bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deciphering the origin of ionized gas in IC 1459 with VLT/MUSE
Authors: Mulcahey C R , Prichard L J , Krajnović D , Jorgenson R A 
Published: April 2021

ABSTRACT
IC 1459 is an early-type galaxy (ETG) with a rapidly counter-rotating stellar core, and is the central galaxy in a gas-rich group of spirals. In this work, we investigate the abundant ionized gas in IC 1459 and present new stellar orbital models to connect its complex array of observed properties and build a more complete picture of its evolution. Using the Multi-Unit Spectroscopic Explorer (MUSE), the optical integral field unit (IFU) on the Very Large Telescope (VLT), we examine the gas and stellar properties of IC 1459 to decipher the origin and powering mechanism of the galaxy’s ionized gas. We detect ionized gas in a non-disc-like structure rotating in the opposite sense to the central stars. Using emission-line flux ratios and velocity dispersion from full-spectral fitting, we find two kinematically distinct regions of shocked emission-line gas in IC 1459, which we distinguished using narrow (σ ≤ 155 km s−1) and broad (σ &gt; 155 km s−1) profiles. Our results imply that the emission-line gas in IC 1459 has a different origin than that of its counter-rotating stellar component. We propose that the ionized gas is from late-stage accretion of gas from the group environment, which occurred long after the formation of the central stellar component. We find that shock heating and AGN activity are both ionizing mechanisms in IC 1459 but that the dominant excitation mechanism is by post-asymptotic giant branch stars from its old stellar population.
The parametrization of gas flows in discs in the Auriga simulations
Authors: Okalidis Periklis , Grand Robert J J , Yates Robert M , Kauffmann Guinevere 
Published: April 2021

ABSTRACT
We study the radial motions of cold, star-forming gas in the secular evolution phase of a set of 14 magnetohydrodynamical cosmological zoom-in simulations of Milky Way-mass galaxies. We study the radial transport of material within the disc plane in a series of concentric rings. For the gas in each ring at a given time we compute two quantities as a function of time and radius: (1) the radial bulk flow of the gas and (2) the radial spread of the gas relative to the bulk flow. Averaging the data from all the haloes, we find that the radial spread increases with radius in the form of a power law with strong secondary dependencies on the fraction of accreted material and the local radial velocity dispersion of the gas. We find that the bulk motion of gas is well described in the inner disc regions by a radially independent mean inwards flow speed of $-2.4\, \rm {km\ s}^{-1}$. The spread around this value relates to the change in angular momentum of the gas and also the amount of accreted material. These scalings from fully cosmological, MHD simulations of galaxy formation can then be used in semi-analytic models to better parametrize the radial flow of gas in discs.
The SAMI Galaxy Survey: stellar population and structural trends across the Fundamental Plane
Authors: D’Eugenio Francesco , Colless Matthew , Scott Nicholas , van der Wel Arjen , Davies Roger L , van de Sande Jesse , Sweet Sarah M , Oh Sree , Groves Brent , Sharp Rob , Owers Matt S , Bland-Hawthorn Joss , Croom Scott M , Brough Sarah , Bryant Julia J , Goodwin Michael , Lawrence Jon S , Lorente Nuria P F , Richards Samuel N 
Published: April 2021

ABSTRACT
We study the Fundamental Plane (FP) for a volume- and luminosity-limited sample of 560 early-type galaxies from the SAMI survey. Using r-band sizes and luminosities from new multi-Gaussian expansion photometric measurements, and treating luminosity as the dependent variable, the FP has coefficients a = 1.294 ± 0.039, b = 0.912 ± 0.025, and zero-point c = 7.067 ± 0.078. We leverage the high signal-to-noise ratio of SAMI integral field spectroscopy, to determine how structural and stellar population observables affect the scatter about the FP. The FP residuals correlate most strongly (8σ significance) with luminosity-weighted simple stellar population (SSP) age. In contrast, the structural observables surface mass density, rotation-to-dispersion ratio, Sérsic index, and projected shape all show little or no significant correlation. We connect the FP residuals to the empirical relation between age (or stellar mass-to-light ratio Υ⋆ ) and surface mass density, the best predictor of SSP age amongst parameters based on FP observables. We show that the FP residuals (anti)correlate with the residuals of the relation between surface density and Υ⋆ . This correlation implies that part of the FP scatter is due to the broad age and Υ⋆ distribution at any given surface mass density. Using virial mass and Υ⋆, we construct a simulated FP and compare it to the observed FP. We find that, while the empirical relations between observed stellar population relations and FP observables are responsible for most (75 per cent) of the FP scatter, on their own they do not explain the observed tilt of the FP away from the virial plane.
HERMES spectroscopy of normal A and Am stars
Authors: Trust Otto , Jurua Edward , De Cat Peter , Joshi Santosh , Lampens Patricia 
Published: April 2021

