bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of large-scale synchrotron radiation from the molecular envelope of the Sgr B cloud complex at the Galactic centre
Authors: Yusef-Zadeh F , Wardle M , Arendt R , Hewitt J , Hu Y , Lazarian A , Kassim N E , Hyman S , Heywood I 
Published: October 2023

ABSTRACT
We present highly sensitive measurements taken with MeerKAT at 1280 MHz as well as archival Green Bank Telescope (GBT), Murchison Widefield Array, and Very Large Array (VLA) images at 333, 88, and 74 MHz. We report the detection of synchrotron radio emission from the infrared dark cloud associated with the halo of the Sgr B complex on a scale of ∼60 pc. A strong spatial correlation between low-frequency radio continuum emission and dense molecular gas, combined with spectral index measurements, indicates enhanced synchrotron emission by cosmic ray electrons. Correlation of the Fe i 6.4 keV K α line and synchrotron emission provides compelling evidence that the low energy cosmic ray electrons are responsible for producing the K α line emission. The observed synchrotron emission within the halo of the Sgr B cloud complex has a mean spectral index α ∼ −1 ± 1, which gives the magnetic field strength ∼100 µG for cloud densities nH = 104–105 cm−3, and estimated cosmic ray ionization rates between 10−13 and 10−14 s−1. Furthermore, the energy spectrum of primary cosmic ray electrons is constrained to be E−3 ± 1 for typical energies of few hundred MeV. The extrapolation of this spectrum to higher energies is consistent with X-ray and γ-ray emission detected from this cloud. These measurements have important implications on the role that high cosmic ray electron fluxes at the Galactic centre play in production of radio synchrotron emission, the Fe i K α line emission at 6.4 keV, and ∼GeV γ-ray emission throughout the Central Molecular Zone.
Study of the energetic X-ray superflares from the active fast rotator AB doradus
Authors: Didel Shweta , Pandey Jeewan C , Srivastava A K , Singh Gurpreet 
Published: October 2023

ABSTRACT
We present the analyses of intense X-ray flares detected on the active fast rotator AB Dor using observations from the XMM–Newton. A total of 21 flares are detected, and 13 flares are analysed in detail. The total X-ray energy of these flares is found to be in the range of 1034−36 erg, in which the peak flare flux increased up to 34 times from the pre-/post-flaring states for the strongest observed flare. The duration of these flaring events is found to be 0.7 to 5.8 h. The quiescent state X-ray spectra are found to be explained by a three-temperature plasma with average temperatures of 0.29, 0.95, and 1.9 keV, respectively. The temperatures, emission measures, and abundances are found to be varying during the flares. The peak flare temperature was found in the 31–89 MK range, whereas the peak emission measure was 1052.5–54.7 cm−3 . The abundances vary during the flares and increase by a factor of ∼3 from the quiescent value for the strongest detected flare. The variation in individual abundances follows the inverse-FIP effect in quiescent and flare phases. The X-ray light curves of AB Dor are found to exhibit rotational modulation. The semi-loop lengths of the flaring events are derived in the range of 109.9−10.7  cm, whereas the minimum magnetic field to confine the plasma in the flaring loop is estimated between 200 and 700 G.
Can we really pick and choose? Benchmarking various selections of Gaia Enceladus/Sausage stars in observations with simulations
Authors: Carrillo Andreia , Deason Alis J , Fattahi Azadeh , Callingham Thomas M , Grand Robert J J 
Published: October 2023

