bluuebunny/crossref_metadata_2025_split huggingface dataset:
The radio shut-off, glitch, and X-ray burst in 1E 1547.0−5408 interpreted through magnetic reconfiguration
Authors: Suvorov Arthur G 
Published: June 2023

ABSTRACT
A short X-ray burst was observed from the radio-loud magnetar 1E 1547.0–5408 in 2022 April. Unusually however, the source stopped showing radio pulsations $\gtrsim 3\,$ weeks prior to the burst. After recovery, radio timing revealed that the object had also undergone a modest glitch. A model for the overall event is constructed where an initially mild perturbation adjusts the magnetic geometry near the polar caps, leading to shallow fractures. Crustal ejecta or particles leaking from a pair-plasma fireball pollute the magnetospheric gaps, shutting off the pulsar mechanism, but the energy release is not yet large enough to noticeably enhance the X-ray flux. This perturbation gradually ramps, eventuating in a large-scale energy redistribution which fuels the burst. The star’s mass quadrupole moment changes in tandem, issuing a glitch. Some quantitative estimates for the magnetic reconfiguration under this interpretation are provided, based on a quasi-static model where the fluid evolves through a sequence of hydromagnetic equilibria.
Search for the Galactic accelerators of cosmic rays up to the knee with the Pevatron test statistic
Authors: Angüner Ekrem Oğuzhan , Spengler Gerrit , Amato Elena , Casanova Sabrina 
Published: June 2023

ABSTRACT
The Pevatron test statistic (PTS) is applied to data from γ-ray observatories to test for the origin of cosmic rays (CRs) at energies around the knee of the CR spectrum. Several sources are analysed within hadronic emission models. Previously derived results for RX J1713.7−3946, Vela Jr, and HESS J1745−290 are confirmed to demonstrate the concept, reliability, and advantages of the PTS. It is excluded with a significance more than 5σ that the sources RX J1713.7−3946 and Vela Jr are Pevatrons, while strong indications exceeding 4σ are found for excluding HESS J1745−290 as a Pevatron. The importance to resolve source confusion with high angular resolution observations for Pevatrons searches is demonstrated using PTS for the region containing the SNR G106.3+2.7 and the Boomerang nebula. No statistically significant conclusion with respect to Pevatron associations could be drawn from this region, for the diffuse γ-ray emission around the Galactic Centre, and the unidentified γ-ray sources LHAASO J2108+5157, HESS J1702−420A, and MGRO J1908+06. Assuming the entire γ-ray emission from MGRO J1908+06 and the tail region of SNR G106.3+2.7 are hadronic, a statistical indication exceeding 3σ is found for the underlying proton spectrum to extend beyond 350–400 TeV as a power law. This result can indicate that these sources are proton and helium Pevatrons, in which the accelerated particles contribute to the knee of proton and helium spectra observed at Earth.
Hybrid deep learning for blazar classification and correlation search with neutrinos
Authors: Ding Jiacheng , Huang Yunlei , Li Xiao-Dong , Wang Xin , Wang Yang , Yang Lili 
Published: June 2023

ABSTRACT
Since the successful discovery of neutrinos, their origin is still a mystery until the association with TXS 0506+056. More messengers are achievable to study the intrinsic mechanism of extreme phenomena. Recently, Fermi-LAT Collaboration published the fourth catalogue of active galactic nuclei (4LAC), together with Data Release 2 later, including totally 3148 sources. The majority of these objects are blazars, which are classified into flat-spectrum radio quasars (FSRQs), BL Lac-type objects (BLLs), and blazars of uncertain type (BCUs) according to their optical observation feature. The BCUs take up to 38.2 per cent of total, whose classification is quite challenging and manpower consuming. However with the remarkable advances of technology, deep learning has been widely applied in astronomy. In this work, we take the advantage of 11 machine learning algorithms plus the convolutional neural network (CNN)-based deep learning algorithm to classify BCUs based on 10 parameters and the broad-band spectral energy distribution of each object obtained with vou-blazars. On average, this method has impressive performance, reaching above 95 per cent of balanced accuracy for the training sample, best among the studies so far. We correlate the IceCube neutrinos and blazars in 4LAC, found a few possible associations. With the machine learning prediction, we later elaborate the association of these BCUs with neutrinos samples and find out most of the BCUs associated with neutrinos are with low synchrotron peak frequency, which may be due to the energy distribution of high-energy particles. We propose neutrinos might be another feature for objects classification in the future.
Evolution of matter and galaxy clustering in cosmological hydrodynamical simulations
Authors: Einasto Jaan , Hütsi Gert , Liivamägi Lauri-Juhan , Park Changbom , Kim Juhan , Szapudi Istvan , Einasto Maret 
Published: June 2023