ABSTRACT
The nominal Kepler mission provided very high precision photometric data. Using these data, interesting phenomena such as spots, and ‘hump and spike’ features were observed in the light curves of some normal A and metallic lined A stars (Am stars). However, the connection between such phenomena and the chemical peculiarity of the Am stars is still unclear. In order to make progress on these issues, it's important to collect high-resolution spectroscopic data to determine their fundamental parameters and individual chemical abundances. In this paper, we present a spectroscopic study of a sample of ‘hump and spike’ stars in the nominal Kepler field. We used data collected with the High Efficiency and Resolution Mercator Échelle Spectrograph (HERMES). We determined the spectral types of these stars and obtained the atmospheric stellar parameters such as effective temperatures, surface gravities, projected rotational, microturbulent, and radial velocities. We also performed a detailed individual chemical abundance analysis for each target. We confirmed KIC 3459226 and KIC 6266219 as Am stars, KIC 9349245 as a marginal Am star, while KIC 4567097, KIC 4818496, KIC 5524045, KIC 5650229, KIC 7667560, and KIC 9272082 are non-Am stars. To estimate their evolutionary phases, all the stars were placed in the Hertzsprung–Russell diagram. Based on their spectral classification and chemical abundance pattern, we reclassified KIC 6266219 (previously treated as chemically normal) as an Am star (kA3hA7mF1) and KIC 9272082 (previously treated as Am) as non-Am.
Detection of complex organic molecules in young starless core L1521E
Authors: Scibelli Samantha , Shirley Yancy , Vasyunin Anton , Launhardt Ralf 
Published: April 2021

ABSTRACT
Determining the level of chemical complexity within dense starless and gravitationally bound pre-stellar cores is crucial for constructing chemical models, which subsequently constrain the initial chemical conditions of star formation. We have searched for complex organic molecules (COMs) in the young starless core L1521E, and report the first clear detection of dimethyl ether (CH3OCH3), methyl formate (HCOOCH3), and vinyl cyanide (CH2CHCN). Eight transitions of acetaldehyde (CH3CHO) were also detected, five of which (A states) were used to determine an excitation temperature to then calculate column densities for the other oxygen-bearing COMs. If source size was not taken into account (i.e. if filling fraction was assumed to be one), column density was underestimated, and thus we stress the need for higher resolution mapping data. We calculated L1521E COM abundances and compared them to other stages of low-mass star formation, also finding similarities to other starless/pre-stellar cores, suggesting related chemical evolution. The scenario that assumes formation of COMs in gas-phase reactions between precursors formed on grains and then ejected to the cold gas via reactive desorption was tested and was unable to reproduce observed COM abundances, with the exception of CH3CHO. These results suggest that COMs observed in cold gas are formed not by gas-phase reactions alone, but also through surface reactions on interstellar grains. Our observations present a new, unique challenge for existing theoretical astrochemical models.
ExoMol molecular line lists – XLII. Rovibronic molecular line list for the low-lying states of NO
Authors: Qu Qianwei , Yurchenko Sergei N , Tennyson Jonathan 
Published: April 2021

