bluuebunny/crossref_metadata_2025_split huggingface dataset:
A renewed search for radio emission from the variable γ-ray pulsar PSR J2021+4026
Authors: Shaw B , Stappers B W , Weltevrede P , Jordan C A , Mickaliger M B , Lyne A G 
Published: May 2023

ABSTRACT
We undertake the first targeted search at 1.5 GHz for radio emission from the variable γ-ray pulsar PSR J2021+4026. This radio-quiet pulsar assumes one of two stable γ-ray emission states, between which it transitions on a time-scale of years. These transitions, in both γ-ray flux and pulse profile shape, are accompanied by contemporaneous changes to the pulsar’s spin-down rate. A number of radio pulsars are known to exhibit similar correlated variability, which in some cases involves an emission state in which the radio emission ceases to be detectable. In this paper, we perform a search for radio emission from PSR J2021+4026, using archival radio observations recorded when the pulsar was in each of its emission/spin-down states. Using improved techniques, we search for periodic radio emission as well as single pulse phenomena such as giant radio pulses and RRAT-like emission. Our search reveals no evidence of radio emission from PSR J2021+4026. We estimate that the flux density for periodic emission from PSR J2021+4026 does not exceed 0.2 mJy at this frequency. We also estimate single-pulse flux limits for RRAT-like bursts and giant radio pulses to be 0.3 and 100 Jy, respectively. We discuss the transitioning behaviour of PSR J2021+4026 in the context of pulsar glitches, intermittent pulsars and the increasingly common emission-rotation correlation observed in radio pulsars.
Clusters, clouds, and correlations: relating young clusters to giant molecular clouds in M33 and M31
Authors: Peltonen Joshua , Rosolowsky Erik , Johnson L Clifton , Seth Anil C , Dalcanton Julianne , Bell Eric F , Braine Jonathan , Koch Eric W , Lazzarini Margaret , Leroy Adam K , Skillman Evan D , Smercina Adam , Wainer Tobin , Williams Benjamin F 
Published: May 2023

ABSTRACT
We use young clusters and giant molecular clouds (GMCs) in the galaxies M33 and M31 to constrain temporal and spatial scales in the star formation process. In M33, we compare the Panchromatic Hubble Andromeda Treasury: Triangulum Extended Region (PHATTER) catalogue of 1214 clusters with ages measured via colour–magnitude diagram (CMD) fitting to 444 GMCs identified from a new 35 pc resolution Atacama Large Millimeter/submillimeter Array (ALMA) 12CO(2–1) survey. In M31, we compare the Panchromatic Hubble Andromeda Treasury (PHAT) catalogue of 1249 clusters to 251 GMCs measured from a Combined Array for Research in Millimeter-wave Astronomy (CARMA) 12CO(1–0) survey with 20 pc resolution. Through two-point correlation analysis, we find that young clusters have a high probability of being near other young clusters, but correlation between GMCs is suppressed by the cloud identification algorithm. By comparing the positions, we find that younger clusters are closer to GMCs than older clusters. Through cross-correlation analysis of the M33 cluster data, we find that clusters are statistically associated when they are ≤10 Myr old. Utilizing the high precision ages of the clusters, we find that clusters older than ≈18 Myr are uncorrelated with the molecular interstellar medium (ISM). Using the spatial coincidence of the youngest clusters and GMCs in M33, we estimate that clusters spend ≈4–6 Myr inside their parent GMC. Through similar analysis, we find that the GMCs in M33 have a total lifetime of ≈11–15 Myr. We also develop a drift model and show that the above correlations can be explained if the clusters in M33 have a 5–10 km s−1 velocity dispersion relative to the molecular ISM.
Collisional excitation of N+(3P) in interstellar clouds
Authors: Gueguen Marie , Lique François 
Published: May 2023