ABSTRACT
We quantify the evolution of matter and galaxy clustering in cosmological hydrodynamical simulations via correlation and bias functions of matter and galaxies. We use simulations TNG100 and TNG300 with epochs from z = 5 to z = 0. We calculate spatial correlation functions (CFs) of galaxies, ξ(r), for simulated galaxies and dark matter (DM) particles to characterize the evolving cosmic web. We find that bias parameters decrease during the evolution, confirming earlier results. Bias parameters of the lowest luminosity galaxies, b0, estimated from CFs are lower relative to CFs of particle density-limited clustered samples of DM. At low and medium luminosities, bias parameters of galaxies are equal, suggesting that dwarf galaxies reside in the same filamentary web as brighter galaxies. We find that bias parameters b0, estimated from CFs of clustered DM, agree with the expected values from the fraction of particles in the clustered population, b = 1/Fc. The cosmic web contains filamentary structures of various densities, and fractions of matter in the clustered and the unclustered populations are both less than unity. Thus, the CF amplitude of the clustered matter is always higher than that for all matter, i.e. bias parameter must be b &gt; 1. Differences between CFs of galaxies and clustered DM suggest that these functions describe different properties of the cosmic web.
Joint analysis of gravitational-wave and electromagnetic data of mergers: breaking an afterglow model degeneracy in GW170817 and in future events
Authors: Gianfagna Giulia , Piro Luigi , Pannarale Francesco , Van Eerten Hendrik , Ricci Fulvio , Ryan Geoffrey , Troja Eleonora 
Published: June 2023

ABSTRACT
On 2017 August 17, Advanced LIGO and Virgo observed GW170817, the first gravitational-wave (GW) signal from a binary neutron star merger. It was followed by a short-duration gamma-ray burst, GRB 170817A, and by a non-thermal afterglow emission. In this work, a combined simultaneous fit of the electromagnetic (EM, specifically, afterglow) and GW domains is implemented, both using the posterior distribution of a GW standalone analysis as prior distribution to separately process the EM data, and fitting the EM and GW domains simultaneously. These approaches coincide mathematically, as long as the actual posterior of the GW analysis, and not an approximation, is used as prior for the EM analysis. We treat the viewing angle, θv, as shared parameter across the two domains. In the afterglow modelling with a Gaussian structured jet this parameter and the jet core angle, θc, are correlated, leading to high uncertainties on their values. The joint EM + GW analysis relaxes this degeneracy, reducing the uncertainty compared to an EM-only fit. We also apply our methodology to hypothetical GW170817-like events occurring in the next GW observing run at ∼140 and 70 Mpc. At 70 Mpc the existing EM degeneracy is broken, thanks to the inclusion of the GW domain in the analysis. At 140 Mpc, the EM-only fit cannot constrain θv nor θc because of the lack of detections in the afterglow rising phase. Folding the GW data into the analysis leads to tighter constraints on θv, still leaving θc unconstrained, requiring instruments with higher sensitivities, such as Athena.
Eccentricity growth of massive planets inside cavities of protoplanetary discs
Authors: Romanova M M , Koldoba A V , Ustyugova G V , Lai D , Lovelace R V E 
Published: June 2023

ABSTRACT
We carry out hydrodynamical simulations to study the eccentricity growth of a 1–30 Jupiter mass planet located inside the fixed cavity of a protoplanetary disc. The planet exchanges energy and angular momentum with the disc at resonant locations, and its eccentricity grows due to Lindblad resonances. We observe several phases of eccentricity growth where different eccentric Lindblad resonances dominate from 1:3 up to 3:5. The maximum values of eccentricity reached in our simulations are 0.65–0.75. We calculate the eccentricity growth rate for different planet masses and disc parameters and derive analytical dependencies on these parameters. We observe that the growth rate is proportional to both the planet’s mass and the characteristic disc mass for a wide range of parameters. In a separate set of simulations, we derived the width of the 1:3 Lindblad resonance.
Diagnostic value of 18F-fluorodeoxyglucose positron emission tomography and computed tomography for differentiating polymyalgia rheumatica and rheumatoid arthritis: Using classification and regression tree analysis
Authors: Ikuma Daisuke , Sawa Naoki , Yamanouchi Masayuki , Oba Yuki , Mizuno Hiroki , Suwabe Tatsuya , Hoshino Junichi , Ubara Yoshifumi 
Published: June 2023

