bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the stellar populations of backsplash galaxies
Authors: Ferreras I , Böhm A , Umetsu K , Sampaio V , de Carvalho R R 
Published: January 2023

Abstract
Backsplash galaxies are those that traverse and overshoot cluster cores as they fall into these structures. They are affected by environment, and should stand out in contrast to the infalling population. We target galaxies in the vicinity of clusters (R≳R200) and select a sample in projected phase space (PPS), from the compilation of Sampaio et al. based on SDSS data. We present a statistical analysis, comparing two regions in PPS, with the same projected distance to the cluster but different velocity. The analysis relies on the presence of variations in the stellar population content of backsplash galaxies. We find a lower limit in the fractional contribution of ∼5 per cent with respect to the general sample of infalling galaxies at similar group-centric distance when using single line strength analysis, or ∼15-30 per cent when adopting bivariate distributions. The stellar populations show a subtle but significant difference towards older ages, and a higher fraction of quiescent galaxies. We also compare this set with a general field sample, where a substantially larger difference in galaxy properties is found, with the field sample being consistently younger, metal poorer and with a lower fraction of quiescent galaxies. Noting that our ‘cluster’ sample is located outside of the virial radius, we expect this difference to be caused by pre-processing of the infalling galaxies in the overall higher density regions.
Multiwavelength scrutiny of X-ray sources in dwarf galaxies: ULXs versus AGNs
Authors: Thygesen Erica , Plotkin Richard M , Soria Roberto , Reines Amy E , Greene Jenny E , Anderson Gemma E , Baldassare Vivienne F , Owens Milo G , Urquhart Ryan T , Gallo Elena , Miller-Jones James C A , Paul Jeremiah D , Rollings Alexandar P 
Published: January 2023

ABSTRACT
Owing to their quiet evolutionary histories, nearby dwarf galaxies (stellar masses $M_\star \lesssim 3 \times 10^9 \, \mathrm{M}_\odot$) have the potential to teach us about the mechanism(s) that ‘seeded’ the growth of supermassive black holes, and also how the first stellar mass black holes formed and interacted with their environments. Here, we present high spatial resolution observations of three dwarf galaxies in the X-ray (Chandra), the optical/near-infrared (Hubble Space Telescope), and the radio (Karl G. Jansky Very Large Array). These three galaxies were previously identified as hosting candidate active galactic nuclei on the basis of lower resolution X-ray imaging. With our new observations, we find that X-ray sources in two galaxies (SDSS J121326.01+543631.6 and SDSS J122111.29+173819.1) are off-nuclear and lack corresponding radio emission, implying they are likely luminous X-ray binaries. The third galaxy (Mrk 1434) contains two X-ray sources (each with LX ≈ 1040 erg s−1) separated by 2.8 arcsec, has a low metallicity [12 + log(O/H) = 7.8], and emits nebular He ii λ4686 line emission. The northern source has spatially coincident point-like radio emission at 9.0 GHz and extended radio emission at 5.5 GHz. We discuss X-ray binary interpretations (where an ultraluminous X-ray source blows a ‘radio bubble’) and active galactic nucleus interpretations (where an $\approx 4\times 10^5 \, \mathrm{M}_\odot$ black hole launches a jet). In either case, we find that the He ii emission cannot be photoionized by the X-ray source, unless the source was ≈30–90 times more luminous several hundred years ago.
eDIG-CHANGES I: extended Hα emission from the extraplanar diffuse ionized gas (eDIG) around CHANG-ES galaxies
Authors: Lu Li-Yuan , Li Jiang-Tao , Vargas Carlos J , Beck Rainer , Bregman Joel N , Dettmar Ralf-Jürgen , English Jayanne , Fang Taotao , Heald George H , Li Hui , Qu Zhijie , Rand Richard J , Stein Michael , Wang Q Daniel , Wang Jing , Wiegert Theresa , Zheng Yun 
Published: January 2023