ABSTRACT
Large spectroscopic surveys plus Gaia astrometry have shown us that the inner stellar halo of the Galaxy is dominated by the debris of Gaia Enceladus/Sausage (GES). With the richness of data at hand, there are a myriad of ways these accreted stars have been selected. We investigate these GES selections and their effects on the inferred progenitor properties using data constructed from APOGEE and Gaia. We explore selections made in eccentricity, energy-angular momentum (E-Lz), radial action-angular momentum (Jr-Lz), action diamond, and [Mg/Mn]-[Al/Fe] in the observations, selecting between 144 and 1279 GES stars with varying contamination from in-situ and other accreted stars. We also use the Auriga cosmological hydrodynamic simulations to benchmark the different GES dynamical selections. Applying the same observational GES cuts to nine Auriga galaxies with a GES, we find that the Jr-Lz method is best for sample purity and the eccentricity method for completeness. Given the average metallicity of GES (−1.28 &lt; [Fe/H] &lt; −1.18), we use the z = 0 mass–metallicity relationship to find an average $\rm M_{\star }$of ∼4 × 108 M⊙. We adopt a similar procedure and derive $\rm M_{\star }$ for the GES-like systems in Auriga and find that the eccentricity method overestimates the true $\rm M_{\star }$ by ∼2.6 × while E-Lz underestimates by ∼0.7 ×. Lastly, we estimate the total mass of GES to be $\rm 10^{10.5 - 11.1}~{\rm M}_{\odot }$ using the relationship between the metallicity gradient and the GES-to-in-situ energy ratio. In the end, we cannot just ‘pick and choose’ how we select GES stars, and instead should be motivated by the science question.
Disentangling patchy reionization signatures from primordial gravitational waves using CMB E-mode and B-mode polarization
Authors: Jain Divesh , Mukherjee Suvodip , Choudhury Tirthankar Roy 
Published: October 2023

ABSTRACT
The detection of large angular scale B mode in the cosmic microwave background (CMB) polarization signal will open a direct window into not only the primary CMB anisotropies caused by the primordial gravitational waves (PGW) originating in the epoch of inflation, but also the secondary anisotropies imprinted during the epoch of cosmic reionization. The existence of patchiness in the electron density during reionization produces a unique distortion in the CMB B-mode polarization, which can be distinguished from the PGW signal with the aid of spatial frequency modes. In this work, we employ an EB estimator by combining E-mode and B-mode polarization for the τ power spectrum signal generated in a photon-conserving seminumerical reionization model called SCRIPT. We developed a Bayesian framework for the joint detection of the PGW and reionization signal from CMB observations and show the efficacy of this technique for upcoming CMB experiments. We find that, for our model, the τ power spectrum signal effectively tracks the inhomogeneous electron density field, allowing for robust constraints on the patchy B-mode signal. Further, our results indicate that employing the EB estimator for the τ signal will facilitate ground-based CMB-S4 to detect the patchy B-mode signal at approximately ≥2σ confidence level, while observations with space-based PICO will improve this detection to ≥3σ going as high as ≥7σ for extreme reionization models. These findings not only highlight the future potential of these experiments to provide an improved picture of the reionization process but also have important implications towards an unbiased measurement of r.
Exploring dark matter spike distribution around the Galactic centre with stellar orbits
Authors: Shen Zhao-Qiang , Yuan Guan-Wen , Jiang Cheng-Zi , Tsai Yue-Lin Sming , Yuan Qiang , Fan Yi-Zhong 
Published: October 2023

ABSTRACT
Precise measurements of the stellar orbits around Sagittarius A* have established the existence of a supermassive black hole (SMBH) at the Galactic centre (GC). Due to the interplay between the SMBH and dark matter (DM), the DM density profile in the innermost region of the Galaxy, which is crucial for the DM indirect detection, is still an open question. Among the most popular models in the literature, the theoretical spike profile proposed by Gondolo & Silk (GS hereafter) is well adopted. In this work, we investigate the DM spike profile using updated data from the Keck and Very Large Telescope (VLT) telescopes considering that the presence of such an extended mass component may affect the orbits of the S-stars in the GC. We examine the radius and slope of the generalized Navarro–Frenk–White (NFW) spike profile, analyse the Einasto spike, and discuss the influence of DM annihilation on the results. Our findings indicate that an initial slope of γ ≳ 0.92 for the generalized NFW spike profile is ruled out at a 95 per cent confidence level. Additionally, the spike radius Rsp larger than 21.5 pc is rejected at 95 per cent probability for the Einasto spike with α = 0.17, which also contradicts the GS spike model. The constraints with the VLT/GRAVITY upper limits are also projected. Although the GS NFW spike is well constrained by the Keck and VLT observation of S2, an NFW spike with a weak annihilation cusp may still be viable, as long as the DM annihilation cross-section satisfies $\left\langle \sigma v \right\rangle \gtrsim 7.7\times 10^{-27}~{\rm cm^3\, s^{-1}} (m_{\rm DM}/100~{\rm GeV})$ at 95 per cent level.
NIGHT: A compact, near-infrared, high-resolution spectrograph to survey helium in exoplanet systems
Authors: Farret Jentink C , Bourrier V , Lovis C , Allart R , Chazelas B , Lendl M , Dumusque X , Pepe F 
Published: October 2023