ABSTRACT

Objectives
Determining which sites were important to differentiate polymyalgia rheumatica (PMR) from rheumatoid arthritis (RA) using 18F-fluorodeoxyglucose (FDG) positron emission tomography and computed tomography (PET-CT) is challenging.

Methods
Patients with PMR or RA who were undergoing PET-CT were recruited at two mutual-aid hospitals in Japan between 2009 and 2018. Classification and regression tree (CART) analyses were performed to identify FDG uptake patterns that differentiated PMR from RA.

Results
We enrolled 35 patients with PMR and 46 patients with RA. Univariate CART analysis showed that FDG uptake in the shoulder joints, spinous processes of the lumbar vertebrae, pubic symphysis, sternoclavicular joints, ischial tuberosities, greater trochanters, and hip joints differentiated PMR from RA. Multivariate CART analysis revealed that FDG uptake by at least one of the ischial tuberosities had the highest diagnostic value for distinguishing PMR from RA (sensitivity, 77.1%; specificity, 82.6%). We performed the same CART analysis to patients who had not undergone treatment (PMR, n = 28; RA, n = 9). Similar results were obtained, and sensitivity and specificity were increased (sensitivity, 89.3%; specificity, 88.8%).

Conclusions
In PET-CT, FDG uptake by at least one of the ischial tuberosities best discriminates between PMR and RA.
A Seat at the Table for Music Therapy: Perceptions of Music Therapy Within the Hospice Interdisciplinary Team
Authors: Fiore Jennifer , Ridgway Kaitlin , Buttermore Allison 
Published: June 2023

Abstract
Music therapy is a newer profession within hospice, with limited evidence of other disciplines’ perceptions of a music therapist’s role in hospice care. The purpose of this study was to examine if perception differences exist between music therapists and interdisciplinary team (IDT) members regarding how 25 job tasks related to the music therapist’s role within a clinical interdisciplinary hospice team. Two groups consisting of board-certified music therapists (MT-BC) and IDT members completed an online Qualtrics survey to rate how 25 job tasks were perceived to pertain to the music therapist’s role in hospice care. A two-way mixed ANOVA indicated the significant differences between the 2 groups for 13 of the 25 tasks, suggesting less understanding of an MT-BC’s role within a hospice IDT. For the 13 tasks perceived significantly different, a one-way ANOVA was run and indicated significant between discipline perceptual differences for nine of the 13 tasks. Qualitative statements indicated contracted and employed MT-BCs experienced similar perceived barriers of IDT colleagues lack of understanding music therapy and the MT-BC not being able to attend IDT or participate regularly. Overall, required IDT groups’ qualitative statements were positive, with the most common responses across disciplines indicating that MT-BCs elicited positive responses from patients and caregivers, provided a distraction from pain or agitation, and increased patients’ quality of life. The current study’s outcomes highlight the need for music therapists to provide more education to colleagues regarding a music therapist’s role in the hospice setting.
Music Therapy Knowledge, Interest, and Career Recommendations: A Survey of Music Educators
Authors: Springer D Gregory , Gooding Lori F 
Published: June 2023

Abstract
The purpose of this study was to examine high school music teachers’ knowledge of music therapy, interest in music therapy, and career recommendations for music therapy relative to other music careers. High school music teachers (N = 65) from one southeastern state completed a researcher-designed survey instrument designed to investigate these areas. Results indicated varied levels of knowledge about music therapy, although teachers who previously attended institutions that offered music therapy degree programs provided higher knowledge ratings than those who had not attended institutions with music therapy programs. Additionally, participants reported a relatively high interest in music therapy and a willingness to promote it as a career to their students. Participants reported that they were most likely to recommend music education as a career to their students, followed by music performance and music therapy. In response to open-ended questions, participants indicated that they believed personal characteristics were the most important qualities of prospective music therapists and that musical characteristics were the most important qualities of prospective music educators. They also expressed an interest in more information about music therapy, especially related to job characteristics. Implications of these findings and suggestions for future research are discussed.
Generalised interrelations among mutation rates drive the genomic compliance of Chargaff's second parity rule
Authors: Pflughaupt Patrick , Sahakyan Aleksandr B 
Published: June 2023