ABSTRACT
The extraplanar diffuse ionized gas (eDIG) represents the cool/warm ionized gas reservoir around galaxies. We present spatial analysis of the Hα images of 22 nearby edge-on spiral galaxies taken with the Apache Point Observatory 3.5-m telescope (eDIG-CHANGES). We conduct an exponential fit to the vertical Hα intensity profiles of the galaxies, of which 16 can be decomposed into thin + thick disk components. The median value of the Hα scale height of the thick disk is $\langle h_{\rm H\alpha }\rangle =1.13\pm 0.14\rm ~kpc$. We further examine the dependence of hHα on the stellar mass, SFR, and SFR surface density (SFRSD) of the galaxies. We find a tight sublinear correlation between hHα and SFR, expressed in hHα ∝ SFRα, where α ≈ 0.29. Moreover, the offset of individual galaxies from the best-fit SFR-hHα relation, expressed in hHα/SFRα, shows significant anti-correlation with SFRSD. We further compare the vertical extension of the eDIG to multi-wavelength measurements of other CGM phases. We find the eDIG slightly more extended than the neutral gas. This indicates the existence of some extended ionizing sources, in addition to the leaking photons from the disk star formation regions. Most galaxies have an X-ray scale height smaller than Hα, suggesting the majority of the X-ray photons are actually from the thick disk instead of the extended CGM. hHα is comparable to the L-band radio continuum scale height. This indicates that the thermal and non-thermal electrons have similar spatial distributions, a natural result if both are transported outwards by a galactic wind. This further indicates the thermal gas, cosmic rays, and magnetic field may be close to energy equipartition.
Photometric variable stars in the young open cluster NGC 6823
Authors: Lata Sneh , Chen W P , Pandey J C , Dileep Athul , Ai Zhong-Han , Hojaev Alisher S , Panwar Neelam , Joshi Santosh , Mondal Soumen , Biswas Siddhartha , Bhatt B C 
Published: January 2023

ABSTRACT
We present stellar variability towards the young open cluster NGC 6823. Time series V- and I-band CCD photometry led to identification and characterization of 88 variable stars, of which only 14 have been previously recognized. We ascertain the membership of each variable with optical UBVI and infrared photometry, and with Gaia EDR3 parallax and proper motion data. Seventy two variable stars are found to be cluster members, of which 25 are main sequence stars and 48 are pre-main-sequence stars. The probable cluster members collectively suggest an isochrone age of the cluster to be about 2 Myrs based on the GAIA photometry. With the colour and magnitude, as well as the shape of the light curve, we have classified the main sequence variables into β Cep, δ Scuti, slowly pulsating B type, and new class variables. Among the pre-main-sequence variables, eight are classical T Tauri variables, and four are Herbig Ae/Be objects, whereas the remaining belong to the weak-lined T Tauri population. The variable nature of 32 stars is validated with TESS light curves. Our work provides refined classification of variability of pre-main-sequence and main-sequence cluster members of the active star-forming complex, Sharpless 86. Despite no strong evidence of the disc-locking mechanism in the present sample of TTSs, one TTS with larger Δ(I − K) is found to be a slow rotator.
MAXI J1820+070 X-ray spectral-timing reveals the nature of the accretion flow in black hole binaries
Authors: Kawamura Tenyo , Done Chris , Axelsson Magnus , Takahashi Tadayuki 
Published: January 2023

ABSTRACT
Black hole X-ray binaries display significant stochastic variability on short time-scales (0.01–100 s), with a complex pattern of lags in correlated variability seen in different energy bands. This behaviour is generally interpreted in a model where slow fluctuations stirred up at large radii propagate down through the accretion flow, modulating faster fluctuations generated at smaller radii. Coupling this scenario with radially stratified emission opens the way to measure the propagation time-scale from data, allowing direct tests of the accretion flow structure. We previously developed a model based on this picture and showed that it could fit the Neutron star Interior Composition Explorer (NICER; 0.5–10 keV) data from the brightest recent black hole transient, MAXI J1820+070. However, here we show it fails when extrapolated to higher energy variability data from the Insight-Hard X-ray Modulation Telescope(HXMT). We extend our model so that the spectrum emitted at each radius changes shape in response to fluctuations (pivoting) rather than just changing normalization. This gives the strong suppression of fractional variability as a function of energy seen in the data. The derived propagation time-scale is slower than predicted by a magnetically arrested disc (MAD), despite this system showing a strong jet. Our new model jointly fits the spectrum and variability up to 50 keV, though still cannot match all the data above this. Nonetheless, the good fit from 3 to 40 keV means the quasi-periodic oscillation (QPO) can most easily be explained as an extrinsic modulation of the flow, such as produced in the Lense–Thirring precession, rather than arising in an additional spectral-timing component such as the jet.
MaLAdapt Reveals Novel Targets of Adaptive Introgression From Neanderthals and Denisovans in Worldwide Human Populations
Authors: Zhang Xinjun , Kim Bernard , Singh Armaan , Sankararaman Sriram , Durvasula Arun , Lohmueller Kirk E 
Published: January 2023