ABSTRACT
The detection of the N+ ion in ionized interstellar regions, as well as its use as a tracer for atomic nitrogen (N) in interstellar media, makes it an interesting ion from the astrophysical point of view. Accurate determination of the N+ abundance in the interstellar clouds requires detailed modelling of its excitation conditions. Hence, collisional excitation induced by the dominant interstellar species has to be studied. In this paper, we study the collisional excitation of N+ by He and H2. We provide new potential energy surfaces describing the interactions between N+ and He and between N+ and H2 considered as a structureless collider. Quantum calculations of the excitation cross-sections for collisions of N+ with He and H2 are provided, as well as the first excitation rate coefficients for N+ induced by these two species. The results are compared to collisional data for the excitation induced by electrons. It is shown that the excitation of N+ by a neutral collider can play a significant role in weakly ionized regions as well as in warm molecular clouds.
MeerKAT caught a Mini Mouse: serendipitous detection of a young radio pulsar escaping its birth site
Authors: Motta S E , Turner J D , Stappers B , Fender R P , Heywood I , Kramer M , Barr E D 
Published: May 2023

ABSTRACT
In MeerKAT observations pointed at a Galactic X-ray binary located on the Galactic plane, we serendipitously discovered a radio nebula with cometary-like morphology. The feature, which we named ‘the Mini Mouse’ based on its similarity with the previously discovered ‘Mouse’ nebula, points back towards the previously unidentified candidate supernova remnant G45.24+0.18. We observed the location of the Mini Mouse with MeerKAT in two different observations, and we localized with arcsecond precision the 138-ms radio pulsar PSR J1914+1054g, recently discovered by the FAST telescope, to a position consistent with the head of the nebula. We confirm a dispersion measure of about 418 pc cm−3 corresponding to a distance between 7.8 and 8.8 kpc based on models of the electron distribution. Using our accurate localization and two period measurements spaced 90 d apart, we calculate a period derivative of (2.7 ± 0.3) × 10 −14 s s−1. We derive a characteristic age of approximately 82 kyr and a spin-down luminosity of 4 × 1035 erg s−1. For a pulsar age comparable with the characteristic age, we find that the projected velocity of the neutron star is between 320 and 360 km s−1 if it was born at the location of the supernova remnant. The size of the proposed remnant appears small if compared with the pulsar characteristic age; however, the relatively high density of the environment near the Galactic plane could explain a suppressed expansion rate and thus a smaller remnant.
Evolution of radioactive elements in the LMC: predictions for future γ-ray surveys
Authors: Vasini Arianna , Matteucci F , Spitoni E , Siegert Thomas 
Published: May 2023

ABSTRACT
Short-lived radionuclides, such as 26Al and 60Fe, are tracers of star formation. Therefore, their abundances can unravel the recent star formation history of the host galaxy. In view of future γ-ray surveys, we predict the masses and fluxes of these two elements in the Large Magellanic Cloud (LMC) using new chemical evolution models. Our best model reproduces the abundance patterns of [α/Fe] ratios, the gas mass, the average metallicity, the present time supernova and nova rates observed in LMC. We show three main results: (i) the best model for the LMC suggests a star formation rate very mild at the beginning with a recent burst, and a Salpeter-like initial mass function. (ii) The predicted mass of 26Al is 0.33 M⊙, 2/3 produced by massive stars and 1/3 by novae. (iii) The predicted mass of 60Fe is 0.44 M⊙, entirely produced by massive stars. This result suggests a larger fraction of 60Fe, at variance with the Milky Way. The explanation for this lies in the adopted initial mass function, that for the LMC contains more massive stars than for the Milky Way. These predictions can be useful for the COSI-SMEX mission planned for launch in 2027. The expected γ-ray line fluxes for the 1.809 MeV line of 26Al and the 1.173 and 1.332 MeV lines of 60Fe are in the range of (0.2–$2.7)\times 10^{-6}\, \mathrm{ph\, cm^{-2}\, s^{-1}}$ and (0.7–$2.8)\times 10^{-7}\, \mathrm{ph\, cm^{-2}\, s^{-1}}$, respectively. This new instrument could have the sensitivity to detect the upper end of the predicted 1.8 MeV flux within its nominal two-yr mission.
The properties of wind and jet from a super-Eddington accretion flow around a supermassive black hole
Authors: Yang Hai , Yuan Feng , Kwan Tom , Dai Lixin 
Published: May 2023