Abstract
Chargaff's second parity rule (PR-2), where the complementary base and k-mer contents are matching within the same strand of a double stranded DNA (dsDNA), is a phenomenon that invited many explanations. The strict compliance of nearly all nuclear dsDNA to PR-2 implies that the explanation should also be similarly adamant. In this work, we revisited the possibility of mutation rates driving PR-2 compliance. Starting from the assumption-free approach, we constructed kinetic equations for unconstrained simulations. The results were analysed for their PR-2 compliance by employing symbolic regression and machine learning techniques. We arrived to a generalised set of mutation rate interrelations in place in most species that allow for their full PR-2 compliance. Importantly, our constraints explain PR-2 in genomes out of the scope of the prior explanations based on the equilibration under mutation rates with simpler no-strand-bias constraints. We thus reinstate the role of mutation rates in PR-2 through its molecular core, now shown, under our formulation, to be tolerant to previously noted strand biases and incomplete compositional equilibration. We further investigate the time for any genome to reach PR-2, showing that it is generally earlier than the compositional equilibrium, and well within the age of life on Earth.
Reverse transcriptases prime DNA synthesis
Authors: Zabrady Matej , Zabrady Katerina , Li Arthur W H , Doherty Aidan J 
Published: June 2023

Abstract
The discovery of reverse transcriptases (RTs) challenged the central dogma by establishing that genetic information can also flow from RNA to DNA. Although they act as DNA polymerases, RTs are distantly related to replicases that also possess de novo primase activity. Here we identify that CRISPR associated RTs (CARTs) directly prime DNA synthesis on both RNA and DNA. We demonstrate that RT-dependent priming is utilized by some CRISPR-Cas complexes to synthesise new spacers and integrate these into CRISPR arrays. Expanding our analyses, we show that primer synthesis activity is conserved in representatives of other major RT classes, including group II intron RT, telomerase and retroviruses. Together, these findings establish a conserved innate ability of RTs to catalyse de novo DNA primer synthesis, independently of accessory domains or alternative priming mechanisms, which likely plays important roles in a wide variety of biological pathways.
Insights into a viral motor: the structure of the HK97 packaging termination assembly
Authors: Hawkins Dorothy E D P , Bayfield Oliver W , Fung Herman K H , Grba Daniel N , Huet Alexis , Conway James F , Antson Alfred A 
Published: June 2023

Abstract
Double-stranded DNA viruses utilise machinery, made of terminase proteins, to package viral DNA into the capsid. For cos bacteriophage, a defined signal, recognised by small terminase, flanks each genome unit. Here we present the first structural data for a cos virus DNA packaging motor, assembled from the bacteriophage HK97 terminase proteins, procapsids encompassing the portal protein, and DNA containing a cos site. The cryo-EM structure is consistent with the packaging termination state adopted after DNA cleavage, with DNA density within the large terminase assembly ending abruptly at the portal protein entrance. Retention of the large terminase complex after cleavage of the short DNA substrate suggests that motor dissociation from the capsid requires headful pressure, in common with pac viruses. Interestingly, the clip domain of the 12-subunit portal protein does not adhere to C12 symmetry, indicating asymmetry induced by binding of the large terminase/DNA. The motor assembly is also highly asymmetric, showing a ring of 5 large terminase monomers, tilted against the portal. Variable degrees of extension between N- and C-terminal domains of individual subunits suggest a mechanism of DNA translocation driven by inter-domain contraction and relaxation.
Interplay of endonucleolytic and exonucleolytic processing in the 3′-end formation of a mitochondrial nad2 RNA precursor in Arabidopsis
Authors: Wang Chuande , Quadrado Martine , Mireau Hakim 
Published: June 2023