ABSTRACT
An accurate line list, called XABC, is computed for nitric oxide which covers its pure rotational, vibrational and rovibronic spectra. A mixture of empirical and theoretical electronic transition dipole moments are used for the final calculation of 14N16O rovibronic $\mathrm{A}\, ^2\Sigma ^+$ – $\mathrm{X}\, ^2\Pi$, $\mathrm{B}\, ^2\Pi$ – X2Π, and $\mathrm{C}\, ^2\Pi$ – $\mathrm{X}\, ^2\Pi$ which correspond to the γ, β, and δ band systems, respectively, as well as minor improvements to transitions within the $\mathrm{X}\, ^2\Pi$ ground state. The work is a major update of the ExoMol NOname line list. It provides a high-accuracy NO ultraviolet line list covering the complicated regions where the $\mathrm{B}\, ^2\Pi$-$\mathrm{C}\, ^2\Pi$ states interact. XABC provides comprehensive data for the lowest four doublet states of NO in the region of λ &gt; 160 nm ($\tilde{\nu } \lt 63~000~\mathrm{cm}^{-1}$) for the analysis of atmospheric NO on Earth, Venus, or Mars, other astronomical observations and applications. The data are available via www.exomol.com.
Strong evidence of low levels of solar activity during the Maunder Minimum
Authors: Carrasco V M S , Hayakawa H , Kuroyanagi C , Gallego M C , Vaquero J M 
Published: April 2021

ABSTRACT
The Maunder Minimum (MM) was a period of prolonged solar activity minimum between 1645 and 1715. Several works have identified a significant number of problematic spotless days in the MM included in existing data bases. We have found a list of exact spotless (in the second half of 1709) and spot days (January and August 1709) provided by Johann Heinrich Müller. We computed the most probable value and upper/lower limits of the active day fraction (ADF) from Müller's data using the hypergeometrical probability distribution. Our sample is not strictly random because Müller recorded observations in consecutive days when he observed sunspots. Therefore, our result represents an upper threshold of solar activity for 1709. We compared this result with annual values of the ADF calculated for the Dalton Minimum and the most recent solar cycles. We concluded that, although 1709 is one of the most active years in the MM, it was less active than most years both in the Dalton Minimum and in the most recent solar cycles. Therefore, the solar activity level estimated in this work for 1709 represents robust evidence of low solar activity levels in the MM.
Impact of initial mass functions on the dynamical channel of gravitational wave sources
Authors: Wang Long , Fujii Michiko S , Tanikawa Ataru 
Published: April 2021

ABSTRACT
Dynamically formed black hole (BH) binaries (BBHs) are important sources of gravitational waves (GWs). Globular clusters (GCs) provide a major environment to produce such BBHs, but the total mass of the known GCs is small compared to that in the Galaxy; thus, the fraction of BBHs formed in GCs is also small. However, this assumes that GCs contain a canonical initial mass function (IMF) similar to that of field stars. This might not be true because several studies suggest that extreme dense and metal-poor environment can result in top-heavy IMFs, where GCs may originate. Although GCs with top-heavy IMFs were easily disrupted or have become dark clusters, the contribution to the GW sources can be significant. Using a high-performance and accurate N-body code, petar, we investigate the effect of varying IMFs by carrying out four star-by-star simulations of dense GCs with the initial mass of 5 × 105 M⊙ and the half-mass radius of 2 pc. We find that the BBH merger rate does not monotonically correlate with the slope of IMFs. Due to a rapid expansion, top-heavy IMFs lead to less efficient formation of merging BBHs. The formation rate continuously decreases as the cluster expands because of the dynamical heating caused by BHs. However, in star clusters with a top-heavier IMF, the total number of BHs is larger, and therefore, the final contribution to merging BBHs can still be more than that from clusters with the standard IMF, if the initial cluster mass and density are higher than those used in our model.
Optical and ultraviolet monitoring of the black hole X-ray binary MAXI J1820+070/ASASSN-18ey for 18 months
Authors: Sai Hanna , Wang Xiaofeng , Wu Jianfeng , Lin Jie , Feng Hua , Zhang Tianmeng , Li Wenxiong , Zhang Jujia , Mo Jun , Sun Tianrui , Ehgamberdiev Shuhrat A , Mirzaqulov Davron , Rui Liming , Lin Weili , Zhao Xulin , Lin Han , Zhang Jicheng , Zhang Xinghan , Zhao Yong , Li Xue , Xiang Danfeng , Wang Lingzhi , Wu Chengyuan 
Published: April 2021