ABSTRACT
Wind and jet are important medium of active galactic nucleus (AGN) feedback thus it is crucial to obtain their properties for the feedback study. In this paper we investigate the properties of wind and jet launched from a magnetized super-Eddington accretion flow around a supermassive black hole. For this aim, we have performed radiation magnetohydrodynamical simulation of a magnetically arrested super-Eddington accretion flows. We then have analysed the simulation data by the ‘virtual particle trajectory’ approach and obtained the mass flux, poloidal, and toroidal velocities, and mass-flux-weighted momentum and energy fluxes of wind and jet. The mass flux is found to be two to six times higher than that obtained based on the time-averaged streamline method widely used in literature. The momentum flux of wind is found to be larger than that of jet, while the total energy flux of jet is at most three times larger than that of wind. These results are similar to the case of hot accretion flows and imply that winds likely play a more important role than jet in AGN feedback. The acceleration mechanism of wind and jet is analysed and found to be dominated by Lorentz force rather than radiation force.
Skew spectrum and smoothed skewness of 21-cm signals from epoch of reionization
Authors: Ma Qing-Bo , Peng Ling 
Published: May 2023

ABSTRACT
Due to the non-linear ionizing and heating processes, the 21-cm signals from epoch of reionization (EoR) are expected to have strong non-Gaussian fluctuations. In this paper, we use the seminumerical simulations to study the non-Gaussian statistics, i.e. skew spectrum and smoothed skewness of the 21-cm signals from EoR. We find the 21-cm skew spectrum and smoothed skewness have similar evolution features with the 21-cm bispectrum. All of them are sensitive to the EoR models, while not too much to the cosmic volume applied. With the SKA1-low telescope as reference, we find both the skew spectrum and smoothed skewness have much higher signal-to-noise ratios than the 21-cm bispectrum.
Spontaneous resolution of inflammatory myopathy involving the masseter muscle following COVID-19 mRNA vaccination
Authors: Tada Tomomi , Murao Haruka , Shiratani Reo , Park JeongHoon , Hideshima Makoto , Kanki Hideaki , Ishikawa Nachi , Shibahara Takayuki , Fujimoto Jun , Higa Shinji 
Published: May 2023

ABSTRACT
According to previous reports, most cases of inflammatory myopathy following messenger RNA (mRNA) vaccination can be classified as idiopathic inflammatory myopathy, particularly dermatomyositis, owing to their similar clinical features and courses. However, some patients have different clinical features and courses. We report a rare case of transient inflammatory myopathy involving the masseter muscle following the third dose of coronavirus disease 2019 (COVID-19) mRNA vaccination. An 80-year-old woman presented with a history of fever and fatigue for 3 months soon after receiving the third COVID-19 mRNA vaccination. Her symptoms progressed to jaw pain and inability to open her mouth. She also experienced mild proximal muscle weakness in the lower limbs but no skin manifestations or daily difficulties. Fat-saturated T2-weighted magnetic resonance imaging showed bilateral high-intensity signals for the masseter and quadriceps muscles. The patient experienced spontaneous resolution of fever and improvement of symptoms 5 months after onset. The timing of the onset of symptoms, the lack of detectable autoantibodies, and the atypical presentation of myopathy in the masseter muscles, in addition to the spontaneous mild course of the disease, all indicate the substantial role of mRNA vaccination in this myopathy. Since then, the patient has been followed up for 4 months without any recurrence of symptoms or any additional treatment. It is important to recognise that the course of myopathy after COVID-19 mRNA vaccination could be different from that of typical idiopathic inflammatory myopathies.
MULocDeep web service for protein localization prediction and visualization at subcellular and suborganellar levels
Authors: Jiang Yuexu , Jiang Lei , Akhil Chopparapu Sai , Wang Duolin , Zhang Ziyang , Zhang Weinan , Xu Dong 
Published: May 2023