Abstract
Adaptive introgression (AI) facilitates local adaptation in a wide range of species. Many state-of-the-art methods detect AI with ad-hoc approaches that identify summary statistic outliers or intersect scans for positive selection with scans for introgressed genomic regions. Although widely used, approaches intersecting outliers are vulnerable to a high false-negative rate as the power of different methods varies, especially for complex introgression events. Moreover, population genetic processes unrelated to AI, such as background selection or heterosis, may create similar genomic signals to AI, compromising the reliability of methods that rely on neutral null distributions. In recent years, machine learning (ML) methods have been increasingly applied to population genetic questions. Here, we present a ML-based method called MaLAdapt for identifying AI loci from genome-wide sequencing data. Using an Extra-Trees Classifier algorithm, our method combines information from a large number of biologically meaningful summary statistics to capture a powerful composite signature of AI across the genome. In contrast to existing methods, MaLAdapt is especially well-powered to detect AI with mild beneficial effects, including selection on standing archaic variation, and is robust to non-AI selective sweeps, heterosis from deleterious mutations, and demographic misspecification. Furthermore, MaLAdapt outperforms existing methods for detecting AI based on the analysis of simulated data and the validation of empirical signals through visual inspection of haplotype patterns. We apply MaLAdapt to the 1000 Genomes Project human genomic data and discover novel AI candidate regions in non-African populations, including genes that are enriched in functionally important biological pathways regulating metabolism and immune responses.
Development of ANCA-associated vasculitis followed by SARS-CoV-2 vaccination in a patient with HLA-DRB1*09:01 allele
Authors: Kawamura Takuro , Nakazawa Daigo , Nishio Saori , Isozaki Taiki , Komatsumoto Maki , Atsumi Tatsuya 
Published: January 2023

ABSTRACT
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), presents with severe pneumonia and fatal systemic complications. Currently, SARS-CoV-2 vaccines are effective in reducing the risk of new onset and getting worse of the disease. However, autoimmune diseases such as antineutrophil cytoplasmic antibody (ANCA)–associated vasculitis (AAV) have been reported to develop after COVID-19 vaccine administration. A 71-year-old woman presented with fever, malaise, urinary abnormalities, and renal dysfunction after receiving the COVID-19 vaccine (Pfizer-BioNTech). We clinically diagnosed AAV with her manifestations and serological test (myeloperoxidase-ANCA-positive). Her clinical findings were improved after immunosuppressive therapy. We examined her genetic susceptibility to AAV, and we found that her allele was HLA-DRB1*09:01, which is a risk allele of myeloperoxidase-AAV. Mechanistically, SARS-CoV-2 vaccines would activate immunity, including neutrophils, and trigger AAV onset in this patient with a genetic risk to develop AAV. The pathophysiology of this case would share with that of autoimmune/inflammatory syndrome induced by adjuvants in the absence of external adjuvants.
The putative metal-binding proteome of the Coronaviridae family
Authors: Dixit Himisha , Upadhyay Vipin , Kulharia Mahesh , Verma Shailender Kumar 
Published: January 2023