ABSTRACT
MAXI J1820+070 is a low-mass black hole X-ray binary system with high luminosity in both optical and X-ray bands during its outburst periods. We present extensive photometry in the X-ray, ultraviolet, and optical bands, as well as densely cadenced optical spectra, covering the phase from the beginning of the optical outburst to ∼550 days. During the rebrightening process, the optical emission precedes the X-ray by 20.80 ± 2.85 days. The spectra are characterized by blue continua and emission features of Balmer series, He i, and He ii lines and a broad Bowen blend. The pseudo equivalent widths (pEWs) of emission lines are found to show anticorrelations with the X-ray flux measured at comparable phases, due to increased suppression by the optical continuum. At around the X-ray peak, the full widths at half-maximum (FWHMs) of Hβ and He ii λ4686 tend to stabilize at 19.4 and 21.8 Å, corresponding to the line-forming regions at radii of 1.7 and 1.3 R⊙ within the disc. We further analysed the absolute fluxes of the lines and found that the fluxes of Hβ and He ii λ4686 show positive correlations with the X-ray flux, favouring the suggestion that the irradiation model is responsible for the optical emission. However, the fact that X-ray emission experiences a dramatic flux drop at t ∼ 200 days after the outburst, while the optical flux only shows a little variation, suggests that additional energy such as viscous energy may contribute to the optical radiation, in addition to X-ray irradiation.
An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic
Authors: Kumar Sudhir , Tao Qiqing , Weaver Steven , Sanderford Maxwell , Caraballo-Ortiz Marcos A , Sharma Sudip , Pond Sergei L K , Miura Sayaka 
Published: April 2021

Abstract
Global sequencing of genomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to reveal new genetic variants that are the key to unraveling its early evolutionary history and tracking its global spread over time. Here we present the heretofore cryptic mutational history and spatiotemporal dynamics of SARS-CoV-2 from an analysis of thousands of high-quality genomes. We report the likely most recent common ancestor of SARS-CoV-2, reconstructed through a novel application and advancement of computational methods initially developed to infer the mutational history of tumor cells in a patient. This progenitor genome differs from genomes of the first coronaviruses sampled in China by three variants, implying that none of the earliest patients represent the index case or gave rise to all the human infections. However, multiple coronavirus infections in China and the United States harbored the progenitor genetic fingerprint in January 2020 and later, suggesting that the progenitor was spreading worldwide months before and after the first reported cases of COVID-19 in China. Mutations of the progenitor and its offshoots have produced many dominant coronavirus strains that have spread episodically over time. Fingerprinting based on common mutations reveals that the same coronavirus lineage has dominated North America for most of the pandemic in 2020. There have been multiple replacements of predominant coronavirus strains in Europe and Asia as well as continued presence of multiple high-frequency strains in Asia and North America. We have developed a continually updating dashboard of global evolution and spatiotemporal trends of SARS-CoV-2 spread (http://sars2evo.datamonkey.org/).
MEGA11: Molecular Evolutionary Genetics Analysis Version 11
Authors: Tamura Koichiro , Stecher Glen , Kumar Sudhir 
Published: April 2021

Abstract
The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses. They are supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor, and an extended Tree Explorer to display timetrees. Also added is a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface has been made more responsive and interactive for very big data sets. These enhancements will improve the user experience, quality of results, and the pace of biological discovery. Natively compiled graphical user interface and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from www.megasoftware.net.
RNA sequencing and proteomic profiling reveal different alterations by dietary methylmercury in the hippocampal transcriptome and proteome in BALB/c mice
Authors: Mellingen Ragnhild Marie , Myrmel Lene Secher , Lie Kai Kristoffer , Rasinger Josef Daniel , Madsen Lise , Nøstbakken Ole Jakob 
Published: April 2021