Abstract
Initiation and termination of plant mitochondrial transcription are poorly controlled steps. Precursor transcripts are thus often longer than necessary, and 3′-end processing as well as control of RNA stability are essential to produce mature mRNAs in plant mitochondria. Plant mitochondrial 3′ ends are determined by 3′-to-5′ exonucleolytic trimming until the progression of mitochondrial exonucleases along transcripts is stopped by stable RNA structures or RNA binding proteins. In this analysis, we investigated the function of the endonucleolytic mitochondrial stability factor 1 (EMS1) pentatricopeptide repeat (PPR) protein and showed that it is essential for the production and the stabilization of the mature form of the nad2 exons 1–2 precursor transcript, whose 3′ end corresponds to the 5′ half of the nad2 trans-intron 2. The accumulation of an extended rather than a truncated form of this transcript in ems1 mutant plants suggests that the role of EMS1 in 3′ end formation is not strictly limited to blocking the passage of 3′-5′ exonucleolytic activity, but that 3′ end formation of the nad2 exons 1–2 transcript involves an EMS1-dependent endonucleolytic cleavage. This study demonstrates that the formation of the 3′ end of mitochondrial transcripts may involve an interplay of endonucleolytic and exonucleolytic processing mediated by PPR proteins.
Rarely acquired type II-A CRISPR-Cas spacers mediate anti-viral immunity through the targeting of a non-canonical PAM sequence
Authors: Kenney Claire T , Marraffini Luciano A 
Published: June 2023

Abstract
The Streptococcus pyogenes type II-A CRISPR-Cas systems provides adaptive immunity through the acquisition of short DNA sequences from invading viral genomes, called spacers. Spacers are transcribed into short RNA guides that match regions of the viral genome followed by a conserved NGG DNA motif, known as the PAM. These RNA guides, in turn, are used by the Cas9 nuclease to find and destroy complementary DNA targets within the viral genome. While most of the spacers present in bacterial populations that survive phage infection target protospacers flanked by NGG sequences, there is a small fraction that target non-canonical PAMs. Whether these spacers originate through accidental acquisition of phage sequences and/or provide efficient defense is unknown. Here we found that many of them match phage target regions flanked by an NAGG PAM. Despite being scarcely present in bacterial populations, NAGG spacers provide substantial immunity in vivo and generate RNA guides that support robust DNA cleavage by Cas9 in vitro; with both activities comparable to spacers that target sequences followed by the canonical AGG PAM. In contrast, acquisition experiments showed that NAGG spacers are acquired at very low frequencies. We therefore conclude that discrimination against these sequences occurs during immunization of the host. Our results reveal unexpected differences in PAM recognition during the spacer acquisition and targeting stages of the type II-A CRISPR-Cas immune response.
Dual chemical labeling enables nucleotide-resolution mapping of DNA abasic sites and common alkylation damage in human mitochondrial DNA
Authors: Liu Chaoxing , Le Brandon H , Xu Wenyan , Yang Ching-Hsin , Chen Yu Hsuan , Zhao Linlin 
Published: June 2023

Abstract
Mitochondrial DNA (mtDNA) modifications play an emerging role in innate immunity and inflammatory diseases. Nonetheless, relatively little is known regarding the locations of mtDNA modifications. Such information is critically important for deciphering their roles in mtDNA instability, mtDNA-mediated immune and inflammatory responses, and mitochondrial disorders. The affinity probe-based enrichment of lesion-containing DNA represents a key strategy for sequencing DNA modifications. Existing methods are limited in the enrichment specificity of abasic (AP) sites, a prevalent DNA modification and repair intermediate. Herein, we devise a novel approach, termed dual chemical labeling-assisted sequencing (DCL-seq), for mapping AP sites. DCL-seq features two designer compounds for enriching and mapping AP sites specifically at single-nucleotide resolution. For proof of principle, we mapped AP sites in mtDNA from HeLa cells under different biological conditions. The resulting AP site maps coincide with mtDNA regions with low TFAM (mitochondrial transcription factor A) coverage and with potential G-quadruplex-forming sequences. In addition, we demonstrated the broader applicability of the method in sequencing other DNA modifications in mtDNA, such as N7-methyl-2′-deoxyguanosine and N3-methyl-2′-deoxyadenosine, when coupled with a lesion-specific repair enzyme. Together, DCL-seq holds the promise to sequence multiple DNA modifications in various biological samples.