ABSTRACT
Among highly irradiated exoplanets, some have been found to undergo significant hydrodynamic expansion traced by atmospheric escape. To better understand these processes in the context of planetary evolution, we propose NIGHT (the Near-Infrared Gatherer of Helium Transits). NIGHT is a high-resolution spectrograph dedicated to surveying and temporally monitoring He i triplet absorption at 1083 nm in stellar and planetary atmospheres. In this paper, we outline our scientific objectives, requirements, and cost-efficient design. Our simulations, based on previous detections and modelling using the current exoplanet population, determine our requirements and survey targets. With a spectral resolution of 70 000 on a 2-m telescope, NIGHT can accurately resolve the helium triplet and detect 1 per cent peak absorption in 118 known exoplanets in a single transit. Additionally, it can search for 3σ temporal variations of 0.4 per cent in 66 exoplanets in-between two transits. These are conservative estimates considering the ongoing detections of transiting planets amenable to atmospheric characterization. We find that instrumental stability at 40 m s−1, less stringent than for radial velocity monitoring, is sufficient for transmission spectroscopy in He i. As such, NIGHT can utilize mostly off-the-shelf components, ensuring cost-efficiency. A fibre-fed system allows for flexibility as a visitor instrument on a variety of telescopes, making it ideal for follow-up observations after JWST or ground-based detections. Over a few years of surveying, NIGHT could offer detailed insights into the mechanisms shaping the hot Neptune desert and close-in planet population by significantly expanding the statistical sample of planets with known evaporating atmospheres. First light is expected in 2024.
Characterization of acetonitrile ice irradiated by X-rays employing the procoda code – II. Desorption processes
Authors: Carvalho G A , Pilling S , Gerasimenko S 
Published: October 2023

ABSTRACT
In this work, we focus on the study of radiation-induced desorption processes that occurred in acetonitrile ice irradiated by broad-band X-rays (6 eV to 2 keV) monitored by Fourier transform infrared spectroscopy at different radiation fluences. In a previous work, we used the procoda code to derive the chemical evolution of the ice. Here, we have observed that the acetonitrile desorbed column density is at least two orders of magnitude larger than the desorbed column densities of daughter or granddaughter molecular species at chemical equilibrium stage. This indicates that total desorption column density is mainly governed by the father molecule, as also previously hypothesized in experimental studies. This occurs basically because the acetonitrile column density is larger than the other ones. In particular, at chemical equilibrium acetonitrile desorption column density represents almost 98 per cent of the total, while it is close to 1 per cent for H, CN, and CH2, the species with larger molecular desorption percentages at chemical equilibrium. Another derived quantity is what we called intrinsic desorption rate, which is a number per second for individual species. Some of the larger intrinsic desorption rates were 6.2 × 10−6 (CH3CN), 6.2 × 10−6 (CN), 5.7 × 10−6 (H), 5.7 × 10−6 (CH2), and 4.4 × 10−6 (C2N2). These results help to put constraints in astrochemical models and can also be useful to clarify some astronomical radio observations.
Effect of graded levels of selenium supplementation as selenite on expression of selenosugars, selenocysteine, and other selenometabolites in rat liver
Authors: Bierla Katarzyna , Szpunar Joanna , Lobinski Ryszard , Sunde Roger A 
Published: October 2023

