plants
Authors: Chen Zhaodan , Liu Fan , Zeng Mengzhu , Wang Lei , Liu Hanmei , Sun Yujing , Wang Lan , Zhang Zhichao , Chen Zhiyuan , Xu Yuanpeng , Zhang Mingmei , Xia Yeqiang , Ye Wenwu , Dong Suomeng , Govers Francine , Wang Yan , Wang Yuanchao 
Published: January 2023

Abstract
Elicitins are a large family of secreted proteins in Phytophthora. Clade 1 elicitins were identified decades ago as potent elicitors of immune responses in Nicotiana species, but the mechanisms underlying elicitin recognition are largely unknown. Here we identified an elicitin receptor in Nicotiana benthamiana that we named REL for Responsive to ELicitins. REL is a receptor-like protein (RLP) with an extracellular leucine-rich repeat (LRR) domain that mediates Phytophthora resistance by binding elicitins. Silencing or knocking out REL in N. benthamiana abolished elicitin-triggered cell death and immune responses. Domain deletion and site-directed mutagenesis revealed that the island domain (ID) located within the LRR domain of REL is crucial for elicitin recognition. In addition, sequence polymorphism in the ID underpins the genetic diversity of REL homologs in various Nicotiana species in elicitin recognition and binding. Remarkably, REL is phylogenetically distant from the elicitin response (ELR) protein, an LRR–RLP that was previously identified in the wild potato species Solanum microdontum and REL and ELR differ in the way they bind and recognize elicitins. Our findings provide insights into the molecular basis of plant innate immunity and highlight a convergent evolution of immune receptors towards perceiving the same elicitor.