Abstract
Predicting protein localization and understanding its mechanisms are critical in biology and pathology. In this context, we propose a new web application of MULocDeep with improved performance, result interpretation, and visualization. By transferring the original model into species-specific models, MULocDeep achieved competitive prediction performance at the subcellular level against other state-of-the-art methods. It uniquely provides a comprehensive localization prediction at the suborganellar level. Besides prediction, our web service quantifies the contribution of single amino acids to localization for individual proteins; for a group of proteins, common motifs or potential targeting-related regions can be derived. Furthermore, the visualizations of targeting mechanism analyses can be downloaded for publication-ready figures. The MULocDeep web service is available at https://www.mu-loc.org/.
DNA modifications impact natural transformation of Acinetobacter baumannii
Authors: Vesel Nina , Iseli Christian , Guex Nicolas , Lemopoulos Alexandre , Blokesch Melanie 
Published: May 2023

Abstract
Acinetobacter baumannii is a dangerous nosocomial pathogen, especially due to its ability to rapidly acquire new genetic traits, including antibiotic resistance genes (ARG). In A. baumannii, natural competence for transformation, one of the primary modes of horizontal gene transfer (HGT), is thought to contribute to ARG acquisition and has therefore been intensively studied. However, knowledge regarding the potential role of epigenetic DNA modification(s) on this process remains lacking. Here, we demonstrate that the methylome pattern of diverse A. baumannii strains differs substantially and that these epigenetic marks influence the fate of transforming DNA. Specifically, we describe a methylome-dependent phenomenon that impacts intra- and inter-species DNA exchange by the competent A. baumannii strain A118. We go on to identify and characterize an A118-specific restriction-modification (RM) system that impairs transformation when the incoming DNA lacks a specific methylation signature. Collectively, our work contributes towards a more holistic understanding of HGT in this organism and may also aid future endeavors towards tackling the spread of novel ARGs. In particular, our results suggest that DNA exchanges between bacteria that share similar epigenomes are favored and could therefore guide future research into identifying the reservoir(s) of dangerous genetic traits for this multi-drug resistant pathogen.
Epigenetic plasticity safeguards heterochromatin configuration in mammals
Authors: Fukuda Kei , Shimi Takeshi , Shimura Chikako , Ono Takao , Suzuki Takehiro , Onoue Kenta , Okayama Satoko , Miura Hisashi , Hiratani Ichiro , Ikeda Kazuho , Okada Yasushi , Dohmae Naoshi , Yonemura Shigenobu , Inoue Azusa , Kimura Hiroshi , Shinkai Yoichi 
Published: May 2023

Abstract
Heterochromatin is a key architectural feature of eukaryotic chromosomes critical for cell type-specific gene expression and genome stability. In the mammalian nucleus, heterochromatin segregates from transcriptionally active genomic regions and exists in large, condensed, and inactive nuclear compartments. However, the mechanisms underlying the spatial organization of heterochromatin need to be better understood. Histone H3 lysine 9 trimethylation (H3K9me3) and lysine 27 trimethylation (H3K27me3) are two major epigenetic modifications that enrich constitutive and facultative heterochromatin, respectively. Mammals have at least five H3K9 methyltransferases (SUV39H1, SUV39H2, SETDB1, G9a and GLP) and two H3K27 methyltransferases (EZH1 and EZH2). In this study, we addressed the role of H3K9 and H3K27 methylation in heterochromatin organization using a combination of mutant cells for five H3K9 methyltransferases and an EZH1/2 dual inhibitor, DS3201. We showed that H3K27me3, which is normally segregated from H3K9me3, was redistributed to regions targeted by H3K9me3 after the loss of H3K9 methylation and that the loss of both H3K9 and H3K27 methylation resulted in impaired condensation and spatial organization of heterochromatin. Our data demonstrate that the H3K27me3 pathway safeguards heterochromatin organization after the loss of H3K9 methylation in mammalian cells.
Single-stranded DNA recruitment mechanism in replication origin unwinding by DnaA initiator protein and HU, an evolutionary ubiquitous nucleoid protein
Authors: Yoshida Ryusei , Ozaki Shogo , Kawakami Hironori , Katayama Tsutomu 
Published: May 2023