Abstract
Metalloproteins are well-known for playing various physicochemical processes in all life forms, including viruses. Some life-threatening viruses (such as some members of the Coronaviridae family of viruses) are emerged and remerged frequently and are rapidly transmitted throughout the globe. This study aims to identify and characterize the metal-binding proteins (MBPs) of the Coronaviridae family of viruses and further provides insight into the MBP’s role in sustaining and propagating viruses inside a host cell and in the outer environment. In this study, the available proteome of the Coronaviridae family was exploited. Identified potential MBPs were analyzed for their functional domains, structural aspects, and subcellular localization. We also demonstrate phylogenetic aspects of all predicted MBPs among other Coronaviridae family members to understand the evolutionary trend among their respective hosts. A total of 256 proteins from 51 different species of coronaviruses are predicted as MBPs. These MBPs perform various key roles in the replication and survival of viruses within the host cell. Cysteine, aspartic acid, threonine, and glutamine are key amino acid residues interacting with respective metal ions. Our observations also indicate that the metalloproteins of this family of viruses circulated and evolved in different hosts, which supports the zoonotic nature of coronaviruses. The comprehensive information on MBPs of the Coronaviridae family may be further helpful in designing novel therapeutic metalloprotein targets. Moreover, the study of viral MBPs can also help to understand the roles of MBPs in virus pathogenesis and virus–host interactions.
CRISPR-Cas9 recognition of enzymatically synthesized base-modified nucleic acids
Authors: Yang Hui , Eremeeva Elena , Abramov Mikhail , Jacquemyn Maarten , Groaz Elisabetta , Daelemans Dirk , Herdewijn Piet 
Published: January 2023

Abstract
An enzymatic method has been successfully established enabling the generation of partially base-modified RNA (previously named RZA) constructs, in which all G residues were replaced by isomorphic fluorescent thienoguanosine (thG) analogs, as well as fully modified RZA featuring thG, 5-bromocytosine, 7-deazaadenine and 5-chlorouracil. The transcriptional efficiency of emissive fully modified RZA was found to benefit from the use of various T7 RNA polymerase variants. Moreover, dthG could be incorporated into PCR products by Taq DNA polymerase together with the other three base-modified nucleotides. Notably, the obtained RNA products containing thG as well as thG together with 5-bromocytosine could function as effectively as natural sgRNAs in an in vitro CRISPR-Cas9 cleavage assay. N1-Methylpseudouridine was also demonstrated to be a faithful non-canonical substitute of uridine to direct Cas9 nuclease cleavage when incorporated in sgRNA. The Cas9 inactivation by 7-deazapurines indicated the importance of the 7-nitrogen atom of purines in both sgRNA and PAM site for achieving efficient Cas9 cleavage. Additional aspects of this study are discussed in relation to the significance of sgRNA–protein and PAM–-protein interactions that were not highlighted by the Cas9–sgRNA–DNA complex crystal structure. These findings could expand the impact and therapeutic value of CRISPR-Cas9 and other RNA-based technologies.
The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection
Authors: Rigden Daniel J , Fernández Xosé M 
Published: January 2023

Abstract
The 2023 Nucleic Acids Research Database Issue contains 178 papers ranging across biology and related fields. There are 90 papers reporting on new databases and 82 updates from resources previously published in the Issue. Six more papers are updates from databases most recently published elsewhere. Major nucleic acid databases reporting updates include Genbank, ENA, ChIPBase, JASPAR, mirDIP and the Issue's first Breakthrough Article, NACDDB for Circular Dichroism data. Updates from BMRB and RCSB cover experimental protein structural data while AlphaFold 2 computational structure predictions feature widely. STRING and REBASE are stand-out updates in the signalling and enzymes section. Immunology-related databases include CEDAR, the second Breakthrough Article, for cancer epitopes and receptors alongside returning IPD-IMGT/HLA and the new PGG.MHC. Genomics-related resources include Ensembl, GWAS Central and UCSC Genome Browser. Major returning databases for drugs and their targets include Open Targets, DrugCentral, CTD and Pubchem. The EMPIAR image archive appears in the Issue for the first time. The entire database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been updated, revisiting 463 entries, adding 92 new resources and eliminating 96 discontinued URLs so bringing the current total to 1764 databases. It is available at http://www.oxfordjournals.org/nar/database/c/.
The DEAD-box protein Dbp6 is an ATPase and RNA annealase interacting with the peptidyl transferase center (PTC) of the ribosome
Authors: Khreiss Ali , Capeyrou Régine , Lebaron Simon , Albert Benjamin , Bohnsack Katherine E , Bohnsack Markus T , Henry Yves , Henras Anthony K , Humbert Odile 
Published: January 2023