Abstract
Using high pressure liquid chromatography (HPLC) coupled with selenium-specific inductively coupled plasma mass spectrometry (ICP–MS) and molecule specific (Orbitrap MS/MS) detection, we previously found that far more selenium (Se) is present as selenosugar (seleno-N-acetyl galactosamine) in Se-adequate turkey liver than is present as selenocysteine (Sec) in true selenoproteins, and that selenosugars account for half of the Se in high-Se turkey liver. To expand these observations to mammals, we studied Se metabolism in rats fed graded levels of selenite from 0 to 5 μg Se/g for 4 wk. In Se-adequate (0.24 μg Se/g) rats, 43% of liver Se was present as Sec, 32% was present as selenosugars, and 22% as inorganic Se bound to protein. In liver of rats fed 5 μg Se/g as selenite, the quantity of Sec remained at the Se-adequate plateau (11% of total Se), 22% was present as low molecular weight (LMW) selenosugars with substantial additional selenosugars linked to protein, but 64% was present as inorganic Se bound to protein. No selenomethionine was found at any level of selenite supplementation. Below the Se requirement, Se is preferentially incorporated into Sec-selenoproteins. Above the dietary Se requirement, selenosugars become by far the major LMW water soluble Se species in liver, and levels of selenosugar-decorated proteins are far higher than Sec-selenoproteins, making these selenosugar-decorated proteins the major Se-containing protein species in liver with high Se supplementation. This accumulation of selenosugars linked to cysteines on proteins or the build-up of inorganic Se bound to protein may underlie Se toxicity at the molecular level.
‘SAXS-osmometer’ method provides measurement of DNA pressure in viral capsids and delivers an empirical equation of state
Authors: Villanueva Valencia José Ramón , Li Dong , Casjens Sherwood R , Evilevitch Alex 
Published: October 2023

Abstract
We present a novel method that provides a measurement of DNA pressure in viral capsids using small angle X-ray scattering (SAXS). This method, unlike our previous assay, does not require triggering genome release with a viral receptor. Thus, it can be used to determine the existence of a pressurized genome state in a wide range of virus systems, even if the receptor is not known, leading to a better understanding of the processes of viral genome uncoating and encapsidation in the course of infection. Furthermore, by measuring DNA pressure for a collection of bacteriophages with varying DNA packing densities, we derived an empirical equation of state (EOS) that accurately predicts the relation between the capsid pressure and the packaged DNA density and includes the contribution of both DNA–DNA interaction energy and DNA bending stress to the total DNA pressure. We believe that our SAXS-osmometer method and the EOS, combined, provide the necessary tools to investigate physico-chemical properties of confined DNA condensates and mechanisms of infection, and may also provide essential data for the design of viral vectors in gene therapy applications and development of antivirals that target the pressurized genome state.
High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins
Authors: Martin Vincentius , Zhuang Farica , Zhang Yuning , Pinheiro Kyle , Gordân Raluca 
Published: October 2023

Abstract
Cooperative DNA-binding by transcription factor (TF) proteins is critical for eukaryotic gene regulation. In the human genome, many regulatory regions contain TF-binding sites in close proximity to each other, which can facilitate cooperative interactions. However, binding site proximity does not necessarily imply cooperative binding, as TFs can also bind independently to each of their neighboring target sites. Currently, the rules that drive cooperative TF binding are not well understood. In addition, it is oftentimes difficult to infer direct TF–TF cooperativity from existing DNA-binding data. Here, we show that in vitro binding assays using DNA libraries of a few thousand genomic sequences with putative cooperative TF-binding events can be used to develop accurate models of cooperativity and to gain insights into cooperative binding mechanisms. Using factors ETS1 and RUNX1 as our case study, we show that the distance and orientation between ETS1 sites are critical determinants of cooperative ETS1–ETS1 binding, while cooperative ETS1–RUNX1 interactions show more flexibility in distance and orientation and can be accurately predicted based on the affinity and sequence/shape features of the binding sites. The approach described here, combining custom experimental design with machine-learning modeling, can be easily applied to study the cooperative DNA-binding patterns of any TFs.
scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse
Authors: Huang Xuemei , Song Chao , Zhang Guorui , Li Ye , Zhao Yu , Zhang Qinyi , Zhang Yuexin , Fan Shifan , Zhao Jun , Xie Liyuan , Li Chunquan 
Published: October 2023