Abstract
The Escherichia coli replication origin oriC contains the initiator ATP-DnaA-Oligomerization Region (DOR) and its flanking duplex unwinding element (DUE). In the Left-DOR subregion, ATP-DnaA forms a pentamer by binding to R1, R5M and three other DnaA boxes. The DNA-bending protein IHF binds sequence-specifically to the interspace between R1 and R5M boxes, promoting DUE unwinding, which is sustained predominantly by binding of R1/R5M-bound DnaAs to the single-stranded DUE (ssDUE). The present study describes DUE unwinding mechanisms promoted by DnaA and IHF-structural homolog HU, a ubiquitous protein in eubacterial species that binds DNA sequence-non-specifically, preferring bent DNA. Similar to IHF, HU promoted DUE unwinding dependent on ssDUE binding of R1/R5M-bound DnaAs. Unlike IHF, HU strictly required R1/R5M-bound DnaAs and interactions between the two DnaAs. Notably, HU site-specifically bound the R1-R5M interspace in a manner stimulated by ATP-DnaA and ssDUE. These findings suggest a model that interactions between the two DnaAs trigger DNA bending within the R1/R5M-interspace and initial DUE unwinding, which promotes site-specific HU binding that stabilizes the overall complex and DUE unwinding. Moreover, HU site-specifically bound the replication origin of the ancestral bacterium Thermotoga maritima depending on the cognate ATP-DnaA. The ssDUE recruitment mechanism could be evolutionarily conserved in eubacteria.
GenomeFLTR: filtering reads made easy
Authors: Dotan Edo , Alburquerque Michael , Wygoda Elya , Huchon Dorothée , Pupko Tal 
Published: May 2023

Abstract
In the last decade, advances in sequencing technology have led to an exponential increase in genomic data. These new data have dramatically changed our understanding of the evolution and function of genes and genomes. Despite improvements in sequencing technologies, identifying contaminated reads remains a complex task for many research groups. Here, we introduce GenomeFLTR, a new web server to filter contaminated reads. Reads are compared against existing sequence databases from various representative organisms to detect potential contaminants. The main features implemented in GenomeFLTR are: (i) automated updating of the relevant databases; (ii) fast comparison of each read against the database; (iii) the ability to create user-specified databases; (iv) a user-friendly interactive dashboard to investigate the origin and frequency of the contaminations; (v) the generation of a contamination-free file. Availability: https://genomefltr.tau.ac.il/.
An evaluation of biobanking and therapeutic clinical trial representation among adult glioma patients from rural and urban Utah
Authors: Earl Emma R , Colman Howard , Mendez Joe , Jensen Randy L , Karsy Michael 
Published: May 2023

Abstract

Background
Social determinants of health (SDOHs)—specifically those related to rurality, health care accessibility, and income—may play as-yet-unidentified roles in prognosis for glioma patients, and their impact on access to clinical trials is important to understand. We examined SDOHs of patients enrolled in glioma clinical trials and evaluate disparities in trial participation and outcomes between rural and urban patients.

Methods
We retrospectively identified patients enrolled in glioma clinical trials at Huntsman Cancer Institute (HCI) from May 2012 to May 2022 to evaluate clinical trial participation. We used multivariable models to evaluate SDOHs and geographic information system mapping to assess representation across Utah’s counties. We utilized the most recent 10-year datasets of patients treated for glioma at HCI and from the Utah Cancer Registry to analyze survival and incidence, respectively.

Results
A total of 570 participants (68 trials) resided in Utah, 84.4% from urban counties, 13.5% from rural counties, and 2.1% from frontier (least-populous) counties. Nineteen counties (65.5%) were underrepresented in trials (enrolled participants vs. eligible), 1 (3.5%) was represented in a near-1:1 ratio, and 9 (31.0%) were overrepresented. Counties with greater enrollment had greater population densities, highest per-capita income, and proximity to HCI. Among patients treated at HCI, patients from rural/frontier counties had equivalent survival with urban patients across nearly all glioma types, including glioblastomas, despite underrepresentation in clinical trials.

Conclusions
By highlighting disparities in clinical trial enrollment, our results can support efforts to improve recruitment in underrepresented regions, which can assist providers in delivering equitable care for all patients.