Abstract
Ribosomes are ribozymes, hence correct folding of the rRNAs during ribosome biogenesis is crucial to ensure catalytic activity. RNA helicases, which can modulate RNA–RNA and RNA/protein interactions, are proposed to participate in rRNA tridimensional folding. Here, we analyze the biochemical properties of Dbp6, a DEAD-box RNA helicase required for the conversion of the initial 90S pre-ribosomal particle into the first pre-60S particle. We demonstrate that in vitro, Dbp6 shows ATPase as well as annealing and clamping activities negatively regulated by ATP. Mutations in Dbp6 core motifs involved in ATP binding and ATP hydrolysis are lethal and impair Dbp6 ATPase activity but increase its RNA binding and RNA annealing activities. These data suggest that correct regulation of these activities is important for Dbp6 function in vivo. Using in vivo cross-linking (CRAC) experiments, we show that Dbp6 interacts with 25S rRNA sequences located in the 5′ domain I and in the peptidyl transferase center (PTC), and also crosslinks to snoRNAs hybridizing to the immature PTC. We propose that the ATPase and RNA clamping/annealing activities of Dbp6 modulate interactions of snoRNAs with the immature PTC and/or contribute directly to the folding of this region.
Dissecting Trypanosoma brucei RRP44 function in the maturation of segmented ribosomal RNA using a regulated genetic complementation system
Authors: Guerra-Slompo Eloise Pavão , Cesaro Giovanna , Guimarães Beatriz Gomes , Zanchin Nilson Ivo Tonin 
Published: January 2023

Abstract
Trypanosoma brucei belongs to a group of protozoans presenting fragmented large subunit rRNA. Its LSU rRNA equivalent to the 25S/28S rRNA of other eukaryotes is split into six fragments, requiring additional processing for removal of the extra spacer sequences. We have used a genetic complementation strategy to further investigate the T. brucei RRP44 nuclease in pre-rRNA maturation. TbRRP44 contains both a PIN and a RNB domain whose homologues are found in association with the exosome complex. We found that the exonucleolytic activity of the RNB domain as well as the physical presence of the PIN domain are essential for TbRRP44 function, while a catalytic site mutation in the PIN domain has no detectable effect on cell growth. A new endonucleolytic cleavage site in ITS1 was identified. In addition to the 5.8S rRNA 3′-end maturation, TbRRP44 is required for degradation of the excised 5′-ETS and for removal of part of ITS1 during maturation of the 18S rRNA 3′-end. TbRRP44 deficiency leads to accumulation of many LSU intermediate precursors, most of them not detected in control cells. TbRRP44 is also required for U3 snoRNA and spliced leader processing, indicating that TbRRP44 may have a wide role in RNA processing in T. brucei.
The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements
Authors: Botelho João , Cazares Adrian , Schulenburg Hinrich 
Published: January 2023

Abstract
Mobile genetic elements (MGEs) mediate the shuffling of genes among organisms. They contribute to the spread of virulence and antibiotic resistance (AMR) genes in human pathogens, such as the particularly problematic group of ESKAPE pathogens. Here, we performed the first systematic analysis of MGEs, including plasmids, prophages, and integrative and conjugative/mobilizable elements (ICEs/IMEs), across all ESKAPE pathogens. We found that different MGE types are asymmetrically distributed across these pathogens, and that most horizontal gene transfer (HGT) events are restricted by phylum or genus. We show that the MGEs proteome is involved in diverse functional processes and distinguish widespread proteins within the ESKAPE context. Moreover, anti-CRISPRs and AMR genes are overrepresented in the ESKAPE mobilome. Our results also underscore species-specific trends shaping the number of MGEs, AMR, and virulence genes across pairs of conspecific ESKAPE genomes with and without CRISPR-Cas systems. Finally, we observed that CRISPR spacers found on prophages, ICEs/IMEs, and plasmids have different targeting biases: while plasmid and prophage CRISPRs almost exclusively target other plasmids and prophages, respectively, ICEs/IMEs CRISPRs preferentially target prophages. Overall, our study highlights the general importance of the ESKAPE mobilome in contributing to the spread of AMR and mediating conflict among MGEs.