Abstract
Gene regulatory networks (GRNs) are interpretable graph models encompassing the regulatory interactions between transcription factors (TFs) and their downstream target genes. Making sense of the topology and dynamics of GRNs is fundamental to interpreting the mechanisms of disease etiology and translating corresponding findings into novel therapies. Recent advances in single-cell multi-omics techniques have prompted the computational inference of GRNs from single-cell transcriptomic and epigenomic data at an unprecedented resolution. Here, we present scGRN (https://bio.liclab.net/scGRN/), a comprehensive single-cell multi-omics gene regulatory network platform of human and mouse. The current version of scGRN catalogs 237 051 cell type-specific GRNs (62 999 692 TF–target gene pairs), covering 160 tissues/cell lines and 1324 single-cell samples. scGRN is the first resource documenting large-scale cell type-specific GRN information of diverse human and mouse conditions inferred from single-cell multi-omics data. We have implemented multiple online tools for effective GRN analysis, including differential TF–target network analysis, TF enrichment analysis, and pathway downstream analysis. We also provided details about TF binding to promoters, super-enhancers and typical enhancers of target genes in GRNs. Taken together, scGRN is an integrative and useful platform for searching, browsing, analyzing, visualizing and downloading GRNs of interest, enabling insight into the differences in regulatory mechanisms across diverse conditions.
AGIDB: a versatile database for genotype imputation and variant decoding across species
Authors: Zhang Kaili , Liang Jiete , Fu Yuhua , Chu Jinyu , Fu Liangliang , Wang Yongfei , Li Wangjiao , Zhou You , Li Jinhua , Yin Xiaoxiao , Wang Haiyan , Liu Xiaolei , Mou Chunyan , Wang Chonglong , Wang Heng , Dong Xinxing , Yan Dawei , Yu Mei , Zhao Shuhong , Li Xinyun , Ma Yunlong 
Published: October 2023

Abstract
The high cost of large-scale, high-coverage whole-genome sequencing has limited its application in genomics and genetics research. The common approach has been to impute whole-genome sequence variants obtained from a few individuals for a larger population of interest individually genotyped using SNP chip. An alternative involves low-coverage whole-genome sequencing (lcWGS) of all individuals in the larger population, followed by imputation to sequence resolution. To overcome limitations of processing lcWGS data and meeting specific genotype imputation requirements, we developed AGIDB (https://agidb.pro), a website comprising tools and database with an unprecedented sample size and comprehensive variant decoding for animals. AGIDB integrates whole-genome sequencing and chip data from 17 360 and 174 945 individuals, respectively, across 89 species to identify over one billion variants, totaling a massive 688.57 TB of processed data. AGIDB focuses on integrating multiple genotype imputation scenarios. It also provides user-friendly searching and data analysis modules that enable comprehensive annotation of genetic variants for specific populations. To meet a wide range of research requirements, AGIDB offers downloadable reference panels for each species in addition to its extensive dataset, variant decoding and utility tools. We hope that AGIDB will become a key foundational resource in genetics and breeding, providing robust support to researchers.
dbAPIS: a database of

a

nti-

p

rokaryotic

i

mmune

s

ystem genes
Authors: Yan Yuchen , Zheng Jinfang , Zhang Xinpeng , Yin Yanbin 
Published: October 2023

Abstract
Anti-prokaryotic immune system (APIS) proteins, typically encoded by phages, prophages, and plasmids, inhibit prokaryotic immune systems (e.g. restriction modification, toxin-antitoxin, CRISPR-Cas). A growing number of APIS genes have been characterized and dispersed in the literature. Here we developed dbAPIS (https://bcb.unl.edu/dbAPIS), as the first literature curated data repository for experimentally verified APIS genes and their associated protein families. The key features of dbAPIS include: (i) experimentally verified APIS genes with their protein sequences, functional annotation, PDB or AlphaFold predicted structures, genomic context, sequence and structural homologs from different microbiome/virome databases; (ii) classification of APIS proteins into sequence-based families and construction of hidden Markov models (HMMs); (iii) user-friendly web interface for data browsing by the inhibited immune system types or by the hosts, and functions for searching and batch downloading of pre-computed data; (iv) Inclusion of all types of APIS proteins (except for anti-CRISPRs) that inhibit a variety of prokaryotic defense systems (e.g. RM, TA, CBASS, Thoeris, Gabija). The current release of dbAPIS contains 41 verified APIS proteins and ∼4400 sequence homologs of 92 families and 38 clans. dbAPIS will facilitate the discovery of novel anti-defense genes and genomic islands in phages, by providing a user-friendly data repository and a web resource for an easy homology search against known APIS proteins.