Abstract
Methylmercury (MeHg) is a highly neurotoxic form of mercury (Hg) present in seafood. Here, we recorded and compared proteomic and transcriptomic changes in hippocampus of male BALB/c mice exposed to two doses of MeHg. Mice were fed diets spiked with 0.28 mg MeHg kg–1, 5 mg MeHg kg–1, or an unspiked control diet for 77 days. Total mercury content was significantly (P &lt; 0.05) increased in brain tissue of both MeHg-exposed groups (18 ± 2 mg Hg kg–1 and 0.56 ± 0.06 mg Hg kg–1). Hippocampal protein and ribonucleic acid (RNA) expression levels were significantly altered both in tissues from mice receiving a low dose MeHg (20 proteins/294 RNA transcripts) and a high dose MeHg (61 proteins/876 RNA transcripts). The majority but not all the differentially expressed features in hippocampus were dose dependent. The combined use of transcriptomic and proteomic profiling data provided insight on the influence of MeHg on neurotoxicity, energy metabolism, and oxidative stress through several regulated features and pathways, including RXR function and superoxide radical degradation.
HDAC3 controls male fertility through enzyme-independent transcriptional regulation at the meiotic exit of spermatogenesis
Authors: Yin Huiqi , Kang Zhenlong , Zhang Yingwen , Gong Yingyun , Liu Mengrou , Xue Yanfeng , He Wenxiu , Wang Yanfeng , Zhang Shuya , Xu Qiushi , Fu Kaiqiang , Zheng Bangjin , Xie Jie , Zhang Jinwen , Wang Yuanyuan , Lin Mingyan , Zhang Yihan , Feng Hua , Xin Changpeng , Guan Yichun , Huang Chaoyang , Guo Xuejiang , Wang P Jeremy , Baur Joseph A , Zheng Ke , Sun Zheng , Ye Lan 
Published: April 2021

AbstractThe transition from meiotic spermatocytes to postmeiotic haploid germ cells constitutes an essential step in spermatogenesis. The epigenomic regulatory mechanisms underlying this transition remain unclear. Here, we find a prominent transcriptomic switch from the late spermatocytes to the early round spermatids during the meiotic-to-postmeiotic transition, which is associated with robust histone acetylation changes across the genome. Among histone deacetylases (HDACs) and acetyltransferases, we find that HDAC3 is selectively expressed in the late meiotic and early haploid stages. Three independent mouse lines with the testis-specific knockout of HDAC3 show infertility and defects in meiotic exit with an arrest at the late stage of meiosis or early stage of round spermatids. Stage-specific RNA-seq and histone acetylation ChIP-seq analyses reveal that HDAC3 represses meiotic/spermatogonial genes and activates postmeiotic haploid gene programs during meiotic exit, with associated histone acetylation alterations. Unexpectedly, abolishing HDAC3 catalytic activity by missense mutations in the nuclear receptor corepressor (NCOR or SMRT) does not cause infertility, despite causing histone hyperacetylation as HDAC3 knockout, demonstrating that HDAC3 enzyme activity is not required for spermatogenesis. Motif analysis of the HDAC3 cistrome in the testes identified SOX30, which has a similar spatiotemporal expression pattern as HDAC3 during spermatogenesis. Depletion of SOX30 in the testes abolishes the genomic recruitment of the HDAC3 to the binding sites. Collectively, these results establish the SOX30/HDAC3 signaling as a key regulator of the transcriptional program in a deacetylase-independent manner during the meiotic-to-postmeiotic transition in spermatogenesis.
The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota
Authors: Pascal Andreu Victòria , Roel-Touris Jorge , Dodd Dylan , Fischbach Michael A , Medema Marnix H 
Published: April 2021

Abstract
Anaerobic bacteria from the human microbiome produce a wide array of molecules at high concentrations that can directly or indirectly affect the host. The production of these molecules, mostly derived from their primary metabolism, is frequently encoded in metabolic gene clusters (MGCs). However, despite the importance of microbiome-derived primary metabolites, no tool existed to predict the gene clusters responsible for their production. For this reason, we recently introduced gutSMASH. gutSMASH can predict 41 different known pathways, including MGCs involved in bioenergetics, but also putative ones that are candidates for novel pathway discovery. To make the tool more user-friendly and accessible, we here present the gutSMASH web server, hosted at https://gutsmash.bioinformatics.nl/. The user can either input the GenBank assembly accession or upload a genome file in FASTA or GenBank format. Optionally, the user can enable additional analyses to obtain further insights into the predicted MGCs. An interactive HTML output (viewable online or downloadable for offline use) provides a user-friendly way to browse functional gene annotations and sequence comparisons with reference gene clusters as well as gene clusters predicted in other genomes. Thus, this web server provides the community with a streamlined and user-friendly interface to analyze the metabolic potential of gut microbiomes.